Transformative Rendering of Internet Resources

Science.gov (United States)

2012-10-01

using either the Firefox or Google Chrome rendering engine. The rendering server then captures a screen shot of the page and creates code that positions...be compromised at web pages the hackers had built for that hacking competition to exploit that particular OS /browser configuration. During...of risk with no benefit. They include: - The rendering server is hosted on a Linux-based operating system ( OS ). The OS is much more secure than the

Technical analysis of volume-rendering algorithms: application in low-contrast structures using liver vascularisation as a model

International Nuclear Information System (INIS)

Cademartiri, Filippo; Luccichenti, Giacomo; Runza, Giuseppe; Bartolotta, Tommaso Vincenzo; Midiri, Massimo; Gualerzi, Massimo; Brambilla, Lorenzo; Coruzzi, Paolo; Soliani, Paolo; Sianesi, Mario

2005-01-01

Purpose: To assess the influence of pre-set volume rendering opacity curves (OC) on image quality and to identify which absolute parameters (density of aorta, hepatic parenchyma and portal vein) affect visualization of portal vascular structures (low-contrast structures). Materials and methods: Twenty-two patients underwent a dual-phase spiral CT with the following parameters: collimation 3 mm, pitch 2, increment 1 mm. Three scans were performed: one without contrast medium and the latter two after the injection of contrast material (conventionally identified as 'arterial' and 'portal'). The images were sent to a workstation running on an NT platform equipped with post-processing software allowing three-dimensional (3D) reconstructions to generate volume-rendered images of the vascular supply to the liver. Correlation between the absolute values of aorta, liver and portal vein density, OC parameters, and image quality were assessed. Results: 3D images generated using pre-set OC obtained a much mower overall quality score than those produced with OC set by the operator. High contrast between the liver and the portal vein, for example during the portal vascular phase, allows wider windows, thus improving image quality. Conversely, the OC in the parenchymal phase scans must have a high gradient in order to better differentiate between the vascular structures and the surrounding hepatic parenchyma. Conclusions: Image features considered to be of interest by the operator cannot be simplified by the mean of pre-set OC. Due to their strong individual variability automatic 3D algorithms cannot be universally applied: they should be adapted to both image and patient characteristics [it

Distributed rendering for multiview parallax displays

Science.gov (United States)

Annen, T.; Matusik, W.; Pfister, H.; Seidel, H.-P.; Zwicker, M.

2006-02-01

3D display technology holds great promise for the future of television, virtual reality, entertainment, and visualization. Multiview parallax displays deliver stereoscopic views without glasses to arbitrary positions within the viewing zone. These systems must include a high-performance and scalable 3D rendering subsystem in order to generate multiple views at real-time frame rates. This paper describes a distributed rendering system for large-scale multiview parallax displays built with a network of PCs, commodity graphics accelerators, multiple projectors, and multiview screens. The main challenge is to render various perspective views of the scene and assign rendering tasks effectively. In this paper we investigate two different approaches: Optical multiplexing for lenticular screens and software multiplexing for parallax-barrier displays. We describe the construction of large-scale multi-projector 3D display systems using lenticular and parallax-barrier technology. We have developed different distributed rendering algorithms using the Chromium stream-processing framework and evaluate the trade-offs and performance bottlenecks. Our results show that Chromium is well suited for interactive rendering on multiview parallax displays.

Sketchy Rendering for Information Visualization

NARCIS (Netherlands)

Wood, Jo; Isenberg, Petra; Isenberg, Tobias; Dykes, Jason; Boukhelifa, Nadia; Slingsby, Aidan

2012-01-01

We present and evaluate a framework for constructing sketchy style information visualizations that mimic data graphics drawn by hand. We provide an alternative renderer for the Processing graphics environment that redefines core drawing primitives including line, polygon and ellipse rendering. These

Rendering Falling Leaves on Graphics Hardware

OpenAIRE

Marcos Balsa; Pere-Pau Vázquez

2008-01-01

There is a growing interest in simulating natural phenomena in computer graphics applications. Animating natural scenes in real time is one of the most challenging problems due to the inherent complexity of their structure, formed by millions of geometric entities, and the interactions that happen within. An example of natural scenario that is needed for games or simulation programs are forests. Forests are difficult to render because the huge amount of geometric entities and the large amount...

Real-time photorealistic stereoscopic rendering of fire

Science.gov (United States)

Rose, Benjamin M.; McAllister, David F.

2007-02-01

We propose a method for real-time photorealistic stereo rendering of the natural phenomenon of fire. Applications include the use of virtual reality in fire fighting, military training, and entertainment. Rendering fire in real-time presents a challenge because of the transparency and non-static fluid-like behavior of fire. It is well known that, in general, methods that are effective for monoscopic rendering are not necessarily easily extended to stereo rendering because monoscopic methods often do not provide the depth information necessary to produce the parallax required for binocular disparity in stereoscopic rendering. We investigate the existing techniques used for monoscopic rendering of fire and discuss their suitability for extension to real-time stereo rendering. Methods include the use of precomputed textures, dynamic generation of textures, and rendering models resulting from the approximation of solutions of fluid dynamics equations through the use of ray-tracing algorithms. We have found that in order to attain real-time frame rates, our method based on billboarding is effective. Slicing is used to simulate depth. Texture mapping or 2D images are mapped onto polygons and alpha blending is used to treat transparency. We can use video recordings or prerendered high-quality images of fire as textures to attain photorealistic stereo.

Parametric model of the scala tympani for haptic-rendered cochlear implantation.

Science.gov (United States)

Todd, Catherine; Naghdy, Fazel

2005-01-01

A parametric model of the human scala tympani has been designed for use in a haptic-rendered computer simulation of cochlear implant surgery. It will be the first surgical simulator of this kind. A geometric model of the Scala Tympani has been derived from measured data for this purpose. The model is compared with two existing descriptions of the cochlear spiral. A first approximation of the basilar membrane is also produced. The structures are imported into a force-rendering software application for system development.

Transform coding for hardware-accelerated volume rendering.

Science.gov (United States)

Fout, Nathaniel; Ma, Kwan-Liu

2007-01-01

Hardware-accelerated volume rendering using the GPU is now the standard approach for real-time volume rendering, although limited graphics memory can present a problem when rendering large volume data sets. Volumetric compression in which the decompression is coupled to rendering has been shown to be an effective solution to this problem; however, most existing techniques were developed in the context of software volume rendering, and all but the simplest approaches are prohibitive in a real-time hardware-accelerated volume rendering context. In this paper we present a novel block-based transform coding scheme designed specifically with real-time volume rendering in mind, such that the decompression is fast without sacrificing compression quality. This is made possible by consolidating the inverse transform with dequantization in such a way as to allow most of the reprojection to be precomputed. Furthermore, we take advantage of the freedom afforded by off-line compression in order to optimize the encoding as much as possible while hiding this complexity from the decoder. In this context we develop a new block classification scheme which allows us to preserve perceptually important features in the compression. The result of this work is an asymmetric transform coding scheme that allows very large volumes to be compressed and then decompressed in real-time while rendering on the GPU.

Interactive Molecular Graphics for Augmented Reality Using HoloLens.

Science.gov (United States)

Müller, Christoph; Krone, Michael; Huber, Markus; Biener, Verena; Herr, Dominik; Koch, Steffen; Reina, Guido; Weiskopf, Daniel; Ertl, Thomas

2018-06-13

Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft's HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight. Consequently, insights from best practises for powerful desktop hardware may not be transferable. Therefore, we evaluate the capabilities of the HoloLens hardware for modern, GPU-enabled, high-quality rendering methods for the space-filling model commonly used in molecular visualisation. We also assess the scalability for large molecular data sets. Based on the results, we discuss ideas and possibilities for immersive molecular analytics. Besides more obvious benefits like the stereoscopic rendering offered by the device, this specifically includes natural user interfaces that use physical navigation instead of the traditional virtual one. Furthermore, we consider different scenarios for such an immersive system, ranging from educational use to collaborative scenarios.

Apparatus for rendering at least a portion of a device inoperable and related methods

Energy Technology Data Exchange (ETDEWEB)

Daniels, Michael A.; Steffler, Eric D.; Hartenstein, Steven D.; Wallace, Ronald S.

2016-11-08

Apparatus for rendering at least a portion of a device inoperable may include a containment structure having a first compartment that is configured to receive a device therein and a movable member configured to receive a cartridge having reactant material therein. The movable member is configured to be inserted into the first compartment of the containment structure and to ignite the reactant material within the cartridge. Methods of rendering at least a portion of a device inoperable may include disposing the device into the first compartment of the containment structure, inserting the movable member into the first compartment of the containment structure, igniting the reactant material in the cartridge, and expelling molten metal onto the device.

Photoionization and molecular structure

International Nuclear Information System (INIS)

Palma, A.

1983-01-01

A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

Relationship between chromatin structure and sensitivity to molecularly targeted auger electron radiation therapy.

NARCIS (Netherlands)

Terry, S.Y.A.; Vallis, K.A.

2012-01-01

PURPOSE: The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. METHODS AND MATERIALS: Chromatin structure was

RenderGAN: Generating Realistic Labeled Data

Directory of Open Access Journals (Sweden)

Leon Sixt

2018-06-01

Full Text Available Deep Convolutional Neuronal Networks (DCNNs are showing remarkable performance on many computer vision tasks. Due to their large parameter space, they require many labeled samples when trained in a supervised setting. The costs of annotating data manually can render the use of DCNNs infeasible. We present a novel framework called RenderGAN that can generate large amounts of realistic, labeled images by combining a 3D model and the Generative Adversarial Network framework. In our approach, image augmentations (e.g., lighting, background, and detail are learned from unlabeled data such that the generated images are strikingly realistic while preserving the labels known from the 3D model. We apply the RenderGAN framework to generate images of barcode-like markers that are attached to honeybees. Training a DCNN on data generated by the RenderGAN yields considerably better performance than training it on various baselines.

Physically based rendering from theory to implementation

CERN Document Server

Pharr, Matt

2010-01-01

"Physically Based Rendering, 2nd Edition" describes both the mathematical theory behind a modern photorealistic rendering system as well as its practical implementation. A method - known as 'literate programming'- combines human-readable documentation and source code into a single reference that is specifically designed to aid comprehension. The result is a stunning achievement in graphics education. Through the ideas and software in this book, you will learn to design and employ a full-featured rendering system for creating stunning imagery. This book features new sections on subsurface scattering, Metropolis light transport, precomputed light transport, multispectral rendering, and much more. It includes a companion site complete with source code for the rendering system described in the book, with support for Windows, OS X, and Linux. Code and text are tightly woven together through a unique indexing feature that lists each function, variable, and method on the page that they are first described.

Molecular Structure of Human-Liver Glycogen.

Directory of Open Access Journals (Sweden)

Bin Deng

Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

Energy Technology Data Exchange (ETDEWEB)

Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

2012-11-01

We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

Advanced Material Rendering in Blender

Czech Academy of Sciences Publication Activity Database

Hatka, Martin; Haindl, Michal

2012-01-01

Roč. 11, č. 2 (2012), s. 15-23 ISSN 1081-1451 R&D Projects: GA ČR GAP103/11/0335; GA ČR GA102/08/0593 Grant - others:CESNET(CZ) 387/2010; CESNET(CZ) 409/2011 Institutional support: RVO:67985556 Keywords : realistic material rendering * bidirectional texture function * Blender Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2013/RO/haindl-advanced material rendering in blender.pdf

Realistic Real-Time Outdoor Rendering in Augmented Reality

Science.gov (United States)

Kolivand, Hoshang; Sunar, Mohd Shahrizal

2014-01-01

Realistic rendering techniques of outdoor Augmented Reality (AR) has been an attractive topic since the last two decades considering the sizeable amount of publications in computer graphics. Realistic virtual objects in outdoor rendering AR systems require sophisticated effects such as: shadows, daylight and interactions between sky colours and virtual as well as real objects. A few realistic rendering techniques have been designed to overcome this obstacle, most of which are related to non real-time rendering. However, the problem still remains, especially in outdoor rendering. This paper proposed a much newer, unique technique to achieve realistic real-time outdoor rendering, while taking into account the interaction between sky colours and objects in AR systems with respect to shadows in any specific location, date and time. This approach involves three main phases, which cover different outdoor AR rendering requirements. Firstly, sky colour was generated with respect to the position of the sun. Second step involves the shadow generation algorithm, Z-Partitioning: Gaussian and Fog Shadow Maps (Z-GaF Shadow Maps). Lastly, a technique to integrate sky colours and shadows through its effects on virtual objects in the AR system, is introduced. The experimental results reveal that the proposed technique has significantly improved the realism of real-time outdoor AR rendering, thus solving the problem of realistic AR systems. PMID:25268480

Realistic real-time outdoor rendering in augmented reality.

Directory of Open Access Journals (Sweden)

Hoshang Kolivand

Full Text Available Realistic rendering techniques of outdoor Augmented Reality (AR has been an attractive topic since the last two decades considering the sizeable amount of publications in computer graphics. Realistic virtual objects in outdoor rendering AR systems require sophisticated effects such as: shadows, daylight and interactions between sky colours and virtual as well as real objects. A few realistic rendering techniques have been designed to overcome this obstacle, most of which are related to non real-time rendering. However, the problem still remains, especially in outdoor rendering. This paper proposed a much newer, unique technique to achieve realistic real-time outdoor rendering, while taking into account the interaction between sky colours and objects in AR systems with respect to shadows in any specific location, date and time. This approach involves three main phases, which cover different outdoor AR rendering requirements. Firstly, sky colour was generated with respect to the position of the sun. Second step involves the shadow generation algorithm, Z-Partitioning: Gaussian and Fog Shadow Maps (Z-GaF Shadow Maps. Lastly, a technique to integrate sky colours and shadows through its effects on virtual objects in the AR system, is introduced. The experimental results reveal that the proposed technique has significantly improved the realism of real-time outdoor AR rendering, thus solving the problem of realistic AR systems.

RenderSelect: a Cloud Broker Framework for Cloud Renderfarm Services

OpenAIRE

Ruby, Annette J; Aisha, Banu W; Subash, Chandran P

2016-01-01

In the 3D studios the animation scene files undergo a process called as rendering, where the 3D wire frame models are converted into 3D photorealistic images. As the rendering process is both a computationally intensive and a time consuming task, the cloud services based rendering in cloud render farms is gaining popularity among the animators. Though cloud render farms offer many benefits, the animators hesitate to move from their traditional offline rendering to cloud services based render ...

[Hybrid 3-D rendering of the thorax and surface-based virtual bronchoscopy in surgical and interventional therapy control].

Science.gov (United States)

Seemann, M D; Gebicke, K; Luboldt, W; Albes, J M; Vollmar, J; Schäfer, J F; Beinert, T; Englmeier, K H; Bitzer, M; Claussen, C D

2001-07-01

The aim of this study was to demonstrate the possibilities of a hybrid rendering method, the combination of a color-coded surface and volume rendering method, with the feasibility of performing surface-based virtual endoscopy with different representation models in the operative and interventional therapy control of the chest. In 6 consecutive patients with partial lung resection (n = 2) and lung transplantation (n = 4) a thin-section spiral computed tomography of the chest was performed. The tracheobronchial system and the introduced metallic stents were visualized using a color-coded surface rendering method. The remaining thoracic structures were visualized using a volume rendering method. For virtual bronchoscopy, the tracheobronchial system was visualized using a triangle surface model, a shaded-surface model and a transparent shaded-surface model. The hybrid 3D visualization uses the advantages of both the color-coded surface and volume rendering methods and facilitates a clear representation of the tracheobronchial system and the complex topographical relationship of morphological and pathological changes without loss of diagnostic information. Performing virtual bronchoscopy with the transparent shaded-surface model facilitates a reasonable to optimal, simultaneous visualization and assessment of the surface structure of the tracheobronchial system and the surrounding mediastinal structures and lesions. Hybrid rendering relieve the morphological assessment of anatomical and pathological changes without the need for time-consuming detailed analysis and presentation of source images. Performing virtual bronchoscopy with a transparent shaded-surface model offers a promising alternative to flexible fiberoptic bronchoscopy.

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study.

Science.gov (United States)

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K

2017-11-21

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (C d ) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of C d with positive and negative surface potentials.

Image Based Rendering and Virtual Reality

DEFF Research Database (Denmark)

Livatino, Salvatore

The Presentation concerns with an overview of Image Based Rendering approaches and their use on Virtual Reality, including Virtual Photography and Cinematography, and Mobile Robot Navigation.......The Presentation concerns with an overview of Image Based Rendering approaches and their use on Virtual Reality, including Virtual Photography and Cinematography, and Mobile Robot Navigation....

Earth mortars and earth-lime renders

Directory of Open Access Journals (Sweden)

Maria Fernandes

2008-01-01

Full Text Available Earth surface coatings play a decorative architectural role, apart from their function as wall protection. In Portuguese vernacular architecture, earth mortars were usually applied on stone masonry, while earth renders and plasters were used on indoors surface coatings. Limestone exists only in certain areas of the country and consequently lime was not easily available everywhere, especially on granite and schist regions where stone masonry was a current building technique. In the central west coast of Portugal, the lime slaking procedure entailed slaking the quicklime mixed with earth (sandy soil, in a pit; the resulting mixture would then be combined in a mortar or plaster. This was also the procedure for manufactured adobes stabilized with lime. Adobe buildings with earth-lime renderings and plasters were also traditional in the same region, using lime putty and lime wash for final coat and decoration. Classic decoration on earth architecture from the 18th-19th century was in many countries a consequence of the François Cointeraux (1740-1830 manuals - Les Cahiers d'Architecture Rurale" (1793 - a French guide for earth architecture and building construction. This manual arrived to Portugal in the beginning of XIX century, but was never translated to Portuguese. References about decoration for earth houses were explained on this manual, as well as procedures about earth-lime renders and ornamentation of earth walls; in fact, these procedures are exactly the same as the ones used in adobe buildings in this Portuguese region. The specific purpose of the present paper is to show some cases of earth mortars, renders and plasters on stone buildings in Portugal and to explain the methods of producing earth-lime renders, and also to show some examples of rendering and coating with earth-lime in Portuguese adobe vernacular architecture.

Immersive volume rendering of blood vessels

Science.gov (United States)

Long, Gregory; Kim, Han Suk; Marsden, Alison; Bazilevs, Yuri; Schulze, Jürgen P.

2012-03-01

In this paper, we present a novel method of visualizing flow in blood vessels. Our approach reads unstructured tetrahedral data, resamples it, and uses slice based 3D texture volume rendering. Due to the sparse structure of blood vessels, we utilize an octree to efficiently store the resampled data by discarding empty regions of the volume. We use animation to convey time series data, wireframe surface to give structure, and utilize the StarCAVE, a 3D virtual reality environment, to add a fully immersive element to the visualization. Our tool has great value in interdisciplinary work, helping scientists collaborate with clinicians, by improving the understanding of blood flow simulations. Full immersion in the flow field allows for a more intuitive understanding of the flow phenomena, and can be a great help to medical experts for treatment planning.

Prediction of molecular crystal structures

International Nuclear Information System (INIS)

Beyer, Theresa

2001-01-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

Prediction of molecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Beyer, Theresa

2001-07-01

The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

CSMB | Center For Structural Molecular Biology

Data.gov (United States)

Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

A concept of volume rendering guided search process to analyze medical data set.

Science.gov (United States)

Zhou, Jianlong; Xiao, Chun; Wang, Zhiyan; Takatsuka, Masahiro

2008-03-01

This paper firstly presents an approach of parallel coordinates based parameter control panel (PCP). The PCP is used to control parameters of focal region-based volume rendering (FRVR) during data analysis. It uses a parallel coordinates style interface. Different rendering parameters represented with nodes on each axis, and renditions based on related parameters are connected using polylines to show dependencies between renditions and parameters. Based on the PCP, a concept of volume rendering guided search process is proposed. The search pipeline is divided into four phases. Different parameters of FRVR are recorded and modulated in the PCP during search phases. The concept shows that volume visualization could play the role of guiding a search process in the rendition space to help users to efficiently find local structures of interest. The usability of the proposed approach is evaluated to show its effectiveness.

Evaluating progressive-rendering algorithms in appearance design tasks.

Science.gov (United States)

Jiawei Ou; Karlik, Ondrej; Křivánek, Jaroslav; Pellacini, Fabio

2013-01-01

Progressive rendering is becoming a popular alternative to precomputational approaches to appearance design. However, progressive algorithms create images exhibiting visual artifacts at early stages. A user study investigated these artifacts' effects on user performance in appearance design tasks. Novice and expert subjects performed lighting and material editing tasks with four algorithms: random path tracing, quasirandom path tracing, progressive photon mapping, and virtual-point-light rendering. Both the novices and experts strongly preferred path tracing to progressive photon mapping and virtual-point-light rendering. None of the participants preferred random path tracing to quasirandom path tracing or vice versa; the same situation held between progressive photon mapping and virtual-point-light rendering. The user workflow didn’t differ significantly with the four algorithms. The Web Extras include a video showing how four progressive-rendering algorithms converged (at http://youtu.be/ck-Gevl1e9s), the source code used, and other supplementary materials.

Exploring RNA structure by integrative molecular modelling

DEFF Research Database (Denmark)

Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

2010-01-01

RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

Efficient Algorithms for Real-Time GPU Volumetric Cloud Rendering with Enhanced Geometry

OpenAIRE

Carlos Jiménez de Parga; Sebastián Rubén Gómez Palomo

2018-01-01

This paper presents several new techniques for volumetric cloud rendering using efficient algorithms and data structures based on ray-tracing methods for cumulus generation, achieving an optimum balance between realism and performance. These techniques target applications such as flight simulations, computer games, and educational software, even with conventional graphics hardware. The contours of clouds are defined by implicit mathematical expressions or triangulated structures inside which ...

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering

KAUST Repository

Sicat, Ronell Barrera

2014-12-31

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined in the 4D domain jointly comprising the 3D volume and its 1D intensity range. Crucially, the computation of sparse pdf volumes exploits data coherence in 4D, resulting in a sparse representation with surprisingly low storage requirements. At run time, we dynamically apply transfer functions to the pdfs using simple and fast convolutions. Whereas standard low-pass filtering and down-sampling incur visible differences between resolution levels, the use of pdfs facilitates consistent results independent of the resolution level used. We describe the efficient out-of-core computation of large-scale sparse pdf volumes, using a novel iterative simplification procedure of a mixture of 4D Gaussians. Finally, our data structure is optimized to facilitate interactive multi-resolution volume rendering on GPUs.

Moisture movements in render on brick wall

DEFF Research Database (Denmark)

Hansen, Kurt Kielsgaard; Munch, Thomas Astrup; Thorsen, Peter Schjørmann

2003-01-01

A three-layer render on brick wall used for building facades is studied in the laboratory. The vertical render surface is held in contact with water for 24 hours simulating driving rain while it is measured with non-destructive X-ray equipment every hour in order to follow the moisture front...

Sketchy Rendering for Information Visualization.

Science.gov (United States)

Wood, J; Isenberg, P; Isenberg, T; Dykes, J; Boukhelifa, N; Slingsby, A

2012-12-01

We present and evaluate a framework for constructing sketchy style information visualizations that mimic data graphics drawn by hand. We provide an alternative renderer for the Processing graphics environment that redefines core drawing primitives including line, polygon and ellipse rendering. These primitives allow higher-level graphical features such as bar charts, line charts, treemaps and node-link diagrams to be drawn in a sketchy style with a specified degree of sketchiness. The framework is designed to be easily integrated into existing visualization implementations with minimal programming modification or design effort. We show examples of use for statistical graphics, conveying spatial imprecision and for enhancing aesthetic and narrative qualities of visualization. We evaluate user perception of sketchiness of areal features through a series of stimulus-response tests in order to assess users' ability to place sketchiness on a ratio scale, and to estimate area. Results suggest relative area judgment is compromised by sketchy rendering and that its influence is dependent on the shape being rendered. They show that degree of sketchiness may be judged on an ordinal scale but that its judgement varies strongly between individuals. We evaluate higher-level impacts of sketchiness through user testing of scenarios that encourage user engagement with data visualization and willingness to critique visualization design. Results suggest that where a visualization is clearly sketchy, engagement may be increased and that attitudes to participating in visualization annotation are more positive. The results of our work have implications for effective information visualization design that go beyond the traditional role of sketching as a tool for prototyping or its use for an indication of general uncertainty.

Local and Global Illumination in the Volume Rendering Integral

Energy Technology Data Exchange (ETDEWEB)

Max, N; Chen, M

2005-10-21

This article is intended as an update of the major survey by Max [1] on optical models for direct volume rendering. It provides a brief overview of the subject scope covered by [1], and brings recent developments, such as new shadow algorithms and refraction rendering, into the perspective. In particular, we examine three fundamentals aspects of direct volume rendering, namely the volume rendering integral, local illumination models and global illumination models, in a wavelength-independent manner. We review the developments on spectral volume rendering, in which visible light are considered as a form of electromagnetic radiation, optical models are implemented in conjunction with representations of spectral power distribution. This survey can provide a basis for, and encourage, new efforts for developing and using complex illumination models to achieve better realism and perception through optical correctness.

Efficient Algorithms for Real-Time GPU Volumetric Cloud Rendering with Enhanced Geometry

Directory of Open Access Journals (Sweden)

Carlos Jiménez de Parga

2018-04-01

Full Text Available This paper presents several new techniques for volumetric cloud rendering using efficient algorithms and data structures based on ray-tracing methods for cumulus generation, achieving an optimum balance between realism and performance. These techniques target applications such as flight simulations, computer games, and educational software, even with conventional graphics hardware. The contours of clouds are defined by implicit mathematical expressions or triangulated structures inside which volumetric rendering is performed. Novel techniques are used to reproduce the asymmetrical nature of clouds and the effects of light-scattering, with low computing costs. The work includes a new method to create randomized fractal clouds using a recursive grammar. The graphical results are comparable to those produced by state-of-the-art, hyper-realistic algorithms. These methods provide real-time performance, and are superior to particle-based systems. These outcomes suggest that our methods offer a good balance between realism and performance, and are suitable for use in the standard graphics industry.

Three-dimensional rendering of otolith growth using phase contrast synchrotron tomography.

Science.gov (United States)

Mapp, J J I; Fisher, M H; Atwood, R C; Bell, G D; Greco, M K; Songer, S; Hunter, E

2016-05-01

A three-dimensional computer reconstruction of a plaice Pleuronectes platessa otolith is presented from data acquired by the Diamond Light synchrotron, beamline I12, X-ray source, a high energy (53-150 keV) source particularly well suited to the study of dense objects. The data allowed non-destructive rendering of otolith structure, and for the first time allows otolith annuli (internal ring structures) to be analysed in X-ray tomographic images. © 2016 The Fisheries Society of the British Isles.

Standardized rendering from IR surveillance motion imagery

Science.gov (United States)

Prokoski, F. J.

2014-06-01

Government agencies, including defense and law enforcement, increasingly make use of video from surveillance systems and camera phones owned by non-government entities.Making advanced and standardized motion imaging technology available to private and commercial users at cost-effective prices would benefit all parties. In particular, incorporating thermal infrared into commercial surveillance systems offers substantial benefits beyond night vision capability. Face rendering is a process to facilitate exploitation of thermal infrared surveillance imagery from the general area of a crime scene, to assist investigations with and without cooperating eyewitnesses. Face rendering automatically generates greyscale representations similar to police artist sketches for faces in surveillance imagery collected from proximate locations and times to a crime under investigation. Near-realtime generation of face renderings can provide law enforcement with an investigation tool to assess witness memory and credibility, and integrate reports from multiple eyewitnesses, Renderings can be quickly disseminated through social media to warn of a person who may pose an immediate threat, and to solicit the public's help in identifying possible suspects and witnesses. Renderings are pose-standardized so as to not divulge the presence and location of eyewitnesses and surveillance cameras. Incorporation of thermal infrared imaging into commercial surveillance systems will significantly improve system performance, and reduce manual review times, at an incremental cost that will continue to decrease. Benefits to criminal justice would include improved reliability of eyewitness testimony and improved accuracy of distinguishing among minority groups in eyewitness and surveillance identifications.

Real-time 3-dimensional fetal echocardiography with an instantaneous volume-rendered display: early description and pictorial essay.

Science.gov (United States)

Sklansky, Mark S; DeVore, Greggory R; Wong, Pierre C

2004-02-01

Random fetal motion, rapid fetal heart rates, and cumbersome processing algorithms have limited reconstructive approaches to 3-dimensional fetal cardiac imaging. Given the recent development of real-time, instantaneous volume-rendered sonographic displays of volume data, we sought to apply this technology to fetal cardiac imaging. We obtained 1 to 6 volume data sets on each of 30 fetal hearts referred for formal fetal echocardiography. Each volume data set was acquired over 2 to 8 seconds and stored on the system's hard drive. Rendered images were subsequently processed to optimize translucency, smoothing, and orientation and cropped to reveal "surgeon's eye views" of clinically relevant anatomic structures. Qualitative comparison was made with conventional fetal echocardiography for each subject. Volume-rendered displays identified all major abnormalities but failed to identify small ventricular septal defects in 2 patients. Important planes and views not visualized during the actual scans were generated with minimal processing of rendered image displays. Volume-rendered displays tended to have slightly inferior image quality compared with conventional 2-dimensional images. Real-time 3-dimensional echocardiography with instantaneous volume-rendered displays of the fetal heart represents a new approach to fetal cardiac imaging with tremendous clinical potential.

Remote volume rendering pipeline for mHealth applications

Science.gov (United States)

Gutenko, Ievgeniia; Petkov, Kaloian; Papadopoulos, Charilaos; Zhao, Xin; Park, Ji Hwan; Kaufman, Arie; Cha, Ronald

2014-03-01

We introduce a novel remote volume rendering pipeline for medical visualization targeted for mHealth (mobile health) applications. The necessity of such a pipeline stems from the large size of the medical imaging data produced by current CT and MRI scanners with respect to the complexity of the volumetric rendering algorithms. For example, the resolution of typical CT Angiography (CTA) data easily reaches 512^3 voxels and can exceed 6 gigabytes in size by spanning over the time domain while capturing a beating heart. This explosion in data size makes data transfers to mobile devices challenging, and even when the transfer problem is resolved the rendering performance of the device still remains a bottleneck. To deal with this issue, we propose a thin-client architecture, where the entirety of the data resides on a remote server where the image is rendered and then streamed to the client mobile device. We utilize the display and interaction capabilities of the mobile device, while performing interactive volume rendering on a server capable of handling large datasets. Specifically, upon user interaction the volume is rendered on the server and encoded into an H.264 video stream. H.264 is ubiquitously hardware accelerated, resulting in faster compression and lower power requirements. The choice of low-latency CPU- and GPU-based encoders is particularly important in enabling the interactive nature of our system. We demonstrate a prototype of our framework using various medical datasets on commodity tablet devices.

A Sort-Last Rendering System over an Optical Backplane

Directory of Open Access Journals (Sweden)

Yasuhiro Kirihata

2005-06-01

Full Text Available Sort-Last is a computer graphics technique for rendering extremely large data sets on clusters of computers. Sort-Last works by dividing the data set into even-sized chunks for parallel rendering and then composing the images to form the final result. Since sort-last rendering requires the movement of large amounts of image data among cluster nodes, the network interconnecting the nodes becomes a major bottleneck. In this paper, we describe a sort-last rendering system implemented on a cluster of computers whose nodes are connected by an all-optical switch. The rendering system introduces the notion of the Photonic Computing Engine, a computing system built dynamically by using the optical switch to create dedicated network connections among cluster nodes. The sort-last volume rendering algorithm was implemented on the Photonic Computing Engine, and its performance is evaluated. Prelimi- nary experiments show that performance is affected by the image composition time and average payload size. In an attempt to stabilize the performance of the system, we have designed a flow control mechanism that uses feedback messages to dynamically adjust the data flow rate within the computing engine.

Learning surface molecular structures via machine vision

Science.gov (United States)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

GPU Pro 5 advanced rendering techniques

CERN Document Server

Engel, Wolfgang

2014-01-01

In GPU Pro5: Advanced Rendering Techniques, section editors Wolfgang Engel, Christopher Oat, Carsten Dachsbacher, Michal Valient, Wessam Bahnassi, and Marius Bjorge have once again assembled a high-quality collection of cutting-edge techniques for advanced graphics processing unit (GPU) programming. Divided into six sections, the book covers rendering, lighting, effects in image space, mobile devices, 3D engine design, and compute. It explores rasterization of liquids, ray tracing of art assets that would otherwise be used in a rasterized engine, physically based area lights, volumetric light

Fast algorithm for the rendering of three-dimensional surfaces

Science.gov (United States)

Pritt, Mark D.

1994-02-01

It is often desirable to draw a detailed and realistic representation of surface data on a computer graphics display. One such representation is a 3D shaded surface. Conventional techniques for rendering shaded surfaces are slow, however, and require substantial computational power. Furthermore, many techniques suffer from aliasing effects, which appear as jagged lines and edges. This paper describes an algorithm for the fast rendering of shaded surfaces without aliasing effects. It is much faster than conventional ray tracing and polygon-based rendering techniques and is suitable for interactive use. On an IBM RISC System/6000TM workstation it renders a 1000 X 1000 surface in about 7 seconds.

Innovative Lime Pozzolana Renders for Reconstruction of Historical Buildings

International Nuclear Information System (INIS)

Vejmelkova, E.; Maca, P.; Konvalinka, P.; Cerny, R.

2011-01-01

Bulk density, matrix density, open porosity, compressive strength, bending strength, water sorptivity, moisture diffusivity, water vapor diffusion coefficient, thermal conductivity, specific heat capacity and thermal diffusivity of two innovative renovation renders on limepozzolana basis are analyzed. The obtained results are compared with reference lime plaster and two commercial renovation renders, and conclusions on the applicability of the particular renders in practical reconstruction works are drawn. (author)

Rotational structure in molecular infrared spectra

CERN Document Server

di Lauro, Carlo

2013-01-01

Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

Science.gov (United States)

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

Using neutrosophic graph cut segmentation algorithm for qualified rendering image selection in thyroid elastography video.

Science.gov (United States)

Guo, Yanhui; Jiang, Shuang-Quan; Sun, Baiqing; Siuly, Siuly; Şengür, Abdulkadir; Tian, Jia-Wei

2017-12-01

Recently, elastography has become very popular in clinical investigation for thyroid cancer detection and diagnosis. In elastogram, the stress results of the thyroid are displayed using pseudo colors. Due to variation of the rendering results in different frames, it is difficult for radiologists to manually select the qualified frame image quickly and efficiently. The purpose of this study is to find the qualified rendering result in the thyroid elastogram. This paper employs an efficient thyroid ultrasound image segmentation algorithm based on neutrosophic graph cut to find the qualified rendering images. Firstly, a thyroid ultrasound image is mapped into neutrosophic set, and an indeterminacy filter is constructed to reduce the indeterminacy of the spatial and intensity information in the image. A graph is defined on the image and the weight for each pixel is represented using the value after indeterminacy filtering. The segmentation results are obtained using a maximum-flow algorithm on the graph. Then the anatomic structure is identified in thyroid ultrasound image. Finally the rendering colors on these anatomic regions are extracted and validated to find the frames which satisfy the selection criteria. To test the performance of the proposed method, a thyroid elastogram dataset is built and totally 33 cases were collected. An experienced radiologist manually evaluates the selection results of the proposed method. Experimental results demonstrate that the proposed method finds the qualified rendering frame with 100% accuracy. The proposed scheme assists the radiologists to diagnose the thyroid diseases using the qualified rendering images.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

Directory of Open Access Journals (Sweden)

Rong Shen

2015-10-01

Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

Validation of a colour rendering index based on memory colours

OpenAIRE

Smet, Kevin; Jost-Boissard, Sophie; Ryckaert, Wouter; Deconinck, Geert; Hanselaer, Peter

2010-01-01

In this paper the performance of a colour rendering index based on memory colours is investigated in comparison with the current CIE Colour Rendering Index, the NIST Colour Quality Scale and visual appreciation results obtained at CNRS at Lyon University for a set of 3000K and 4000K LED light sources. The Pearson and Spearman correlation coefficients between each colour rendering metric and the two sets of visual results were calculated. It was found that the memory colour based colour render...

