GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
Identifieur interne : 002737 ( Main/Merge ); précédent : 002736; suivant : 002738GPU‐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
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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. 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38040 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.upmf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-51016" type="indirect"><org type="institution" xml:id="struct-51016" status="OLD"><orgName>Université Joseph Fourier</orgName><orgName type="acronym">UJF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 53 - 38041 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.ujf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-300275" type="indirect"><org type="institution" xml:id="struct-300275" status="VALID"><orgName>Institut National Polytechnique de Grenoble (INPG)</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle><tutelle name="UMR5217" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="IdRef">02636817X</idno><idno type="ISNI">0000000122597504</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName><orgName type="university">Université Pierre-Mendès-France</orgName><orgName type="institution" wicri:auto="newGroup">Université de Grenoble</orgName><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName><orgName type="university">Université Joseph Fourier</orgName><orgName type="institution" wicri:auto="newGroup">Université de Grenoble</orgName></affiliation></author><author><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-489" status="VALID"><orgName>Laboratoire de biochimie théorique [Paris]</orgName><orgName type="acronym">LBT</orgName><desc><address><addrLine>13 Rue Pierre et Marie Curie 75005 PARIS</addrLine><country key="FR"></country></address><ref type="url">http://www.ibpc.fr/UPR9080/</ref></desc><listRelation><relation active="#struct-300301" type="direct"></relation><relation name="UPR9080" active="#struct-441569" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-300301" type="direct"><org type="institution" xml:id="struct-300301" status="VALID"><orgName>Université Paris Diderot - Paris 7</orgName><orgName type="acronym">UP7</orgName><desc><address><addrLine>5 rue Thomas-Mann - 75205 Paris cedex 13</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-paris-diderot.fr</ref></desc></org></tutelle><tutelle name="UPR9080" active="#struct-441569" type="direct"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="IdRef">02636817X</idno><idno type="ISNI">0000000122597504</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country></affiliation></author></analytic><idno type="DOI">10.1002/jcc.21861</idno><series><title level="j">Journal of Computational Chemistry</title><idno type="ISSN">0192-8651</idno><imprint><date type="datePub">2011-10</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></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.</div></front></TEI></HAL><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids</title><author><name sortKey="Chavent, Matthieu" sort="Chavent, Matthieu" uniqKey="Chavent M" first="Matthieu" last="Chavent">Matthieu Chavent</name></author><author><name sortKey="Vanel, Antoine" sort="Vanel, Antoine" uniqKey="Vanel A" first="Antoine" last="Vanel">Antoine Vanel</name></author><author><name sortKey="Tek, Alex" sort="Tek, Alex" uniqKey="Tek A" first="Alex" last="Tek">Alex Tek</name></author><author><name sortKey="Levy, Bruno" sort="Levy, Bruno" uniqKey="Levy B" first="Bruno" last="Levy">Bruno Levy</name></author><author><name sortKey="Robert, Sophie" sort="Robert, Sophie" uniqKey="Robert S" first="Sophie" last="Robert">Sophie Robert</name></author><author><name sortKey="Raffin, Bruno" sort="Raffin, Bruno" uniqKey="Raffin B" first="Bruno" last="Raffin">Bruno Raffin</name></author><author><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:4910C825C89928F4FEF5F9B427762EFC736207E6</idno><date when="2011" year="2011">2011</date><idno type="doi">10.1002/jcc.21861</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-ZBDNPGXZ-2/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001122</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001122</idno><idno type="wicri:Area/Istex/Curation">001106</idno><idno type="wicri:Area/Istex/Checkpoint">000595</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000595</idno><idno type="wicri:doubleKey">0192-8651:2011:Chavent M:gpu:accelerated:atom</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids</title><author><name sortKey="Chavent, Matthieu" sort="Chavent, Matthieu" uniqKey="Chavent M" first="Matthieu" last="Chavent">Matthieu Chavent</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Biochimie Théorique, Institut de Biologie Physico‐Chimique, CNRS UPR 9080/Université Paris‐7, 13, rue Pierre et Marie Curie, F‐75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>CEA, DAM, DIF, 91297 Arpajon</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Arpajon</settlement></placeName></affiliation></author><author><name sortKey="Vanel, Antoine" sort="Vanel, Antoine" uniqKey="Vanel A" first="Antoine" last="Vanel">Antoine Vanel</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>INRIA, Laboratoire d'Informatique de Grenoble, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Tek, Alex" sort="Tek, Alex" uniqKey="Tek A" first="Alex" last="Tek">Alex Tek</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Biochimie Théorique, Institut de Biologie Physico‐Chimique, CNRS UPR 9080/Université Paris‐7, 13, rue Pierre et Marie Curie, F‐75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Levy, Bruno" sort="Levy, Bruno" uniqKey="Levy B" first="Bruno" last="Levy">Bruno Levy</name><affiliation wicri:level="4"><country xml:lang="fr">France</country><wicri:regionArea>Equipe ALICE, Nancy Université, LORIA, INRIA Nancy grand‐Est, 54506 Vandoeuvre‐les‐Nancy Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Vandoeuvre‐les‐Nancy</settlement></placeName><orgName type="university">Nancy-Université</orgName></affiliation></author><author><name sortKey="Robert, Sophie" sort="Robert, Sophie" uniqKey="Robert S" first="Sophie" last="Robert">Sophie Robert</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire d'Informatique Fondamentale d'Orléans (LIFO), 45067, Orléans Cedex 02</wicri:regionArea><placeName><region type="region" nuts="2">Centre-Val de Loire</region><region type="old region" nuts="2">Région Centre</region><settlement type="city">Orléans</settlement></placeName></affiliation></author><author><name sortKey="Raffin, Bruno" sort="Raffin, Bruno" uniqKey="Raffin B" first="Bruno" last="Raffin">Bruno Raffin</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>INRIA, Laboratoire d'Informatique de Grenoble, Grenoble</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author><author><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire de Biochimie Théorique, Institut de Biologie Physico‐Chimique, CNRS UPR 9080/Université Paris‐7, 13, rue Pierre et Marie Curie, F‐75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Allemagne</country></affiliation><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Correspondence address: Laboratoire de Biochimie Théorique, Institut de Biologie Physico‐Chimique, CNRS UPR 9080/Université Paris‐7, 13, rue Pierre et Marie Curie, F‐75005 Paris</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Journal of Computational Chemistry</title><title level="j" type="alt">JOURNAL OF COMPUTATIONAL CHEMISTRY</title><idno type="ISSN">0192-8651</idno><idno type="eISSN">1096-987X</idno><imprint><biblScope unit="vol">32</biblScope><biblScope unit="issue">13</biblScope><biblScope unit="page" from="2924">2924</biblScope><biblScope unit="page" to="2935">2935</biblScope><biblScope unit="page-count">12</biblScope><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2011-10">2011-10</date></imprint><idno type="ISSN">0192-8651</idno></series></biblStruct></sourceDesc><seriesStmt><idno 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></ISTEX></double></record>Pour manipuler ce document sous Unix (Dilib)
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