GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
Identifieur interne : 002695 ( Main/Exploration ); précédent : 002694; suivant : 002696GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
Auteurs : Matthieu Chavent [France] ; Antoine Vanel [France] ; Alex Tek [France] ; Bruno Levy [France] ; Sophie Robert [France] ; Bruno Raffin [France] ; Marc Baaden [France, Allemagne]Source :
- Journal of Computational Chemistry [ 0192-8651 ] ; 2011-10.
English descriptors
- Teeft :
- Acta crystallogr, Active pixels, Algebraic equation, Atom radii, Atom spheres, Atom type, Baaden, Benchmark, Biol, Biol crystallogr, Case studies, Chavent, Classical representations, Color figure, Comput, Comput chem, Comput graph, Computational, Computational chemistry, Covalent bonds, Datasets, Different types, Direction vector, Electronics engineers, Flowvrnano platform, Focus point, Fragment shader, Frame rate, Frame rates, General equation, General quadric, Graph model, Graphics, Graphics card, Graphics cards, High cost, Hydrogen bonds, Hyperballs, Hyperballs figure, Hyperballs implementation, Hyperballs method, Hyperballs representation, Hyperboloid, Hyperboloid bonds, Hyperboloid equation, Ieee, Ieee trans, Large amount, Large number, Licorice, Licorice representations, Lipid membrane, Mathematical basis, Matrix, Matrix form, Matrix operations, Molecular representations, Molecular systems, Noncovalent bonds, Nucleic acids, Nvidia, Online issue, Origin vector, Pixel, Plane positions, Probe sphere, Professional graphics card, Quadric equation, Quadric surface, Quadric surfaces, Representation, Residue name, Rvdw, Shader, Significant performance gain, Simulation, Smooth links, Sphere scale hyperboloid scale, Spring network model, Spring networks, Such bonds, Trajectory, Translation matrix, Vertex shader, View point, Visualization, Waals spheres, Water molecules, Wiley periodicals.
Abstract
Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball‐and‐stick, space‐filling van der Waals spheres, and approximated solvent‐accessible surfaces using GPUs. We introduce HyperBalls, an improved ball‐and‐stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse‐grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray‐casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Url:
- https://api.istex.fr/ark:/67375/WNG-ZBDNPGXZ-2/fulltext.pdf
- https://hal.archives-ouvertes.fr/hal-00645162
DOI: 10.1002/jcc.21861
Affiliations:
- Allemagne, France
- Auvergne-Rhône-Alpes, Centre-Val de Loire, Grand Est, Lorraine (région), Rhône-Alpes, Région Centre, Île-de-France
- Arpajon, Grenoble, Orléans, Paris, Vandoeuvre‐les‐Nancy
- Nancy-Université
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Le document en format XML
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type="ISSN">0192-8651</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Acta crystallogr</term><term>Active pixels</term><term>Algebraic equation</term><term>Atom radii</term><term>Atom spheres</term><term>Atom type</term><term>Baaden</term><term>Benchmark</term><term>Biol</term><term>Biol crystallogr</term><term>Case studies</term><term>Chavent</term><term>Classical representations</term><term>Color figure</term><term>Comput</term><term>Comput chem</term><term>Comput graph</term><term>Computational</term><term>Computational chemistry</term><term>Covalent bonds</term><term>Datasets</term><term>Different types</term><term>Direction vector</term><term>Electronics engineers</term><term>Flowvrnano platform</term><term>Focus point</term><term>Fragment shader</term><term>Frame rate</term><term>Frame rates</term><term>General equation</term><term>General quadric</term><term>Graph model</term><term>Graphics</term><term>Graphics card</term><term>Graphics cards</term><term>High cost</term><term>Hydrogen bonds</term><term>Hyperballs</term><term>Hyperballs figure</term><term>Hyperballs implementation</term><term>Hyperballs method</term><term>Hyperballs representation</term><term>Hyperboloid</term><term>Hyperboloid bonds</term><term>Hyperboloid equation</term><term>Ieee</term><term>Ieee trans</term><term>Large amount</term><term>Large number</term><term>Licorice</term><term>Licorice representations</term><term>Lipid membrane</term><term>Mathematical basis</term><term>Matrix</term><term>Matrix form</term><term>Matrix operations</term><term>Molecular representations</term><term>Molecular systems</term><term>Noncovalent bonds</term><term>Nucleic acids</term><term>Nvidia</term><term>Online issue</term><term>Origin vector</term><term>Pixel</term><term>Plane positions</term><term>Probe sphere</term><term>Professional graphics card</term><term>Quadric equation</term><term>Quadric surface</term><term>Quadric surfaces</term><term>Representation</term><term>Residue name</term><term>Rvdw</term><term>Shader</term><term>Significant performance gain</term><term>Simulation</term><term>Smooth links</term><term>Sphere scale hyperboloid scale</term><term>Spring network model</term><term>Spring networks</term><term>Such bonds</term><term>Trajectory</term><term>Translation matrix</term><term>Vertex shader</term><term>View point</term><term>Visualization</term><term>Waals spheres</term><term>Water molecules</term><term>Wiley periodicals</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball‐and‐stick, space‐filling van der Waals spheres, and approximated solvent‐accessible surfaces using GPUs. We introduce HyperBalls, an improved ball‐and‐stick representation replacing tubes, linking the atom spheres by hyperboloids that can smoothly connect them. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of noncovalent bonds. It is furthermore well suited to represent coarse‐grained models and spring networks. All these representations can be defined by a single general algebraic equation that is adapted for the ray‐casting technique and is well suited for execution on the GPU. Using GPU capabilities, this implementation can routinely, accurately, and interactively render molecules ranging from a few atoms up to huge macromolecular assemblies with more than 500,000 particles. In simple cases, based only on spheres, we have been able to display up to two million atoms smoothly. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Centre-Val de Loire</li><li>Grand Est</li><li>Lorraine (région)</li><li>Rhône-Alpes</li><li>Région Centre</li><li>Île-de-France</li></region><settlement><li>Arpajon</li><li>Grenoble</li><li>Orléans</li><li>Paris</li><li>Vandoeuvre‐les‐Nancy</li></settlement><orgName><li>Nancy-Université</li></orgName></list><tree><country name="France"><region name="Île-de-France"><name sortKey="Chavent, Matthieu" sort="Chavent, Matthieu" uniqKey="Chavent M" first="Matthieu" last="Chavent">Matthieu Chavent</name></region><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><name sortKey="Chavent, Matthieu" sort="Chavent, Matthieu" uniqKey="Chavent M" first="Matthieu" last="Chavent">Matthieu Chavent</name><name sortKey="Levy, Bruno" sort="Levy, Bruno" uniqKey="Levy B" first="Bruno" last="Levy">Bruno Levy</name><name sortKey="Raffin, Bruno" sort="Raffin, Bruno" uniqKey="Raffin B" first="Bruno" last="Raffin">Bruno Raffin</name><name sortKey="Robert, Sophie" sort="Robert, Sophie" uniqKey="Robert S" first="Sophie" last="Robert">Sophie Robert</name><name sortKey="Tek, Alex" sort="Tek, Alex" uniqKey="Tek A" first="Alex" last="Tek">Alex Tek</name><name sortKey="Vanel, Antoine" sort="Vanel, Antoine" uniqKey="Vanel A" first="Antoine" last="Vanel">Antoine Vanel</name></country><country name="Allemagne"><noRegion><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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