Media Presentation Synchronisation for Non-monolithic Rendering Architectures

NARCIS (Netherlands)

I. Vaishnavi (Ishan); D.C.A. Bulterman (Dick); P.S. Cesar Garcia (Pablo Santiago); B. Gao (Bo)

2007-01-01

htmlabstractNon-monolithic renderers are physically distributed media playback engines. Non-monolithic renderers may use a number of different underlying network connection types to transmit media items belonging to a presentation. There is therefore a need for a media based and inter-network- type

Extreme simplification and rendering of point sets using algebraic multigrid

NARCIS (Netherlands)

Reniers, D.; Telea, A.C.

2009-01-01

We present a novel approach for extreme simplification of point set models, in the context of real-time rendering. Point sets are often rendered using simple point primitives, such as oriented discs. However, this requires using many primitives to render even moderately simple shapes. Often, one

Volume rendering in treatment planning for moving targets

Energy Technology Data Exchange (ETDEWEB)

Gemmel, Alexander [GSI-Biophysics, Darmstadt (Germany); Massachusetts General Hospital, Boston (United States); Wolfgang, John A.; Chen, George T.Y. [Massachusetts General Hospital, Boston (United States)

2009-07-01

Advances in computer technologies have facilitated the development of tools for 3-dimensional visualization of CT-data sets with volume rendering. The company Fovia has introduced a high definition volume rendering engine (HDVR trademark by Fovia Inc., Palo Alto, USA) that is capable of representing large CT data sets with high user interactivity even on standard PCs. Fovia provides a software development kit (SDK) that offers control of all the features of the rendering engine. We extended the SDK by functionalities specific to the task of treatment planning for moving tumors. This included navigation of the patient's anatomy in beam's eye view, fast point-and-click measurement of lung tumor trajectories as well as estimation of range perturbations due to motion by calculation of (differential) water equivalent path lengths for protons and carbon ions on 4D-CT data sets. We present patient examples to demonstrate the advantages and disadvantages of volume rendered images as compared to standard 2-dimensional axial plane images. Furthermore, we show an example of a range perturbation analysis. We conclude that volume rendering is a powerful technique for the representation and analysis of large time resolved data sets in treatment planning.

Fast DRR splat rendering using common consumer graphics hardware

International Nuclear Information System (INIS)

Spoerk, Jakob; Bergmann, Helmar; Wanschitz, Felix; Dong, Shuo; Birkfellner, Wolfgang

2007-01-01

Digitally rendered radiographs (DRR) are a vital part of various medical image processing applications such as 2D/3D registration for patient pose determination in image-guided radiotherapy procedures. This paper presents a technique to accelerate DRR creation by using conventional graphics hardware for the rendering process. DRR computation itself is done by an efficient volume rendering method named wobbled splatting. For programming the graphics hardware, NVIDIAs C for Graphics (Cg) is used. The description of an algorithm used for rendering DRRs on the graphics hardware is presented, together with a benchmark comparing this technique to a CPU-based wobbled splatting program. Results show a reduction of rendering time by about 70%-90% depending on the amount of data. For instance, rendering a volume of 2x10 6 voxels is feasible at an update rate of 38 Hz compared to 6 Hz on a common Intel-based PC using the graphics processing unit (GPU) of a conventional graphics adapter. In addition, wobbled splatting using graphics hardware for DRR computation provides higher resolution DRRs with comparable image quality due to special processing characteristics of the GPU. We conclude that DRR generation on common graphics hardware using the freely available Cg environment is a major step toward 2D/3D registration in clinical routine

Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1980-01-01

Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

Technical analysis of volume-rendering algorithms: application in low-contrast structures using liver vascularisation as a model; Analisi tecnica degli algoritmi di volume rendering: applicazione alle strutture a basso contrsto usando come modello la vascolarizzazione epatica

Energy Technology Data Exchange (ETDEWEB)

Cademartiri, Filippo [Erasmus Medical Center, Rotterdam (Netherlands); Luccichenti, Giacomo [Fondazione Biomedica Europea ONLUS, Roma (Italy); Runza, Giuseppe; Bartolotta, Tommaso Vincenzo; Midiri, Massimo [Palermo Univ., Palermo (Italy). Sezione di scienze radiologiche; Gualerzi, Massimo; Brambilla, Lorenzo; Coruzzi, Paolo [Parma Univ., Parma (Italy). UO di prevenzione e riabilitazione vascolare, Fondazione Don C. Gnocchi ONLUS; Soliani, Paolo; Sianesi, Mario [Parma Univ., Parma (Italy). Dipartimento di chirurgia

2005-04-01

Purpose: To assess the influence of pre-set volume rendering opacity curves (OC) on image quality and to identify which absolute parameters (density of aorta, hepatic parenchyma and portal vein) affect visualization of portal vascular structures (low-contrast structures). Materials and methods: Twenty-two patients underwent a dual-phase spiral CT with the following parameters: collimation 3 mm, pitch 2, increment 1 mm. Three scans were performed: one without contrast medium and the latter two after the injection of contrast material (conventionally identified as 'arterial' and 'portal'). The images were sent to a workstation running on an NT platform equipped with post-processing software allowing three-dimensional (3D) reconstructions to generate volume-rendered images of the vascular supply to the liver. Correlation between the absolute values of aorta, liver and portal vein density, OC parameters, and image quality were assessed. Results: 3D images generated using pre-set OC obtained a much mower overall quality score than those produced with OC set by the operator. High contrast between the liver and the portal vein, for example during the portal vascular phase, allows wider windows, thus improving image quality. Conversely, the OC in the parenchymal phase scans must have a high gradient in order to better differentiate between the vascular structures and the surrounding hepatic parenchyma. Conclusions: Image features considered to be of interest by the operator cannot be simplified by the mean of pre-set OC. Due to their strong individual variability automatic 3D algorithms cannot be universally applied: they should be adapted to both image and patient characteristics. [Italian] Scopo: Valutare l'influenza delle curve di opacit� (CO) preimpostate del volume-rendering sulla qualit� delle immagini, ed identificare quali parametri assoluti (attenzione dell'aorta, del parenchima epatico e della vena porta) influenzano la

3D rendering and interactive visualization technology in large industry CT

International Nuclear Information System (INIS)

Xiao Yongshun; Zhang Li; Chen Zhiqiang; Kang Kejun

2002-01-01

The author introduces the applications of interactive 3D rendering technology in the large ICT. It summarizes and comments on the iso-surfaces rendering and the direct volume rendering methods used in ICT. The author emphasizes on the technical analysis of the 3D rendering process of ICT volume data sets, and summarizes the difficulties of the inspection subsystem design in large ICT

3D rendering and interactive visualization technology in large industry CT

International Nuclear Information System (INIS)

Xiao Yongshun; Zhang Li; Chen Zhiqiang; Kang Kejun

2001-01-01

This paper introduces the applications of interactive 3D rendering technology in the large ICT. It summarizes and comments on the iso-surfaces rendering and the direct volume rendering methods used in ICT. The paper emphasizes on the technical analysis of the 3D rendering process of ICT volume data sets, and summarizes the difficulties of the inspection subsystem design in large ICT

A Real-Time Sound Field Rendering Processor

Directory of Open Access Journals (Sweden)

Tan Yiyu

2017-12-01

Full Text Available Real-time sound field renderings are computationally intensive and memory-intensive. Traditional rendering systems based on computer simulations suffer from memory bandwidth and arithmetic units. The computation is time-consuming, and the sample rate of the output sound is low because of the long computation time at each time step. In this work, a processor with a hybrid architecture is proposed to speed up computation and improve the sample rate of the output sound, and an interface is developed for system scalability through simply cascading many chips to enlarge the simulated area. To render a three-minute Beethoven wave sound in a small shoe-box room with dimensions of 1.28 m × 1.28 m × 0.64 m, the field programming gate array (FPGA-based prototype machine with the proposed architecture carries out the sound rendering at run-time while the software simulation with the OpenMP parallelization takes about 12.70 min on a personal computer (PC with 32 GB random access memory (RAM and an Intel i7-6800K six-core processor running at 3.4 GHz. The throughput in the software simulation is about 194 M grids/s while it is 51.2 G grids/s in the prototype machine even if the clock frequency of the prototype machine is much lower than that of the PC. The rendering processor with a processing element (PE and interfaces consumes about 238,515 gates after fabricated by the 0.18 µm processing technology from the ROHM semiconductor Co., Ltd. (Kyoto Japan, and the power consumption is about 143.8 mW.

Simplification of Visual Rendering in Simulated Prosthetic Vision Facilitates Navigation.

Science.gov (United States)

Vergnieux, Victor; Macé, Marc J-M; Jouffrais, Christophe

2017-09-01

Visual neuroprostheses are still limited and simulated prosthetic vision (SPV) is used to evaluate potential and forthcoming functionality of these implants. SPV has been used to evaluate the minimum requirement on visual neuroprosthetic characteristics to restore various functions such as reading, objects and face recognition, object grasping, etc. Some of these studies focused on obstacle avoidance but only a few investigated orientation or navigation abilities with prosthetic vision. The resolution of current arrays of electrodes is not sufficient to allow navigation tasks without additional processing of the visual input. In this study, we simulated a low resolution array (15 × 18 electrodes, similar to a forthcoming generation of arrays) and evaluated the navigation abilities restored when visual information was processed with various computer vision algorithms to enhance the visual rendering. Three main visual rendering strategies were compared to a control rendering in a wayfinding task within an unknown environment. The control rendering corresponded to a resizing of the original image onto the electrode array size, according to the average brightness of the pixels. In the first rendering strategy, vision distance was limited to 3, 6, or 9 m, respectively. In the second strategy, the rendering was not based on the brightness of the image pixels, but on the distance between the user and the elements in the field of view. In the last rendering strategy, only the edges of the environments were displayed, similar to a wireframe rendering. All the tested renderings, except the 3 m limitation of the viewing distance, improved navigation performance and decreased cognitive load. Interestingly, the distance-based and wireframe renderings also improved the cognitive mapping of the unknown environment. These results show that low resolution implants are usable for wayfinding if specific computer vision algorithms are used to select and display appropriate

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

Blender cycles lighting and rendering cookbook

CERN Document Server

Iraci, Bernardo

2013-01-01

An in-depth guide full of step-by-step recipes to explore the concepts behind the usage of Cycles. Packed with illustrations, and lots of tips and tricks; the easy-to-understand nature of the book will help the reader understand even the most complex concepts with ease.If you are a digital artist who already knows your way around Blender, and you want to learn about the new Cycles' rendering engine, this is the book for you. Even experts will be able to pick up new tips and tricks to make the most of the rendering capabilities of Cycles.

Three-dimensional rendering of segmented object using matlab - biomed 2010.

Science.gov (United States)

Anderson, Jeffrey R; Barrett, Steven F

2010-01-01

The three-dimensional rendering of microscopic objects is a difficult and challenging task that often requires specialized image processing techniques. Previous work has been described of a semi-automatic segmentation process of fluorescently stained neurons collected as a sequence of slice images with a confocal laser scanning microscope. Once properly segmented, each individual object can be rendered and studied as a three-dimensional virtual object. This paper describes the work associated with the design and development of Matlab files to create three-dimensional images from the segmented object data previously mentioned. Part of the motivation for this work is to integrate both the segmentation and rendering processes into one software application, providing a seamless transition from the segmentation tasks to the rendering and visualization tasks. Previously these tasks were accomplished on two different computer systems, windows and Linux. This transition basically limits the usefulness of the segmentation and rendering applications to those who have both computer systems readily available. The focus of this work is to create custom Matlab image processing algorithms for object rendering and visualization, and merge these capabilities to the Matlab files that were developed especially for the image segmentation task. The completed Matlab application will contain both the segmentation and rendering processes in a single graphical user interface, or GUI. This process for rendering three-dimensional images in Matlab requires that a sequence of two-dimensional binary images, representing a cross-sectional slice of the object, be reassembled in a 3D space, and covered with a surface. Additional segmented objects can be rendered in the same 3D space. The surface properties of each object can be varied by the user to aid in the study and analysis of the objects. This inter-active process becomes a powerful visual tool to study and understand microscopic objects.

Real-Time Location-Based Rendering of Urban Underground Pipelines

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Wei Li

2018-01-01

Full Text Available The concealment and complex spatial relationships of urban underground pipelines present challenges in managing them. Recently, augmented reality (AR has been a hot topic around the world, because it can enhance our perception of reality by overlaying information about the environment and its objects onto the real world. Using AR, underground pipelines can be displayed accurately, intuitively, and in real time. We analyzed the characteristics of AR and their application in underground pipeline management. We mainly focused on the AR pipeline rendering procedure based on the BeiDou Navigation Satellite System (BDS and simultaneous localization and mapping (SLAM technology. First, in aiming to improve the spatial accuracy of pipeline rendering, we used differential corrections received from the Ground-Based Augmentation System to compute the precise coordinates of users in real time, which helped us accurately retrieve and draw pipelines near the users, and by scene recognition the accuracy can be further improved. Second, in terms of pipeline rendering, we used Visual-Inertial Odometry (VIO to track the rendered objects and made some improvements to visual effects, which can provide steady dynamic tracking of pipelines even in relatively markerless environments and outdoors. Finally, we used the occlusion method based on real-time 3D reconstruction to realistically express the immersion effect of underground pipelines. We compared our methods to the existing methods and concluded that the method proposed in this research improves the spatial accuracy of pipeline rendering and the portability of the equipment. Moreover, the updating of our rendering procedure corresponded with the moving of the user’s location, thus we achieved a dynamic rendering of pipelines in the real environment.

Visualization of normal and abnormal inner ear with volume rendering technique using multislice spiral CT

International Nuclear Information System (INIS)

Ma Hui; Han Ping; Liang Bo; Lei Ziqiao; Liu Fang; Tian Zhiliang

2006-01-01

Objective: To evaluate the ability of the volume rendering technique to display the normal and abnormal inner ear structures. Methods: Forty normal earand 61 abnormal inner ears (40 congenital inner ear malformations, 7 labyrinthitis ossificans, and 14 inner ear erosion caused by cholesteatomas) were examined with a MSCT scanner. Axial imaging were performed using the following parameters: 120 kV, 100 mAs, 0.75 mm slice thickness, a pitch factor of 1. The axial images of interested ears were reconstructed with 0.1 mm reconstruction increment and a FOV of 50 mm. The 3D reconstructions were done with volume rendering technique on the workstation. Results: In the subjects without ear disorders a high quality 3D visualization of the inner ear could be achieved. In the patients with inner ear' disorders all inner ear malformations could be clearly displayed on 3D images as follows: (1) Michel deformity (one ear): There was complete absence of all cochlear and vestibular structures. (2) common cavity deformity (3 ears): The cochlea and vestibule were represented by a cystic cavity and couldn't be differentiated from each other. (3)incomplete partition type I (3 ears): The cochlea lacked the entire modiolus and cribriform area, resulting in a cystic appearance. (4) incomplete partition type II (Mondini deformity) (5 ears): The cochlea consisted of 1.5 turns, in which the middle and apical turns coalesced to form a cystic apex. (5) vestibular and semicircular canal malformations (14 ears): Cochlea was normal, vestibule dilated, semicircular canals were absent, hypoplastic or enlarged. (6) dilated vestibular aqueduct (14 ears): The vestibular aqueduct was bell-mouthed. In 7 patients with labyrinthifis ossificans, 3D images failed to clearly show the completeinner ears in 4 ears because of too high ossifications in the membranous labyrinth. In the other 3 ears volume rendering could display the thin cochlea basal turn and the intermittent semicircular canals. In the patients

Interactive dual-volume rendering visualization with real-time fusion and transfer function enhancement

Science.gov (United States)

Macready, Hugh; Kim, Jinman; Feng, David; Cai, Weidong

2006-03-01

Dual-modality imaging scanners combining functional PET and anatomical CT constitute a challenge in volumetric visualization that can be limited by the high computational demand and expense. This study aims at providing physicians with multi-dimensional visualization tools, in order to navigate and manipulate the data running on a consumer PC. We have maximized the utilization of pixel-shader architecture of the low-cost graphic hardware and the texture-based volume rendering to provide visualization tools with high degree of interactivity. All the software was developed using OpenGL and Silicon Graphics Inc. Volumizer, tested on a Pentium mobile CPU on a PC notebook with 64M graphic memory. We render the individual modalities separately, and performing real-time per-voxel fusion. We designed a novel "alpha-spike" transfer function to interactively identify structure of interest from volume rendering of PET/CT. This works by assigning a non-linear opacity to the voxels, thus, allowing the physician to selectively eliminate or reveal information from the PET/CT volumes. As the PET and CT are rendered independently, manipulations can be applied to individual volumes, for instance, the application of transfer function to CT to reveal the lung boundary while adjusting the fusion ration between the CT and PET to enhance the contrast of a tumour region, with the resultant manipulated data sets fused together in real-time as the adjustments are made. In addition to conventional navigation and manipulation tools, such as scaling, LUT, volume slicing, and others, our strategy permits efficient visualization of PET/CT volume rendering which can potentially aid in interpretation and diagnosis.

An interactive tool for CT volume rendering and sagittal plane-picking of the prostate for radiotherapy treatment planning

International Nuclear Information System (INIS)

Jani, Ashesh B.; Pelizzari, Charles A.; Chen, George T.Y.; Grzezcszuk, Robert P.; Vijayakumar, Srinivasan

1997-01-01

Objective: Accurate and precise target volume and critical structure definition is a basic necessity in radiotherapy. The prostate, particularly the apex (an important potential site of recurrence in prostate cancer patients), is a challenging structure to define using any modality, including conventional axial CT. Invasive or expensive techniques, such as retrograde urethrography or MRI, could be avoided if localization of the prostate were possible using information already available on the planning CT. Our primary objective was to build a software tool to determine whether volume rendering and sagittal plane-picking, which are CT-based, noninvasive visualization techniques, were of utility in radiotherapy treatment planning for the prostate. Methods: Using AVS (Application Visualization System) on a Silicon Graphics Indigo 2 High Impact workstation, we have developed a tool that enables the clinician to efficiently navigate a CT volume and to use volume rendering and sagittal plane-picking to better define structures at any anatomic site. We applied the tool to the specific example of the prostate to compare the two visualization techniques with the current standard of axial CT. The prostate was defined on 80-slice CT scans (scanning thickness 4mm, pixel size 2mm x 2mm) of prostate cancer patients using axial CT images, volume-rendered CT images, and sagittal plane-picked images. Results: The navigation of the prostate using the different visualization techniques qualitatively demonstrated that the sagittal plane-picked images, and even more so the volume-rendered images, revealed the prostate (particularly the lower border) better in relationship to the surrounding regional anatomy (bladder, rectum, pelvis, and penile structures) than did the axial images. A quantitative comparison of the target volumes obtained by navigating using the different visualization techniques demonstrated that, when compared to the prostate volume defined on axial CT, a larger volume

Molecular Structure of Membrane Tethers

NARCIS (Netherlands)

Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

2012-01-01

Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains

Structures of Life: The Role of Molecular Structures in Scientists' Work

NARCIS (Netherlands)

Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J

2008-01-01

The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

Conservation of the historical render in the Church of Nossa Senhora da Assunção in Elvas

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Sofia Salema

2008-01-01

Full Text Available In this paper we present a practical case of conservation of the historical renders in the pyramidal tower of the Church of Nossa Senhora da Assunção in Elvas (Portugal, carried out by the former IPPAR (Portuguese Institute of Architectonic Heritage, now Regional Direction of Culture of Alentejo. Awareness of the value and of the risks facing these renders points towards the necessity to safeguard their material authenticity. During the works of conservation of the main façade, under the layers of non decorated recovering render, a previous decorated render, simulating stone masonry, with raised joints reproducing stone divisions and the internal structure in solid brick, was discovered. After material and historical analysis we came to the conclusion that it was highly probable that this render was contemporary to the construction of the Church and, as such, it seemed essential to conserve and restore this covering as historical evidence and cultural heritage. Treatment of the pyramidal tower render included removal of the non original recover mortars, survey of ancient materials, execution of technical and decorative scheme, surfaces' cleaning and consolidation of the weaker original old mortars. In order to fill the gaps in the original surface, specific lime mortars, prepared with washed sand and standard grain size, were used. Restoration techniques were used to reconstitute and integrate the lacunas. These actions not only conserved the workmanship, but also reconstructed the decorative structure and a reading clarity, allowing the identification of restoration without the connotation of a mimetic integration. This joint action, only possible with the help of the conservation and restoration team, puts into evidence the possibility of continuous evaluation and learning. It is clear that, in cases where there are unknown, unpredictable factors, due to the specific work and value of the materials, it is possible to change the course

Advances in Rosetta structure prediction for difficult molecular-replacement problems

International Nuclear Information System (INIS)

DiMaio, Frank

2013-01-01

Modeling advances using Rosetta structure prediction to aid in solving difficult molecular-replacement problems are discussed. Recent work has shown the effectiveness of structure-prediction methods in solving difficult molecular-replacement problems. The Rosetta protein structure modeling suite can aid in the solution of difficult molecular-replacement problems using templates from 15 to 25% sequence identity; Rosetta refinement guided by noisy density has consistently led to solved structures where other methods fail. In this paper, an overview of the use of Rosetta for these difficult molecular-replacement problems is provided and new modeling developments that further improve model quality are described. Several variations to the method are introduced that significantly reduce the time needed to generate a model and the sampling required to improve the starting template. The improvements are benchmarked on a set of nine difficult cases and it is shown that this improved method obtains consistently better models in less running time. Finally, strategies for best using Rosetta to solve difficult molecular-replacement problems are presented and future directions for the role of structure-prediction methods in crystallography are discussed

High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL

Science.gov (United States)

Stone, John E.; Messmer, Peter; Sisneros, Robert; Schulten, Klaus

2016-01-01

Large scale molecular dynamics simulations produce terabytes of data that is impractical to transfer to remote facilities. It is therefore necessary to perform visualization tasks in-situ as the data are generated, or by running interactive remote visualization sessions and batch analyses co-located with direct access to high performance storage systems. A significant challenge for deploying visualization software within clouds, clusters, and supercomputers involves the operating system software required to initialize and manage graphics acceleration hardware. Recently, it has become possible for applications to use the Embedded-system Graphics Library (EGL) to eliminate the requirement for windowing system software on compute nodes, thereby eliminating a significant obstacle to broader use of high performance visualization applications. We outline the potential benefits of this approach in the context of visualization applications used in the cloud, on commodity clusters, and supercomputers. We discuss the implementation of EGL support in VMD, a widely used molecular visualization application, and we outline benefits of the approach for molecular visualization tasks on petascale computers, clouds, and remote visualization servers. We then provide a brief evaluation of the use of EGL in VMD, with tests using developmental graphics drivers on conventional workstations and on Amazon EC2 G2 GPU-accelerated cloud instance types. We expect that the techniques described here will be of broad benefit to many other visualization applications. PMID:27747137

Emission of VOC's from modified rendering process

International Nuclear Information System (INIS)

Bhatti, Z.A.; Raja, I.A.; Saddique, M.; Langenhove, H.V.

2005-01-01

Rendering technique for processing of dead animal and slaughterhouse wastes into valuable products. It involves cooking of raw material and later Sterilization was added to reduce the Bovine Spongiform Encephalopathy (BSE). Studies have been carried out on rendering emission, with the normal cooking process. Our study shows, that the sterilization step in rendering process increases the emission of volatile organic compounds (VOC's). Gas samples, containing VOC's, were analyzed by the GC/MS (Gas Chromatograph and Mass Spectrometry). The most important groups of compounds- alcohols and cyclic hydrocarbons were identified. In the group of alcohol; 1-butanol, l-pentanol and l-hexanol compounds were found while in the group of cyclic hydrocarbon; methyl cyclopentane and cyclohexane compounds were detected. Other groups like aldehyde, sulphur containing compounds, ketone and furan were also found. Some compounds, like l-pentanol, 2-methyl propanal, dimethyl disulfide and dimethyl trisulfide, which belong to these groups, cause malodor. It is important to know these compounds to treat odorous gasses. (author)

A kinesthetic washout filter for force-feedback rendering.

Science.gov (United States)

Danieau, Fabien; Lecuyer, Anatole; Guillotel, Philippe; Fleureau, Julien; Mollet, Nicolas; Christie, Marc

2015-01-01

Today haptic feedback can be designed and associated to audiovisual content (haptic-audiovisuals or HAV). Although there are multiple means to create individual haptic effects, the issue of how to properly adapt such effects on force-feedback devices has not been addressed and is mostly a manual endeavor. We propose a new approach for the haptic rendering of HAV, based on a washout filter for force-feedback devices. A body model and an inverse kinematics algorithm simulate the user's kinesthetic perception. Then, the haptic rendering is adapted in order to handle transitions between haptic effects and to optimize the amplitude of effects regarding the device capabilities. Results of a user study show that this new haptic rendering can successfully improve the HAV experience.

Processing-in-Memory Enabled Graphics Processors for 3D Rendering

Energy Technology Data Exchange (ETDEWEB)

Xie, Chenhao; Song, Shuaiwen; Wang, Jing; Zhang, Weigong; Fu, Xin

2017-02-06

The performance of 3D rendering of Graphics Processing Unit that convents 3D vector stream into 2D frame with 3D image effects significantly impact users’ gaming experience on modern computer systems. Due to the high texture throughput in 3D rendering, main memory bandwidth becomes a critical obstacle for improving the overall rendering performance. 3D stacked memory systems such as Hybrid Memory Cube (HMC) provide opportunities to significantly overcome the memory wall by directly connecting logic controllers to DRAM dies. Based on the observation that texel fetches significantly impact off-chip memory traffic, we propose two architectural designs to enable Processing-In-Memory based GPU for efficient 3D rendering.

Molecular structure of dextran sulphate sodium in aqueous environment

Science.gov (United States)

Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

2018-03-01

Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

RAY TRACING RENDER MENGGUNAKAN FRAGMENT ANTI ALIASING

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Febriliyan Samopa

2008-07-01

Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Rendering is generating surface and three-dimensional effects on an object displayed on a monitor screen. Ray tracing as a rendering method that traces ray for each image pixel has a drawback, that is, aliasing (jaggies effect. There are some methods for executing anti aliasing. One of those methods is OGSS (Ordered Grid Super Sampling. OGSS is able to perform aliasing well. However, this method requires more computation time since sampling of all pixels in the image will be increased. Fragment Anti Aliasing (FAA is a new alternative method that can cope with the drawback. FAA will check the image when performing rendering to a scene. Jaggies effect is only happened at curve and gradient object. Therefore, only this part of object that will experience sampling magnification. After this sampling magnification and the pixel values are computed, then downsample is performed to retrieve the original pixel values. Experimental results show that the software can implement ray tracing well in order to form images, and it can implement FAA and OGSS technique to perform anti aliasing. In general, rendering using FAA is faster than using OGSS

Molecular structure and motion in zero field magnetic resonance

International Nuclear Information System (INIS)

Jarvie, T.P.

1989-10-01

Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

Ab initio study of structural and mechanical property of solid molecular hydrogens

Science.gov (United States)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Simulation and training of lumbar punctures using haptic volume rendering and a 6DOF haptic device

Science.gov (United States)

Färber, Matthias; Heller, Julika; Handels, Heinz

2007-03-01

The lumbar puncture is performed by inserting a needle into the spinal chord of the patient to inject medicaments or to extract liquor. The training of this procedure is usually done on the patient guided by experienced supervisors. A virtual reality lumbar puncture simulator has been developed in order to minimize the training costs and the patient's risk. We use a haptic device with six degrees of freedom (6DOF) to feedback forces that resist needle insertion and rotation. An improved haptic volume rendering approach is used to calculate the forces. This approach makes use of label data of relevant structures like skin, bone, muscles or fat and original CT data that contributes information about image structures that can not be segmented. A real-time 3D visualization with optional stereo view shows the punctured region. 2D visualizations of orthogonal slices enable a detailed impression of the anatomical context. The input data consisting of CT and label data and surface models of relevant structures is defined in an XML file together with haptic rendering and visualization parameters. In a first evaluation the visible human male data has been used to generate a virtual training body. Several users with different medical experience tested the lumbar puncture trainer. The simulator gives a good haptic and visual impression of the needle insertion and the haptic volume rendering technique enables the feeling of unsegmented structures. Especially, the restriction of transversal needle movement together with rotation constraints enabled by the 6DOF device facilitate a realistic puncture simulation.

Digital color acquisition, perception, coding and rendering

CERN Document Server

Fernandez-Maloigne, Christine; Macaire, Ludovic

2013-01-01

In this book the authors identify the basic concepts and recent advances in the acquisition, perception, coding and rendering of color. The fundamental aspects related to the science of colorimetry in relation to physiology (the human visual system) are addressed, as are constancy and color appearance. It also addresses the more technical aspects related to sensors and the color management screen. Particular attention is paid to the notion of color rendering in computer graphics. Beyond color, the authors also look at coding, compression, protection and quality of color images and videos.

LOD 1 VS. LOD 2 - Preliminary Investigations Into Differences in Mobile Rendering Performance

Science.gov (United States)

Ellul, C.; Altenbuchner, J.

2013-09-01

The increasing availability, size and detail of 3D City Model datasets has led to a challenge when rendering such data on mobile devices. Understanding the limitations to the usability of such models on these devices is particularly important given the broadening range of applications - such as pollution or noise modelling, tourism, planning, solar potential - for which these datasets and resulting visualisations can be utilized. Much 3D City Model data is created by extrusion of 2D topographic datasets, resulting in what is known as Level of Detail (LoD) 1 buildings - with flat roofs. However, in the UK the National Mapping Agency (the Ordnance Survey, OS) is now releasing test datasets to Level of Detail (LoD) 2 - i.e. including roof structures. These datasets are designed to integrate with the LoD 1 datasets provided by the OS, and provide additional detail in particular on larger buildings and in town centres. The availability of such integrated datasets at two different Levels of Detail permits investigation into the impact of the additional roof structures (and hence the display of a more realistic 3D City Model) on rendering performance on a mobile device. This paper describes preliminary work carried out to investigate this issue, for the test area of the city of Sheffield (in the UK Midlands). The data is stored in a 3D spatial database as triangles and then extracted and served as a web-based data stream which is queried by an App developed on the mobile device (using the Android environment, Java and OpenGL for graphics). Initial tests have been carried out on two dataset sizes, for the city centre and a larger area, rendering the data onto a tablet to compare results. Results of 52 seconds for rendering LoD 1 data, and 72 seconds for LoD 1 mixed with LoD 2 data, show that the impact of LoD 2 is significant.

Nanohashtag structures based on carbon nanotubes and molecular linkers

Science.gov (United States)

Frye, Connor W.; Rybolt, Thomas R.

2018-03-01

Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

Cellular and Molecular Basis of Cerebellar Development

Directory of Open Access Journals (Sweden)

Salvador eMartinez

2013-06-01

Full Text Available Historically, the molecular and cellular mechanisms of cerebellar development were investigated through structural descriptions and studying spontaneous mutations in animal models and humans. Advances in experimental embryology, genetic engineering and neuroimaging techniques render today the possibility to approach the analysis of molecular mechanisms underlying histogenesis and morphogenesis of the cerebellum by experimental designs. Several genes and molecules were identified to be involved in the cerebellar plate regionalization, specification and differentiation of cerebellar neurons, as well as the establishment of cellular migratory routes and the subsequent neuronal connectivity. Indeed, pattern formation of the cerebellum requires the adequate orchestration of both key morphogenetic signals, arising from distinct brain regions, and local expression of specific transcription factors. Thus, the present review wants to revisit and discuss these morphogenetic and molecular mechanisms taking place during cerebellar development in order to understand causal processes regulating cerebellar cytoarchitecture, its highly topographically ordered circuitry and its role in brain function.

Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

2017-08-05

The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

Design and Implementation of High-Performance GIS Dynamic Objects Rendering Engine

Science.gov (United States)

Zhong, Y.; Wang, S.; Li, R.; Yun, W.; Song, G.

2017-12-01

Spatio-temporal dynamic visualization is more vivid than static visualization. It important to use dynamic visualization techniques to reveal the variation process and trend vividly and comprehensively for the geographical phenomenon. To deal with challenges caused by dynamic visualization of both 2D and 3D spatial dynamic targets, especially for different spatial data types require high-performance GIS dynamic objects rendering engine. The main approach for improving the rendering engine with vast dynamic targets relies on key technologies of high-performance GIS, including memory computing, parallel computing, GPU computing and high-performance algorisms. In this study, high-performance GIS dynamic objects rendering engine is designed and implemented for solving the problem based on hybrid accelerative techniques. The high-performance GIS rendering engine contains GPU computing, OpenGL technology, and high-performance algorism with the advantage of 64-bit memory computing. It processes 2D, 3D dynamic target data efficiently and runs smoothly with vast dynamic target data. The prototype system of high-performance GIS dynamic objects rendering engine is developed based SuperMap GIS iObjects. The experiments are designed for large-scale spatial data visualization, the results showed that the high-performance GIS dynamic objects rendering engine have the advantage of high performance. Rendering two-dimensional and three-dimensional dynamic objects achieve 20 times faster on GPU than on CPU.

Haptic rendering for simulation of fine manipulation

CERN Document Server

Wang, Dangxiao; Zhang, Yuru

2014-01-01

This book introduces the latest progress in six degrees of freedom (6-DoF) haptic rendering with the focus on a new approach for simulating force/torque feedback in performing tasks that require dexterous manipulation skills. One of the major challenges in 6-DoF haptic rendering is to resolve the conflict between high speed and high fidelity requirements, especially in simulating a tool interacting with both rigid and deformable objects in a narrow space and with fine features. The book presents a configuration-based optimization approach to tackle this challenge. Addressing a key issue in man

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

Science.gov (United States)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P R2 = 0.87, RSD = 0.74, P R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

GRAPHICS-IMAGE MIXED METHOD FOR LARGE-SCALE BUILDINGS RENDERING

Directory of Open Access Journals (Sweden)

Y. Zhou

2018-05-01

Full Text Available Urban 3D model data is huge and unstructured, LOD and Out-of-core algorithm are usually used to reduce the amount of data that drawn in each frame to improve the rendering efficiency. When the scene is large enough, even the complex optimization algorithm is difficult to achieve better results. Based on the traditional study, a novel idea was developed. We propose a graphics and image mixed method for large-scale buildings rendering. Firstly, the view field is divided into several regions, the graphics-image mixed method used to render the scene on both screen and FBO, then blending the FBO with scree. The algorithm is tested on the huge CityGML model data in the urban areas of New York which contained 188195 public building models, and compared with the Cesium platform. The experiment result shows the system was running smoothly. The experimental results confirm that the algorithm can achieve more massive building scene roaming under the same hardware conditions, and can rendering the scene without vision loss.

Enhancement method for rendered images of home decoration based on SLIC superpixels

Science.gov (United States)

Dai, Yutong; Jiang, Xiaotong

2018-04-01

Rendering technology has been widely used in the home decoration industry in recent years for images of home decoration design. However, due to the fact that rendered images of home decoration design rely heavily on the parameters of renderer and the lights of scenes, most rendered images in this industry require further optimization afterwards. To reduce workload and enhance rendered images automatically, an algorithm utilizing neural networks is proposed in this manuscript. In addition, considering few extreme conditions such as strong sunlight and lights, SLIC superpixels based segmentation is used to choose out these bright areas of an image and enhance them independently. Finally, these chosen areas are merged with the entire image. Experimental results show that the proposed method effectively enhances the rendered images when compared with some existing algorithms. Besides, the proposed strategy is proven to be adaptable especially to those images with obvious bright parts.

View compensated compression of volume rendered images for remote visualization.

Science.gov (United States)

Lalgudi, Hariharan G; Marcellin, Michael W; Bilgin, Ali; Oh, Han; Nadar, Mariappan S

2009-07-01

Remote visualization of volumetric images has gained importance over the past few years in medical and industrial applications. Volume visualization is a computationally intensive process, often requiring hardware acceleration to achieve a real time viewing experience. One remote visualization model that can accomplish this would transmit rendered images from a server, based on viewpoint requests from a client. For constrained server-client bandwidth, an efficient compression scheme is vital for transmitting high quality rendered images. In this paper, we present a new view compensation scheme that utilizes the geometric relationship between viewpoints to exploit the correlation between successive rendered images. The proposed method obviates motion estimation between rendered images, enabling significant reduction to the complexity of a compressor. Additionally, the view compensation scheme, in conjunction with JPEG2000 performs better than AVC, the state of the art video compression standard.

Near-term nanotechnology: the molecular fabrication of nanostructured materials

Science.gov (United States)

Gillett, Stephen L.

1996-09-01

The remarkably short timescales commonly predicted for achieving full molecular nanotechnology (MNT) are not realistic, as an enormous investment must be made up-front for a distant and ill-defined payoff. The reason is that technology, per se, is not an economic driver; economics instead drives technology. Hence, markets that could motivate the ongoing, incremental development of MNT must be sought. Such markets exist: they fundamentally consist of the molecular assembly of nano structured materials such as semipermeable membranes, catalysts, perfect crystalline fibres, and others. Although in theory atomically precise, such materials have no molecular moving parts and thus will be both easier to build and more robust. Some of these applications (e.g. catalysis), moreover, have huge, mature markets. Once a demand is established, further incremental development of primitive molecular assemblers, or `molecular looms', might then justify the analogies with the explosive development of computer hardware over the last few decades. Finally, the fact that many such applications are likely to be rendered obsolete by full MNT is irrelevant to their interim value as technology drivers.

Real-time volume rendering of digital medical images on an iOS device

Science.gov (United States)

Noon, Christian; Holub, Joseph; Winer, Eliot

2013-03-01

Performing high quality 3D visualizations on mobile devices, while tantalizingly close in many areas, is still a quite difficult task. This is especially true for 3D volume rendering of digital medical images. Allowing this would empower medical personnel a powerful tool to diagnose and treat patients and train the next generation of physicians. This research focuses on performing real time volume rendering of digital medical images on iOS devices using custom developed GPU shaders for orthogonal texture slicing. An interactive volume renderer was designed and developed with several new features including dynamic modification of render resolutions, an incremental render loop, a shader-based clipping algorithm to support OpenGL ES 2.0, and an internal backface culling algorithm for properly sorting rendered geometry with alpha blending. The application was developed using several application programming interfaces (APIs) such as OpenSceneGraph (OSG) as the primary graphics renderer coupled with iOS Cocoa Touch for user interaction, and DCMTK for DICOM I/O. The developed application rendered volume datasets over 450 slices up to 50-60 frames per second, depending on the specific model of the iOS device. All rendering is done locally on the device so no Internet connection is required.

Molecular structure descriptors in the computer-aided design of biologically active compounds

International Nuclear Information System (INIS)

Raevsky, Oleg A

1999-01-01

The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

Cloud-based Monte Carlo modelling of BSSRDF for the rendering of human skin appearance (Conference Presentation)

Science.gov (United States)

Doronin, Alexander; Rushmeier, Holly E.; Meglinski, Igor; Bykov, Alexander V.

2016-03-01

We present a new Monte Carlo based approach for the modelling of Bidirectional Scattering-Surface Reflectance Distribution Function (BSSRDF) for accurate rendering of human skin appearance. The variations of both skin tissues structure and the major chromophores are taken into account correspondingly to the different ethnic and age groups. The computational solution utilizes HTML5, accelerated by the graphics processing units (GPUs), and therefore is convenient for the practical use at the most of modern computer-based devices and operating systems. The results of imitation of human skin reflectance spectra, corresponding skin colours and examples of 3D faces rendering are presented and compared with the results of phantom studies.

Freely-available, true-color volume rendering software and cryohistology data sets for virtual exploration of the temporal bone anatomy.

Science.gov (United States)

Kahrs, Lüder Alexander; Labadie, Robert Frederick

2013-01-01

Cadaveric dissection of temporal bone anatomy is not always possible or feasible in certain educational environments. Volume rendering using CT and/or MRI helps understanding spatial relationships, but they suffer in nonrealistic depictions especially regarding color of anatomical structures. Freely available, nonstained histological data sets and software which are able to render such data sets in realistic color could overcome this limitation and be a very effective teaching tool. With recent availability of specialized public-domain software, volume rendering of true-color, histological data sets is now possible. We present both feasibility as well as step-by-step instructions to allow processing of publicly available data sets (Visible Female Human and Visible Ear) into easily navigable 3-dimensional models using free software. Example renderings are shown to demonstrate the utility of these free methods in virtual exploration of the complex anatomy of the temporal bone. After exploring the data sets, the Visible Ear appears more natural than the Visible Human. We provide directions for an easy-to-use, open-source software in conjunction with freely available histological data sets. This work facilitates self-education of spatial relationships of anatomical structures inside the human temporal bone as well as it allows exploration of surgical approaches prior to cadaveric testing and/or clinical implementation. Copyright © 2013 S. Karger AG, Basel.

Integral image rendering procedure for aberration correction and size measurement.

Science.gov (United States)

Sommer, Holger; Ihrig, Andreas; Ebenau, Melanie; Flühs, Dirk; Spaan, Bernhard; Eichmann, Marion

2014-05-20

The challenge in rendering integral images is to use as much information preserved by the light field as possible to reconstruct a captured scene in a three-dimensional way. We propose a rendering algorithm based on the projection of rays through a detailed simulation of the optical path, considering all the physical properties and locations of the optical elements. The rendered images contain information about the correct size of imaged objects without the need to calibrate the imaging device. Additionally, aberrations of the optical system may be corrected, depending on the setup of the integral imaging device. We show simulation data that illustrates the aberration correction ability and experimental data from our plenoptic camera, which illustrates the capability of our proposed algorithm to measure size and distance. We believe this rendering procedure will be useful in the future for three-dimensional ophthalmic imaging of the human retina.

Light Field Rendering for Head Mounted Displays using Pixel Reprojection

DEFF Research Database (Denmark)

Hansen, Anne Juhler; Klein, Jákup; Kraus, Martin

2017-01-01

Light field displays have advantages over traditional stereoscopic head mounted displays, for example, because they can overcome the vergence-accommodation conflict. However, rendering light fields can be a heavy task for computers due to the number of images that have to be rendered. Since much ...

Light Field Rendering for Head Mounted Displays using Pixel Reprojection

DEFF Research Database (Denmark)

Hansen, Anne Juhler; Klein, Jákup; Kraus, Martin

2017-01-01

of the information of the different images is redundant, we use pixel reprojection from the corner cameras to compute the remaining images in the light field. We compare the reprojected images with directly rendered images in a user test. In most cases, the users were unable to distinguish the images. In extreme...... cases, the reprojection approach is not capable of creating the light field. We conclude that pixel reprojection is a feasible method for rendering light fields as far as quality of perspective and diffuse shading is concerned, but render time needs to be reduced to make the method practical....

Architecture for high performance stereoscopic game rendering on Android

Science.gov (United States)

Flack, Julien; Sanderson, Hugh; Shetty, Sampath

2014-03-01

Stereoscopic gaming is a popular source of content for consumer 3D display systems. There has been a significant shift in the gaming industry towards casual games for mobile devices running on the Android™ Operating System and driven by ARM™ and other low power processors. Such systems are now being integrated directly into the next generation of 3D TVs potentially removing the requirement for an external games console. Although native stereo support has been integrated into some high profile titles on established platforms like Windows PC and PS3 there is a lack of GPU independent 3D support for the emerging Android platform. We describe a framework for enabling stereoscopic 3D gaming on Android for applications on mobile devices, set top boxes and TVs. A core component of the architecture is a 3D game driver, which is integrated into the Android OpenGL™ ES graphics stack to convert existing 2D graphics applications into stereoscopic 3D in real-time. The architecture includes a method of analyzing 2D games and using rule based Artificial Intelligence (AI) to position separate objects in 3D space. We describe an innovative stereo 3D rendering technique to separate the views in the depth domain and render directly into the display buffer. The advantages of the stereo renderer are demonstrated by characterizing the performance in comparison to more traditional render techniques, including depth based image rendering, both in terms of frame rates and impact on battery consumption.

Extreme Simplification and Rendering of Point Sets using Algebraic Multigrid

NARCIS (Netherlands)

Reniers, Dennie; Telea, Alexandru

2005-01-01

We present a novel approach for extreme simplification of point set models in the context of real-time rendering. Point sets are often rendered using simple point primitives, such as oriented discs. However efficient, simple primitives are less effective in approximating large surface areas. A large

Ab initio molecular crystal structures, spectra, and phase diagrams.

Science.gov (United States)

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

Science.gov (United States)

DiMaio, Frank

2017-01-01

Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

Rendering potential wearable robot designs with the LOPES gait trainer.

Science.gov (United States)

Koopman, B; van Asseldonk, E H F; van der Kooij, H; van Dijk, W; Ronsse, R

2011-01-01

In recent years, wearable robots (WRs) for rehabilitation, personal assistance, or human augmentation are gaining increasing interest. To make these devices more energy efficient, radical changes to the mechanical structure of the device are being considered. However, it remains very difficult to predict how people will respond to, and interact with, WRs that differ in terms of mechanical design. Users may adjust their gait pattern in response to the mechanical restrictions or properties of the device. The goal of this pilot study is to show the feasibility of rendering the mechanical properties of different potential WR designs using the robotic gait training device LOPES. This paper describes a new method that selectively cancels the dynamics of LOPES itself and adds the dynamics of the rendered WR using two parallel inverse models. Adaptive frequency oscillators were used to get estimates of the joint position, velocity, and acceleration. Using the inverse models, different WR designs can be evaluated, eliminating the need to build several prototypes. As a proof of principle, we simulated the effect of a very simple WR that consisted of a mass attached to the ankles. Preliminary results show that we are partially able to cancel the dynamics of LOPES. Additionally, the simulation of the mass showed an increase in muscle activity but not in the same level as during the control, where subjects actually carried the mass. In conclusion, the results in this paper suggest that LOPES can be used to render different WRs. In addition, it is very likely that the results can be further optimized when more effort is put in retrieving proper estimations for the velocity and acceleration, which are required for the inverse models. © 2011 IEEE

Density functional study of molecular interactions in secondary structures of proteins.

Science.gov (United States)

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

2007-09-02

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

Color-coded volume rendering for three-dimensional reconstructions of CT data

International Nuclear Information System (INIS)

Rieker, O.; Mildenberger, P.; Thelen, M.

1999-01-01

Purpose: To evaluate a technique of colored three-dimensional reconstructions without segmentation. Material and methods: Color-coded volume rendered images were reconstructed from the volume data of 25 thoracic, abdominal, musculoskeletal, and vascular helical CT scans using commercial software. The CT volume rendered voxels were encoded with color in the following manner. Opacity, hue, lightness, and chroma were assigned to each of four classes defined by CT number. Color-coded reconstructions were compared to the corresponding grey-scale coded reconstructions. Results: Color-coded volume rendering enabled realistic visualization of pathologic findings when there was sufficient difference in CT density. Segmentation was necessary in some cases to demonstrate small details in a complex volume. Conclusion: Color-coded volume rendering allowed lifelike visualisation of CT volumes without the need of segmentation in most cases. (orig.) [de

Physically-Based Rendering of Particle-Based Fluids with Light Transport Effects

Science.gov (United States)

Beddiaf, Ali; Babahenini, Mohamed Chaouki

2018-03-01

Recent interactive rendering approaches aim to efficiently produce images. However, time constraints deeply affect their output accuracy and realism (many light phenomena are poorly or not supported at all). To remedy this issue, in this paper, we propose a physically-based fluid rendering approach. First, while state-of-the-art methods focus on isosurface rendering with only two refractions, our proposal (1) considers the fluid as a heterogeneous participating medium with refractive boundaries, and (2) supports both multiple refractions and scattering. Second, the proposed solution is fully particle-based in the sense that no particles transformation into a grid is required. This interesting feature makes it able to handle many particle types (water, bubble, foam, and sand). On top of that, a medium with different fluids (color, phase function, etc.) can also be rendered.

An improved method of continuous LOD based on fractal theory in terrain rendering

Science.gov (United States)

Lin, Lan; Li, Lijun

2007-11-01

With the improvement of computer graphic hardware capability, the algorithm of 3D terrain rendering is going into the hot topic of real-time visualization. In order to solve conflict between the rendering speed and reality of rendering, this paper gives an improved method of terrain rendering which improves the traditional continuous level of detail technique based on fractal theory. This method proposes that the program needn't to operate the memory repeatedly to obtain different resolution terrain model, instead, obtains the fractal characteristic parameters of different region according to the movement of the viewpoint. Experimental results show that the method guarantees the authenticity of landscape, and increases the real-time 3D terrain rendering speed.

PMG: online generation of high-quality molecular pictures and storyboarded animations

Science.gov (United States)

Autin, Ludovic; Tufféry, Pierre

2007-01-01

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html. PMID:17478496

High Fidelity Haptic Rendering

CERN Document Server

Otaduy, Miguel A

2006-01-01

The human haptic system, among all senses, provides unique and bidirectional communication between humans and their physical environment. Yet, to date, most human-computer interactive systems have focused primarily on the graphical rendering of visual information and, to a lesser extent, on the display of auditory information. Extending the frontier of visual computing, haptic interfaces, or force feedback devices, have the potential to increase the quality of human-computer interaction by accommodating the sense of touch. They provide an attractive augmentation to visual display and enhance t

On the design of a real-time volume rendering engine

NARCIS (Netherlands)

Smit, Jaap; Wessels, H.L.F.; van der Horst, A.; Bentum, Marinus Jan

1992-01-01

An architecture for a Real-Time Volume Rendering Engine (RT-VRE) is given, capable of computing 750 × 750 × 512 samples from a 3D dataset at a rate of 25 images per second. The RT-VRE uses for this purpose 64 dedicated rendering chips, cooperating with 16 RISC-processors. A plane interpolator

On the design of a real-time volume rendering engine

NARCIS (Netherlands)

Smit, Jaap; Wessels, H.J.; van der Horst, A.; Bentum, Marinus Jan

1995-01-01

An architecture for a Real-Time Volume Rendering Engine (RT-VRE) is given, capable of computing 750 × 750 × 512 samples from a 3D dataset at a rate of 25 images per second. The RT-VRE uses for this purpose 64 dedicated rendering chips, cooperating with 16 RISC-processors. A plane interpolator

Electronic structure of molecular Rydberg states of some small molecules and molecular ion

International Nuclear Information System (INIS)

Sun Biao; Li Jiaming

1993-01-01

Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

Geometric and electronic structures of molecular ions from high energy collisions

International Nuclear Information System (INIS)

Groeneveld, K.O.

1983-01-01

This chapter examines the characteristics of heavy ion collision and of beam foil spectroscopy. It discusses the kinematic consequences of the high energies and presents results from ''Coulomb explosion'' and structure determination of molecular ions. It demonstrates that studies of molecular ions with accelerators can provide electronic and geometric structure information of molecules or molecular ions and points out that the understanding of the microscopic processes at such high energies is incomplete and needs further experimental and theoretical efforts

Molecular dynamic analysis of the structure of dendrimers

Energy Technology Data Exchange (ETDEWEB)

Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

Molecular dynamic analysis of the structure of dendrimers

International Nuclear Information System (INIS)

Canetta, E.; Maino, G.

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

Functionality and Performance Visualization of the Distributed High Quality Volume Renderer (HVR)

KAUST Repository

Shaheen, Sara

2012-07-01

Volume rendering systems are designed to provide means to enable scientists and a variety of experts to interactively explore volume data through 3D views of the volume. However, volume rendering techniques are computationally intensive tasks. Moreover, parallel distributed volume rendering systems and multi-threading architectures were suggested as natural solutions to provide an acceptable volume rendering performance for very large volume data sizes, such as Electron Microscopy data (EM). This in turn adds another level of complexity when developing and manipulating volume rendering systems. Given that distributed parallel volume rendering systems are among the most complex systems to develop, trace and debug, it is obvious that traditional debugging tools do not provide enough support. As a consequence, there is a great demand to provide tools that are able to facilitate the manipulation of such systems. This can be achieved by utilizing the power of compute graphics in designing visual representations that reflect how the system works and that visualize the current performance state of the system.The work presented is categorized within the field of software Visualization, where Visualization is used to serve visualizing and understanding various software. In this thesis, a number of visual representations that reflect a number of functionality and performance aspects of the distributed HVR, a high quality volume renderer system that uses various techniques to visualize large volume sizes interactively. This work is provided to visualize different stages of the parallel volume rendering pipeline of HVR. This is along with means of performance analysis through a number of flexible and dynamic visualizations that reflect the current state of the system and enables manipulation of them at runtime. Those visualization are aimed to facilitate debugging, understanding and analyzing the distributed HVR.

Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

Science.gov (United States)

Murphy, Peter M.

2007-01-01

A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

Characteristics studies of molecular structures in drugs

Directory of Open Access Journals (Sweden)

Wei Gao

2017-05-01

Full Text Available In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined. Furthermore, the Wiener related indices of distance-regular structure are also considered.

Fast rendering of scanned room geometries

DEFF Research Database (Denmark)

Olesen, Søren Krarup; Markovic, Milos; Hammershøi, Dorte

2014-01-01

Room acoustics are rendered in Virtual Realities based on models of the real world. These are typically rather coarse representations of the true geometry resulting in room impulse responses with a lack of natural detail. This problem can be overcome by using data scanned by sensors, such as e...

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

Science.gov (United States)

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

On-the-fly generation and rendering of infinite cities on the GPU

KAUST Repository

Steinberger, Markus

2014-05-01

In this paper, we present a new approach for shape-grammar-based generation and rendering of huge cities in real-time on the graphics processing unit (GPU). Traditional approaches rely on evaluating a shape grammar and storing the geometry produced as a preprocessing step. During rendering, the pregenerated data is then streamed to the GPU. By interweaving generation and rendering, we overcome the problems and limitations of streaming pregenerated data. Using our methods of visibility pruning and adaptive level of detail, we are able to dynamically generate only the geometry needed to render the current view in real-time directly on the GPU. We also present a robust and efficient way to dynamically update a scene\\'s derivation tree and geometry, enabling us to exploit frame-to-frame coherence. Our combined generation and rendering is significantly faster than all previous work. For detailed scenes, we are capable of generating geometry more rapidly than even just copying pregenerated data from main memory, enabling us to render cities with thousands of buildings at up to 100 frames per second, even with the camera moving at supersonic speed. © 2014 The Author(s) Computer Graphics Forum © 2014 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.

On-the-fly generation and rendering of infinite cities on the GPU

KAUST Repository

Steinberger, Markus; Kenzel, Michael; Kainz, Bernhard K.; Wonka, Peter; Schmalstieg, Dieter

2014-01-01

In this paper, we present a new approach for shape-grammar-based generation and rendering of huge cities in real-time on the graphics processing unit (GPU). Traditional approaches rely on evaluating a shape grammar and storing the geometry produced as a preprocessing step. During rendering, the pregenerated data is then streamed to the GPU. By interweaving generation and rendering, we overcome the problems and limitations of streaming pregenerated data. Using our methods of visibility pruning and adaptive level of detail, we are able to dynamically generate only the geometry needed to render the current view in real-time directly on the GPU. We also present a robust and efficient way to dynamically update a scene's derivation tree and geometry, enabling us to exploit frame-to-frame coherence. Our combined generation and rendering is significantly faster than all previous work. For detailed scenes, we are capable of generating geometry more rapidly than even just copying pregenerated data from main memory, enabling us to render cities with thousands of buildings at up to 100 frames per second, even with the camera moving at supersonic speed. © 2014 The Author(s) Computer Graphics Forum © 2014 The Eurographics Association and John Wiley & Sons Ltd. Published by John Wiley & Sons Ltd.

Democratizing rendering for multiple viewers in surround VR systems

KAUST Repository

Schulze, Jü rgen P.; Acevedo-Feliz, Daniel; Mangan, John; Prudhomme, Andrew; Nguyen, Phi Khanh; Weber, Philip P.

2012-01-01

We present a new approach for how multiple users' views can be rendered in a surround virtual environment without using special multi-view hardware. It is based on the idea that different parts of the screen are often viewed by different users, so that they can be rendered from their own view point, or at least from a point closer to their view point than traditionally expected. The vast majority of 3D virtual reality systems are designed for one head-tracked user, and a number of passive viewers. Only the head tracked user gets to see the correct view of the scene, everybody else sees a distorted image. We reduce this problem by algorithmically democratizing the rendering view point among all tracked users. Researchers have proposed solutions for multiple tracked users, but most of them require major changes to the display hardware of the VR system, such as additional projectors or custom VR glasses. Our approach does not require additional hardware, except the ability to track each participating user. We propose three versions of our multi-viewer algorithm. Each of them balances image distortion and frame rate in different ways, making them more or less suitable for certain application scenarios. Our most sophisticated algorithm renders each pixel from its own, optimized camera perspective, which depends on all tracked users' head positions and orientations. © 2012 IEEE.

Democratizing rendering for multiple viewers in surround VR systems

KAUST Repository

Schulze, Jürgen P.

2012-03-01

We present a new approach for how multiple users\\' views can be rendered in a surround virtual environment without using special multi-view hardware. It is based on the idea that different parts of the screen are often viewed by different users, so that they can be rendered from their own view point, or at least from a point closer to their view point than traditionally expected. The vast majority of 3D virtual reality systems are designed for one head-tracked user, and a number of passive viewers. Only the head tracked user gets to see the correct view of the scene, everybody else sees a distorted image. We reduce this problem by algorithmically democratizing the rendering view point among all tracked users. Researchers have proposed solutions for multiple tracked users, but most of them require major changes to the display hardware of the VR system, such as additional projectors or custom VR glasses. Our approach does not require additional hardware, except the ability to track each participating user. We propose three versions of our multi-viewer algorithm. Each of them balances image distortion and frame rate in different ways, making them more or less suitable for certain application scenarios. Our most sophisticated algorithm renders each pixel from its own, optimized camera perspective, which depends on all tracked users\\' head positions and orientations. © 2012 IEEE.

Use of volume-rendered images in registration of nuclear medicine studies

International Nuclear Information System (INIS)

Wallis, J.W.; Miller, T.R.; Hsu, S.S.

1995-01-01

A simple operator-guided alignment technique based on volume-rendered images was developed to register tomographic nuclear medicine studies. For each of 2 three-dimensional data sets to be registered, volume-rendered images were generated in 3 orthogonal projections (x,y,z) using the method of maximum-activity projection. Registration was achieved as follows: (a) One of the rendering orientations (e.g. x) was chosen for manipulation; (b) The two dimensional rendering was translated and rotated under operator control to achieve the best alignment as determined by visual assessment; (c) This rotation and translation was then applied to the underlying three-dimensional data set, with updating of the rendered images in each of the orthogonal projections; (d) Another orientation was chosen, and the process repeated. Since manipulation was performed on the small two-dimensional rendered image, feedback was instantaneous. To aid in the visual alignment, difference images and flicker images (toggling between the two data sets) were displayed. Accuracy was assessed by analysis of separate clinical data sets acquired without patient movement. After arbitrary rotation and translation of one of the two data sets, the 2 data sets were registered. Mean registration error was 0.36 pixels, corresponding to a 2.44 mm registration error. Thus, accurate registration can be achieved in under 10 minutes using this simple technique. The accuracy of registration was assessed with use of duplicate SPECT studies originating from separate reconstructions of the data from each of the detectors of a triple-head gamma camera

Gesture Interaction Browser-Based 3D Molecular Viewer.

Science.gov (United States)

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2016-01-01

The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

Relation between molecular electronic structure and nuclear spin-induced circular dichroism

DEFF Research Database (Denmark)

Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

2017-01-01

with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

Lighting design for globally illuminated volume rendering.

Science.gov (United States)

Zhang, Yubo; Ma, Kwan-Liu

2013-12-01

With the evolution of graphics hardware, high quality global illumination becomes available for real-time volume rendering. Compared to local illumination, global illumination can produce realistic shading effects which are closer to real world scenes, and has proven useful for enhancing volume data visualization to enable better depth and shape perception. However, setting up optimal lighting could be a nontrivial task for average users. There were lighting design works for volume visualization but they did not consider global light transportation. In this paper, we present a lighting design method for volume visualization employing global illumination. The resulting system takes into account view and transfer-function dependent content of the volume data to automatically generate an optimized three-point lighting environment. Our method fully exploits the back light which is not used by previous volume visualization systems. By also including global shadow and multiple scattering, our lighting system can effectively enhance the depth and shape perception of volumetric features of interest. In addition, we propose an automatic tone mapping operator which recovers visual details from overexposed areas while maintaining sufficient contrast in the dark areas. We show that our method is effective for visualizing volume datasets with complex structures. The structural information is more clearly and correctly presented under the automatically generated light sources.

Detecting Molecular Features of Spectra Mainly Associated with Structural and Non-Structural Carbohydrates in Co-Products from BioEthanol Production Using DRIFT with Uni- and Multivariate Molecular Spectral Analyses

Science.gov (United States)

Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

2011-01-01

The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485–1188 cm−1), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm−1 with region and baseline: ca. 1292–1198 cm−1), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187–950 cm−1), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm−1 with region and baseline: ca. 952–910 cm−1), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm−1 with region and baseline: ca. 880–827 cm−1), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm−1 with baseline: ca. 1485–1188 cm−1), H_1370 (structural carbohydrate, peak height at ca. 1370 cm−1 with a baseline: ca. 1485–1188 cm−1). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P carbohydrate of A_928 (17.3 vs. 2.0) and A_860 (20.7 vs. 7.6) than their co-products from bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292–1198 cm−1 and A_CHO (total CHO) at 1187–950 cm−1 with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This

Method of producing hydrogen, and rendering a contaminated biomass inert

Science.gov (United States)

Bingham, Dennis N [Idaho Falls, ID; Klingler, Kerry M [Idaho Falls, ID; Wilding, Bruce M [Idaho Falls, ID

2010-02-23

A method for rendering a contaminated biomass inert includes providing a first composition, providing a second composition, reacting the first and second compositions together to form an alkaline hydroxide, providing a contaminated biomass feedstock and reacting the alkaline hydroxide with the contaminated biomass feedstock to render the contaminated biomass feedstock inert and further producing hydrogen gas, and a byproduct that includes the first composition.

Molecular structure and correlations in liquid D-2-propanol through neutron diffraction

International Nuclear Information System (INIS)

Sahoo, A.; Sarkar, S.; Joarder, R.N.; Krishna, P.S.R.

2003-01-01

Like t-butanol, 2-propanol molecules are quite big with substantial amount of asymmetry in the structure and so the analysis of the neutron diffraction data is tricky. A modified method of analysis, similar to one for liquid t-butanol, enables extraction of the detailed molecular conformation and intermolecular correlations through neutron diffraction. The pre-peak in the structure function, a signature of chain molecular association together with partially identified inter-molecular correlations yield some information about the nature of possible H-bonded molecular clusters in the liquid state. (author)

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

Science.gov (United States)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Rendering Visible: Painting and Sexuate Subjectivity

Science.gov (United States)

Daley, Linda

2015-01-01

In this essay, I examine Luce Irigaray's aesthetic of sexual difference, which she develops by extrapolating from Paul Klee's idea that the role of painting is to render the non-visible rather than represent the visible. This idea is the premise of her analyses of phenomenology and psychoanalysis and their respective contributions to understanding…

Free-viewpoint depth image based rendering

NARCIS (Netherlands)

Zinger, S.; Do, Q.L.; With, de P.H.N.

2010-01-01

In 3D TV research, one approach is to employ multiple cameras for creating a 3D multi-view signal with the aim to make interactive free-viewpoint selection possible in 3D TV media. This paper explores a new rendering algorithm that enables to compute a free-viewpoint between two reference views from

Influence of rendering methods on yield and quality of chicken fat recovered from broiler skin

Directory of Open Access Journals (Sweden)

Liang-Kun Lin

2017-06-01

Full Text Available Objective In order to utilize fat from broiler byproducts efficiently, it is necessary to develop an appropriate rendering procedure and establish quality information for the rendered fat. A study was therefore undertaken to evaluate the influence of rendering methods on the amounts and general properties of the fat recovered from broiler skin. Methods The yield and quality of the broiler skin fat rendered through high and lower energy microwave rendering (3.6 W/g for 10 min and 2.4 W/g for 10 min for high power microwave rendering (HPMR and high power microwave rendering (LPMR, respectively, oven baking (OB, at 180°C for 40 min, and water cooking (WC, boiling for 40 min were compared. Results Microwave-rendered skin exhibited the highest yields and fat recovery rates, followed by OB, and WC fats (p<0.05. HPMR fat had the highest L*, a*, and b* values, whereas WC fat had the highest moisture content, acid values, and thiobarbituric acid (TBA values (p<0.05. There was no significant difference in the acid value, peroxide value, and TBA values between HPMR and LPMR fats. Conclusion Microwave rendering at a power level of 3.6 W/g for 10 min is suggested base on the yield and quality of chicken fat.

Beaming teaching application: recording techniques for spatial xylophone sound rendering

DEFF Research Database (Denmark)

Markovic, Milos; Madsen, Esben; Olesen, Søren Krarup

2012-01-01

BEAMING is a telepresence research project aiming at providing a multimodal interaction between two or more participants located at distant locations. One of the BEAMING applications allows a distant teacher to give a xylophone playing lecture to the students. Therefore, rendering of the xylophon...... to spatial improvements mainly in terms of the Apparent Source Width (ASW). Rendered examples are subjectively evaluated in listening tests by comparing them with binaural recording....

Molecular dynamics of the structure and thermodynamics of dusty ...

African Journals Online (AJOL)

The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

Chromium Renderserver: Scalable and Open Source Remote RenderingInfrastructure

Energy Technology Data Exchange (ETDEWEB)

Paul, Brian; Ahern, Sean; Bethel, E. Wes; Brugger, Eric; Cook,Rich; Daniel, Jamison; Lewis, Ken; Owen, Jens; Southard, Dale

2007-12-01

Chromium Renderserver (CRRS) is software infrastructure thatprovides the ability for one or more users to run and view image outputfrom unmodified, interactive OpenGL and X11 applications on a remote,parallel computational platform equipped with graphics hardwareaccelerators via industry-standard Layer 7 network protocolsand clientviewers. The new contributions of this work include a solution to theproblem of synchronizing X11 and OpenGL command streams, remote deliveryof parallel hardware-accelerated rendering, and a performance analysis ofseveral different optimizations that are generally applicable to avariety of rendering architectures. CRRSis fully operational, Open Sourcesoftware.

Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages.

Science.gov (United States)

Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang

2017-10-18

The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

In Vivo CT Direct Volume Rendering: A Three-Dimensional Anatomical Description of the Heart

International Nuclear Information System (INIS)

Cutroneo, Giuseppina; Bruschetta, Daniele; Trimarchi, Fabio; Cacciola, Alberto; Cinquegrani, Maria; Duca, Antonio; Rizzo, Giuseppina; Alati, Emanuela; Gaeta, Michele; Milardi, Demetrio

2016-01-01

Since cardiac anatomy continues to play an important role in the practice of medicine and in the development of medical devices, the study of the heart in three dimensions is particularly useful to understand its real structure, function and proper location in the body. This study demonstrates a fine use of direct volume rendering, processing the data set images obtained by Computed Tomography (CT) of the heart of 5 subjects with age range between 18 and 42 years (2 male, 3 female), with no history of any overt cardiac disease. The cardiac structure in CT images was first extracted from the thorax by marking manually the regions of interest on the computer, and then it was stacked to create new volumetric data. The use of a specific algorithm allowed us to observe with a good perception of depth the heart and the skeleton of the thorax at the same time. Besides, in all examined subjects, it was possible to depict its structure and its position within the body and to study the integrity of papillary muscles, the fibrous tissue of cardiac valve and chordae tendineae and the course of coronary arteries. Our results demonstrated that one of the greatest advantages of algorithmic modifications of direct volume rendering parameters is that this method provides much necessary information in a single radiologic study. It implies a better accuracy in the study of the heart, being complementary to other diagnostic methods and facilitating the therapeutic plans

A point-based rendering approach for real-time interaction on mobile devices

Institute of Scientific and Technical Information of China (English)

LIANG XiaoHui; ZHAO QinPing; HE ZhiYing; XIE Ke; LIU YuBo

2009-01-01

Mobile device is an Important interactive platform. Due to the limitation of computation, memory, display area and energy, how to realize the efficient and real-time interaction of 3D models based on mobile devices is an important research topic. Considering features of mobile devices, this paper adopts remote rendering mode and point models, and then, proposes a transmission and rendering approach that could interact in real time. First, improved simplification algorithm based on MLS and display resolution of mobile devices is proposed. Then, a hierarchy selection of point models and a QoS transmission control strategy are given based on interest area of operator, interest degree of object in the virtual environment and rendering error. They can save the energy consumption. Finally, the rendering and interaction of point models are completed on mobile devices. The experiments show that our method is efficient.

An Insight towards Conceptual Understanding: Looking into the Molecular Structures of Compounds

Science.gov (United States)

Uyulgan, Melis Arzu; Akkuzu, Nalan

2016-01-01

The subject of molecular structures is one of the most important and complex subject in chemistry which a majority of the undergraduate students have difficulties to understand its concepts and characteristics correctly. To comprehend the molecular structures and their characteristics the students need to understand related subjects such as Lewis…

Depth of Field Effects for Interactive Direct Volume Rendering

KAUST Repository

Schott, Mathias; Pascal Grosset, A.V.; Martin, Tobias; Pegoraro, Vincent; Smith, Sean T.; Hansen, Charles D.

2011-01-01

In this paper, a method for interactive direct volume rendering is proposed for computing depth of field effects, which previously were shown to aid observers in depth and size perception of synthetically generated images. The presented technique extends those benefits to volume rendering visualizations of 3D scalar fields from CT/MRI scanners or numerical simulations. It is based on incremental filtering and as such does not depend on any precomputation, thus allowing interactive explorations of volumetric data sets via on-the-fly editing of the shading model parameters or (multi-dimensional) transfer functions. © 2011 The Author(s).

Depth of Field Effects for Interactive Direct Volume Rendering

KAUST Repository

Schott, Mathias

2011-06-01

In this paper, a method for interactive direct volume rendering is proposed for computing depth of field effects, which previously were shown to aid observers in depth and size perception of synthetically generated images. The presented technique extends those benefits to volume rendering visualizations of 3D scalar fields from CT/MRI scanners or numerical simulations. It is based on incremental filtering and as such does not depend on any precomputation, thus allowing interactive explorations of volumetric data sets via on-the-fly editing of the shading model parameters or (multi-dimensional) transfer functions. © 2011 The Author(s).

Anisotropic 3D texture synthesis with application to volume rendering

DEFF Research Database (Denmark)

Laursen, Lasse Farnung; Ersbøll, Bjarne Kjær; Bærentzen, Jakob Andreas

2011-01-01

images using a 12.1 megapixel camera. Next, we extend the volume rendering pipeline by creating a transfer function which yields not only color and opacity from the input intensity, but also texture coordinates for our synthesized 3D texture. Thus, we add texture to the volume rendered images....... This method is applied to a high quality visualization of a pig carcass, where samples of meat, bone, and fat have been used to produce the anisotropic 3D textures....

Graphical User Interfaces for Volume Rendering Applications in Medical Imaging

OpenAIRE

Lindfors, Lisa; Lindmark, Hanna

2002-01-01

Volume rendering applications are used in medical imaging in order to facilitate the analysis of three-dimensional image data. This study focuses on how to improve the usability of graphical user interfaces of these systems, by gathering user requirements. This is achieved by evaluations of existing systems, together with interviews and observations at clinics in Sweden that use volume rendering to some extent. The usability of the applications of today is not sufficient, according to the use...

Clustered deep shadow maps for integrated polyhedral and volume rendering

KAUST Repository

Bornik, Alexander

2012-01-01

This paper presents a hardware-accelerated approach for shadow computation in scenes containing both complex volumetric objects and polyhedral models. Our system is the first hardware accelerated complete implementation of deep shadow maps, which unifies the computation of volumetric and geometric shadows. Up to now such unified computation was limited to software-only rendering . Previous hardware accelerated techniques can handle only geometric or only volumetric scenes - both resulting in the loss of important properties of the original concept. Our approach supports interactive rendering of polyhedrally bounded volumetric objects on the GPU based on ray casting. The ray casting can be conveniently used for both the shadow map computation and the rendering. We show how anti-aliased high-quality shadows are feasible in scenes composed of multiple overlapping translucent objects, and how sparse scenes can be handled efficiently using clustered deep shadow maps. © 2012 Springer-Verlag.

Energy-related atomic and molecular structure and scattering studies: Final report

International Nuclear Information System (INIS)

1987-01-01

The general goals of the DOE research concerned the use of molecular beams techniques in the study of atomic and molecular polarizabilities and the study of the interactions between electrons and highly polar molecules. Both of these goals are directly relevant to the general problem of the role played by long-range forces in atomic and molecular physics. Details related to this motivation can be found in the published literature. Here we will describe in general terms the work performed under DOE sponsorship in the atomic beams laboratory at NYU. Our original intent was to exploit techniques developed at NYU, mainly in the study of simple atomic systems, to the more complex atomic and molecular systems that are related to DOE interests. These included the developing understanding of the structure of molecular systems, particularly of alkali halide molecules, and the study of the interactions of electrons with such molecules. The structure experiments would serve as critical experimental benchmarks for computational techniques on molecular properties, including both molecular wave functions and derivative properties of them, such as vibrational and rotational constants, but in particular of molecular electric dipole polarizabilities. We believe that we have at least to some extent fulfilled these goals. 16 refs., 1 fig

Molecular biological methods (DGGE) as a tool to investigate nitrification inhibition in wastewater treatment.

Science.gov (United States)

Kreuzinger, N; Farnleitner, A; Wandl, G; Hornek, R; Mach, R

2003-01-01

Incomplete nitrification at an activated sludge plant for biological pre-treatment of rendering plant effluents led to a detailed investigation on the origin and solution of this problem. Preliminary studies revealed that an inhibition of ammonia oxidising microorganisms (AOM) by process waters of the rendering plant was responsible for the situation. We were able to show a correlation between the existence of specific AOM and nitrification capacity expressed as oxygen uptake rate for maximal nitrification (OURNmax). Only Nitrosospira sp. was found in the activated sludge of the rendering plant and another industrial wastewater treatment plant with problems in nitrification, while reference plants without nitrification problems showed Nitrosomonas spp. as the predominant ammonia oxidising bacteria. By accompanying engineering investigations and experiments (cross-feeding experiments, operation of a two-stage laboratory plant) with molecular biological methods (DGGE--Denaturing Gradient Gel Electrophoresis) we were able to elaborate an applicable solution for the rendering plant. Laboratory experiments with a two-stage process layout finally provided complete nitrification overcoming the inhibiting nature of process waters from the rendering plant. DGGE analysis of the second stage activated sludge from the laboratory plant showed a shift in population structure from Nitrosospira sp. towards Nitrosomonas spp. simultaneous to the increase of nitrification capacity. Nitrification capacities comparable to full-scale municipal wastewater treatment plants could be maintained for more than two months. As the design of wastewater treatment plants for nitrification is linked to the growth characteristics of Nitrosomonas spp., established criteria can be applied for the redesign of the full-scale plant.

Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

Science.gov (United States)

Yu, Peiqiang; Damiran, Daalkhaijav

2011-06-01

Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

Molecular characterization of a proteolysis-resistant lipase from Bacillus pumilus SG2

Directory of Open Access Journals (Sweden)

R. Sangeetha

2014-06-01

Full Text Available Proteolysis-resistant lipases can be well exploited by industrial processes which employ both lipase and protease as biocatalysts. A proteolysis resistant lipase from Bacillus pumilus SG2 was isolated, purified and characterized earlier. The lipase was resistant to native and commercial proteases. In the present work, we have characterized the lip gene which encodes the proteolysis-resistant lipase from Bacillus pumilus SG2. The parameters and structural details of lipase were analysed. The lip gene consisted of 650 bp. The experimental molecular weight of SG2 lipase was nearly double that of its theoretical molecular weight, thus suggesting the existence of the functional lipase as a covalent dimer. The proteolytic cleavage sites of the lipase would have been made inaccessible by dimerisation, thus rendering the lipase resistant to protease.

Molecular orientation and electronic structure at organic heterojunction interfaces

Energy Technology Data Exchange (ETDEWEB)

Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

2015-10-01

Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

Evaluation and Improvement of the CIE Metameric and Colour Rendering Index

Directory of Open Access Journals (Sweden)

Radovan Slavuj

2015-12-01

Full Text Available All artificial light sources are intended to simulate daylight and its properties of color rendering or ability of colour discrimination. Two indices, defined by the CIE, are used to quantify quality of the artificial light sources. First is Color Rendering Index which quantifies ability of light sources to render colours and other is the Metemerism Index which describes metamerism potential of given light source. Calculation of both indices are defined by CIE and has been a subject of discussion and change in past. In this work particularly, the problem of sample number and type used in calculation is addressed here and evaluated. It is noticed that both indices depends on the choice and sample number and that they should be determined based on application.

Effect of steam explosion pre-treatment on molecular structure of ...

African Journals Online (AJOL)

Purpose: To examine the effect of steam-explosion (SE) strength on the molecular ... pressure-holding time on the molecular structure of the sweet potato starch were ... overheated liquid and then their pores are filled ... expands and exerts pressure on the cell walls, ... oscillation using distilled water as the dispersing agent.

Coulomb-explosion technique for determining geometrical structures of molecular ions

International Nuclear Information System (INIS)

Gemmell, D.S.

1981-01-01

Traditional experimental techniques (e.g. studies on photon absorption or emission) for determining the sterochemical structures of neutral molecules are extremeley difficult to apply to molecular ions because of problems in obtaining a sufficient spatial density of the ions to be studied. Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the sterochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2+ , HeH + , CH + , NH + , OH + , N 2+ , O 2+ , etc.) with an accuracy of approx. 0.01 A. H 3+ has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2+ , N 2 O + , C 3 H 3+ , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2+ ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 --- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

Dynamic Resolution in GPU-Accelerated Volume Rendering to Autostereoscopic Multiview Lenticular Displays

Directory of Open Access Journals (Sweden)

Daniel Ruijters

2008-09-01

Full Text Available The generation of multiview stereoscopic images of large volume rendered data demands an enormous amount of calculations. We propose a method for hardware accelerated volume rendering of medical data sets to multiview lenticular displays, offering interactive manipulation throughout. The method is based on buffering GPU-accelerated direct volume rendered visualizations of the individual views from their respective focal spot positions, and composing the output signal for the multiview lenticular screen in a second pass. This compositing phase is facilitated by the fact that the view assignment per subpixel is static, and therefore can be precomputed. We decoupled the resolution of the individual views from the resolution of the composited signal, and adjust the resolution on-the-fly, depending on the available processing resources, in order to maintain interactive refresh rates. The optimal resolution for the volume rendered views is determined by means of an analysis of the lattice of the output signal for the lenticular screen in the Fourier domain.

Experiencing "Macbeth": From Text Rendering to Multicultural Performance.

Science.gov (United States)

Reisin, Gail

1993-01-01

Shows how one teacher used innovative methods in teaching William Shakespeare's "Macbeth." Outlines student assignments including text renderings, rewriting a scene from the play, and creating a multicultural scrapbook for the play. (HB)

Evaluation of obstructive airway lesions in complex congenital heart disease using composite volume-rendered images from multislice CT

International Nuclear Information System (INIS)

Choo, Ki Seok; Kim, Chang Won; Lee, Tae Hong; Kim, Suk; Kim, Kun Il; Lee, Hyoung Doo; Ban, Ji Eun; Sung, Si Chan; Chang, Yun Hee

2006-01-01

Multislice CT (MSCT) allows high-quality volume-rendered (VR) and composite volume-rendered images. To investigate the clinical usefulness of composite VR images in the evaluation of the relationship between cardiovascular structures and the airway in children with complex congenital heart disease (CHD). Four- or 16-slice MSCT scanning was performed consecutively in 77 children (mean age 6.4 months) with CHD and respiratory symptoms, a chest radiographic abnormality, or abnormal course of the pulmonary artery on ECHO. MSCT scanning was performed during breathing or after sedation. Contrast medium (2 ml/kg) was administered through a pedal venous route or arm vein in all patients. The VR technique was used to reconstruct the cardiovascular structures and airway, and then both VR images were composed using the commercial software (VoxelPlus 2 ; Daejeon, Korea). Stenoses were seen in the trachea in 1 patient and in the bronchi in 14 patients (19%). Other patients with complex CHD did not have significant airway stenoses. Composite VR images with MSCT can provide more exact airway images in relationship to the surrounding cardiovascular structures and thus help in optimizing management strategies in treating CHD. (orig.)

Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

International Nuclear Information System (INIS)

Wang, J.; Gutierre, M.S.

2010-01-01

This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

Long-term thermophilic mono-digestion of rendering wastes and co-digestion with potato pulp

International Nuclear Information System (INIS)

Bayr, S.; Ojanperä, M.; Kaparaju, P.; Rintala, J.

2014-01-01

Highlights: • Rendering wastes’ mono-digestion and co-digestion with potato pulp were studied. • CSTR process with OLR of 1.5 kg VS/m 3 d, HRT of 50 d was unstable in mono-digestion. • Free NH 3 inhibited mono-digestion of rendering wastes. • CSTR process with OLR of 1.5 kg VS/m 3 d, HRT of 50 d was stable in co-digestion. • Co-digestion increased methane yield somewhat compared to mono-digestion. - Abstract: In this study, mono-digestion of rendering wastes and co-digestion of rendering wastes with potato pulp were studied for the first time in continuous stirred tank reactor (CSTR) experiments at 55 °C. Rendering wastes have high protein and lipid contents and are considered good substrates for methane production. However, accumulation of digestion intermediate products viz., volatile fatty acids (VFAs), long chain fatty acids (LCFAs) and ammonia nitrogen (NH 4 -N and/or free NH 3 ) can cause process imbalance during the digestion. Mono-digestion of rendering wastes at an organic loading rate (OLR) of 1.5 kg volatile solids (VS)/m 3 d and hydraulic retention time (HRT) of 50 d was unstable and resulted in methane yields of 450 dm 3 /kg VS fed . On the other hand, co-digestion of rendering wastes with potato pulp (60% wet weight, WW) at the same OLR and HRT improved the process stability and increased methane yields (500–680 dm 3 /kg VS fed ). Thus, it can be concluded that co-digestion of rendering wastes with potato pulp could improve the process stability and methane yields from these difficult to treat industrial waste materials

ACCELERATION RENDERING METHOD ON RAY TRACING WITH ANGLE COMPARISON AND DISTANCE COMPARISON

Directory of Open Access Journals (Sweden)

Liliana liliana

2007-01-01

Full Text Available In computer graphics applications, to produce realistic images, a method that is often used is ray tracing. Ray tracing does not only model local illumination but also global illumination. Local illumination count ambient, diffuse and specular effects only, but global illumination also count mirroring and transparency. Local illumination count effects from the lamp(s but global illumination count effects from other object(s too. Objects that are usually modeled are primitive objects and mesh objects. The advantage of mesh modeling is various, interesting and real-like shape. Mesh contains many primitive objects like triangle or square (rare. A problem in mesh object modeling is long rendering time. It is because every ray must be checked with a lot of triangle of the mesh. Added by ray from other objects checking, the number of ray that traced will increase. It causes the increasing of rendering time. To solve this problem, in this research, new methods are developed to make the rendering process of mesh object faster. The new methods are angle comparison and distance comparison. These methods are used to reduce the number of ray checking. The rays predicted will not intersect with the mesh, are not checked weather the ray intersects the mesh. With angle comparison, if using small angle to compare, the rendering process will be fast. This method has disadvantage, if the shape of each triangle is big, some triangles will be corrupted. If the angle to compare is bigger, mesh corruption can be avoided but the rendering time will be longer than without comparison. With distance comparison, the rendering time is less than without comparison, and no triangle will be corrupted.

Building bridges between cellular and molecular structural biology.

Science.gov (United States)

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Molecular structure of the lecithin ripple phase

Science.gov (United States)

de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

2005-04-01

Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation | structural model

31 CFR 515.548 - Services rendered by Cuba to United States aircraft.

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Services rendered by Cuba to United... REGULATIONS Licenses, Authorizations, and Statements of Licensing Policy § 515.548 Services rendered by Cuba to United States aircraft. Specific licenses are issued for payment to Cuba of charges for services...

GPU Pro advanced rendering techniques

CERN Document Server

Engel, Wolfgang

2010-01-01

This book covers essential tools and techniques for programming the graphics processing unit. Brought to you by Wolfgang Engel and the same team of editors who made the ShaderX series a success, this volume covers advanced rendering techniques, engine design, GPGPU techniques, related mathematical techniques, and game postmortems. A special emphasis is placed on handheld programming to account for the increased importance of graphics on mobile devices, especially the iPhone and iPod touch.Example programs and source code can be downloaded from the book's CRC Press web page. 

A cache-friendly sampling strategy for texture-based volume rendering on GPU

Directory of Open Access Journals (Sweden)

Junpeng Wang

2017-06-01

Full Text Available The texture-based volume rendering is a memory-intensive algorithm. Its performance relies heavily on the performance of the texture cache. However, most existing texture-based volume rendering methods blindly map computational resources to texture memory and result in incoherent memory access patterns, causing low cache hit rates in certain cases. The distance between samples taken by threads of an atomic scheduling unit (e.g. a warp of 32 threads in CUDA of the GPU is a crucial factor that affects the texture cache performance. Based on this fact, we present a new sampling strategy, called Warp Marching, for the ray-casting algorithm of texture-based volume rendering. The effects of different sample organizations and different thread-pixel mappings in the ray-casting algorithm are thoroughly analyzed. Also, a pipeline manner color blending approach is introduced and the power of warp-level GPU operations is leveraged to improve the efficiency of parallel executions on the GPU. In addition, the rendering performance of the Warp Marching is view-independent, and it outperforms existing empty space skipping techniques in scenarios that need to render large dynamic volumes in a low resolution image. Through a series of micro-benchmarking and real-life data experiments, we rigorously analyze our sampling strategies and demonstrate significant performance enhancements over existing sampling methods.

COMPANION ANIMALS SYMPOSIUM: Rendered ingredients significantly influence sustainability, quality, and safety of pet food.

Science.gov (United States)

Meeker, D L; Meisinger, J L

2015-03-01

The rendering industry collects and safely processes approximately 25 million t of animal byproducts each year in the United States. Rendering plants process a variety of raw materials from food animal production, principally offal from slaughterhouses, but include whole animals that die on farms or in transit and other materials such as bone, feathers, and blood. By recycling these byproducts into various protein, fat, and mineral products, including meat and bone meal, hydrolyzed feather meal, blood meal, and various types of animal fats and greases, the sustainability of food animal production is greatly enhanced. The rendering industry is conscious of its role in the prevention of disease and microbiological control and providing safe feed ingredients for livestock, poultry, aquaculture, and pets. The processing of otherwise low-value OM from the livestock production and meat processing industries through rendering drastically reduces the amount of waste. If not rendered, biological materials would be deposited in landfills, burned, buried, or inappropriately dumped with large amounts of carbon dioxide, ammonia, and other compounds polluting air and water. The majority of rendered protein products are used as animal feed. Rendered products are especially valuable to the livestock and pet food industries because of their high protein content, digestible AA levels (especially lysine), mineral availability (especially calcium and phosphorous), and relatively low cost in relation to their nutrient value. The use of these reclaimed and recycled materials in pet food is a much more sustainable model than using human food for pets.

Matching rendered and real world images by digital image processing

Science.gov (United States)

Mitjà, Carles; Bover, Toni; Bigas, Miquel; Escofet, Jaume

2010-05-01

Recent advances in computer-generated images (CGI) have been used in commercial and industrial photography providing a broad scope in product advertising. Mixing real world images with those rendered from virtual space software shows a more or less visible mismatching between corresponding image quality performance. Rendered images are produced by software which quality performance is only limited by the resolution output. Real world images are taken with cameras with some amount of image degradation factors as lens residual aberrations, diffraction, sensor low pass anti aliasing filters, color pattern demosaicing, etc. The effect of all those image quality degradation factors can be characterized by the system Point Spread Function (PSF). Because the image is the convolution of the object by the system PSF, its characterization shows the amount of image degradation added to any taken picture. This work explores the use of image processing to degrade the rendered images following the parameters indicated by the real system PSF, attempting to match both virtual and real world image qualities. The system MTF is determined by the slanted edge method both in laboratory conditions and in the real picture environment in order to compare the influence of the working conditions on the device performance; an approximation to the system PSF is derived from the two measurements. The rendered images are filtered through a Gaussian filter obtained from the taking system PSF. Results with and without filtering are shown and compared measuring the contrast achieved in different final image regions.

Fine- and hyperfine-structure effects in molecular photoionization. II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

Energy Technology Data Exchange (ETDEWEB)

Germann, Matthias; Willitsch, Stefan, E-mail: stefan.willitsch@unibas.ch [Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel (Switzerland)

2016-07-28

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine-structure effects in one-photon ionization of molecules presented in Paper I [M. Germann and S. Willitsch, J. Chem. Phys. 145, 044314 (2016)]. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including the hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments.

Clinical application of three-dimensional spiral CT cerebral angiography with volume rendering

International Nuclear Information System (INIS)

Duan Shaoyin; Huang Xi'en; Kang Jianghe; Zhang Dantong; Lin Qingchi; Cai Guoxiang; Xu Meixin; Pang Ruilin

2002-01-01

Objective: To study the methodology and assess the clinical value of three-dimensional CT angiography (3D-CTA) with volume rendering (VR) in cerebral vessels. Methods: Sixty-two patients were examined by means of 3D-CTA with volume rendering. VR was used in the reconstruction of 3D images, and the demonstration of normal vessels and vascular lesions were particularly analyzed. At the same time, comparisons were made between the images of VR and SSD, MIP, and also between the diagnosis of VR-CTA and DSA or postoperative results. Results: In VR images, cerebral vessel routes and vessel cavities were showed clearly, while the relationship among vascular lesions, surrounding vessels, and neighboring structure was distinguished. 50 cases (80.6%) were found positive, 48 of which were correct and 2 were false-positive compared with DSA or postoperative results. The accurate rate of diagnosis was 96.0%. There was no obvious difference in showing the cerebral vessel among the images of VR, SSD and MIP (P > 0.25). Conclusion: Three-dimensional CT cerebral angiography with VR is a new noninvasive effective method. It can even partly replace the DSA. The 3D-images have the characteristics of showing the cerebral vascular cavity and overlapped vessels without cutting the skull

Bending of conjugated molecular wires and its effect on electron conduction properties

International Nuclear Information System (INIS)

Das, Bidisa

2010-01-01

The electronic structure and electron transport properties of simple conjugated molecular wires like oligophenylene ethynylene (OPE) and oligophenylene vinylene (OPV) are studied under compression. If artificially confined to a given shorter length, the oligomers tend to bend and bending causes a loss in the overlap of the conjugated molecular orbitals. Theoretical modeling of electronic transport has been carried out for all undistorted and compressed OPE/OPV oligomers. OPV exists in step-like or V-like conformations and they have the same stability with very similar frontier molecular orbitals. The conductances of these molecular wires are calculated when inserted between two gold probes and the conductances for OPV are found to be comparable to OPE when the interfaces are same. The conductance decreases with bending due to the gradual loss in overlap of the molecular orbitals. It is also found that the conductances of the molecular wires decrease very strongly if the terminal sulfur atom is simultaneously bonded to hydrogen and a gold surface, thus reflecting the importance of the interface in determining the conductance in two-probe systems. From the conductance studies it may be concluded that if one or more benzene rings of OPE are rotated from coplanar conditions, the orthogonal molecular orbitals may completely block the electronic transport, rendering the molecule insulating.

Long-term thermophilic mono-digestion of rendering wastes and co-digestion with potato pulp

Energy Technology Data Exchange (ETDEWEB)

Bayr, S., E-mail: suvi.bayr@jyu.fi; Ojanperä, M.; Kaparaju, P.; Rintala, J.

2014-10-15

Highlights: • Rendering wastes’ mono-digestion and co-digestion with potato pulp were studied. • CSTR process with OLR of 1.5 kg VS/m{sup 3} d, HRT of 50 d was unstable in mono-digestion. • Free NH{sub 3} inhibited mono-digestion of rendering wastes. • CSTR process with OLR of 1.5 kg VS/m{sup 3} d, HRT of 50 d was stable in co-digestion. • Co-digestion increased methane yield somewhat compared to mono-digestion. - Abstract: In this study, mono-digestion of rendering wastes and co-digestion of rendering wastes with potato pulp were studied for the first time in continuous stirred tank reactor (CSTR) experiments at 55 °C. Rendering wastes have high protein and lipid contents and are considered good substrates for methane production. However, accumulation of digestion intermediate products viz., volatile fatty acids (VFAs), long chain fatty acids (LCFAs) and ammonia nitrogen (NH{sub 4}-N and/or free NH{sub 3}) can cause process imbalance during the digestion. Mono-digestion of rendering wastes at an organic loading rate (OLR) of 1.5 kg volatile solids (VS)/m{sup 3} d and hydraulic retention time (HRT) of 50 d was unstable and resulted in methane yields of 450 dm{sup 3}/kg VS{sub fed}. On the other hand, co-digestion of rendering wastes with potato pulp (60% wet weight, WW) at the same OLR and HRT improved the process stability and increased methane yields (500–680 dm{sup 3}/kg VS{sub fed}). Thus, it can be concluded that co-digestion of rendering wastes with potato pulp could improve the process stability and methane yields from these difficult to treat industrial waste materials.

Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data

KAUST Repository

Ibrahim, Mohamed

2017-08-28

Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.

Screen-Space Normal Distribution Function Caching for Consistent Multi-Resolution Rendering of Large Particle Data

KAUST Repository

Ibrahim, Mohamed; Wickenhauser, Patrick; Rautek, Peter; Reina, Guido; Hadwiger, Markus

2017-01-01

Molecular dynamics (MD) simulations are crucial to investigating important processes in physics and thermodynamics. The simulated atoms are usually visualized as hard spheres with Phong shading, where individual particles and their local density can be perceived well in close-up views. However, for large-scale simulations with 10 million particles or more, the visualization of large fields-of-view usually suffers from strong aliasing artifacts, because the mismatch between data size and output resolution leads to severe under-sampling of the geometry. Excessive super-sampling can alleviate this problem, but is prohibitively expensive. This paper presents a novel visualization method for large-scale particle data that addresses aliasing while enabling interactive high-quality rendering. We introduce the novel concept of screen-space normal distribution functions (S-NDFs) for particle data. S-NDFs represent the distribution of surface normals that map to a given pixel in screen space, which enables high-quality re-lighting without re-rendering particles. In order to facilitate interactive zooming, we cache S-NDFs in a screen-space mipmap (S-MIP). Together, these two concepts enable interactive, scale-consistent re-lighting and shading changes, as well as zooming, without having to re-sample the particle data. We show how our method facilitates the interactive exploration of real-world large-scale MD simulation data in different scenarios.

Electronic structure of surface-supported bis(phthalocyaninato) terbium(III) single molecular magnets.

Science.gov (United States)

Vitali, Lucia; Fabris, Stefano; Conte, Adriano Mosca; Brink, Susan; Ruben, Mario; Baroni, Stefano; Kern, Klaus

2008-10-01

The electronic structure of isolated bis(phthalocyaninato) terbium(III) molecules, a novel single-molecular-magnet (SMM), supported on the Cu(111) surface has been characterized by density functional theory and scanning tunneling spectroscopy. These studies reveal that the interaction with the metal surface preserves both the molecular structure and the large spin magnetic moment of the metal center. The 4f electron states are not perturbed by the adsorption while a strong molecular/metal interaction can induce the suppression of the minor spin contribution delocalized over the molecular ligands. The calculations show that the inherent spin magnetic moment of the molecule is only weakly affected by the interaction with the surface and suggest that the SMM character might be preserved.

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Directory of Open Access Journals (Sweden)

Catherine L Worth

Full Text Available BACKGROUND: Up until recently the only available experimental (high resolution structure of a G-protein-coupled receptor (GPCR was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY: We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s for building a comparative molecular model. CONCLUSIONS: The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying

Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.

Science.gov (United States)

Worth, Catherine L; Kleinau, Gunnar; Krause, Gerd

2009-09-16

Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will

Construction and Evaluation of an Ultra Low Latency Frameless Renderer for VR.

Science.gov (United States)

Friston, Sebastian; Steed, Anthony; Tilbury, Simon; Gaydadjiev, Georgi

2016-04-01

Latency - the delay between a user's action and the response to this action - is known to be detrimental to virtual reality. Latency is typically considered to be a discrete value characterising a delay, constant in time and space - but this characterisation is incomplete. Latency changes across the display during scan-out, and how it does so is dependent on the rendering approach used. In this study, we present an ultra-low latency real-time ray-casting renderer for virtual reality, implemented on an FPGA. Our renderer has a latency of ~1 ms from 'tracker to pixel'. Its frameless nature means that the region of the display with the lowest latency immediately follows the scan-beam. This is in contrast to frame-based systems such as those using typical GPUs, for which the latency increases as scan-out proceeds. Using a series of high and low speed videos of our system in use, we confirm its latency of ~1 ms. We examine how the renderer performs when driving a traditional sequential scan-out display on a readily available HMO, the Oculus Rift OK2. We contrast this with an equivalent apparatus built using a GPU. Using captured human head motion and a set of image quality measures, we assess the ability of these systems to faithfully recreate the stimuli of an ideal virtual reality system - one with a zero latency tracker, renderer and display running at 1 kHz. Finally, we examine the results of these quality measures, and how each rendering approach is affected by velocity of movement and display persistence. We find that our system, with a lower average latency, can more faithfully draw what the ideal virtual reality system would. Further, we find that with low display persistence, the sensitivity to velocity of both systems is lowered, but that it is much lower for ours.

The lime renderings from plaza de la Corredera, Córdoba

Directory of Open Access Journals (Sweden)

González, T.

2002-09-01

Full Text Available The causes of the pathologies found on the lime renderings from Plaza de la Corredera façades are analysed in this study. For this purpose, the mineralogical and chemical analyses of the building materials -brickwork and rendering mortar- has been carried out, as well as their physical, hydric and mechanical properties have been determined. The obtained results from both unaltered and altered materials, and the analysis of the rendering's raw materials, have allowed us to establish that rendering deterioration is connected to the presence of saline compounds (gypsum, halite, which existing in the brickwork substratum, have been removed due to the water saturation of such brickwork. The main cause responsible of the alteration forms - efflorescence, crusts, grain-disintegration, bulging, flaking found on the renderings, has been the salts precipitation (halite, hexahydrite, epsomite in their way towards the external surface.

En este estudio se analizan las causas de las patologías de los revocos de cal de las fachadas de la Plaza de la Corredera. Para ello se ha realizado el análisis mineralógico y químico de los materiales de construcción - fábrica de ladrillo y mortero de revestimiento- y se han determinado sus propiedades físicas, hídricas y mecánicas. Mediante la comparación de los resultados obtenidos en los materiales inalterados y en los alterados, así como una vez analizadas las materias primas utilizadas en la realización del revoco, se ha podido establecer que la alteración de este último está relacionada con la existencia de compuestos salinos (yeso, halita que, presentes en el substrato de fábrica de ladrillo, se han exudado por saturación de agua de la misma. La precipitación de las sales (halita, hexahidrita, epsomita en su migración hacia el exterior ha sido la principal responsable de las formas de alteración -eflorescencias, costras, arenización, abombamientos, descamaciones- que aparecen sobre los

Structure of a molecular liquid GeI4

International Nuclear Information System (INIS)

Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

2016-01-01

A molecular liquid GeI 4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge–I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I–I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å −1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed. (paper)

Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

DEFF Research Database (Denmark)

Snow, M.; Bain, N.; Black, J.

2004-01-01

The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

Molecular Descriptors Family on Structure Activity Relationships 1. Review of the Methodology

Directory of Open Access Journals (Sweden)

Lorentz JÄNTSCHI

2005-01-01

Full Text Available This review cumulates the knowledge about the use of Molecular Descriptors Family usage on Structure Activity Relationships. The methodology is augmented through the general Structure Activity Relationships methodology. The obtained models in a series of five papers are quantitatively analyzed by comparing with previous reported results by using of the correlated correlations tests. The scores for a series of 13 data sets unpublished yet results are presented. Two unrestricted online access portals to the Molecular Descriptors Family Structure Activity Relationship models results are given.

Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

Science.gov (United States)

Walsh, Tiffany R

2017-07-18

An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

Science.gov (United States)

Couvineau, Alain; Laburthe, Marc

2012-05-01

The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

Insurance of professional responsibility at medical aid rendering

Directory of Open Access Journals (Sweden)

Abyzova N.V.

2011-12-01

Full Text Available The article discusses the necessity of adoption of professional responsibility insurance act into the public health service. It is considered as the basic mechanism of compensation in case of damage to a patient at medical aid rendering

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

International Nuclear Information System (INIS)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

2010-01-01

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Energy Technology Data Exchange (ETDEWEB)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-08-15

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.

NATO Advanced Study Institute on Electronic Structure of Polymers and Molecular Crystals

CERN Document Server

Ladik, János

1975-01-01

The NATO Advanced Study Institute on "Electronic Structure of Polymers and Molecular Crystals" was held at the Facultes Universi­ taires de Namur (F.U.N.) from September 1st till September 14th, 1974. We wish to express our appreciation to the NATO Scientific Affairs Division whose generous support made this Institute possible and to the Facultes Universitaires de Namur and the Societe Chimique de Belgique which provided fellowships and travel grants to a number of students. This volume contains the main lectures about the basic principles of the field and about different recent developments of the theory of the electronic structure of polymers and molecular crystals. The school started with the presentation of the basic SCF-LCAO theory of the electronic structure of periodic polymers and molecular crystals (contributions by Ladik, Andre & Delhalle) showing how a combination of quantum chemical and solid state physical methods can provide band structures for these systems. The numerical aspects of these ...

Crystal structure and pair potentials: A molecular-dynamics study

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1980-10-06

With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

Science.gov (United States)

Yip, Hin-Lap

Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

TransCut: interactive rendering of translucent cutouts.

Science.gov (United States)

Li, Dongping; Sun, Xin; Ren, Zhong; Lin, Stephen; Tong, Yiying; Guo, Baining; Zhou, Kun

2013-03-01

We present TransCut, a technique for interactive rendering of translucent objects undergoing fracturing and cutting operations. As the object is fractured or cut open, the user can directly examine and intuitively understand the complex translucent interior, as well as edit material properties through painting on cross sections and recombining the broken pieces—all with immediate and realistic visual feedback. This new mode of interaction with translucent volumes is made possible with two technical contributions. The first is a novel solver for the diffusion equation (DE) over a tetrahedral mesh that produces high-quality results comparable to the state-of-art finite element method (FEM) of Arbree et al. but at substantially higher speeds. This accuracy and efficiency is obtained by computing the discrete divergences of the diffusion equation and constructing the DE matrix using analytic formulas derived for linear finite elements. The second contribution is a multiresolution algorithm to significantly accelerate our DE solver while adapting to the frequent changes in topological structure of dynamic objects. The entire multiresolution DE solver is highly parallel and easily implemented on the GPU. We believe TransCut provides a novel visual effect for heterogeneous translucent objects undergoing fracturing and cutting operations.

The Atom in a Molecule: Implications for Molecular Structure and Properties

Science.gov (United States)

2016-05-23

Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry

Reflection curves—new computation and rendering techniques

Directory of Open Access Journals (Sweden)

Dan-Eugen Ulmet

2004-05-01

Full Text Available Reflection curves on surfaces are important tools for free-form surface interrogation. They are essential for industrial 3D CAD/CAM systems and for rendering purposes. In this note, new approaches regarding the computation and rendering of reflection curves on surfaces are introduced. These approaches are designed to take the advantage of the graphics libraries of recent releases of commercial systems such as the OpenInventor toolkit (developed by Silicon Graphics or Matlab (developed by The Math Works. A new relation between reflection curves and contour curves is derived; this theoretical result is used for a straightforward Matlab implementation of reflection curves. A new type of reflection curves is also generated using the OpenInventor texture and environment mapping implementations. This allows the computation, rendering, and animation of reflection curves at interactive rates, which makes it particularly useful for industrial applications.

Cement-Based Renders Manufactured with Phase-Change Materials: Applications and Feasibility

Directory of Open Access Journals (Sweden)

Luigi Coppola

2016-01-01

Full Text Available The paper focuses on the evaluation of the rheological and mechanical performances of cement-based renders manufactured with phase-change materials (PCM in form of microencapsulated paraffin for innovative and ecofriendly residential buildings. Specifically, cement-based renders were manufactured by incorporating different amount of paraffin microcapsules—ranging from 5% to 20% by weight with respect to binder. Specific mass, entrained or entrapped air, and setting time were evaluated on fresh mortars. Compressive strength was measured over time to evaluate the effect of the PCM addition on the hydration kinetics of cement. Drying shrinkage was also evaluated. Experimental results confirmed that the compressive strength decreases as the amount of PCM increases. Furthermore, the higher the PCM content, the higher the drying shrinkage. The results confirm the possibility of manufacturing cement-based renders containing up to 20% by weight of PCM microcapsules with respect to binder.

Hardware-accelerated Point Generation and Rendering of Point-based Impostors

DEFF Research Database (Denmark)

Bærentzen, Jakob Andreas

2005-01-01

This paper presents a novel scheme for generating points from triangle models. The method is fast and lends itself well to implementation using graphics hardware. The triangle to point conversion is done by rendering the models, and the rendering may be performed procedurally or by a black box API....... I describe the technique in detail and discuss how the generated point sets can easily be used as impostors for the original triangle models used to create the points. Since the points reside solely in GPU memory, these impostors are fairly efficient. Source code is available online....

The Visualization Toolkit (VTK): Rewriting the rendering code for modern graphics cards

Science.gov (United States)

Hanwell, Marcus D.; Martin, Kenneth M.; Chaudhary, Aashish; Avila, Lisa S.

2015-09-01

The Visualization Toolkit (VTK) is an open source, permissively licensed, cross-platform toolkit for scientific data processing, visualization, and data analysis. It is over two decades old, originally developed for a very different graphics card architecture. Modern graphics cards feature fully programmable, highly parallelized architectures with large core counts. VTK's rendering code was rewritten to take advantage of modern graphics cards, maintaining most of the toolkit's programming interfaces. This offers the opportunity to compare the performance of old and new rendering code on the same systems/cards. Significant improvements in rendering speeds and memory footprints mean that scientific data can be visualized in greater detail than ever before. The widespread use of VTK means that these improvements will reap significant benefits.

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...

Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

DEFF Research Database (Denmark)

Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

1999-01-01

2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

Molecular structure and DFT investigations on new cobalt(II ...

Indian Academy of Sciences (India)

tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

International Nuclear Information System (INIS)

Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

2013-01-01

Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts

Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

Science.gov (United States)

Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

2018-04-24

In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

VIDEO ANIMASI 3D PENGENALAN RUMAH ADAT DAN ALAT MUSIK KEPRI DENGAN MENGUNAKAN TEKNIK RENDER CEL-SHADING

Directory of Open Access Journals (Sweden)

Jianfranco Irfian Asnawi

2016-11-01

Full Text Available Animasi ini berjudul "video animasi 3D rumah adat dan alat musik Kepulauan Riau dengan menggunakan teknik render cel-shading" merupakan video yang bertujuan memperkenalkan alat-alat musik yang berasal dari kepulauan riau, Animasi ini akan diterapkan dengan menggunakan teknik render cel-shading. Cel-shading adalah teknik render yang menampilkan grafik 3D yang menyerupai gambar tangan, seperti gambar komik dan kartun. Teknik ini juga sudah di terapkan dalam game 3D yang ternyata menarik banyak perhatian peminat. Teknik ini akan di terapkan kedalam animasi 3D "video animasi rumah adat dan alat musik kepulauan riau dengan menggunakan teknik render cel-shading" Animasi di rancang menggunakan skenario dan storyboard kemudian di implementasikan dalam software 3D MAYA AUTODESK dengan menggunakan teknik render cel-shading. Setelah diterapkan maka di dapatkan definisi keberhasilan dari teknik render cel shading di bandingkan dengan teknik render global illumination seperti dari kecepatan dalam merender dan tingkat kecerahan warna pada video. Kata kunci: animasi, game 3D, cel-shading.

Visualization of plasma collision phenomenon by particle based rendering

International Nuclear Information System (INIS)

Yamamoto, Takeshi; Takagishi, Hironori; Hasegawa, Kyoko; Nakata, Susumu; Tanaka, Satoshi; Tanaka, Kazuo

2012-01-01

In this paper, we visualize plasma collision phenomenon based on XYT-space (space and time) volume data for supporting research in plasma physics. We create 3D volume data in the XYT-space by piling up a time series of XY-plane photo images taken in experiment. As a result, we can visualize as one still image all the time behavior of the plasma plume. Besides, we adopt 'fused' visualization based on particle based rendering technique. Using that technique, we can easily fuse volume rendering different materials, and compare physics of different elements in flexible ways. In addition, we propose the method to generate pseudo-3D images from pictures shoot by ICCD of two perspectives on the upper and side. (author)

Specification and time required for the application of a lime-based render inside historic buildings

Directory of Open Access Journals (Sweden)

Vasco Peixoto de Freitas

2008-01-01

Full Text Available Intervention in ancient buildings with historical and architectural value requires traditional techniques, such as the use of lime mortars for internal and external wall renderings. In order to ensure the desired performance, these rendering mortars must be rigorously specified and quality controls have to be performed during application. The choice of mortar composition should take account of factors such as compatibility with the substrate, mechanical requirements and water behaviour. The construction schedule, which used to be considered a second order variable, nowadays plays a decisive role in the selection of the rendering technique, given its effects upon costs. How should lime-based mortars be specified? How much time is required for the application and curing of a lime-based render? This paper reflects upon the feasibility of using traditional lime mortars in three-layer renders inside churches and monasteries under adverse hygrothermal conditions and when time is critical. A case study is presented in which internal lime mortar renderings were applied in a church in Northern Portugal, where the very high relative humidity meant that several months were necessary before the drying process was complete.

ARE: Ada Rendering Engine

Directory of Open Access Journals (Sweden)

Stefano Penge

2009-10-01

Full Text Available E' ormai pratica diffusa, nello sviluppo di applicazioni web, l'utilizzo di template e di potenti template engine per automatizzare la generazione dei contenuti da presentare all'utente. Tuttavia a volte la potenza di tali engine è€ ottenuta mescolando logica e interfaccia, introducendo linguaggi diversi da quelli di descrizione della pagina, o addirittura inventando nuovi linguaggi dedicati.ARE (ADA Rendering Engine è€ pensato per gestire l'intero flusso di creazione del contenuto HTML/XHTML dinamico, la selezione del corretto template, CSS, JavaScript e la produzione dell'output separando completamente logica e interfaccia. I templates utilizzati sono puro HTML senza parti in altri linguaggi, e possono quindi essere gestiti e visualizzati autonomamente. Il codice HTML generato è€ uniforme e parametrizzato.E' composto da due moduli, CORE (Common Output Rendering Engine e ALE (ADA Layout Engine.Il primo (CORE viene utilizzato per la generazione OO degli elementi del DOM ed è pensato per aiutare lo sviluppatore nella produzione di codice valido rispetto al DTD utilizzato. CORE genera automaticamente gli elementi del DOM in base al DTD impostato nella configurazioneIl secondo (ALE viene utilizzato come template engine per selezionare automaticamente in base ad alcuni parametri (modulo, profilo utente, tipologia del nodo, del corso, preferenze di installazione il template HTML, i CSS e i file JavaScript appropriati. ALE permette di usare templates di default e microtemplates ricorsivi per semplificare il lavoro del grafico.I due moduli possono in ogni caso essere utilizzati indipendentemente l'uno dall'altro. E' possibile generare e renderizzare una pagina HTML utilizzando solo CORE oppure inviare gli oggetti CORE al template engine ALE che provvede a renderizzare la pagina HTML. Viceversa è possibile generare HTML senza utilizzare CORE ed inviarlo al template engine ALECORE è alla prima release ed è€ già utilizzato all

Molecular structure determination from x-ray scattering patterns of laser-aligned symmetric-top molecules

International Nuclear Information System (INIS)

Ho, P. J.; Starodub, D.; Saldin, D. K.; Shneerson, V. L.; Ourmazd, A.; Santra, R.

2009-01-01

We investigate the molecular structure information contained in the x-ray diffraction patterns of an ensemble of rigid CF 3 Br molecules aligned by an intense laser pulse at finite rotational temperature. The diffraction patterns are calculated at an x-ray photon energy of 20 keV to probe molecular structure at angstrom-scale resolution. We find that a structural reconstruction algorithm based on iterative phase retrieval fails to extract a reliable structure. However, the high atomic number of Br compared with C or F allows each diffraction pattern to be treated as a hologram. Using this approach, the azimuthal projection of the molecular electron density about the alignment axis may be retrieved.

Sparse PDF Volumes for Consistent Multi-Resolution Volume Rendering

KAUST Repository

Sicat, Ronell Barrera; Kruger, Jens; Moller, Torsten; Hadwiger, Markus

2014-01-01

This paper presents a new multi-resolution volume representation called sparse pdf volumes, which enables consistent multi-resolution volume rendering based on probability density functions (pdfs) of voxel neighborhoods. These pdfs are defined

Tactile display for virtual 3D shape rendering

CERN Document Server

Mansutti, Alessandro; Bordegoni, Monica; Cugini, Umberto

2017-01-01

This book describes a novel system for the simultaneous visual and tactile rendering of product shapes which allows designers to simultaneously touch and see new product shapes during the conceptual phase of product development. This system offers important advantages, including potential cost and time savings, compared with the standard product design process in which digital 3D models and physical prototypes are often repeatedly modified until an optimal design is achieved. The system consists of a tactile display that is able to represent, within a real environment, the shape of a product. Designers can explore the rendered surface by touching curves lying on the product shape, selecting those curves that can be considered style features and evaluating their aesthetic quality. In order to physically represent these selected curves, a flexible surface is modeled by means of servo-actuated modules controlling a physical deforming strip. The tactile display is designed so as to be portable, low cost, modular,...

Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

Science.gov (United States)

Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

2018-04-01

The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

Science.gov (United States)

2017-05-05

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

Science.gov (United States)

Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

3D reconstruction from X-ray fluoroscopy for clinical veterinary medicine using differential volume rendering

International Nuclear Information System (INIS)

Khongsomboon, K.; Hamamoto, Kazuhiko; Kondo, Shozo

2007-01-01

3D reconstruction from ordinary X-ray equipment which is not CT or MRI is required in clinical veterinary medicine. Authors have already proposed a 3D reconstruction technique from X-ray photograph to present bone structure. Although the reconstruction is useful for veterinary medicine, the technique has two problems. One is about exposure of X-ray and the other is about data acquisition process. An x-ray equipment which is not special one but can solve the problems is X-ray fluoroscopy. Therefore, in this paper, we propose a method for 3D-reconstruction from X-ray fluoroscopy for clinical veterinary medicine. Fluoroscopy is usually used to observe a movement of organ or to identify a position of organ for surgery by weak X-ray intensity. Since fluoroscopy can output a observed result as movie, the previous two problems which are caused by use of X-ray photograph can be solved. However, a new problem arises due to weak X-ray intensity. Although fluoroscopy can present information of not only bone structure but soft tissues, the contrast is very low and it is very difficult to recognize some soft tissues. It is very useful to be able to observe not only bone structure but soft tissues clearly by ordinary X-ray equipment in the field of clinical veterinary medicine. To solve this problem, this paper proposes a new method to determine opacity in volume rendering process. The opacity is determined according to 3D differential coefficient of 3D reconstruction. This differential volume rendering can present a 3D structure image of multiple organs volumetrically and clearly for clinical veterinary medicine. This paper shows results of simulation and experimental investigation of small dog and evaluation by veterinarians. (author)

16O + 16O molecular structures of superdeformed states in S isotopes

Science.gov (United States)

Taniguchi, Y.

2017-06-01

Structures of excited states in S isotopes are investigated by using the antisymmetrized molecular dynamics and generator coordinate method (GCM). The GCM basis wave functions are calculated via energy variation with a constraint on the quadrupole deformation parameter β. By applying the GCM after parity and angular momentum projections, the coexistence of positive- and negative-parity superdeformed (SD) bands are predicted in 33-36S except for negative-parity states in 36S. The SD bands have structures of 16O + 16O + valence neutron(s) in molecular orbitals around the two 16O cores in a cluster picture. The configurations of the valence neutron(s) in the SD states are δ and/or π molecular orbitals.

Laser-induced blurring of molecular structure information in high harmonic spectroscopy

DEFF Research Database (Denmark)

Risoud, Francois; Leveque, Camille; Labeye, Marie

2017-01-01

High harmonic spectroscopy gives access to molecular structure with Angstrom resolution. Such information is encoded in the destructive interferences occurring between the harmonic emissions from the different parts of the molecule. By solving the time-dependent Schrodinger equation, either....... These findings have important consequences for molecular imaging and orbital tomography using high harmonic spectroscopy....

Entropy in molecular recognition by proteins.

Science.gov (United States)

Caro, José A; Harpole, Kyle W; Kasinath, Vignesh; Lim, Jackwee; Granja, Jeffrey; Valentine, Kathleen G; Sharp, Kim A; Wand, A Joshua

2017-06-20

Molecular recognition by proteins is fundamental to molecular biology. Dissection of the thermodynamic energy terms governing protein-ligand interactions has proven difficult, with determination of entropic contributions being particularly elusive. NMR relaxation measurements have suggested that changes in protein conformational entropy can be quantitatively obtained through a dynamical proxy, but the generality of this relationship has not been shown. Twenty-eight protein-ligand complexes are used to show a quantitative relationship between measures of fast side-chain motion and the underlying conformational entropy. We find that the contribution of conformational entropy can range from favorable to unfavorable, which demonstrates the potential of this thermodynamic variable to modulate protein-ligand interactions. For about one-quarter of these complexes, the absence of conformational entropy would render the resulting affinity biologically meaningless. The dynamical proxy for conformational entropy or "entropy meter" also allows for refinement of the contributions of solvent entropy and the loss in rotational-translational entropy accompanying formation of high-affinity complexes. Furthermore, structure-based application of the approach can also provide insight into long-lived specific water-protein interactions that escape the generic treatments of solvent entropy based simply on changes in accessible surface area. These results provide a comprehensive and unified view of the general role of entropy in high-affinity molecular recognition by proteins.

Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

Science.gov (United States)

Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

2018-03-06

Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

Radionuclide cisternography: SPECT and 3D-rendering

International Nuclear Information System (INIS)

Henkes, H.; Huber, G.; Piepgras, U.; Hierholzer, J.; Cordes, M.

1991-01-01

Radionuclide cisternography is indicated in the clinical work-up for hydrocephalus, when searching for CSF leaks, and when testing whether or not intracranial cystic lesions are communicating with the adjacent subarachnoid space. This paper demonstrates the feasibility and diagnostic value of SPECT and subsequent 3D surface rendering in addition to conventional rectilinear CSF imaging in eight patients. Planar images allowed the evaluation of CSF circulation and the detection of CSF fistula. They were advantageous in examinations 48 h after application of 111 In-DTPA. SPECT scans, generated 4-24 h after tracer application, were superior in the delineation of basal cisterns, especially in early scans; this was helpful in patients with pooling due to CSF fistula and in cystic lesions near the skull base. A major drawback was the limited image quality of delayed scans, when the SPECT data were degraded by a low count rate. 3D surface rendering was easily feasible from SPECT data and yielded high quality images. The presentation of the spatial distribution of nuclide-contaminated CSF proved especially helpful in the area of the basal cisterns. (orig.) [de

Machine learning for the structure-energy-property landscapes of molecular crystals.

Science.gov (United States)

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

Energy Technology Data Exchange (ETDEWEB)

Prates, Luciana Louzada [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

2017-05-16

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structures within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.

Using photoelectron diffraction to determine complex molecular adsorption structures

International Nuclear Information System (INIS)

Woodruff, D P

2010-01-01

Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

Molecular symmetry: Why permutation-inversion (PI) groups don't render the point groups obsolete

Science.gov (United States)

Groner, Peter

2018-01-01

The analysis of spectra of molecules with internal large-amplitude motions (LAMs) requires molecular symmetry (MS) groups that are larger than and significantly different from the more familiar point groups. MS groups are described often by the permutation-inversion (PI) group method. It is shown that point groups still can and should play a significant role together with the PI groups for a class of molecules with internal rotors. In molecules of this class, several simple internal rotors are attached to a rigid molecular frame. The PI groups for this class are semidirect products like H ^ F, where the invariant subgroup H is a direct product of cyclic groups and F is a point group. This result is used to derive meaningful labels for MS groups, and to derive correlation tables between MS groups and point groups. MS groups of this class have many parallels to space groups of crystalline solids.

Emotion rendering in auditory simulations of imagined walking styles

DEFF Research Database (Denmark)

Turchet, Luca; Rodá, Antonio

2016-01-01

This paper investigated how different emotional states of a walker can be rendered and recognized by means of footstep sounds synthesis algorithms. In a first experiment, participants were asked to render, according to imagined walking scenarios, five emotions (aggressive, happy, neutral, sad......, and tender) by manipulating the parameters of synthetic footstep sounds simulating various combinations of surface materials and shoes types. Results allowed to identify, for the involved emotions and sound conditions, the mean values and ranges of variation of two parameters, sound level and temporal...... distance between consecutive steps. Results were in accordance with those reported in previous studies on real walking, suggesting that expression of emotions in walking is independent from the real or imagined motor activity. In a second experiment participants were asked to identify the emotions...

Frequency Analysis of Gradient Estimators in Volume Rendering

NARCIS (Netherlands)

Bentum, Marinus Jan; Lichtenbelt, Barthold B.A.; Malzbender, Tom

1996-01-01

Gradient information is used in volume rendering to classify and color samples along a ray. In this paper, we present an analysis of the theoretically ideal gradient estimator and compare it to some commonly used gradient estimators. A new method is presented to calculate the gradient at arbitrary

Electron Scattering Studies of Gas Phase Molecular Structure at High Temperature

Science.gov (United States)

Mawhorter, Richard J., Jr.

A high precision counting electron diffraction study of the structure of gaseous sulfur dioxide as a function of temperature from 300(DEGREES) to 1000(DEGREES)K is presented. The results agree well with current theory, and yield insight into the effects of anharmonicity on molecular structure. Another aspect of molecular structure is the molecular charge density distribution. The difference (DELTA)(sigma) is between the electron scattering cross sections for the actual molecule and independent atom model (IAM) are a sensitive measure of the change in this distribution due to bond formation. These difference cross sections have been calculated using ab initio methods, and the results for a wide range of simple polyatomic molecules are presented. Such calculations are routinely done for a single, fixed molecular geometry, an approach which neglects the effects of the vibrational motion of real molecules. The effect of vibrational averaging is studied in detail for the three normal vibrational modes of H(,2)O in the ground state. The effects are small, lending credence to the practice of comparing cross sections calculated at a fixed geometry with inherently averaged experimental data. The efficacy of the standard formula used to account for vibrational averaging in the IAM is also examined. Finally, the nature of the ionic bond is probed with an experimental study of the structure of alkali chlorides, NaCl, KCl, RbCl, and CsCl, in the gas phase. Temperatures from 840-960(DEGREES)K were required to achieve the necessary vapor pressures of approximately 0.01 torr. A planar rhombic structure for the dimer molecule is confirmed, with a fairly uniform decrease of the chlorine-alkali-chlorine angle as the alkalis increase in size. The experiment also yields information on the amount of dimer present in the vapor, and these results are compared with thermodynamic values.

Factors affecting extension workers in their rendering of effective ...

African Journals Online (AJOL)

Factors affecting extension workers in their rendering of effective service to pre and ... Small, micro and medium entrepreneurs play an important role in economic ... such as production, marketing and management to adequately service the ...

Molecular epidemiology and population structure of bovine Streptococcus uberis

DEFF Research Database (Denmark)

Rato, M G; Bexiga, R; Nunes, S F

2008-01-01

The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

International Nuclear Information System (INIS)

Sidhu, Navdeep S.; Schreiber, Kathrin; Pröpper, Kevin; Becker, Stefan; Usón, Isabel; Sheldrick, George M.; Gärtner, Jutta; Krätzner, Ralph; Steinfeld, Robert

2014-01-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder

Structure of sulfamidase provides insight into the molecular pathology of mucopolysaccharidosis IIIA

Energy Technology Data Exchange (ETDEWEB)

Sidhu, Navdeep S. [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Schreiber, Kathrin [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany); Pröpper, Kevin [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Becker, Stefan [Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); Usón, Isabel [Instituto de Biologia Molecular de Barcelona (IBMB–CSIC), Barcelona Science Park, Baldiri Reixach 15, 08028 Barcelona (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); Sheldrick, George M. [University of Göttingen, Tammannstrasse 4, 37077 Göttingen (Germany); Gärtner, Jutta; Krätzner, Ralph, E-mail: rkraetz@gwdg.de; Steinfeld, Robert, E-mail: rkraetz@gwdg.de [University of Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen (Germany)

2014-05-01

Mucopolysaccharidosis IIIA is a fatal neurodegenerative disease that typically manifests itself in childhood and is caused by mutations in the gene for the lysosomal enzyme sulfamidase. The first structure of this enzyme is presented, which provides insight into the molecular basis of disease-causing mutations, and the enzymatic mechanism is proposed. Mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities, is caused by an inherited deficiency of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). More than 100 mutations in the SGSH gene have been found to reduce or eliminate its enzymatic activity. However, the molecular understanding of the effect of these mutations has been confined by a lack of structural data for this enzyme. Here, the crystal structure of glycosylated SGSH is presented at 2 Å resolution. Despite the low sequence identity between this unique N-sulfatase and the group of O-sulfatases, they share a similar overall fold and active-site architecture, including a catalytic formylglycine, a divalent metal-binding site and a sulfate-binding site. However, a highly conserved lysine in O-sulfatases is replaced in SGSH by an arginine (Arg282) that is positioned to bind the N-linked sulfate substrate. The structure also provides insight into the diverse effects of pathogenic mutations on SGSH function in mucopolysaccharidosis type IIIA and convincing evidence for the molecular consequences of many missense mutations. Further, the molecular characterization of SGSH mutations will lay the groundwork for the development of structure-based drug design for this devastating neurodegenerative disorder.

Tunneling and resonant conductance in one-dimensional molecular structures

International Nuclear Information System (INIS)

Kozhushner, M.A.; Posvyanskii, V.S.; Oleynik, I.I.

2005-01-01

We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

Science.gov (United States)

Cati, Dilovan S; Stoeckli-Evans, Helen

2017-05-01

The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

Irregular Morphing for Real-Time Rendering of Large Terrain

Directory of Open Access Journals (Sweden)

S. Kalem

2016-06-01

Full Text Available The following paper proposes an alternative approach to the real-time adaptive triangulation problem. A new region-based multi-resolution approach for terrain rendering is described which improves on-the-fly the distribution of the density of triangles inside the tile after selecting appropriate Level-Of-Detail by an adaptive sampling. This proposed approach organizes the heightmap into a QuadTree of tiles that are processed independently. This technique combines the benefits of both Triangular Irregular Network approach and region-based multi-resolution approach by improving the distribution of the density of triangles inside the tile. Our technique morphs the initial regular grid of the tile to deformed grid in order to minimize approximation error. The proposed technique strives to combine large tile size and real-time processing while guaranteeing an upper bound on the screen space error. Thus, this approach adapts terrain rendering process to local surface characteristics and enables on-the-fly handling of large amount of terrain data. Morphing is based-on the multi-resolution wavelet analysis. The use of the D2WT multi-resolution analysis of the terrain height-map speeds up processing and permits to satisfy an interactive terrain rendering. Tests and experiments demonstrate that Haar B-Spline wavelet, well known for its properties of localization and its compact support, is suitable for fast and accurate redistribution. Such technique could be exploited in client-server architecture for supporting interactive high-quality remote visualization of very large terrain.

Virtual endoscopy and 3D volume rendering in the management of frontal sinus fractures.

Science.gov (United States)

Belina, Stanko; Cuk, Viseslav; Klapan, Ivica

2009-12-01

Frontal sinus fractures (FSF) are commonly caused by traffic accidents, assaults, industrial accidents and gunshot wounds. Classical roentgenography has high proportion of false negative findings in cases of FSF and is not particularly useful in examining the severity of damage to the frontal sinus posterior table and the nasofrontal duct region. High resolution computed tomography was inavoidable during the management of such patients but it may produce large quantity of 2D images. Postprocessing of datasets acquired by high resolution computer tomography from patients with severe head trauma may offer a valuable additional help in diagnostics and surgery planning. We performed virtual endoscopy (VE) and 3D volume rendering (3DVR) on high resolution CT data acquired from a 54-year-old man with with both anterior and posterior frontal sinus wall fracture in order to demonstrate advantages and disadvantages of these methods. Data acquisition was done by Siemens Somatom Emotion scanner and postprocessing was performed with Syngo 2006G software. VE and 3DVR were performed in a man who suffered blunt trauma to his forehead and nose in an traffic accident. Left frontal sinus anterior wall fracture without dislocation and fracture of tabula interna with dislocation were found. 3D position and orientation of fracture lines were shown in by 3D rendering software. We concluded that VE and 3DVR can clearly display the anatomic structure of the paranasal sinuses and nasopharyngeal cavity, revealing damage to the sinus wall caused by a fracture and its relationship to surrounding anatomical structures.

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

Science.gov (United States)

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

2014-12-19

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

Haptic rendering foundations, algorithms, and applications

CERN Document Server

Lin, Ming C

2008-01-01

For a long time, human beings have dreamed of a virtual world where it is possible to interact with synthetic entities as if they were real. It has been shown that the ability to touch virtual objects increases the sense of presence in virtual environments. This book provides an authoritative overview of state-of-theart haptic rendering algorithms and their applications. The authors examine various approaches and techniques for designing touch-enabled interfaces for a number of applications, including medical training, model design, and maintainability analysis for virtual prototyping, scienti

GPU Pro 4 advanced rendering techniques

CERN Document Server

Engel, Wolfgang

2013-01-01

GPU Pro4: Advanced Rendering Techniques presents ready-to-use ideas and procedures that can help solve many of your day-to-day graphics programming challenges. Focusing on interactive media and games, the book covers up-to-date methods producing real-time graphics. Section editors Wolfgang Engel, Christopher Oat, Carsten Dachsbacher, Michal Valient, Wessam Bahnassi, and Sebastien St-Laurent have once again assembled a high-quality collection of cutting-edge techniques for advanced graphics processing unit (GPU) programming. Divided into six sections, the book begins with discussions on the abi

GPU PRO 3 Advanced rendering techniques

CERN Document Server

Engel, Wolfgang

2012-01-01

GPU Pro3, the third volume in the GPU Pro book series, offers practical tips and techniques for creating real-time graphics that are useful to beginners and seasoned game and graphics programmers alike. Section editors Wolfgang Engel, Christopher Oat, Carsten Dachsbacher, Wessam Bahnassi, and Sebastien St-Laurent have once again brought together a high-quality collection of cutting-edge techniques for advanced GPU programming. With contributions by more than 50 experts, GPU Pro3: Advanced Rendering Techniques covers battle-tested tips and tricks for creating interesting geometry, realistic sha

Design of Carborane Molecular Architectures via Electronic Structure Computations

International Nuclear Information System (INIS)

Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

2009-01-01

Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

Validation of Thermal Lethality against Salmonella enterica in Poultry Offal during Rendering.

Science.gov (United States)

Jones-Ibarra, Amie-Marie; Acuff, Gary R; Alvarado, Christine Z; Taylor, T Matthew

2017-09-01

Recent outbreaks of human disease following contact with companion animal foods cross-contaminated with enteric pathogens, such as Salmonella enterica, have resulted in increased concern regarding the microbiological safety of animal foods. Additionally, the U.S. Food and Drug Administration Food Safety Modernization Act and its implementing rules have stipulated the implementation of current good manufacturing practices and food safety preventive controls for livestock and companion animal foods. Animal foods and feeds are sometimes formulated to include thermally rendered animal by-product meals. The objective of this research was to determine the thermal inactivation of S. enterica in poultry offal during rendering at differing temperatures. Raw poultry offal was obtained from a commercial renderer and inoculated with a mixture of Salmonella serovars Senftenberg, Enteritidis, and Gallinarum (an avian pathogen) prior to being subjected to heating at 150, 155, or 160°F (65.5, 68.3, or 71.1°C) for up to 15 min. Following heat application, surviving Salmonella bacteria were enumerated. Mean D-values for the Salmonella cocktail at 150, 155, and 160°F were 0.254 ± 0.045, 0.172 ± 0.012, and 0.086 ± 0.004 min, respectively, indicative of increasing susceptibility to increased application of heat during processing. The mean thermal process constant (z-value) was 21.948 ± 3.87°F. Results indicate that a 7.0-log-cycle inactivation of Salmonella may be obtained from the cumulative lethality encountered during the heating come-up period and subsequent rendering of raw poultry offal at temperatures not less than 150°F. Current poultry rendering procedures are anticipated to be effective for achieving necessary pathogen control when completed under sanitary conditions.

Marine Biotoxins: Laboratory Culture and Molecular Structure

Science.gov (United States)

1991-01-21

ciguateric carnivorous fishes in concentrations ranging from I to 10 ppb. Its molecular structure has been elucidated. It has been isolated from toxic...American Chemical Society, Washington, DC, 1984, pp 217-329. 6. Med. J. Australia 1986, 145 (11/12), 558; 584-5M). 7. "Toxic Plants and Animals A Guide...isolated and grown in the laboratory. Lethality of crude acetone and methanol extracts were assa~ed by ip injection into mice. In vitro cytotoxicity and

Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement

Energy Technology Data Exchange (ETDEWEB)

Bibby, Jaclyn [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Keegan, Ronan M. [Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom)

2013-11-01

Processing of NMR structures for molecular replacement by AMPLE works well. AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

Semiconductive 3-D haloplumbate framework hybrids with high color rendering index white-light emission.

Science.gov (United States)

Wang, Guan-E; Xu, Gang; Wang, Ming-Sheng; Cai, Li-Zhen; Li, Wen-Hua; Guo, Guo-Cong

2015-12-01

Single-component white light materials may create great opportunities for novel conventional lighting applications and display systems; however, their reported color rendering index (CRI) values, one of the key parameters for lighting, are less than 90, which does not satisfy the demand of color-critical upmarket applications, such as photography, cinematography, and art galleries. In this work, two semiconductive chloroplumbate (chloride anion of lead(ii)) hybrids, obtained using a new inorganic-organic hybrid strategy, show unprecedented 3-D inorganic framework structures and white-light-emitting properties with high CRI values around 90, one of which shows the highest value to date.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

Directory of Open Access Journals (Sweden)

Dallakian Pavel

2011-02-01

Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

Two-dimensional dynamics of a free molecular chain with a secondary structure

DEFF Research Database (Denmark)

Zolotaryuk, Alexander; Christiansen, Peter Leth; Savin, A.V.

1996-01-01

A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model of an anharmo......A simple two-dimensional (2D) model of an isolated (free) molecular chain with primary and secondary structures has been suggested and investigated both analytically and numerically. This model can be considered as the simplest generalization of the well-known Fermi-Pasta-Ulam model...

Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

KAUST Repository

Hayes, Sophia C.

2016-09-27

Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

KAUST Repository

Hayes, Sophia C.; Pieridou, Galatia; Vezie, Michelle; Few, Sheridan; Bronstein, Hugo; Meager, Iain; McCulloch, Iain; Nelson, Jenny

2016-01-01

Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

Science.gov (United States)

Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

2016-09-07

Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

The effect of depth compression on multiview rendering quality

NARCIS (Netherlands)

Merkle, P.; Morvan, Y.; Smolic, A.; Farin, D.S.; Mueller, K..; With, de P.H.N.; Wiegand, T.

2010-01-01

This paper presents a comparative study on different techniques for depth-image compression and its implications on the quality of multiview video plus depth virtual view rendering. A novel coding algorithm for depth images that concentrates on their special characteristics, namely smooth regions

Learning Molecular Structures in a Tangible Augmented Reality Environment

Science.gov (United States)

Asai, Kikuo; Takase, Norio

2011-01-01

This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

Digital tomosynthesis rendering of joint margins for arthritis assessment

Science.gov (United States)

Duryea, Jeffrey W.; Neumann, Gesa; Yoshioka, Hiroshi; Dobbins, James T., III

2004-05-01

PURPOSE: Rheumatoid arthritis (RA) of the hand is a significant healthcare problem. Techniques to accurately quantity the structural changes from RA are crucial for the development and prescription of therapies. Analysis of radiographic joint space width (JSW) is widely used and has demonstrated promise. However, radiography presents a 2D view of the joint. In this study we performed tomosynthesis reconstructions of proximal interphalangeal (PIP), and metacarpophalangeal (MCP) joints to measure the 3D joint structure. METHODS: We performed a reader study using simulated radiographs of 12 MCP and 12 PIP joints from skeletal specimens imaged with micro-CT. The tomosynthesis technique provided images of reconstructed planes with 0.75 mm spacing, which were presented to 2 readers with a computer tool. The readers were instructed to delineate the joint surfaces on tomosynthetic slices where they could visualize the margins. We performed a quantitative analysis of 5 slices surrounding the central portion of each joint. Reader-determined JSW was compared to a gold standard. As a figure of merit we calculated the average root-mean square deviation (RMSD). RESULTS: RMSD was 0.22 mm for both joints. For the individual joints, RMSD was 0.18 mm (MCP), and 0.26 mm (PIP). The reduced performance for the smaller PIP joints suggests that a slice spacing less than 0.75 mm may be more appropriate. CONCLUSIONS: We have demonstrated the capability of limited 3D rendering of joint surfaces using digital tomosynthesis. This technique promises to provide an improved method to visualize the structural changes of RA.

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

Science.gov (United States)

Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

Effects of molecular structure on microscopic heat transport in chain polymer liquids

International Nuclear Information System (INIS)

Matsubara, Hiroki; Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

2015-01-01

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T c ) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

Effects of molecular structure on microscopic heat transport in chain polymer liquids

Energy Technology Data Exchange (ETDEWEB)

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

Confocal imaging of whole vertebrate embryos reveals novel insights into molecular and cellular mechanisms of organ development

Science.gov (United States)

Hadel, Diana M.; Keller, Bradley B.; Sandell, Lisa L.

2014-03-01

Confocal microscopy has been an invaluable tool for studying cellular or sub-cellular biological processes. The study of vertebrate embryology is based largely on examination of whole embryos and organs. The application of confocal microscopy to immunostained whole mount embryos, combined with three dimensional (3D) image reconstruction technologies, opens new avenues for synthesizing molecular, cellular and anatomical analysis of vertebrate development. Optical cropping of the region of interest enables visualization of structures that are morphologically complex or obscured, and solid surface rendering of fluorescent signal facilitates understanding of 3D structures. We have applied these technologies to whole mount immunostained mouse embryos to visualize developmental morphogenesis of the mammalian inner ear and heart. Using molecular markers of neuron development and transgenic reporters of neural crest cell lineage we have examined development of inner ear neurons that originate from the otic vesicle, along with the supporting glial cells that derive from the neural crest. The image analysis reveals a previously unrecognized coordinated spatial organization between migratory neural crest cells and neurons of the cochleovestibular nerve. The images also enable visualization of early cochlear spiral nerve morphogenesis relative to the developing cochlea, demonstrating a heretofore unknown association of neural crest cells with extending peripheral neurite projections. We performed similar analysis of embryonic hearts in mouse and chick, documenting the distribution of adhesion molecules during septation of the outflow tract and remodeling of aortic arches. Surface rendering of lumen space defines the morphology in a manner similar to resin injection casting and micro-CT.

Exponential Repulsion Improves Structural Predictability of Molecular Docking

Czech Academy of Sciences Publication Activity Database

Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

2016-01-01

Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

Splitting of α-Helical Structure as Molecular Basis for Abolishing an Amyloid Formation by Multiple Glycosylation: A Molecular Dynamics Simulation Study

Energy Technology Data Exchange (ETDEWEB)

Choi, Youngjin [Hoseo University, Asan (Korea, Republic of); Cho, Eunae; Jung, Seunho [Konkuk University, Seoul (Korea, Republic of)

2016-07-15

Molecular details played by glycosylation are complicated by the subtle nature of variations in the glycan structure, and this complexity is one of the research barriers to establish structure-function relationship on the protein modification. This is particularly true for understanding the exact structural consequence of the glycosylation of the biological proteins. The present MD simulation revealed molecular-level mechanism of the glycosylation effect on the peptide to understand the experimentally observed phenomenon for inhibiting amyloid formation in the model peptide. The galactose residue on the Ser17 undermined the helical integrity of main protein region by enhancing sugar–amino acid interaction and perturbing natural interactions between amino acid residues.

7 CFR 54.1016 - Advance information concerning service rendered.

Science.gov (United States)

2010-01-01

... MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS INSPECTION ACT... rendered. Upon request of any applicant, all or any part of the contents of any report issued to the...

Molecular motion and structure in plastics

International Nuclear Information System (INIS)

Doolan, K.R.; Baxter, M.

2000-01-01

Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

Science.gov (United States)

Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

2016-01-01

Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

A Single Swede Midge (Diptera: Cecidomyiidae) Larva Can Render Cauliflower Unmarketable.

Science.gov (United States)

Stratton, Chase A; Hodgdon, Elisabeth A; Zuckerman, Samuel G; Shelton, Anthony M; Chen, Yolanda H

2018-05-01

Swede midge, Contarinia nasturtii Kieffer (Diptera: Cecidomyiidae), is an invasive pest causing significant damage on Brassica crops in the Northeastern United States and Eastern Canada. Heading brassicas, like cauliflower, appear to be particularly susceptible. Swede midge is difficult to control because larvae feed concealed inside meristematic tissues of the plant. In order to develop damage and marketability thresholds necessary for integrated pest management, it is important to determine how many larvae render plants unmarketable and whether the timing of infestation affects the severity of damage. We manipulated larval density (0, 1, 3, 5, 10, or 20) per plant and the timing of infestation (30, 55, and 80 d after seeding) on cauliflower in the lab and field to answer the following questions: 1) What is the swede midge damage threshold? 2) How many swede midge larvae can render cauliflower crowns unmarketable? and 3) Does the age of cauliflower at infestation influence the severity of damage and marketability? We found that even a single larva can cause mild twisting and scarring in the crown rendering cauliflower unmarketable 52% of the time, with more larvae causing more severe damage and additional losses, regardless of cauliflower age at infestation.

Structure and properties of sodium aluminosilicate glasses from molecular dynamics simulations

DEFF Research Database (Denmark)

Xiang, Ye; Du, Jincheng; Smedskjær, Morten Mattrup

2013-01-01

the recent Corning® Gorilla® Glass. In this paper, the structures of sodium aluminosilicate glasses with a wide range of Al/Na ratios (from 1.5 to 0.6) have been studied using classical molecular dynamics simulations in a system containing around 3000 atoms, with the aim to understand the structural role...

Mastering Mental Ray Rendering Techniques for 3D and CAD Professionals

CERN Document Server

O'Connor, Jennifer

2010-01-01

Proven techniques for using mental ray effectively. If you're a busy artist seeking high-end results for your 3D, design, or architecture renders using mental ray, this is the perfect book for you. It distills the highly technical nature of rendering into easy-to-follow steps and tutorials that you can apply immediately to your own projects. The book uses 3ds Max and 3ds Max Design to show the integration with mental ray, but users of any 3D or CAD software can learn valuable techniques for incorporating mental ray into their pipelines.: Takes you under the hood of mental ray, a stand-alone or

Structure-Activity Relationships on the Molecular Descriptors Family Project at the End

Directory of Open Access Journals (Sweden)

Lorentz JÄNTSCHI

2007-12-01

Full Text Available Molecular Descriptors Family (MDF on the Structure-Activity Relationships (SAR, a promising approach in investigation and quantification of the link between 2D and 3D structural information and the activity, and its potential in the analysis of the biological active compounds is summarized. The approach, attempts to correlate molecular descriptors family generated and calculated on a set of biological active compounds with their observed activity. The estimation as well as prediction abilities of the approach are presented. The obtained MDF SAR models can be used to predict the biological activity of unknown substrates in a series of compounds.

The molecular structure of the insoluble organic matter isolated from Murchison carbonaceous chondrite.

Science.gov (United States)

Robert, F.; Derenne, S.

2009-04-01

During these last 10 years, our group has characterized the various molecular moieties of the insoluble organic matter (IOM) isolated from carbonaceous meteorites with the aim of reconstructing its overall molecular structure. Indeed, a precise knowledge of the structure of an organic macromolecule contains irreplaceable information that traces its mechanisms of synthesis and its conditions of formation. Such a modelled structure will be presented. Carbonaceous chondrites contain up to 3 wt % of carbon that is under the form of soluble and insoluble fractions. The IOM, which constitutes more than 75 wt% of the bulk organic matter, was isolated from the bulk rock through successive acid dissolutions. The chemical structure of the isolated IOM has been studied by both (1) destructive and (2) non destructive methods. Methods include thermal and chemical degradations followed by GC/MS, spectroscopic techniques (nuclear magnetic resonance, Fourier transform infra red spectroscopy; X-ray absorption near-edge spectroscopy, electron paramagnetic resonance) along with high resolution transmission electron microscopy. Although each technique alone cannot provide definite information on the chemical structure of such a complex material, the combination of the results can be used to reconstruct the molecular structure of the IOM. The proposed structure accounts for all these measured parameters. The details of this structure reveal information of the conditions of its formation in space and allow to discuss the mechanisms of organo-synthesis in the cosmochemical context of the formation of the solar system.

Water driven leaching of biocides from paints and renders

DEFF Research Database (Denmark)

Bester, Kai; Vollertsen, Jes; Bollmann, Ulla E

) were so high, that rather professional urban gardening (flower and greenhouses) than handling of biocides from construction materials seem to be able to explain the findings. While the use in agriculture is restricted, the use in greenhouses is currently considered legal in Denmark. Leaching....../partitioning: Considering material properties, it was found out that, for all of the compounds the sorption (and leaching) is highly pH-dependent. It must be take into account that the pH in the porewater of the tested render materials is between 9 and 10 while the rainwater is around 5, thus making prediction difficult...... at this stage. For some of the compounds the sorption is dependent on the amount of polymer in the render, while it is only rarely of importance which polymer is used. Considering the interaction of weather with the leaching of biocides from real walls it turned out that a lot of parameters such as irradiation...

Photoionization-regulated star formation and the structure of molecular clouds

Science.gov (United States)

Mckee, Christopher F.

1989-01-01

A model for the rate of low-mass star formation in Galactic molecular clouds and for the influence of this star formation on the structure and evolution of the clouds is presented. The rate of energy injection by newly formed stars is estimated, and the effect of this energy injection on the size of the cloud is determined. It is shown that the observed rate of star formation appears adequate to support the observed clouds against gravitational collapse. The rate of photoionization-regulated star formation is estimated and it is shown to be in agreement with estimates of the observed rate of star formation if the observed molecular cloud parameters are used. The mean cloud extinction and the Galactic star formation rate per unit mass of molecular gas are predicted theoretically from the condition that photionization-regulated star formation be in equilibrium. A simple model for the evolution of isolated molecular clouds is developed.

Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

NARCIS (Netherlands)

Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

The Role of Molecular Structure and Conformation in Polymer Electronics

NARCIS (Netherlands)

von Hauff, Elizabeth

2011-01-01

ABSTRACT Conjugated polymers have unique material properties that make them promising for a wide range of applications. The potential lies in the virtually infinite possibilities for creating new materials for specific applications by simply chemically tuning the molecular structure. Conjugated

Autostereoscopic image creation by hyperview matrix controlled single pixel rendering

Science.gov (United States)

Grasnick, Armin

2017-06-01

technology just with a simple equation. This formula can be utilized to create a specific hyperview matrix for a certain 3D display - independent of the technology used. A hyperview matrix may contain the references to loads of images and act as an instruction for a subsequent rendering process of particular pixels. Naturally, a single pixel will deliver an image with no resolution and does not provide any idea of the rendered scene. However, by implementing the method of pixel recycling, a 3D image can be perceived, even if all source images are different. It will be proven that several millions of perspectives can be rendered with the support of GPU rendering and benefit from the hyperview matrix. In result, a conventional autostereoscopic display, which is designed to represent only a few perspectives can be used to show a hyperview image by using a suitable hyperview matrix. It will be shown that a millions-of-views-hyperview-image can be presented on a conventional autostereoscopic display. For such an hyperview image it is required that all pixels of the displays are allocated by different source images. Controlled by the hyperview matrix, an adapted renderer can render a full hyperview image in real-time.

Roles of water in protein structure and function studied by molecular liquid theory.

Science.gov (United States)

Imai, Takashi

2009-01-01

The roles of water in the structure and function of proteins have not been completely elucidated. Although molecular simulation has been widely used for the investigation of protein structure and function, it is not always useful for elucidating the roles of water because the effect of water ranges from atomic to thermodynamic level. The three-dimensional reference interaction site model (3D-RISM) theory, which is a statistical-mechanical theory of molecular liquids, can yield the solvation structure at the atomic level and calculate the thermodynamic quantities from the intermolecular potentials. In the last few years, the author and coworkers have succeeded in applying the 3D-RISM theory to protein aqueous solution systems and demonstrated that the theory is useful for investigating the roles of water. This article reviews some of the recent applications and findings, which are concerned with molecular recognition by protein, protein folding, and the partial molar volume of protein which is related to the pressure effect on protein.

Structural and Molecular Characterization of meso-Substituted Zinc Porphyrins: A DFT Supported Study

Directory of Open Access Journals (Sweden)

Giuseppe Mele

2011-12-01

Full Text Available Structural parameters of a range of over 100 meso-substituted zinc porphyrins were reviewed and compared to show how far the nature of the functional group may affect the interatomic distances and bond angles within the porphyrin core. It was proved that even despite evident deformations of the molecular structure, involving twisting of the porphyrin's central plane, the coupled π-bonding system remains flexible and stable. DFT calculations were applied to a number of selected porphyrins representative for the reviewed compounds to emphasize the relevance of theoretical methods in structural investigations of complex macrocyclic molecular systems. Experimental and DFT-simulated IR spectral data were reported and analyzed in context of the individual molecular features introduced by the meso substituents into the porphyrin moiety base. Raw experimental spectral data, including 1H- and 13C-NMR, UV-Vis, FTIR, XRD, and other relevant physicochemical details have been provided for a specially chosen reference zinc porphyrin functionalized by tert-butylphenyl groups.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

Determination of molecular-ion structures through the use of accelerated beams

International Nuclear Information System (INIS)

Gemmell, D.S.

1987-01-01

In this talk we report on recent research on molecular-ion structures using fast molecular-ion beams provided by Argonne's 5-MV Dynamitron accelerator. The method has become known as the ''Coulomb-explosion'' technique. When molecular-ion projectiles travelling at velocities of a few percent of the velocity of light strike a foil, the electrons that bind the molecular projectiles are almost always totally stripped off within the first few Angstroms of penetration into the solid target. This leaves a cluster of bare (or nearly bare) nuclei which separate rapidly as a result of their mutual Coulomb repulsion. This violent dissociation process in which the initial electrostatic potential energy is converted into kinetic energy of relative motion in the center-of-mass, has been termed a ''Coulomb explosion.'' 4 refs., 2 figs

Three-dimensional volume rendering of the ankle based on magnetic resonance images enables the generation of images comparable to real anatomy.

Science.gov (United States)

Anastasi, Giuseppe; Cutroneo, Giuseppina; Bruschetta, Daniele; Trimarchi, Fabio; Ielitro, Giuseppe; Cammaroto, Simona; Duca, Antonio; Bramanti, Placido; Favaloro, Angelo; Vaccarino, Gianluigi; Milardi, Demetrio

2009-11-01

We have applied high-quality medical imaging techniques to study the structure of the human ankle. Direct volume rendering, using specific algorithms, transforms conventional two-dimensional (2D) magnetic resonance image (MRI) series into 3D volume datasets. This tool allows high-definition visualization of single or multiple structures for diagnostic, research, and teaching purposes. No other image reformatting technique so accurately highlights each anatomic relationship and preserves soft tissue definition. Here, we used this method to study the structure of the human ankle to analyze tendon-bone-muscle relationships. We compared ankle MRI and computerized tomography (CT) images from 17 healthy volunteers, aged 18-30 years (mean 23 years). An additional subject had a partial rupture of the Achilles tendon. The MRI images demonstrated superiority in overall quality of detail compared to the CT images. The MRI series accurately rendered soft tissue and bone in simultaneous image acquisition, whereas CT required several window-reformatting algorithms, with loss of image data quality. We obtained high-quality digital images of the human ankle that were sufficiently accurate for surgical and clinical intervention planning, as well as for teaching human anatomy. Our approach demonstrates that complex anatomical structures such as the ankle, which is rich in articular facets and ligaments, can be easily studied non-invasively using MRI data.

Isotope chemistry and molecular structure. The WINIMAX weighting factor

International Nuclear Information System (INIS)

Lee, M.W.; Bigeleisen, J.

1979-01-01

The modulating coefficients for the finite polynomial expansion of the logarithm of the reduced partition function, lnb (u), of a harmonic oscillator have been obtained for the range of 0 6 . It is shown that this weighting function is near optimum to insure minimum amplitudes of oscillation in the expansion of lnb (u) as a function of the order of the expansion and to include most of the important molecular structure information contained in the moments of the eigenvalues. Beyond Σu/sub i/ 6 , there is little new structural information

Study of Barley Grain Molecular Structure for Ruminants Using DRIFT, FTIR-ATR and Synchrotron Radiation Infrared Microspectroscopy (SR-IMS): A Review

International Nuclear Information System (INIS)

Yu Peiqiang

2012-01-01

Barley inherent structures are highly associated with nutrient utilization and availability in both humans and animals. Barley has different degradation kinetics compared with other cereal grains. It has a relatively higher degradation rate and extent, which often cause digestive disorder in the rumen. Therefore understanding barley inherent structure at cellular and molecular levels and processing-induced structure changes is important, because we can manipulate barley inherent structures and digestive behaviors. Several molecular spectroscopy techniques can be used to detect barley inherent structures at cellular and molecular levels. This article reviews several applications of the IR molecular spectral bioanalytical techniques - DRIFT, FT/IR-ATR and SR-IMS for barley chemistry, molecular structure and molecular nutrition research

Cationic lipids: molecular structure/ transfection activity relationships and interactions with biomembranes.

Science.gov (United States)

Koynova, Rumiana; Tenchov, Boris

2010-01-01

Abstract Synthetic cationic lipids, which form complexes (lipoplexes) with polyanionic DNA, are presently the most widely used constituents of nonviral gene carriers. A large number of cationic amphiphiles have been synthesized and tested in transfection studies. However, due to the complexity of the transfection pathway, no general schemes have emerged for correlating the cationic lipid chemistry with their transfection efficacy and the approaches for optimizing their molecular structures are still largely empirical. Here we summarize data on the relationships between transfection activity and cationic lipid molecular structure and demonstrate that the transfection activity depends in a systematic way on the lipid hydrocarbon chain structure. A number of examples, including a large series of cationic phosphatidylcholine derivatives, show that optimum transfection is displayed by lipids with chain length of approximately 14 carbon atoms and that the transfection efficiency strongly increases with increase of chain unsaturation, specifically upon replacement of saturated with monounsaturated chains.

Adaptive B-spline volume representation of measured BRDF data for photorealistic rendering

Directory of Open Access Journals (Sweden)

Hyungjun Park

2015-01-01

Full Text Available Measured bidirectional reflectance distribution function (BRDF data have been used to represent complex interaction between lights and surface materials for photorealistic rendering. However, their massive size makes it hard to adopt them in practical rendering applications. In this paper, we propose an adaptive method for B-spline volume representation of measured BRDF data. It basically performs approximate B-spline volume lofting, which decomposes the problem into three sub-problems of multiple B-spline curve fitting along u-, v-, and w-parametric directions. Especially, it makes the efficient use of knots in the multiple B-spline curve fitting and thereby accomplishes adaptive knot placement along each parametric direction of a resulting B-spline volume. The proposed method is quite useful to realize efficient data reduction while smoothing out the noises and keeping the overall features of BRDF data well. By applying the B-spline volume models of real materials for rendering, we show that the B-spline volume models are effective in preserving the features of material appearance and are suitable for representing BRDF data.

Developing a Tile-Based Rendering Method to Improve Rendering Speed of 3D Geospatial Data with HTML5 and WebGL

Directory of Open Access Journals (Sweden)

Seokchan Kang

2017-01-01

Full Text Available A dedicated plug-in has been installed to visualize three-dimensional (3D city modeling spatial data in web-based applications. However, plug-in methods are gradually becoming obsolete, owing to their limited performance with respect to installation errors, unsupported cross-browsers, and security vulnerability. Particularly, in 2015, the NPAPI service was terminated in most existing web browsers except Internet Explorer. To overcome these problems, the HTML5/WebGL (next-generation web standard, confirmed in October 2014 technology emerged. In particular, WebGL is able to display 3D spatial data without plug-ins in browsers. In this study, we attempted to identify the requirements and limitations of displaying 3D city modeling spatial data using HTML5/WebGL, and we propose alternative ways based on the bin-packing algorithm that aggregates individual 3D city modeling data including buildings in tile units. The proposed method reduces the operational complexity and the number and volume of transmissions required for rendering processing to improve the speed of 3D data rendering. The proposed method was validated on real data for evaluating its effectiveness in 3D visualization of city modeling data in web-based applications.

Volume rendering based on magnetic resonance imaging: advances in understanding the three-dimensional anatomy of the human knee

Science.gov (United States)

Anastasi, Giuseppe; Bramanti, Placido; Di Bella, Paolo; Favaloro, Angelo; Trimarchi, Fabio; Magaudda, Ludovico; Gaeta, Michele; Scribano, Emanuele; Bruschetta, Daniele; Milardi, Demetrio

2007-01-01

The choice of medical imaging techniques, for the purpose of the present work aimed at studying the anatomy of the knee, derives from the increasing use of images in diagnostics, research and teaching, and the subsequent importance that these methods are gaining within the scientific community. Medical systems using virtual reality techniques also offer a good alternative to traditional methods, and are considered among the most important tools in the areas of research and teaching. In our work we have shown some possible uses of three-dimensional imaging for the study of the morphology of the normal human knee, and its clinical applications. We used the direct volume rendering technique, and created a data set of images and animations to allow us to visualize the single structures of the human knee in three dimensions. Direct volume rendering makes use of specific algorithms to transform conventional two-dimensional magnetic resonance imaging sets of slices into see-through volume data set images. It is a technique which does not require the construction of intermediate geometric representations, and has the advantage of allowing the visualization of a single image of the full data set, using semi-transparent mapping. Digital images of human structures, and in particular of the knee, offer important information about anatomical structures and their relationships, and are of great value in the planning of surgical procedures. On this basis we studied seven volunteers with an average age of 25 years, who underwent magnetic resonance imaging. After elaboration of the data through post-processing, we analysed the structure of the knee in detail. The aim of our investigation was the three-dimensional image, in order to comprehend better the interactions between anatomical structures. We believe that these results, applied to living subjects, widen the frontiers in the areas of teaching, diagnostics, therapy and scientific research. PMID:17645453

Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

OpenAIRE

De Almeida, Wagner B.

2000-01-01

The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

International Nuclear Information System (INIS)

Yu, P.

2007-01-01

The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

Science.gov (United States)

Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

2016-06-01

Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

Molecular Characterization of Macrophage-Biomaterial Interactions

OpenAIRE

Moore, Laura Beth; Kyriakides, Themis R.

2015-01-01

Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulati...

Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

DEFF Research Database (Denmark)

Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

2002-01-01

The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

Model of molecular structure of the insoluble organic matter isolated from Murchison meteorite

Science.gov (United States)

Derenne, Sylvie; Robert, François

2010-09-01

The molecular structure of the insoluble organic matter (IOM) from Murchison meteorite has been investigated by our group for several years using a large set of analytical methods including various spectroscopies (Fourier transform infrared spectroscopy, nuclear magnetic resonance, electron paramagnetic resonance, X-ray absorption near-edge spectroscopy), high resolution electron microscopy, and thermal (pyrolyses in the presence or not of tetramethylammonium hydroxide) and chemical (RuO4 oxidation) degradations. Taken together, these techniques provided a wealth of qualitative and quantitative information, from which we derived 11 elemental and molecular parameters on the same IOM residue. In addition to the basic elemental composition, these parameters describe the distribution of the different types of carbon, nitrogen, and sulfur atoms as well as the size of the polyaromatic units. For this molecular structure, we therefore propose a model which fits with these 11 molecular quantitative parameters. Several cosmochemical implications are derived from this structure. Based on the fact that aromatic moieties are highly substituted and aliphatic chains highly branched, it can be anticipated that the synthesis of this IOM occurred through successive additions of single carbon units in the gas-phase ending by a spontaneous cyclization for chain length ≥7 C. As a whole, these observations favor an organosynthesis in the solar T-Tauri disk.

Leveraging Disturbance Observer Based Torque Control for Improved Impedance Rendering with Series Elastic Actuators

Science.gov (United States)

Mehling, Joshua S.; Holley, James; O'Malley, Marcia K.

2015-01-01

The fidelity with which series elastic actuators (SEAs) render desired impedances is important. Numerous approaches to SEA impedance control have been developed under the premise that high-precision actuator torque control is a prerequisite. Indeed, the design of an inner torque compensator has a significant impact on actuator impedance rendering. The disturbance observer (DOB) based torque control implemented in NASA's Valkyrie robot is considered here and a mathematical model of this torque control, cascaded with an outer impedance compensator, is constructed. While previous work has examined the impact a disturbance observer has on torque control performance, little has been done regarding DOBs and impedance rendering accuracy. Both simulation and a series of experiments are used to demonstrate the significant improvements possible in an SEA's ability to render desired dynamic behaviors when utilizing a DOB. Actuator transparency at low impedances is improved, closed loop hysteresis is reduced, and the actuator's dynamic response to both commands and interaction torques more faithfully matches that of the desired model. All of this is achieved by leveraging DOB based control rather than increasing compensator gains, thus making improved SEA impedance control easier to achieve in practice.

Adsorption and double layer charging in molecular sieve carbons in relation to molecular dimensions and pore structures

International Nuclear Information System (INIS)

Koresh, J.

1982-09-01

The pore structure of a fibrous carbon molecular sieve was studied by adsorption of molecular probes. Mild activation steps enabled the graduated opening of critical pore dimensions in the range 3.1-5.0 A, which keeps adsorption selectivity between molecules differing by 0.2 A in cross section diameter, to be considerably greater than 100/1. High adsorption stereospecificity over a wide pore dimension range enabled the studied adsorbates to be ordered in a sequence of increasing critical molecular dimension. Estimation of molecular dimensions by various experimental methods was discussed and their relevance to nonspherical molecules was evaluated. Polar molecules assume different dimensions depending on whether the carbon surface was polar (oxidized) or not. Hydrogen acquires, surprisingly, large width in accordance with its high liquid molar volume. Adsorbent-adsorbate interactions play a crucial role in determining molecular dimensions. Adsorption of ions from aqueous solutions into the developed ultramicropores of fibrous carbon electrodes was also studied. The dependence of the double layer capacitance and the charging rate on the pore critical dimension and on surface oxidation was studied using linear potential sweep voltametry. (Author)

C9orf72 nucleotide repeat structures initiate molecular cascades of disease.

Science.gov (United States)

Haeusler, Aaron R; Donnelly, Christopher J; Periz, Goran; Simko, Eric A J; Shaw, Patrick G; Kim, Min-Sik; Maragakis, Nicholas J; Troncoso, Juan C; Pandey, Akhilesh; Sattler, Rita; Rothstein, Jeffrey D; Wang, Jiou

2014-03-13

A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner. Specifically, nucleolin, an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases.

North American Rendering: processing high quality protein and fats for feed North American Rendering: processamento de proteínas e gorduras de alta qualidade para alimentos para animais

Directory of Open Access Journals (Sweden)

David L. Meeker

2009-07-01

Full Text Available One third to one half of each animal produced for meat, milk, eggs, and fiber is not consumed by humans. These raw materials are subjected to rendering processes resulting in many useful products. Meat and bone meal, meat meal, poultry meal, hydrolyzed feather meal, blood meal, fish meal, and animal fats are the primary products resulting from the rendering process. The most important and valuable use for these animal by-products is as feed ingredients for livestock, poultry, aquaculture, and companion animals. There are volumes of scientific references validating the nutritional qualities of these products, and there are no scientific reasons for altering the practice of feeding rendered products to animals. Government agencies regulate the processing of food and feed, and the rendering industry is scrutinized often. In addition, industry programs include good manufacturing practices, HACCP, Codes of Practice, and third-party certification. The rendering industry clearly understands its role in the safe and nutritious production of animal feed ingredients and has done it very effectively for over 100 years. The availability of rendered products for animal feeds in the future depends on regulation and the market. Regulatory agencies will determine whether certain raw materials can be used for animal feed. The National Renderers Association (NRA supports the use of science as the basis for regulation while aesthetics, product specifications, and quality differences should be left to the market place. Without the rendering industry, the accumulation of unprocessed animal by-products would impede the meat industries and pose a serious potential hazard to animal and human health.De um terço a metade da produção animal para carne, leite, ovos e fibra, não são consumidos pelos seres humanos. Estes materiais não consumidos são sujeitos a processamento em graxarias e indústrias de alimentos de origem animal, resultando em uma série de produtos

Custom OpenStreetMap Rendering – OpenTrackMap Experience

Directory of Open Access Journals (Sweden)

Radek Bartoň

2010-02-01

Full Text Available After 5 years of its existence, the OpenSteetMap [1] is becoming to be an important and valuable source of a geographic data for all people on the world. Although initially targeted to provide a map of cities for routing services, it can be exploited to other and often unexpected purposes. Such an utilization is an effort to map a network of hiking tracks of the Czech Tourist Club [2].  To support and apply this endeavour, the OpenTrackMap [3] project was started. Its aim is to primarily provide a customized rendering style for Mapnik renderer which emphasizes map features important to tourists and displays a layer with hiking tracks. This article presents obstacles which such project must face and it can be used as a tutorial for other projects of similar type.

Using an electrostatic accelerator to determine the stereochemical structures of molecular ions

International Nuclear Information System (INIS)

Gemmell, D.S.

1980-01-01

Recent high-resolution measurements on the energy and angle distributions of the fragments produced when fast (MeV) molecular-ion beams from an electrostatic accelerator dissociate (Coulomb explode) in thin foils and in gases, offer promising possibilities for deducing the stereochemical structures of the molecular ions constituting the incident beams. Bond lengths have been determined in this way for several diatomic projectiles (H 2 + , HeH + , CH + , NH + , OH + , N 2 + , O 2 + , etc.) with an accuracy of approx. 0.01 A. H 3 + has been demonstrated (for the first time) to be equilateral triangular and the interproton distance measured. Measurements on single fragments from CO 2 + , N 2 O + , C 3 H 3 + , and CH/sub n/ + have revealed the gross structures of the projectiles. An apparatus has recently been constructed at Argonne to permit precise measurements on fragments in coincidence. The apparatus has been tested on a known structure (OH 2 + ). The O-H bond length was found to be 1.0 +- 0.04 A and the H-O-H bond angle was measured as 110 +- 2 0 . These values are in excellent agreement with those found in optical experiments (0.999 A and 110.5 0 ). This Coulomb explosion technique can be expected to be refined in accuracy and to be extended to a wide range of molecular ions whose structures are inaccessible by other means

Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

Science.gov (United States)

Khan, Nazir Ahmad; Booker, Helen; Yu, Peiqiang

2014-07-16

The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value.

Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

International Nuclear Information System (INIS)

Almeida, Wagner B. de

2000-01-01

The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

Science.gov (United States)

Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

2013-01-01

Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Molecular structure input on the web

Directory of Open Access Journals (Sweden)

Ertl Peter

2010-02-01

Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

International Nuclear Information System (INIS)

Tynell, Tommi; Karppinen, Maarit

2014-01-01

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline

ZnO: Hydroquinone superlattice structures fabricated by atomic/molecular layer deposition

Energy Technology Data Exchange (ETDEWEB)

Tynell, Tommi; Karppinen, Maarit, E-mail: maarit.karppinen@aalto.fi

2014-01-31

Here we employ atomic layer deposition in combination with molecular layer deposition to deposit crystalline thin films of ZnO interspersed with single layers of hydroquinone in an effort to create hybrid inorganic–organic superlattice structures. The ratio of the ZnO and hydroquinone deposition cycles is varied between 199:1 and 1:1, and the structure of the resultant thin films is verified with X-ray diffraction and reflectivity techniques. Clear evidence of the formation of a superlattice-type structure is observed in the X-ray reflectivity patterns and the presence of organic bonds in the films corresponding to the structure of hydroquinone is confirmed with Fourier transform infrared spectroscopy measurements. We anticipate that hybrid superlattice structures such as the ones described in this work have the potential to be of great importance for future applications where the precise control of different inorganic and organic layers in hybrid superlattice materials is required. - Highlights: • Inorganic–organic superlattices can be made by atomic/molecular layer deposition. • This is demonstrated here for ZnO and hydroquinone (HQ). • The ratio of the ZnO and HQ layers is varied between 199:1 and 14:1. • The resultant thin films are crystalline.

Doping-free white organic light-emitting diodes without blue molecular emitter: An unexplored approach to achieve high performance via exciplex emission

Science.gov (United States)

Luo, Dongxiang; Xiao, Ye; Hao, Mingming; Zhao, Yu; Yang, Yibin; Gao, Yuan; Liu, Baiquan

2017-02-01

Doping-free white organic light-emitting diodes (DF-WOLEDs) are promising for the low-cost commercialization because of their simplified device structures. However, DF-WOLEDs reported thus far in the literature are based on the use of blue single molecular emitters, whose processing can represent a crucial point in device manufacture. Herein, DF-WOLEDs without the blue single molecular emitter have been demonstrated by managing a blue exciplex system. For the single-molecular-emitter (orange or yellow emitter) DF-WOLEDs, (i) a color rendering index (CRI) of 81 at 1000 cd/m2 can be obtained, which is one of the highest for the single-molecular-emitter WOLEDs, or (ii) a high efficiency of 35.4 lm/W can be yielded. For the dual-molecular-emitter (yellow/red emitters) DF-WOLED, a high CRI of 85 and low correlated color temperature of 2376 K at 1000 cd/m2 have been simultaneously achieved, which has not been reported by previous DF-WOLEDs. Such presented findings may unlock an alternative avenue to the simplified but high-performance WOLEDs.

Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations.

Science.gov (United States)

Ballu, Srilata; Itteboina, Ramesh; Sivan, Sree Kanth; Manga, Vijjulatha

2018-02-01

Filamentous temperature-sensitive protein Z (FtsZ) is a protein encoded by the FtsZ gene that assembles into a Z-ring at the future site of the septum of bacterial cell division. Structurally, FtsZ is a homolog of eukaryotic tubulin but has low sequence similarity; this makes it possible to obtain FtsZ inhibitors without affecting the eukaryotic cell division. Computational studies were performed on a series of substituted 3-arylalkoxybenzamide derivatives reported as inhibitors of FtsZ activity in Staphylococcus aureus. Quantitative structure-activity relationship models (QSAR) models generated showed good statistical reliability, which is evident from r 2 ncv and r 2 loo values. The predictive ability of these models was determined and an acceptable predictive correlation (r 2 Pred ) values were obtained. Finally, we performed molecular dynamics simulations in order to examine the stability of protein-ligand interactions. This facilitated us to compare free binding energies of cocrystal ligand and newly designed molecule B1. The good concordance between the docking results and comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) contour maps afforded obliging clues for the rational modification of molecules to design more potent FtsZ inhibitors.

Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

KAUST Repository

Wang, Haitao; Bai, Fuquan; Jia, Xiaoshi; Cao, Di; Ravva, Mahesh Kumar; Bredas, Jean-Luc; Qu, Songnan; Bai, Binglian; Zhang, Hongxing; Li, Min

2014-01-01

The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

Molecular Characterization of Macrophage-Biomaterial Interactions.

Science.gov (United States)

Moore, Laura Beth; Kyriakides, Themis R

2015-01-01

Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulation. In this review, we discuss the molecular events that contribute to macrophage activation and fusion with a focus on the role of the inflammasome, signaling pathways such as JAK/STAT and NF-κB, and the putative involvement of micro RNAs in the regulation of these processes.

Parallel hierarchical radiosity rendering

Energy Technology Data Exchange (ETDEWEB)

Carter, Michael [Iowa State Univ., Ames, IA (United States)

1993-07-01

In this dissertation, the step-by-step development of a scalable parallel hierarchical radiosity renderer is documented. First, a new look is taken at the traditional radiosity equation, and a new form is presented in which the matrix of linear system coefficients is transformed into a symmetric matrix, thereby simplifying the problem and enabling a new solution technique to be applied. Next, the state-of-the-art hierarchical radiosity methods are examined for their suitability to parallel implementation, and scalability. Significant enhancements are also discovered which both improve their theoretical foundations and improve the images they generate. The resultant hierarchical radiosity algorithm is then examined for sources of parallelism, and for an architectural mapping. Several architectural mappings are discussed. A few key algorithmic changes are suggested during the process of making the algorithm parallel. Next, the performance, efficiency, and scalability of the algorithm are analyzed. The dissertation closes with a discussion of several ideas which have the potential to further enhance the hierarchical radiosity method, or provide an entirely new forum for the application of hierarchical methods.

Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

Energy Technology Data Exchange (ETDEWEB)

Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J., E-mail: fwilliams@qi.fcen.uba.ar [INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química-Física, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Buenos Aires C1428EHA (Argentina)

2015-11-14

The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

VIDEO ANIMASI 3D PENGENALAN RUMAH ADAT DAN ALAT MUSIK KEPRI DENGAN MENGUNAKAN TEKNIK RENDER CEL-SHADING

OpenAIRE

Jianfranco Irfian Asnawi; Afdhol Dzikri

2016-01-01

Animasi ini berjudul "video animasi 3D rumah adat dan alat musik Kepulauan Riau dengan menggunakan teknik render cel-shading" merupakan video yang bertujuan memperkenalkan alat-alat musik yang berasal dari kepulauan riau, Animasi ini akan diterapkan dengan menggunakan teknik render cel-shading. Cel-shading adalah teknik render yang menampilkan grafik 3D yang menyerupai gambar tangan, seperti gambar komik dan kartun. Teknik ini juga sudah di terapkan dalam game 3D yang ternyata menarik banyak ...

Subsurface Scattering-Based Object Rendering Techniques for Real-Time Smartphone Games

Directory of Open Access Journals (Sweden)

Won-Sun Lee

2014-01-01

Full Text Available Subsurface scattering that simulates the path of a light through the material in a scene is one of the advanced rendering techniques in the field of computer graphics society. Since it takes a number of long operations, it cannot be easily implemented in real-time smartphone games. In this paper, we propose a subsurface scattering-based object rendering technique that is optimized for smartphone games. We employ our subsurface scattering method that is utilized for a real-time smartphone game. And an example game is designed to validate how the proposed method can be operated seamlessly in real time. Finally, we show the comparison results between bidirectional reflectance distribution function, bidirectional scattering distribution function, and our proposed subsurface scattering method on a smartphone game.

The effects of multiview depth video compression on multiview rendering

NARCIS (Netherlands)

Merkle, P.; Morvan, Y.; Smolic, A.; Farin, D.S.; Mueller, K.; With, de P.H.N.; Wiegang, T.

2009-01-01

This article investigates the interaction between different techniques for depth compression and view synthesis rendering with multiview video plus scene depth data. Two different approaches for depth coding are compared, namely H.264/MVC, using temporal and inter-view reference images for efficient

Well-ordered monolayers of alkali-doped coronene and picene: Molecular arrangements and electronic structures

Energy Technology Data Exchange (ETDEWEB)

Yano, M.; Endo, M.; Hasegawa, Y.; Okada, R.; Yamada, Y., E-mail: yamada@bk.tsukuba.ac.jp; Sasaki, M. [Institute of Applied Physics, University of Tsukuba, Tsukuba, Ibaraki 305-8573 (Japan)

2014-07-21

Adsorptions of alkali metals (such as K and Li) on monolayers of coronene and picene realize the formation of ordered phases, which serve as well-defined model systems for metal-intercalated aromatic superconductors. Upon alkali-doping of the monolayers of coronene and picene, scanning tunneling microscopy and X-ray absorption spectroscopy revealed the rearrangement of the entire molecular layer. The K-induced reconstruction of both monolayers resulted in the formation of a structure with a herringbone-like arrangement of molecules, suggesting the intercalation of alkali metals between molecular planes. Upon reconstruction, a shift in both the vacuum level and core levels of coronene was observed as a result of a charge transfer from alkali metals to coronene. In addition, a new density of states near the Fermi level was formed in both the doped coronene and the doped picene monolayers. This characteristic electronic feature of the ordered monolayer has been also reported in the multilayer picene films, ensuring that the present monolayer can model the properties of the metal-intercalated aromatic hydrocarbons. It is suggested that the electronic structure near the Fermi level is sensitive to the molecular arrangement, and that both the strict control and determinations of the molecular structure in the doped phase should be important for the determination of the electronic structure of these materials.

Hybrid fur rendering: combining volumetric fur with explicit hair strands

DEFF Research Database (Denmark)

Andersen, Tobias Grønbeck; Falster, Viggo; Frisvad, Jeppe Revall

2016-01-01

Hair is typically modeled and rendered using either explicitly defined hair strand geometry or a volume texture of hair densities. Taken each on their own, these two hair representations have difficulties in the case of animal fur as it consists of very dense and thin undercoat hairs in combination...... with coarse guard hairs. Explicit hair strand geometry is not well-suited for the undercoat hairs, while volume textures are not well-suited for the guard hairs. To efficiently model and render both guard hairs and undercoat hairs, we present a hybrid technique that combines rasterization of explicitly...... defined guard hairs with ray marching of a prismatic shell volume with dynamic resolution. The latter is the key to practical combination of the two techniques, and it also enables a high degree of detail in the undercoat. We demonstrate that our hybrid technique creates a more detailed and soft fur...

The diverse and expanding role of mass spectrometry in structural and molecular biology.

Science.gov (United States)

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Molecular Models of Genetic and Organismic Structures

CERN Document Server

Baianu, I C

2004-01-01

In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

Functional porous composites by blending with solution-processable molecular pores.

Science.gov (United States)

Jiang, S; Chen, L; Briggs, M E; Hasell, T; Cooper, A I

2016-05-25

We present a simple method for rendering non-porous materials porous by solution co-processing with organic cage molecules. This method can be used both for small functional molecules and for polymers, thus creating porous composites by molecular blending, rather than the more traditional approach of supporting functional molecules on pre-frabricated porous supports.

One-Dimensional Haptic Rendering Using Audio Speaker with Displacement Determined by Inductance

Directory of Open Access Journals (Sweden)

Avin Khera

2016-03-01

Full Text Available We report overall design considerations and preliminary results for a new haptic rendering device based on an audio loudspeaker. Our application models tissue properties during microsurgery. For example, the device could respond to the tip of a tool by simulating a particular tissue, displaying a desired compressibility and viscosity, giving way as the tissue is disrupted, or exhibiting independent motion, such as that caused by pulsations in blood pressure. Although limited to one degree of freedom and with a relatively small range of displacement compared to other available haptic rendering devices, our design exhibits high bandwidth, low friction, low hysteresis, and low mass. These features are consistent with modeling interactions with delicate tissues during microsurgery. In addition, our haptic rendering device is designed to be simple and inexpensive to manufacture, in part through an innovative method of measuring displacement by existing variations in the speaker’s inductance as the voice coil moves over the permanent magnet. Low latency and jitter are achieved by running the real-time simulation models on a dedicated microprocessor, while maintaining bidirectional communication with a standard laptop computer for user controls and data logging.

Process for depositing an oxide epitaxially onto a silicon substrate and structures prepared with the process

Science.gov (United States)

McKee, Rodney A.; Walker, Frederick J.

1993-01-01

A process and structure involving a silicon substrate utilizes an ultra high vacuum and molecular beam epitaxy (MBE) methods to grow an epitaxial oxide film upon a surface of the substrate. As the film is grown, the lattice of the compound formed at the silicon interface becomes stabilized, and a base layer comprised of an oxide having a sodium chloride-type lattice structure grows epitaxially upon the compound so as to cover the substrate surface. A perovskite may then be grown epitaxially upon the base layer to render a product which incorporates silicon, with its electronic capabilities, with a perovskite having technologically-significant properties of its own.

Electronic structure and molecular orbital study of hole-transport material triphenylamine derivatives

International Nuclear Information System (INIS)

Wang, B.-C.; Liao, H.-R.; Chang, J.-C.; Chen Likey; Yeh, J.-T.

2007-01-01

Recently, triphenylamine (TPA), 4,4'-bis(phenyl-m-tolylamino)biphenyl (TPD), 4,4'-bis(1-naphthylphenylamino)biphenyl (NPB) and their derivatives are widely used in the organic light-emitting diode (OLED) devices as a hole-transporting material (HTM) layer. We have optimized twenty different structures of HTM materials by using density functional theory (DFT), B3LYP/6-31G method. All these different structures contain mono-amine and diamine TPA derivatives. The energies of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) along with molecular orbitals for these HTMs are also determined. We have found that the central amine nitrogen atom and the phenyl ring, which is next to the central amine nitrogen atom, show significant contribution to the HOMO and LUMO, respectively. The sum of the calculated bond angles (α+β+γ) of the central amine nitrogen atom has been applied to describe the bonding and the energy difference for HOMO and LUMO in these TPA derivatives. Electronic structure calculations have been performed for these TPA derivatives. Again, the LCAO-MO patterns of HOMO and LUMO levels of these derivatives are used to investigate their electron density. A series of electron-transporting steps are predicted for these compounds employing these calculated results

Effects of surface proteins and lipids on molecular structure, thermal properties, and enzymatic hydrolysis of rice starch

Directory of Open Access Journals (Sweden)

Pan HU

Full Text Available Abstract Rice starches with different amylose contents were treated with sodium dodecyl sulfate (SDS to deplete surface proteins and lipids, and the changes in molecular structure, thermal properties, and enzymatic hydrolysis were evaluated. SDS treatment did not significantly change the molecular weight distribution, crystalline structure, short-range ordered degree, and gelatinization properties of starch, but significantly altered the pasting properties and increased the swelling power of starch. The removal of surface proteins and lipids increased the enzymatic hydrolysis and in vitro digestion of starch. The influences of removing surface proteins and lipids from starch on swelling power, pasting properties, and enzymatic hydrolysis were different among the various starches because of the differences in molecular structures of different starch styles. The aforementioned results indicated that removing the surface proteins and lipids from starch did not change the molecular structure but had significant effects on some functional properties.

CT portography by multidetector helical CT. Comparison of three rendering models

International Nuclear Information System (INIS)

Nakayama, Yoshiharu; Imuta, Masanori; Funama, Yoshinori; Kadota, Masataka; Utsunomiya, Daisuke; Shiraishi, Shinya; Hayashida, Yoshiko; Yamashita, Yasuyuki

2002-01-01

The purpose of this study was to assess the value of multidetector CT portography in visualizing varices and portosystemic collaterals in comparison with conventional portography, and to compare the visualizations obtained by three rendering models (volume rendering, VR; minimum intensity projection, MIP; and shaded surface display, SSD). A total of 46 patients with portal hypertension were examined by CT and conventional portography for evaluation of portosystemic collaterals. CT portography was performed by multidetector CT (MD-CT) scanner with a slice thickness of 2.5 mm and table feed of 7.5 mm. Three types of CT portographic models were generated and compared with transarterial portography. Among 46 patients, 48 collaterals were identified on CT transverse images, while 38 collaterals were detected on transarterial portography. Forty-four of 48 collaterals identified on CT transverse images were visualized with the MIP model, while 34 and 29 collaterals were visualized by the VR and SSD methods, respectively. The average CT value for the portal vein and varices was 198 HU with data acquisition of 50 sec after contrast material injection. CT portography by multidetector CT provides excellent images in the visualization of portosystemic collaterals. The images of collaterals produced by MD-CT are superior to those of transarterial portography. Among the three rendering techniques, MIP provides the best visualization of portosystemic collaterals. (author)

CT portography by multidetector helical CT. Comparison of three rendering models

Energy Technology Data Exchange (ETDEWEB)

Nakayama, Yoshiharu; Imuta, Masanori; Funama, Yoshinori; Kadota, Masataka; Utsunomiya, Daisuke; Shiraishi, Shinya; Hayashida, Yoshiko; Yamashita, Yasuyuki [Kumamoto Univ. (Japan). School of Medicine

2002-12-01

The purpose of this study was to assess the value of multidetector CT portography in visualizing varices and portosystemic collaterals in comparison with conventional portography, and to compare the visualizations obtained by three rendering models (volume rendering, VR; minimum intensity projection, MIP; and shaded surface display, SSD). A total of 46 patients with portal hypertension were examined by CT and conventional portography for evaluation of portosystemic collaterals. CT portography was performed by multidetector CT (MD-CT) scanner with a slice thickness of 2.5 mm and table feed of 7.5 mm. Three types of CT portographic models were generated and compared with transarterial portography. Among 46 patients, 48 collaterals were identified on CT transverse images, while 38 collaterals were detected on transarterial portography. Forty-four of 48 collaterals identified on CT transverse images were visualized with the MIP model, while 34 and 29 collaterals were visualized by the VR and SSD methods, respectively. The average CT value for the portal vein and varices was 198 HU with data acquisition of 50 sec after contrast material injection. CT portography by multidetector CT provides excellent images in the visualization of portosystemic collaterals. The images of collaterals produced by MD-CT are superior to those of transarterial portography. Among the three rendering techniques, MIP provides the best visualization of portosystemic collaterals. (author)

Vessel abnormalization: another hallmark of cancer? Molecular mechanisms and therapeutic implications.

Science.gov (United States)

De Bock, Katrien; Cauwenberghs, Sandra; Carmeliet, Peter

2011-02-01

As a result of excessive production of angiogenic molecules, tumor vessels become abnormal in structure and function. By impairing oxygen delivery, abnormal vessels fuel a vicious cycle of non-productive angiogenesis, which creates a hostile microenvironment from where tumor cells escape through leaky vessels and which renders tumors less responsive to chemoradiation. While anti-angiogenic strategies focused on inhibiting new vessel growth and destroying pre-existing vessels, clinical studies showed modest anti-tumor effects. For many solid tumors, anti-VEGF treatment offers greater clinical benefit when combined with chemotherapy. This is partly due to a normalization of the tumor vasculature, which improves cytotoxic drug delivery and efficacy and offers unprecedented opportunities for anti-cancer treatment. Here, we overview key novel molecular players that induce vessel normalization. Copyright © 2010 Elsevier Ltd. All rights reserved.

Variational cellular model of the molecular and crystal electronic structure

International Nuclear Information System (INIS)

Ferreira, L.G.; Leite, J.R.

1977-12-01

A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

Science.gov (United States)

Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

2008-11-05

A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

Post-processing methods of rendering and visualizing 3-D reconstructed tomographic images

Energy Technology Data Exchange (ETDEWEB)

Wong, S.T.C. [Univ. of California, San Francisco, CA (United States)

1997-02-01

The purpose of this presentation is to discuss the computer processing techniques of tomographic images, after they have been generated by imaging scanners, for volume visualization. Volume visualization is concerned with the representation, manipulation, and rendering of volumetric data. Since the first digital images were produced from computed tomography (CT) scanners in the mid 1970s, applications of visualization in medicine have expanded dramatically. Today, three-dimensional (3D) medical visualization has expanded from using CT data, the first inherently digital source of 3D medical data, to using data from various medical imaging modalities, including magnetic resonance scanners, positron emission scanners, digital ultrasound, electronic and confocal microscopy, and other medical imaging modalities. We have advanced from rendering anatomy to aid diagnosis and visualize complex anatomic structures to planning and assisting surgery and radiation treatment. New, more accurate and cost-effective procedures for clinical services and biomedical research have become possible by integrating computer graphics technology with medical images. This trend is particularly noticeable in current market-driven health care environment. For example, interventional imaging, image-guided surgery, and stereotactic and visualization techniques are now stemming into surgical practice. In this presentation, we discuss only computer-display-based approaches of volumetric medical visualization. That is, we assume that the display device available is two-dimensional (2D) in nature and all analysis of multidimensional image data is to be carried out via the 2D screen of the device. There are technologies such as holography and virtual reality that do provide a {open_quotes}true 3D screen{close_quotes}. To confine the scope, this presentation will not discuss such approaches.

Post-processing methods of rendering and visualizing 3-D reconstructed tomographic images

International Nuclear Information System (INIS)

Wong, S.T.C.

1997-01-01

The purpose of this presentation is to discuss the computer processing techniques of tomographic images, after they have been generated by imaging scanners, for volume visualization. Volume visualization is concerned with the representation, manipulation, and rendering of volumetric data. Since the first digital images were produced from computed tomography (CT) scanners in the mid 1970s, applications of visualization in medicine have expanded dramatically. Today, three-dimensional (3D) medical visualization has expanded from using CT data, the first inherently digital source of 3D medical data, to using data from various medical imaging modalities, including magnetic resonance scanners, positron emission scanners, digital ultrasound, electronic and confocal microscopy, and other medical imaging modalities. We have advanced from rendering anatomy to aid diagnosis and visualize complex anatomic structures to planning and assisting surgery and radiation treatment. New, more accurate and cost-effective procedures for clinical services and biomedical research have become possible by integrating computer graphics technology with medical images. This trend is particularly noticeable in current market-driven health care environment. For example, interventional imaging, image-guided surgery, and stereotactic and visualization techniques are now stemming into surgical practice. In this presentation, we discuss only computer-display-based approaches of volumetric medical visualization. That is, we assume that the display device available is two-dimensional (2D) in nature and all analysis of multidimensional image data is to be carried out via the 2D screen of the device. There are technologies such as holography and virtual reality that do provide a open-quotes true 3D screenclose quotes. To confine the scope, this presentation will not discuss such approaches

Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

Science.gov (United States)

He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

2015-09-01

Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multiscale modeling of complex molecular structure and dynamics with MBN Explorer

CERN Document Server

Solov’yov, Ilia A; Solov’yov, Andrey V

2017-01-01

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the meso-scale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potenti...

Rendering LGBTQ+ Visible in Nursing: Embodying the Philosophy of Caring Science.

Science.gov (United States)

Goldberg, Lisa; Rosenburg, Neal; Watson, Jean

2017-06-01

Although health care institutions continue to address the importance of diversity initiatives, the standard(s) for treatment remain historically and institutionally grounded in a sociocultural privileging of heterosexuality. As a result, lesbian, gay, bisexual, transgender, and queer (LGBTQ+) communities in health care remain largely invisible. This marked invisibility serves as a call to action, a renaissance of thinking within redefined boundaries and limitations. We must therefore refocus our habits of attention on the wholeness of persons and the diversity of their storied experiences as embodied through contemporary society. By rethinking current understandings of LGBTQ+ identities through innovative representation(s) of the media, music industry, and pop culture within a caring science philosophy, nurses have a transformative opportunity to render LGBTQ+ visible and in turn render a transformative opportunity for themselves.

The Peshitta Rendering of Psalm 25: Spelling, Synonyms, and Syntax’

NARCIS (Netherlands)

Dyk, J.W.; Loopstra, J.; Sokoloff, M.

2013-01-01

The very act of making a translation implies that the rendered text will differ from the source text. The underlying presupposition is that the grammar, syntax, and semantics of the source and target languages are sufficiently divergent as to warrant a translation. Translations differ in how close

An Extension of Fourier-Wavelet Volume Rendering by View Interpolation

NARCIS (Netherlands)

Westenberg, Michel A.; Roerdink, Jos B.T.M.

2001-01-01

This paper describes an extension to Fourier-wavelet volume rendering (FWVR), which is a Fourier domain implementation of the wavelet X-ray transform. This transform combines integration along the line of sight with a simultaneous 2-D wavelet transform in the view plane perpendicular to this line.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

Science.gov (United States)

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

Directory of Open Access Journals (Sweden)

Natalie Heffernan

2015-01-01

Full Text Available Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis. Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs. These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

Development of volume rendering module for real-time visualization system

International Nuclear Information System (INIS)

Otani, Takayuki; Muramatsu, Kazuhiro

2000-03-01

Volume rendering is a method to visualize the distribution of physical quantities in the three dimensional space from any viewpoint by tracing the ray direction on the ordinary two dimensional monitoring display. It enables to provide the interior information as well as the surfacial one by producing the translucent images. Therefore, it is regarded as a very useful means as well as an important one in the analysis of the computational results of the scientific calculations, although it has, unfortunately, disadvantage to need a large amount of computing time. This report describes algorithm and its performance of the volume rendering soft-ware which was developed as an important functional module in the real-time visualization system PATRAS. This module can directly visualize the computed results on BFC grid. Moreover, it has already realized the speed-up in some parts of the software by the use of a newly developed heuristic technique. This report includes the investigation on the speed-up of the software by parallel processing. (author)

Remote parallel rendering for high-resolution tiled display walls

KAUST Repository

Nachbaur, Daniel; Dumusc, Raphael; Bilgili, Ahmet; Hernando, Juan; Eilemann, Stefan

2014-01-01

© 2014 IEEE. We present a complete, robust and simple to use hardware and software stack delivering remote parallel rendering of complex geometrical and volumetric models to high resolution tiled display walls in a production environment. We describe the setup and configuration, present preliminary benchmarks showing interactive framerates, and describe our contributions for a seamless integration of all the software components.

Remote parallel rendering for high-resolution tiled display walls

KAUST Repository

Nachbaur, Daniel

2014-11-01

© 2014 IEEE. We present a complete, robust and simple to use hardware and software stack delivering remote parallel rendering of complex geometrical and volumetric models to high resolution tiled display walls in a production environment. We describe the setup and configuration, present preliminary benchmarks showing interactive framerates, and describe our contributions for a seamless integration of all the software components.

Molecules and Models The molecular structures of main group element compounds

CERN Document Server

Haaland, Arne

2008-01-01

This book provides a systematic description of the molecular structures and bonding in simple compounds of the main group elements with particular emphasis on bond distances, bond energies and coordination geometries. The description includes the structures of hydrogen, halogen and methyl derivatives of the elements in each group, some of these molecules are ionic, some polar covalent. The survey of molecules whose structures conform to well-established trends is followed byrepresentative examples of molecules that do not conform. We also describe electron donor-acceptor and hydrogen bonded co

Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

KAUST Repository

Li, Haoyuan; Qiu, Yong; Duan, Lian

2016-01-01

A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using

SketchBio: a scientist's 3D interface for molecular modeling and animation.

Science.gov (United States)

Waldon, Shawn M; Thompson, Peter M; Hahn, Patrick J; Taylor, Russell M

2014-10-30

Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

Molecular Docking, Molecular Dynamics, and Structure-Activity Relationship Explorations of 14-Oxygenated N-Methylmorphinan-6-ones as Potent μ-Opioid Receptor Agonists.

Science.gov (United States)

Noha, Stefan M; Schmidhammer, Helmut; Spetea, Mariana

2017-06-21

Among opioids, morphinans are of major importance as the most effective analgesic drugs acting primarily via μ-opioid receptor (μ-OR) activation. Our long-standing efforts in the field of opioid analgesics from the class of morphinans led to N-methylmorphinan-6-ones differently substituted at positions 5 and 14 as μ-OR agonists inducing potent analgesia and fewer undesirable effects. Herein we present the first thorough molecular modeling study and structure-activity relationship (SAR) explorations aided by docking and molecular dynamics (MD) simulations of 14-oxygenated N-methylmorphinan-6-ones to gain insights into their mode of binding to the μ-OR and interaction mechanisms. The structure of activated μ-OR provides an essential model for how ligand/μ-OR binding is encoded within small chemical differences in otherwise structurally similar morphinans. We reveal important molecular interactions that these μ-agonists share and distinguish them. The molecular docking outcomes indicate the crucial role of the relative orientation of the ligand in the μ-OR binding site, influencing the propensity of critical non-covalent interactions that are required to facilitate ligand/μ-OR interactions and receptor activation. The MD simulations point out minor differences in the tendency to form hydrogen bonds by the 4,5α-epoxy group, along with the tendency to affect the 3-7 lock switch. The emerged SARs reveal the subtle interplay between the substituents at positions 5 and 14 in the morphinan scaffold by enabling the identification of key structural elements that determine the distinct pharmacological profiles. This study provides a significant structural basis for understanding ligand binding and μ-OR activation by the 14-oxygenated N-methylmorphinan-6-ones, which should be useful for guiding drug design.

D.Vanwijnsberghe, Autour de la Madeleine Renders

Directory of Open Access Journals (Sweden)

Muriel Verbeeck-Boutin

2008-10-01

Full Text Available Institution fédérale belge de réputation internationale, l’Institut royal du Patrimoine artistique, à Bruxelles,  célèbre cette année son soixantième anniversaire: c’est l’occasion de rappeler le prestige dont jouit depuis des décennies cet institut de recherche, de formation et de diffusion du savoir. Pour souligner l’événement, l’IRPA publie le quatrième volume de la collection Scientia Artis. Il présente sous le titre Autour de la Madeleine Renders un ensemble de recherches qui documentent...

Studies of the surface structures of molecular crystals and of adsorbed molecular monolayers on the (111) crystal faces of platinum and silver by low-energy electron diffraction

International Nuclear Information System (INIS)

Firment, L.E.

1977-01-01

The structures of molecular crystal surfaces were investigated for the first time by the use of low-energy electron diffraction (LEED). The experimental results from a variety of molecular crystals were examined and compared as a first step towards understanding the properties of these surfaces on a microscopic level. The method of sample preparation employed, vapor deposition onto metal single-crystal substrates at low temperatures in ultrahigh vacuum, allowed concurrent study of the structures of adsorbed monolayers on metal surfaces and of the growth processes of molecular films on metal substrates. The systems investigated were ice, ammonia, naphthalene, benzene, the n-paraffins (C 3 to C 8 ), cyclohexane, trioxane, acetic acid, propionic acid, methanol, and methylamine adsorbed and condensed on both Pt(111) and Ag(111) surfaces. Electron-beam-induced damage of the molecular surfaces was observed after electron exposures of 10 -4 A sec cm -2 at 20 eV. Aromatic molecular crystal samples were more resistant to damage than samples of saturated molecules. The quality and orientation of the grown molecular crystal films were influenced by substrate preparation and growth conditions. Forty ordered monolayer structures were observed. 110 figures, 22 tables, 162 references

The History of Molecular Structure Determination Viewed through the Nobel Prizes.

Science.gov (United States)

Jensen, William P.; Palenik, Gus J.; Suh, Il-Hwan

2003-01-01

Discusses the importance of complex molecular structures. Emphasizes their individual significance through examination of the Nobel Prizes of the 20th century. Highlights prizes awarded to Conrad Rontgen, Francis H.C. Crick, James D. Watson, Maurice H.F. Wilkins, and others. (SOE)

Study of the molecular structure and dynamics of bakelite with neutron cross section measurements

International Nuclear Information System (INIS)

Voi, D.L.

1990-06-01

The molecular structure and dynamics of calcined bakelite were studied with neutron transmission and scattering cross section measurements. The total cross sections determined were correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. The total cross section determined showed a deviation smaller than 5% from the literature values. The frequency distribution as well as overall experimental results allowed to suggest a structural model like polycyclic hydrocarbons for bakelite calcined at 800 0 C. (F.E.). 65 refs, 31 figs, 5 tabs

Micro structure processing on plastics by accelerated hydrogen molecular ions

Science.gov (United States)

Hayashi, H.; Hayakawa, S.; Nishikawa, H.

2017-08-01

A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

Nano-structural analysis of fish collagen extracts for new process ...

African Journals Online (AJOL)

GREGORY

2011-12-16

Dec 16, 2011 ... of materials at the atomic, molecular and macromolecular scales. The greater ... renders nanosized particles more active biologically. (Oberdorster et al. ... safety and quality, design of high performing packaging materials ...

3-D volume rendering visualization for calculated distributions of diesel spray; Diesel funmu kyodo suchi keisan kekka no sanjigen volume rendering hyoji

Energy Technology Data Exchange (ETDEWEB)

Yoshizaki, T; Imanishi, H; Nishida, K; Yamashita, H; Hiroyasu, H; Kaneda, K [Hiroshima University, Hiroshima (Japan)

1997-10-01

Three dimensional visualization technique based on volume rendering method has been developed in order to translate calculated results of diesel combustion simulation into realistically spray and flame images. This paper presents an overview of diesel combustion model which has been developed at Hiroshima University, a description of the three dimensional visualization technique, and some examples of spray and flame image generated by this visualization technique. 8 refs., 8 figs., 1 tab.

Physically Based Rendering in the Nightshade NG Visualization Platform

Science.gov (United States)

Berglund, Karrie; Larey-Williams, Trystan; Spearman, Rob; Bogard, Arthur

2015-01-01

This poster describes our work on creating a physically based rendering model in Nightshade NG planetarium simulation and visualization software (project website: NightshadeSoftware.org). We discuss techniques used for rendering realistic scenes in the universe and dealing with astronomical distances in real time on consumer hardware. We also discuss some of the challenges of rewriting the software from scratch, a project which began in 2011.Nightshade NG can be a powerful tool for sharing data and visualizations. The desktop version of the software is free for anyone to download, use, and modify; it runs on Windows and Linux (and eventually Mac). If you are looking to disseminate your data or models, please stop by to discuss how we can work together.Nightshade software is used in literally hundreds of digital planetarium systems worldwide. Countless teachers and astronomy education groups run the software on flat screens. This wide use makes Nightshade an effective tool for dissemination to educators and the public.Nightshade NG is an especially powerful visualization tool when projected on a dome. We invite everyone to enter our inflatable dome in the exhibit hall to see this software in a 3D environment.

The rendering context for stereoscopic 3D web

Science.gov (United States)

Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

2014-03-01

3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3D web page, our 3D browser will create two slightly different images, each representing the left-eye view and right-eye view, both to be combined on the 3D display to generate the illusion of depth. And as the result turns out, elements can be manipulated in a truly 3D space.

Structural insights into the molecular mechanisms of myasthenia gravis and their therapeutic implications

Energy Technology Data Exchange (ETDEWEB)

Noridomi, Kaori; Watanabe, Go; Hansen, Melissa N.; Han, Gye Won; Chen, Lin (USC)

2017-04-25

The nicotinic acetylcholine receptor (nAChR) is a major target of autoantibodies in myasthenia gravis (MG), an autoimmune disease that causes neuromuscular transmission dysfunction. Despite decades of research, the molecular mechanisms underlying MG have not been fully elucidated. Here, we present the crystal structure of the nAChR α1 subunit bound by the Fab fragment of mAb35, a reference monoclonal antibody that causes experimental MG and competes with ~65% of antibodies from MG patients. Our structures reveal for the first time the detailed molecular interactions between MG antibodies and a core region on nAChR α1. These structures suggest a major nAChR-binding mechanism shared by a large number of MG antibodies and the possibility to treat MG by blocking this binding mechanism. Structure-based modeling also provides insights into antibody-mediated nAChR cross-linking known to cause receptor degradation. Our studies establish a structural basis for further mechanistic studies and therapeutic development of MG.

Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

Directory of Open Access Journals (Sweden)

Aparecido R. Silva

2008-05-01

Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

International Nuclear Information System (INIS)

Yu, P.

2008-01-01

More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

Digital representations of the real world how to capture, model, and render visual reality

CERN Document Server

Magnor, Marcus A; Sorkine-Hornung, Olga; Theobalt, Christian

2015-01-01

Create Genuine Visual Realism in Computer Graphics Digital Representations of the Real World: How to Capture, Model, and Render Visual Reality explains how to portray visual worlds with a high degree of realism using the latest video acquisition technology, computer graphics methods, and computer vision algorithms. It explores the integration of new capture modalities, reconstruction approaches, and visual perception into the computer graphics pipeline.Understand the Entire Pipeline from Acquisition, Reconstruction, and Modeling to Realistic Rendering and ApplicationsThe book covers sensors fo

Towards the Availability of the Distributed Cluster Rendering System: Automatic Modeling and Verification

DEFF Research Database (Denmark)

Wang, Kemin; Jiang, Zhengtao; Wang, Yongbin

2012-01-01

, whenever the number of node-n and related parameters vary, we can create the PRISM model file rapidly and then we can use PRISM model checker to verify ralated system properties. At the end of this study, we analyzed and verified the availability distributions of the Distributed Cluster Rendering System......In this study, we proposed a Continuous Time Markov Chain Model towards the availability of n-node clusters of Distributed Rendering System. It's an infinite one, we formalized it, based on the model, we implemented a software, which can automatically model with PRISM language. With the tool...

Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

1991-09-15

We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

NATO Advanced Research Workshop on Vectorization of Advanced Methods for Molecular Electronic Structure

CERN Document Server

1984-01-01

That there have been remarkable advances in the field of molecular electronic structure during the last decade is clear not only to those working in the field but also to anyone else who has used quantum chemical results to guide their own investiga­ tions. The progress in calculating the electronic structures of molecules has occurred through the truly ingenious theoretical and methodological developments that have made computationally tractable the underlying physics of electron distributions around a collection of nuclei. At the same time there has been consider­ able benefit from the great advances in computer technology. The growing sophistication, declining costs and increasing accessibi­ lity of computers have let theorists apply their methods to prob­ lems in virtually all areas of molecular science. Consequently, each year witnesses calculations on larger molecules than in the year before and calculations with greater accuracy and more com­ plete information on molecular properties. We can surel...

16O+16O molecular nature of the superdeformed band of 32S and the evolution of the molecular structure

International Nuclear Information System (INIS)

Kimura, Masaaki; Horiuchi, Hisashi

2004-01-01

The relation between the superdeformed band of 32 S and 16 O+ 16 O molecular bands is studied by the deformed-basis antisymmetrized molecular dynamics with the Gogny D1S force. It is found that the obtained superdeformed band members of S have a considerable amount of the 16 O+ 16 O component. Above the superdeformed band, we have obtained two excited rotational bands which have more prominent character of the 16 O+ 16 O molecular band. These three rotational bands are regarded as a series of 16 O+ 16 O molecular bands which were predicted by using the unique 16 O- 16 O optical potential. As the excitation energy and principal quantum number of the relative motion increase, the 16 O+ 16 O cluster structure becomes more prominent but at the same time, the band members are fragmented into several states

Plant-based food and feed protein structure changes induced by gene-transformation, heating and bio-ethanol processing: a synchrotron-based molecular structure and nutrition research program.

Science.gov (United States)

Yu, Peiqiang

2010-11-01

Unlike traditional "wet" analytical methods which during processing for analysis often result in destruction or alteration of the intrinsic protein structures, advanced synchrotron radiation-based Fourier transform infrared microspectroscopy has been developed as a rapid and nondestructive and bioanalytical technique. This cutting-edge synchrotron-based bioanalytical technology, taking advantages of synchrotron light brightness (million times brighter than sun), is capable of exploring the molecular chemistry or structure of a biological tissue without destruction inherent structures at ultra-spatial resolutions. In this article, a novel approach is introduced to show the potential of the advanced synchrotron-based analytical technology, which can be used to study plant-based food or feed protein molecular structure in relation to nutrient utilization and availability. Recent progress was reported on using synchrotron-based bioanalytical technique synchrotron radiation-based Fourier transform infrared microspectroscopy and diffused reflectance infrared Fourier transform spectroscopy to detect the effects of gene-transformation (Application 1), autoclaving (Application 2), and bio-ethanol processing (Application 3) on plant-based food and feed protein structure changes on a molecular basis. The synchrotron-based technology provides a new approach for plant-based protein structure research at ultra-spatial resolutions at cellular and molecular levels.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

International Nuclear Information System (INIS)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M.

2016-01-01

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors

Energy Technology Data Exchange (ETDEWEB)

Larkey, Nicholas E.; Brucks, Corinne N.; Lansing, Shan S.; Le, Sophia D.; Smith, Natasha M.; Tran, Victoria; Zhang, Lulu; Burrows, Sean M., E-mail: sean.burrows@oregonstate.edu

2016-02-25

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5–9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing. - Highlights: • Challenges facing highly sensitive miRNA biosensor designs are addressed. • Thermodynamic and molecular structure design metrics for reporter+probe biosensors are proposed. • The influence of ideal and non-ideal reporter hairpin structures on reporter+probe formation and signal change are discussed. • 5–9 nM limits of detection were observed with no interference from off-analytes.

Genarris: Random generation of molecular crystal structures and fast screening with a Harris approximation

Science.gov (United States)

Li, Xiayue; Curtis, Farren S.; Rose, Timothy; Schober, Christoph; Vazquez-Mayagoitia, Alvaro; Reuter, Karsten; Oberhofer, Harald; Marom, Noa

2018-06-01

We present Genarris, a Python package that performs configuration space screening for molecular crystals of rigid molecules by random sampling with physical constraints. For fast energy evaluations, Genarris employs a Harris approximation, whereby the total density of a molecular crystal is constructed via superposition of single molecule densities. Dispersion-inclusive density functional theory is then used for the Harris density without performing a self-consistency cycle. Genarris uses machine learning for clustering, based on a relative coordinate descriptor developed specifically for molecular crystals, which is shown to be robust in identifying packing motif similarity. In addition to random structure generation, Genarris offers three workflows based on different sequences of successive clustering and selection steps: the "Rigorous" workflow is an exhaustive exploration of the potential energy landscape, the "Energy" workflow produces a set of low energy structures, and the "Diverse" workflow produces a maximally diverse set of structures. The latter is recommended for generating initial populations for genetic algorithms. Here, the implementation of Genarris is reported and its application is demonstrated for three test cases.

Flight-appropriate 3D Terrain-rendering Toolkit for Synthetic Vision, Phase II

Data.gov (United States)

National Aeronautics and Space Administration — The TerraBlocksTM 3D terrain data format and terrain-block-rendering methodology provides an enabling basis for successful commercial deployment of...

Molecular Dynamics Simulation of the Structure and Properties of Lithium Phosphate Glasses

Energy Technology Data Exchange (ETDEWEB)

Liang, J-J; Cygan, R.T.; Alam, T.M.

1999-07-09

A new forcefield model was developed for the computer simulation of phosphate materials that have many important applications in the electronics and biomedical industries. The model provides a fundamental basis for the evaluation of phosphate glass structure and thermodynamics. Molecular dynamics simulations of a series of lithium phosphate glass compositions were performed using the forcefield model. A high concentration of three-membered rings (P{sub 3}O{sub 3}) occurs in the glass of intermediate composition (0.2 Li{sub 2}O {center_dot} 0.8P{sub 2}O{sub 5}) that corresponds to the minimum in the glass transition temperature curve for the compositional series. Molecular orbital calculations of various phosphate ring clusters indicate an increasing stabilization of the phosphate ring structure going from two- to four-membered rings.

III - V semiconductor structures for biosensor and molecular electronics applications

Energy Technology Data Exchange (ETDEWEB)

Luber, S M

2007-01-15

The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed by a

III - V semiconductor structures for biosensor and molecular electronics applications

Energy Technology Data Exchange (ETDEWEB)

Luber, S.M.

2007-01-15

The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

Uncertainties of Molecular Structural Parameters

International Nuclear Information System (INIS)

Császár, Attila G.

2014-01-01

performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r_e"B"O, and semiexperimental, r_e"S"E) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

Molecular Cloud Structures and Massive Star Formation in N159

Science.gov (United States)

Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

2018-02-01

The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

A circumstellar molecular gas structure associated with the massive young star Cepheus A-HW 2

Science.gov (United States)

Torrelles, Jose M.; Rodriguez, Luis F.; Canto, Jorge; Ho, Paul T. P.

1993-01-01

We report the detection via VLA-D observations of ammonia of a circumstellar high-density molecular gas structure toward the massive young star related to the object Cepheus A-HW 2, a firm candidate for the powering source of the high-velocity molecular outflow in the region. We suggest that the circumstellar molecular gas structure could be related to the circumstellar disk previously suggested from infrared, H2O, and OH maser observations. We consider as a plausible scenario that the double radio continuum source of HW 2 could represent the ionized inner part of the circumstellar disk, in the same way as proposed to explain the double radio source in L1551. The observed motions in the circumstellar molecular gas can be produced by bound motions (e.g., infall or rotation) around a central mass of about 10-20 solar masses (B0.5 V star or earlier).

CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

OpenAIRE

Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

2002-01-01

The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

Deep Exemplar 2D-3D Detection by Adapting from Real to Rendered Views

OpenAIRE

Massa, Francisco; Russell, Bryan; Aubry, Mathieu

2015-01-01

This paper presents an end-to-end convolutional neural network (CNN) for 2D-3D exemplar detection. We demonstrate that the ability to adapt the features of natural images to better align with those of CAD rendered views is critical to the success of our technique. We show that the adaptation can be learned by compositing rendered views of textured object models on natural images. Our approach can be naturally incorporated into a CNN detection pipeline and extends the accuracy and speed benefi...

Refinement of homology-based protein structures by molecular dynamics simulation techniques

NARCIS (Netherlands)

Fan, H; Mark, AE

The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

Science.gov (United States)

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis.

Science.gov (United States)

Wan, Yong; Otsuna, Hideo; Holman, Holly A; Bagley, Brig; Ito, Masayoshi; Lewis, A Kelsey; Colasanto, Mary; Kardon, Gabrielle; Ito, Kei; Hansen, Charles

2017-05-26

Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing tools built on volume visualization pipelines for single channel or red-green-blue (RGB) channels have become inadequate for the new challenges of fluorescence microscopy. For a three-dimensional atlas of the insect nervous system, hundreds of volume channels are rendered simultaneously, whereas fluorescence intensity values from each channel need to be preserved for versatile adjustment and analysis. Although several existing tools have incorporated support of multichannel data using various strategies, the lack of a flexible design has made true many-channel visualization and analysis unavailable. The most common practice for many-channel volume data presentation is still converting and rendering pseudosurfaces, which are inaccurate for both qualitative and quantitative evaluations. Here, we present an alternative design strategy that accommodates the visualization and analysis of about 100 volume channels, each of which can be interactively adjusted, selected, and segmented using freehand tools. Our multichannel visualization includes a multilevel streaming pipeline plus a triple-buffer compositing technique. Our method also preserves original fluorescence intensity values on graphics hardware, a crucial feature that allows graphics-processing-unit (GPU)-based processing for interactive data analysis, such as freehand segmentation. We have implemented the design strategies as a thorough restructuring of our original tool, FluoRender. The redesign of FluoRender not only maintains the existing multichannel capabilities for a greatly extended number of volume channels, but also enables new analysis functions for many-channel data from emerging biomedical-imaging techniques.

Structures and physicochemical properties of molecular aggregates of lipids

International Nuclear Information System (INIS)

Iwahashi, Makio

2005-01-01

Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

Definition of molecular structure: by choice or by appeal to observation?

Science.gov (United States)

Bader, Richard F W

2010-07-22

There are two schools of thought in chemistry: one derived from the valence bond and molecular orbital models of bonding, the other appealing directly to the measurable electron density and the quantum mechanical theorems that determine its behavior, an approach embodied in the quantum theory of atoms in molecules, QTAIM. No one questions the validity of the former approach, and indeed molecular orbital models and QTAIM play complementary roles, the models finding expression in the principles of physics. However, some orbital proponents step beyond the models to impose their personal stamp on their use in interpretive chemistry, by denying the possible existence of a physical basis for the concepts of chemistry. This places them at odds with QTAIM, whose very existence stems from the discovery in the observable topology of the electron density, the definitions of atoms, of the bonding between atoms and hence of molecular structure. Relating these concepts to the electron density provides the necessary link for their ultimate quantum definition. This paper explores in depth the possible causes of the difficulties some have in accepting the quantum basis of structure beginning with the arguments associated with the acceptance of a "bond path" as a criterion for bonding. This identification is based on the finding that all classical structures may be mapped onto molecular graphs consisting of bond paths linking neighboring atoms, a mapping that has no known exceptions and one that is further bolstered by the finding that there are no examples of "missing bond paths". Difficulties arise when the quantum concept is applied to systems that are not amenable to the classical models of bonding. Thus one is faced with the recurring dilemma of science, of having to escape the constraints of a model that requires a change in the existing paradigm, a process that has been in operation since the discovery of new and novel structures necessitated the extension of the Lewis model

Oxytetracycline recovery from aqueous media using computationally designed molecularly imprinted polymers.

Science.gov (United States)

Rodríguez-Dorado, Rosalía; Carro, Antonia M; Chianella, Iva; Karim, Kal; Concheiro, Angel; Lorenzo, Rosa A; Piletsky, Sergey; Alvarez-Lorenzo, Carmen

2016-09-01

Polymers for recovery/removal of the antimicrobial agent oxytetracycline (OTC) from aqueous media were developed with use of computational design and molecular imprinting. 2-Hydroxyethyl methacrylate, 2-acrylamide-2-methylpropane sulfonic acid (AMPS), and mixtures of the two were chosen according to their predicted affinity for OTC and evaluated as functional monomers in molecularly imprinted polymers and nonimprinted polymers. Two levels of AMPS were tested. After bulk polymerization, the polymers were crushed into particles (200-1000 μm). Pressurized liquid extraction was implemented for template removal with a low amount of methanol (less than 20 mL in each extraction) and a few extractions (12-18 for each polymer) in a short period (20 min per extraction). Particle size distribution, microporous structure, and capacity to rebind OTC from aqueous media were evaluated. Adsorption isotherms obtained from OTC solutions (30-110 mg L(-1)) revealed that the polymers prepared with AMPS had the highest affinity for OTC. The uptake capacity depended on the ionic strength as follows: purified water > saline solution (0.9 % NaCl) > seawater (3.5 % NaCl). Polymer particles containing AMPS as a functional monomer showed a remarkable ability to clean water contaminated with OTC. The usefulness of the stationary phase developed for molecularly imprinted solid-phase extraction was also demonstrated. Graphical Abstract Selection of functional monomers by molecular modeling renders polymer networks suitable for removal of pollutants from contaminated aqueous environments, under either dynamic or static conditions.

Structural and spectroscopic properties of the second generation phosphorus-viologen "molecular asterisk".

Science.gov (United States)

Furer, V L; Vandukov, A E; Katir, N; Majoral, J P; El Kadib, A; Caminade, A M; Bousmina, M; Kovalenko, V I

2013-11-01

The FTIR and FT Raman spectra of the second generation phosphorus-viologen "molecular asterisk" G2 built from cyclotriphosphazene core with 12 viologen units and 6 terminal phosphonate groups have been recorded and analyzed. The experimental X-ray data of 1,1-bis(4-formylbenzyl)-4,4'-bipyridinium bis(hexaflurophosphate) was used in molecular modeling studies. The optimization of isolated 1,1-bis(4-formylbenzyl)-4,4'-bipyridinium (BFBP) molecule without counter ions PF6(-) does not lead to significant changes of dihedral angles, thus the molecular conformation does not depend on interactions with the counter ions. The structural optimization and normal mode analysis were performed for G2 on the basis of the density functional theory (DFT). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that G2 has a kind of "egg timer" structure with planar OC6H4CHNN(CH3) fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of G2 were interpreted by means of potential energy distribution. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

Science.gov (United States)

Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

2014-03-01

The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular simulations of electrolyte structure and dynamics in lithium-sulfur battery solvents

Science.gov (United States)

Park, Chanbum; Kanduč, Matej; Chudoba, Richard; Ronneburg, Arne; Risse, Sebastian; Ballauff, Matthias; Dzubiella, Joachim

2018-01-01

The performance of modern lithium-sulfur (Li/S) battery systems critically depends on the electrolyte and solvent compositions. For fundamental molecular insights and rational guidance of experimental developments, efficient and sufficiently accurate molecular simulations are thus in urgent need. Here, we construct a molecular dynamics (MD) computer simulation model of representative state-of-the art electrolyte-solvent systems for Li/S batteries constituted by lithium-bis(trifluoromethane)sulfonimide (LiTFSI) and LiNO3 electrolytes in mixtures of the organic solvents 1,2-dimethoxyethane (DME) and 1,3-dioxolane (DOL). We benchmark and verify our simulations by comparing structural and dynamic features with various available experimental reference systems and demonstrate their applicability for a wide range of electrolyte-solvent compositions. For the state-of-the-art battery solvent, we finally calculate and discuss the detailed composition of the first lithium solvation shell, the temperature dependence of lithium diffusion, as well as the electrolyte conductivities and lithium transference numbers. Our model will serve as a basis for efficient future predictions of electrolyte structure and transport in complex electrode confinements for the optimization of modern Li/S batteries (and related devices).

Rendering of HDR content on LDR displays: an objective approach

Science.gov (United States)

Krasula, Lukáš; Narwaria, Manish; Fliegel, Karel; Le Callet, Patrick

2015-09-01

Dynamic range compression (or tone mapping) of HDR content is an essential step towards rendering it on traditional LDR displays in a meaningful way. This is however non-trivial and one of the reasons is that tone mapping operators (TMOs) usually need content-specific parameters to achieve the said goal. While subjective TMO parameter adjustment is the most accurate, it may not be easily deployable in many practical applications. Its subjective nature can also influence the comparison of different operators. Thus, there is a need for objective TMO parameter selection to automate the rendering process. To that end, we investigate into a new objective method for TMO parameters optimization. Our method is based on quantification of contrast reversal and naturalness. As an important advantage, it does not require any prior knowledge about the input HDR image and works independently on the used TMO. Experimental results using a variety of HDR images and several popular TMOs demonstrate the value of our method in comparison to default TMO parameter settings.

Efficient visibility encoding for dynamic illumination in direct volume rendering.

Science.gov (United States)

Kronander, Joel; Jönsson, Daniel; Löw, Joakim; Ljung, Patric; Ynnerman, Anders; Unger, Jonas

2012-03-01

We present an algorithm that enables real-time dynamic shading in direct volume rendering using general lighting, including directional lights, point lights, and environment maps. Real-time performance is achieved by encoding local and global volumetric visibility using spherical harmonic (SH) basis functions stored in an efficient multiresolution grid over the extent of the volume. Our method enables high-frequency shadows in the spatial domain, but is limited to a low-frequency approximation of visibility and illumination in the angular domain. In a first pass, level of detail (LOD) selection in the grid is based on the current transfer function setting. This enables rapid online computation and SH projection of the local spherical distribution of visibility information. Using a piecewise integration of the SH coefficients over the local regions, the global visibility within the volume is then computed. By representing the light sources using their SH projections, the integral over lighting, visibility, and isotropic phase functions can be efficiently computed during rendering. The utility of our method is demonstrated in several examples showing the generality and interactive performance of the approach.

The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

Science.gov (United States)

Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

2017-07-19

Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

Raman spectroscopy as an advanced structural nanoprobe for conjugated molecular semiconductors

International Nuclear Information System (INIS)

Wood, Sebastian; Hollis, Joseph Razzell; Kim, Ji-Seon

2017-01-01

Raman spectroscopy has emerged as a powerful and important characterisation tool for probing molecular semiconducting materials. The useful optoelectronic properties of these materials arise from the delocalised π -electron density in the conjugated core of the molecule, which also results in large Raman scattering cross-sections and a strong coupling between its electronic states and vibrational modes. For this reason, Raman spectroscopy offers a unique insight into the properties of molecular semiconductors, including: chemical structure, molecular conformation, molecular orientation, and fundamental photo- and electro-chemical processes—all of which are critically important to the performance of a wide range of optical and electronic organic semiconductor devices. Experimentally, Raman spectroscopy is non-intrusive, non-destructive, and requires no special sample preparation, and so is suitable for a wide range of in situ measurements, which are particularly relevant to issues of thermal and photochemical stability. Here we review the development of the family of Raman spectroscopic techniques, which have been applied to the study of conjugated molecular semiconductors. We consider the suitability of each technique for particular circumstances, and the unique insights it can offer, with a particular focus on the significance of these measurements for the continuing development of stable, high performance organic electronic devices. (topical review)

Unconscious neural processing differs with method used to render stimuli invisible

Directory of Open Access Journals (Sweden)

Sergey Victor Fogelson

2014-06-01

Full Text Available Visual stimuli can be kept from awareness using various methods. The extent of processing that a given stimulus receives in the absence of awareness is typically used to make claims about the role of consciousness more generally. The neural processing elicited by a stimulus, however, may also depend on the method used to keep it from awareness, and not only on whether the stimulus reaches awareness. Here we report that the method used to render an image invisible has a dramatic effect on how category information about the unseen stimulus is encoded across the human brain. We collected fMRI data while subjects viewed images of faces and tools, that were rendered invisible using either continuous flash suppression (CFS or chromatic flicker fusion (CFF. In a third condition, we presented the same images under normal fully visible viewing conditions. We found that category information about visible images could be extracted from patterns of fMRI responses throughout areas of neocortex known to be involved in face or tool processing. However, category information about stimuli kept from awareness using CFS could be recovered exclusively within occipital cortex, whereas information about stimuli kept from awareness using CFF was also decodable within temporal and frontal regions. We conclude that unconsciously presented objects are processed differently depending on how they are rendered subjectively invisible. Caution should therefore be used in making generalizations on the basis of any one method about the neural basis of consciousness or the extent of information processing without consciousness.

Unconscious neural processing differs with method used to render stimuli invisible.

Science.gov (United States)

Fogelson, Sergey V; Kohler, Peter J; Miller, Kevin J; Granger, Richard; Tse, Peter U

2014-01-01

Visual stimuli can be kept from awareness using various methods. The extent of processing that a given stimulus receives in the absence of awareness is typically used to make claims about the role of consciousness more generally. The neural processing elicited by a stimulus, however, may also depend on the method used to keep it from awareness, and not only on whether the stimulus reaches awareness. Here we report that the method used to render an image invisible has a dramatic effect on how category information about the unseen stimulus is encoded across the human brain. We collected fMRI data while subjects viewed images of faces and tools, that were rendered invisible using either continuous flash suppression (CFS) or chromatic flicker fusion (CFF). In a third condition, we presented the same images under normal fully visible viewing conditions. We found that category information about visible images could be extracted from patterns of fMRI responses throughout areas of neocortex known to be involved in face or tool processing. However, category information about stimuli kept from awareness using CFS could be recovered exclusively within occipital cortex, whereas information about stimuli kept from awareness using CFF was also decodable within temporal and frontal regions. We conclude that unconsciously presented objects are processed differently depending on how they are rendered subjectively invisible. Caution should therefore be used in making generalizations on the basis of any one method about the neural basis of consciousness or the extent of information processing without consciousness.

Hsp90 molecular chaperone: structure, functions and participation in cardio-vascular pathologies

Directory of Open Access Journals (Sweden)

Kroupskaya I. V.

2009-10-01

Full Text Available The review is devoted to the analysis of structural and functional properties of molecular chaperon Hsp90. Hsp90 is a representative of highly widespread family of heat shock proteins. The protein is found in eubacteria and all branches of eukarya, but it is apparently absent in archaea. It is one of key regulators of numerous signalling pathways, cell growth and development, apoptosis, induction of autoimmunity, and progression of heart failure. The full functional activity of Hsp90 shows up in a complex with other molecular chaperones and co-chaperones. Molecular interactions between chaperones, different signalling proteins and protein-partners are highly crucial for the normal functioning of signalling pathways and their destruction causes an alteration in the cell physiology up to its death.

Structural and Molecular Modeling Features of P2X Receptors

Directory of Open Access Journals (Sweden)

Luiz Anastacio Alves

2014-03-01

Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

Wobbled splatting-a fast perspective volume rendering method for simulation of x-ray images from CT

International Nuclear Information System (INIS)

Birkfellner, Wolfgang; Seemann, Rudolf; Figl, Michael; Hummel, Johann; Ede, Christopher; Homolka, Peter; Yang Xinhui; Niederer, Peter; Bergmann, Helmar

2005-01-01

3D/2D registration, the automatic assignment of a global rigid-body transformation matching the coordinate systems of patient and preoperative volume scan using projection images, is an important topic in image-guided therapy and radiation oncology. A crucial part of most 3D/2D registration algorithms is the fast computation of digitally rendered radiographs (DRRs) to be compared iteratively to radiographs or portal images. Since registration is an iterative process, fast generation of DRRs-which are perspective summed voxel renderings-is desired. In this note, we present a simple and rapid method for generation of DRRs based on splat rendering. As opposed to conventional splatting, antialiasing of the resulting images is not achieved by means of computing a discrete point spread function (a so-called footprint), but by stochastic distortion of either the voxel positions in the volume scan or by the simulation of a focal spot of the x-ray tube with non-zero diameter. Our method generates slightly blurred DRRs suitable for registration purposes at framerates of approximately 10 Hz when rendering volume images with a size of 30 MB. (note)

Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure

Czech Academy of Sciences Publication Activity Database

Réblová, Martina; Réblová, K.; Štěpánek, Václav

2015-01-01

Roč. 35, December 2015 (2015), s. 21-38 ISSN 0031-5850 R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 ; RVO:61388971 Keywords : Barbatosphaeria * molecular systematic * ITS secondary structures Subject RIV: EF - Botanics; EE - Microbiology, Virology (MBU-M) Impact factor: 5.725, year: 2015

Software System for Vocal Rendering of Printed Documents

Directory of Open Access Journals (Sweden)

Marian DARDALA

2008-01-01

Full Text Available The objective of this paper is to present a software system architecture developed to render the printed documents in a vocal form. On the other hand, in the paper are described the software solutions that exist as software components and are necessary for documents processing as well as for multimedia device controlling used by the system. The usefulness of this system is for people with visual disabilities that can access the contents of documents without that they be printed in Braille system or to exist in an audio form.

Flight-appropriate 3D Terrain-rendering Toolkit for Synthetic Vision, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — TerraMetrics proposes an SBIR Phase I R/R&D effort to develop a key 3D terrain-rendering technology that provides the basis for successful commercial deployment...

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

Science.gov (United States)

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Functional Annotation of Ion Channel Structures by Molecular Simulation.

Science.gov (United States)

Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

2016-12-06

Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow

DEFF Research Database (Denmark)

Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter

2015-01-01

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear...... rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates...

The general atomic and molecular electronic structure system HONDO: Version 7.0

International Nuclear Information System (INIS)

Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

1989-01-01

We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

Molecular structure of tetramethylgermane from gas electron diffraction

Science.gov (United States)

Csákvári, Éva; Rozsondai, Béla; Hargittai, István

1991-05-01

The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

Mathematical analysis of compressive/tensile molecular and nuclear structures

Science.gov (United States)

Wang, Dayu

Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

Molecular dynamical and structural studies for the bakelite by neutron cross section measurements

International Nuclear Information System (INIS)

Voi, D.L.

1992-05-01

Neutron reaction cross sections were determined by transmission and scattering measurements, to study the dynamics and molecular structure of calcined bakelites. Total cross sections were determined, with a deviation smaller than 5%, from the literature values, by neutron transmission method and a specially devised approximation. These cross sections were then correlated with data obtained with infra-red spectroscopy, elemental analysis and other techniques to get the probable molecular formulae of bakelite. Double differential scattering cross sections, scattering law values and frequency distributions were determined with 15% error using the neutron inelastic scattering method. The frequency distributions as well as the overall results from all experimental techniques used in this work allowed to suggest a structural model like polycyclic hydrocarbons, for calcined bakelite at 800 0 C. (author)

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

Science.gov (United States)

Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang

2009-03-31

Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

Directory of Open Access Journals (Sweden)

Li Honglin

2009-03-01

Full Text Available Abstract Background Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. Results The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112. Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. Conclusion On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms

Photometric and Colorimeric Comparison of HDR and Spctrally Resolved Rendering Images

DEFF Research Database (Denmark)

Amdemeskel, Mekbib Wubishet; Soreze, Thierry Silvio Claude; Thorseth, Anders

2017-01-01

In this paper, we will demonstrate a comparison between measured colorimetric images, and simulated images from a physics based rendering engine. The colorimetric images are high dynamic range (HDR) and taken with a luminance and colour camera mounted on a goniometer. For the comparison, we have ...

3D-TV Rendering on a Multiprocessor System on a Chip

NARCIS (Netherlands)

Van Eijndhoven, J.T.J.; Li, X.

2006-01-01

This thesis focuses on the issue of mapping 3D-TV rendering applications to a multiprocessor platform. The target platform aims to address tomorrow's multi-media consumer market. The prototype chip, called Wasabi, contains a set of TriMedia processors that communicate viaa shared memory, fast

Molecular design chemical structure generation from the properties of pure organic compounds

CERN Document Server

Horvath, AL

1992-01-01

This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

Complex adaptation-based LDR image rendering for 3D image reconstruction

Science.gov (United States)

Lee, Sung-Hak; Kwon, Hyuk-Ju; Sohng, Kyu-Ik

2014-07-01

A low-dynamic tone-compression technique is developed for realistic image rendering that can make three-dimensional (3D) images similar to realistic scenes by overcoming brightness dimming in the 3D display mode. The 3D surround provides varying conditions for image quality, illuminant adaptation, contrast, gamma, color, sharpness, and so on. In general, gain/offset adjustment, gamma compensation, and histogram equalization have performed well in contrast compression; however, as a result of signal saturation and clipping effects, image details are removed and information is lost on bright and dark areas. Thus, an enhanced image mapping technique is proposed based on space-varying image compression. The performance of contrast compression is enhanced with complex adaptation in a 3D viewing surround combining global and local adaptation. Evaluating local image rendering in view of tone and color expression, noise reduction, and edge compensation confirms that the proposed 3D image-mapping model can compensate for the loss of image quality in the 3D mode.

Anti-symmetrized molecular dynamics: a new insight into the structure of nuclei

International Nuclear Information System (INIS)

Yoshiko, Kanada-En'yo; Masaaki, Kimura; Hisashi, Horiuchi

2003-01-01

The AMD (anti-symmetrized molecular dynamics) theory for nuclear structure is explained by showing its actual applications. First the formulation of AMD including various refined versions is briefly presented and its characteristics are discussed, putting a stress on its nature as an 'ab initio' theory. Then we demonstrate fruitful applications to various structure problems in stable nuclei, in order to explicitly verify the 'ab initio' nature of AMD, especially the ability to describe both mean-field-type structure and cluster structure. Finally, we show the results of applications of AMD to unstable nuclei, from which we see that AMD is powerful in elucidating and understanding various types of nuclear structure of unstable nuclei. (authors)

Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

Science.gov (United States)

Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

2016-05-01

Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

OpenAIRE

Tezuka, Kyoichi; Taguchi, Tatsuhiko; Alavi, Saman; Sum, Amadeu K.; Ohmura, Ryo

2012-01-01

This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...

Electronic structure and molecular dynamics of Na2Li

Science.gov (United States)

Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

Towards structural models of molecular recognition in olfactory receptors.

Science.gov (United States)

Afshar, M; Hubbard, R E; Demaille, J

1998-02-01

The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

Molecular Diagnostics of the Internal Structure of Starspots and Sunspots

Science.gov (United States)

Afram, N.; Berdyugina, S. V.; Fluri, D. M.; Solanki, S. K.; Lagg, A.; Petit, P.; Arnaud, J.

2006-12-01

We have analyzed the usefulness of molecules as a diagnostic tool for studying solar and stellar magnetism with the molecular Zeeman and Paschen-Back effects. In the first part we concentrate on molecules that are observed in sunspots such as MgH and TiO. We present calculated molecular line profiles obtained by assuming magnetic fields of 2-3 kG and compare these synthetic Stokes profiles with spectro-polarimetric observations in sunspots. The good agreement between the theory and observations allows us to turn our attention in the second part to starspots to gain insight into their internal structure. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and compare synthetic Stokes profiles with our recent observations.

USER EVALUATION OF EIGHT LED LIGHT SOURCES WITH DIFFERENTSPECIAL COLOUR RENDERING INDICES R9

DEFF Research Database (Denmark)

Markvart, Jakob; Iversen, Anne; Logadóttir, Ásta

2013-01-01

In this study we evaluated the influence of the special colour rendering index R9 on subjective red colour perception and Caucasian skin appearance among untrained test subjects. The light sources tested are commercially available LED based light sources with similar correlated colour temperature...... and general colour rendering index, but with varying R9. It was found that the test subjects in general are more positive towards light sources with higher R9. The shift from a majority of negative responses to a majority of positive responses is found to occur at R9 values of ~20....

Introductory group theory and its application to molecular structure

CERN Document Server

Ferraro, John R

1975-01-01

The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

Molecular Origin of the Vibrational Structure of Ice Ih.

Science.gov (United States)

Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

2017-06-15

An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

The Scent of Roses and beyond: Molecular Structures, Analysis, and Practical Applications of Odorants

Science.gov (United States)

Mannschreck, Albrecht; von Angerer, Erwin

2011-01-01

A few odorous compounds found in roses are chosen to arouse the reader's interest in their molecular structures. This article differs from some similar reports on odorants mainly by combining the structural description with the presentation of the following types of isomers: constitutional isomers, enantiomers, and diastereomers. The preparation…

Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

Science.gov (United States)

Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

2015-03-06

The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular clouds and galactic spiral structure

International Nuclear Information System (INIS)

Dame, T.M.

1984-02-01

Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

The Effect of Interactive, Three Dimensional, High Speed Simulations on High School Science Students' Conceptions of the Molecular Structure of Water.

Science.gov (United States)

Hakerem, Gita; And Others

The Water and Molecular Networks (WAMNet) Project uses graduate student written Reduced Instruction Set Computing (RISC) computer simulations of the molecular structure of water to assist high school students learn about the nature of water. This study examined: (1) preconceptions concerning the molecular structure of water common among high…

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Science.gov (United States)

Ryan, Michael; Diekhans, Mark; Lien, Stephanie; Liu, Yun; Karchin, Rachel

2009-06-01

LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.

De Novo generation of molecular structures using optimization to select graphs on a given lattice

DEFF Research Database (Denmark)

Bywater, R.P.; Poulsen, Thomas Agersten; Røgen, Peter

2004-01-01

A recurrent problem in organic chemistry is the generation of new molecular structures that conform to some predetermined set of structural constraints that are imposed in an endeavor to build certain required properties into the newly generated structure. An example of this is the pharmacophore...... model, used in medicinal chemistry to guide de novo design or selection of suitable structures from compound databases. We propose here a method that efficiently links up a selected number of required atom positions while at the same time directing the emergent molecular skeleton to avoid forbidden...... positions. The linkage process takes place on a lattice whose unit step length and overall geometry is designed to match typical architectures of organic molecules. We use an optimization method to select from the many different graphs possible. The approach is demonstrated in an example where crystal...

To What Degree Does Handling Concrete Molecular Models Promote the Ability to Translate and Coordinate between 2D and 3D Molecular Structure Representations? A Case Study with Algerian Students

Science.gov (United States)

Mohamed-Salah, Boukhechem; Alain, Dumon

2016-01-01

This study aims to assess whether the handling of concrete ball-and-stick molecular models promotes translation between diagrammatic representations and a concrete model (or vice versa) and the coordination of the different types of structural representations of a given molecular structure. Forty-one Algerian undergraduate students were requested…

Non-Photorealistic Rendering in Chinese Painting of Animals

Institute of Scientific and Technical Information of China (English)

无

2002-01-01

A set of algorithms is proposed in this paper to automatically transform 3D animal models to Chinese painting style. Inspired by real painting process in Chinese painting of animals, we divide the whole rendering process into two parts: borderline stroke making and interior shading. In borderline stroke making process we first find 3D model silhouettes in real-time depending on the viewing direction of a user. After retrieving silhouette information from all model edges, a stroke linking mechanism is applied to link these independent edges into a long stroke. Finally we grow a plain thin silhouette line to a stylus stroke with various widths at each control point and a 2D brush model is combined with it to simulate a Chinese painting stroke. In the interior shading pipeline, three stages are used to convert a Gouraud-shading image to a Chinese painting style image: color quantization, ink diffusion and box filtering. The color quantization stage assigns all pixels in an image into four color levels and each level represents a color layer in a Chinese painting. Ink diffusion stage is used to transfer inks and water between different levels and to grow areas in an irregular way. The box filtering stage blurs sharp borders between different levels to embellish the appearance of final interior shading image. In addition to automatic rendering, an interactive Chinese painting system which is equipped with friendly input devices can be also combined to generate more artistic Chinese painting images manually.

A two-metric proposal to specify the color-rendering properties of light sources for retail lighting

Science.gov (United States)

Freyssinier, Jean Paul; Rea, Mark

2010-08-01

Lighting plays an important role in supporting retail operations, from attracting customers, to enabling the evaluation of merchandise, to facilitating the completion of the sale. Lighting also contributes to the identity, comfort, and visual quality of a retail store. With the increasing availability and quality of white LEDs, retail lighting specifiers are now considering LED lighting in stores. The color rendering of light sources is a key factor in supporting retail lighting goals and thus influences a light source's acceptance by users and specifiers. However, there is limited information on what consumers' color preferences are, and metrics used to describe the color properties of light sources often are equivocal and fail to predict preference. The color rendering of light sources is described in the industry solely by the color rendering index (CRI), which is only indirectly related to human perception. CRI is intended to characterize the appearance of objects illuminated by the source and is increasingly being challenged because new sources are being developed with increasingly exotic spectral power distributions. This paper discusses how CRI might be augmented to better use it in support of the design objectives for retail merchandising. The proposed guidelines include the use of gamut area index as a complementary metric to CRI for assuring good color rendering.

Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations

International Nuclear Information System (INIS)

Rubin, Yu.V.; Belous, L.F.

2012-01-01

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G * ). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30 o : The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

Molecular Imaging of Inflammation in Atherosclerosis

Science.gov (United States)

Wildgruber, Moritz; Swirski, Filip K.; Zernecke, Alma

2013-01-01

Acute rupture of vulnerable plaques frequently leads to myocardial infarction and stroke. Within the last decades, several cellular and molecular players have been identified that promote atherosclerotic lesion formation, maturation and plaque rupture. It is now widely recognized that inflammation of the vessel wall and distinct leukocyte subsets are involved throughout all phases of atherosclerotic lesion development. The mechanisms that render a stable plaque unstable and prone to rupture, however, remain unknown and the identification of the vulnerable plaque remains a major challenge in cardiovascular medicine. Imaging technologies used in the clinic offer minimal information about the underlying biology and potential risk for rupture. New imaging technologies are therefore being developed, and in the preclinical setting have enabled new and dynamic insights into the vessel wall for a better understanding of this complex disease. Molecular imaging has the potential to track biological processes, such as the activity of cellular and molecular biomarkers in vivo and over time. Similarly, novel imaging technologies specifically detect effects of therapies that aim to stabilize vulnerable plaques and silence vascular inflammation. Here we will review the potential of established and new molecular imaging technologies in the setting of atherosclerosis, and discuss the cumbersome steps required for translating molecular imaging approaches into the clinic. PMID:24312156

The structure of quasi-molecular KX-ray spectra from heavy ion collisions

International Nuclear Information System (INIS)

Kaun, K.-N.; Frank, W.; Manfrass, P.

1976-01-01

In the experiments with Ge, Nb, Kr and La ions continuum X-ray spectra having a two-component structure have been observed. Both components atr interpreted as quasi-molecular X-radiation caused by transitions to the 2psigma and 1ssigma states in the quasimolecule

Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene

Directory of Open Access Journals (Sweden)

Kubicki JD

2000-09-01

Full Text Available Molecular simulations (energy minimizations and molecular dynamics of an n-hexane soot model developed by Smith and co-workers (M. S. Akhter, A. R. Chughtai and D. M. Smith, Appl. Spectrosc., 1985, 39, 143; ref. 1 were performed. The MM+ (N. L. Allinger, J. Am. Chem. Soc., 1977, 395, 157; ref. 2 and COMPASS (H. Sun, J. Phys. Chem., 1998, 102, 7338; ref. 3 force fields were tested for their ability to produce realistic soot nanoparticle structure. The interaction of pyrene with the model soot was simulated. Quantum mechanical calculations on smaller soot fragments were carried out. Starting from an initial 2D structure, energy minimizations are not able to produce the observed layering within soot with either force field. Results of molecular dynamics simulations indicate that the COMPASS force field does a reasonably accurate job of reproducing observations of soot structure. Increasing the system size from a 683 to a 2732 atom soot model does not have a significant effect on predicted structures. Neither does the addition of water molecules surrounding the soot model. Pyrene fits within the soot structure without disrupting the interlayer spacing. Polycyclic aromatic hydrocarbons (PAH, such as pyrene, may strongly partition into soot and have slow desorption kinetics because the PAH-soot bonding is similar to soot–soot interactions. Diffusion of PAH into soot micropores may allow the PAH to be irreversibly adsorbed and sequestered so that they partition slowly back into an aqueous phase causing dis-equilibrium between soil organic matter and porewater.

An application of coherence resonances in molecular transition identification

International Nuclear Information System (INIS)

Alekseev, V.A.; Salomaa, R.

1978-01-01

In Λ-type three level configurations having long lived lower levels extremely sharp two photon resonances occur. We want to draw attention to the use of these resonances for distinguishing the hyperfine splitting of lower and upper set of levels of molecular transitions. A new feature in the theoretical model is that the saturator and probe beams are coupled to both transitions rendering possible the appearance of interference between the resonances. (author)

Structure and properties of simple molecular systems at very high density

International Nuclear Information System (INIS)

LeSar, R.

1989-01-01

The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

Directory of Open Access Journals (Sweden)

Drefahl Axel

2011-01-01

Full Text Available Abstract CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity.

Diagnostic Accuracy of the Volume Rendering Images of Multi-Detector CT for the Detection of Lumbar Transverse Process Fractures

Energy Technology Data Exchange (ETDEWEB)

Lee, Yun Hak; Chun, Tong Jin [Dept. of Radiology, Eulji University Hospital, Daejeon (Korea, Republic of)

2012-01-15

To compare the accuracy of three-dimensional computed tomographic (3D CT) volume rendering techniques with axial images of multi-detector row computed tomography to identify lumbar transverse process (LTP) fractures in trauma patients. We retrospectively evaluated 42 patients with back pain as a result of blunt trauma between January and June of 2010. Two radiologists examined the 3D CT volume rendering images independently. The confirmation of a LTP fracture was based on the consensus of the axial images by the two radiologists. The results of 3D CT volume rendering images were compared with the axial images and the diagnostic powers (sensitivity, specificity, and accuracy) were calculated. Seven of the 42 patients had twenty five lumbar transverse process fractures. The diagnostic power of the 3D CT volume rendering technique is as accurate as axial images. Reader 1, sensitivity 96%, specificity 100%, accuracy 99.9%; and Reader 2 sensitivity 100%, specificity 99.8%, accuracy 99.8%. The accordance of the two radiologists was 99.8%. 3D CT volume rendering images can alternate axial images to detect lumbar transverse process fractures with good image quality.

Absolute Molecular Orientation of Isopropanol at Ceria (100) Surfaces: Insight into Catalytic Selectivity from the Interfacial Structure

Energy Technology Data Exchange (ETDEWEB)

Doughty, Benjamin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Goverapet Srinivasan, Sriram [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Indian Inst. of Technology (IIT), Rajasthan (India); Bryantsev, Vyacheslav S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Dongkyu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Ho Nyung [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ma, Ying-Zhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lutterman, Daniel A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2017-06-12

The initial mechanistic steps underlying heterogeneous chemical catalysis can be described in a framework where the composition, structure, and orientation of molecules adsorbed to reactive interfaces are known. However, extracting this vital information is the limiting step in most cases due in part to challenges in probing the interfacial monolayer with enough chemical specificity to characterize the surface molecular constituents. These challenges are exacerbated at complex or spatially heterogeneous interfaces where competing processes and a distribution of local environments can uniquely drive chemistry. To address these limitations, this work presents a distinctive combination of materials synthesis, surface specific optical experiments, and theory to probe and understand molecular structure at catalytic interfaces. Specifically, isopropanol was adsorbed to surfaces of the model CeO₂ catalyst that were synthesized with only the (100) facet exposed. Vibrational sum-frequency generation was used to probe the molecular monolayer, and with the guidance of density functional theory calculations, was used to extract the structure and absolute molecular orientation of isopropanol at the CeO₂ (100) surface. Our results show that isopropanol is readily deprotonated at the surface, and through the measured absolute molecular orientation of isopropanol, we obtain new insight into the selectivity of the (100) surface to form propylene. Our findings reveal key insight into the chemical and physical phenomena taking place at pristine interfaces thereby pointing to intuitive structural arguments to describe catalytic selectivity in more complex systems.

Medicinal Chemistry and Molecular Modeling: An Integration to Teach Drug Structure-Activity Relationship and the Molecular Basis of Drug Action

Science.gov (United States)

Carvalho, Ivone; Borges, Aurea D. L.; Bernardes, Lilian S. C.

2005-01-01

The use of computational chemistry and the protein data bank (PDB) to understand and predict the chemical and molecular basis involved in the drug-receptor interactions is discussed. A geometrical and chemical overview of the great structural similarity in the substrate and inhibitor is provided.

Hardware-accelerated autostereogram rendering for interactive 3D visualization

Science.gov (United States)

Petz, Christoph; Goldluecke, Bastian; Magnor, Marcus

2003-05-01

Single Image Random Dot Stereograms (SIRDS) are an attractive way of depicting three-dimensional objects using conventional display technology. Once trained in decoupling the eyes' convergence and focusing, autostereograms of this kind are able to convey the three-dimensional impression of a scene. We present in this work an algorithm that generates SIRDS at interactive frame rates on a conventional PC. The presented system allows rotating a 3D geometry model and observing the object from arbitrary positions in real-time. Subjective tests show that the perception of a moving or rotating 3D scene presents no problem: The gaze remains focused onto the object. In contrast to conventional SIRDS algorithms, we render multiple pixels in a single step using a texture-based approach, exploiting the parallel-processing architecture of modern graphics hardware. A vertex program determines the parallax for each vertex of the geometry model, and the graphics hardware's texture unit is used to render the dot pattern. No data has to be transferred between main memory and the graphics card for generating the autostereograms, leaving CPU capacity available for other tasks. Frame rates of 25 fps are attained at a resolution of 1024x512 pixels on a standard PC using a consumer-grade nVidia GeForce4 graphics card, demonstrating the real-time capability of the system.

Continuous Surface Rendering, Passing from CAD to Physical Representation

Directory of Open Access Journals (Sweden)

Mario Covarrubias

2013-06-01

Full Text Available This paper describes a desktop-mechatronic interface that has been conceived to support designers in the evaluation of aesthetic virtual shapes. This device allows a continuous and smooth free hand contact interaction on a real and developable plastic tape actuated by a servo-controlled mechanism. The objective in designing this device is to reproduce a virtual surface with a consistent physical rendering well adapted to designers' needs. The desktop-mechatronic interface consists in a servo-actuated plastic strip that has been devised and implemented using seven interpolation points. In fact, by using the MEC (Minimal Energy Curve Spline approach, a developable real surface is rendered taking into account the CAD geometry of the virtual shapes. In this paper, we describe the working principles of the interface by using both absolute and relative approaches to control the position on each single control point on the MEC spline. Then, we describe the methodology that has been implemented, passing from the CAD geometry, linked to VisualNastran in order to maintain the parametric properties of the virtual shape. Then, we present the co-simulation between VisualNastran and MATLAB/Simulink used for achieving this goal and controlling the system and finally, we present the results of the subsequent testing session specifically carried out to evaluate the accuracy and the effectiveness of the mechatronic device.

Tomographic image reconstruction and rendering with texture-mapping hardware

International Nuclear Information System (INIS)

Azevedo, S.G.; Cabral, B.K.; Foran, J.

1994-07-01

The image reconstruction problem, also known as the inverse Radon transform, for x-ray computed tomography (CT) is found in numerous applications in medicine and industry. The most common algorithm used in these cases is filtered backprojection (FBP), which, while a simple procedure, is time-consuming for large images on any type of computational engine. Specially-designed, dedicated parallel processors are commonly used in medical CT scanners, whose results are then passed to graphics workstation for rendering and analysis. However, a fast direct FBP algorithm can be implemented on modern texture-mapping hardware in current high-end workstation platforms. This is done by casting the FBP algorithm as an image warping operation with summing. Texture-mapping hardware, such as that on the Silicon Graphics Reality Engine (TM), shows around 600 times speedup of backprojection over a CPU-based implementation (a 100 Mhz R4400 in this case). This technique has the further advantages of flexibility and rapid programming. In addition, the same hardware can be used for both image reconstruction and for volumetric rendering. The techniques can also be used to accelerate iterative reconstruction algorithms. The hardware architecture also allows more complex operations than straight-ray backprojection if they are required, including fan-beam, cone-beam, and curved ray paths, with little or no speed penalties

Molecular structures from density functional calculations with simulated annealing