GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.
Identifieur interne : 002540 ( Hal/Corpus ); précédent : 002539; suivant : 002541GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.
Auteurs : Matthieu Chavent ; Antoine Vanel ; Alex Tek ; Bruno Levy ; Sophie Robert ; Bruno Raffin ; Marc BaadenSource :
- Journal of Computational Chemistry [ 0192-8651 ] ; 2011-10.
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.
Url:
DOI: 10.1002/jcc.21861
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Hal:hal-00645162Le document en format XML
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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></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 api="V3"><titleStmt><title xml:lang="en">GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.</title><author role="aut"><persName><forename type="first">Matthieu</forename><surname>Chavent</surname></persName><email></email><idno type="halauthor">367427</idno><affiliation ref="#struct-2358"></affiliation><affiliation ref="#struct-3174"></affiliation><affiliation ref="#struct-489"></affiliation></author><author role="aut"><persName><forename type="first">Antoine</forename><surname>Vanel</surname></persName><email></email><idno type="halauthor">663140</idno><affiliation ref="#struct-44973"></affiliation></author><author role="aut"><persName><forename type="first">Alex</forename><surname>Tek</surname></persName><email></email><idno type="halauthor">663141</idno><affiliation ref="#struct-489"></affiliation></author><author role="aut"><persName><forename type="first">Bruno</forename><surname>Levy</surname></persName><email></email><idno type="idhal">bruno-levy</idno><idno type="halauthor">608613</idno><idno type="arXiv">http://arxiv.org/a/brlevy</idno><affiliation ref="#struct-3174"></affiliation></author><author role="aut"><persName><forename type="first">Sophie</forename><surname>Robert</surname></persName><email></email><idno type="idhal">sophie-robert</idno><idno type="halauthor">112246</idno><affiliation ref="#struct-1625"></affiliation></author><author role="aut"><persName><forename type="first">Bruno</forename><surname>Raffin</surname></persName><email></email><idno type="idhal">bruno-raffin</idno><idno type="halauthor">54119</idno><affiliation ref="#struct-44973"></affiliation></author><author role="crp"><persName><forename type="first">Marc</forename><surname>Baaden</surname></persName><email>baaden@smplinux.de</email><ptr type="url" target="http://www.baaden.ibpc.fr"></ptr><idno type="halauthor">663134</idno><affiliation ref="#struct-489"></affiliation></author><editor role="depositor"><persName><forename>Marc</forename><surname>Baaden</surname></persName><email>baaden@smplinux.de</email></editor></titleStmt><editionStmt><edition n="v1" type="current"><date type="whenSubmitted">2011-11-26 23:54:49</date><date type="whenModified">2016-05-18 08:55:19</date><date type="whenReleased">2011-11-26 23:54:49</date><date type="whenProduced">2011-10</date></edition><respStmt><resp>contributor</resp><name key="104717"><persName><forename>Marc</forename><surname>Baaden</surname></persName><email>baaden@smplinux.de</email></name></respStmt></editionStmt><publicationStmt><distributor>CCSD</distributor><idno type="halId">hal-00645162</idno><idno type="halUri">https://hal.archives-ouvertes.fr/hal-00645162</idno><idno type="halBibtex">chavent:hal-00645162</idno><idno type="halRefHtml">Journal of Computational Chemistry, Wiley, 2011, 32 (13), pp.2924-35. <10.1002/jcc.21861></idno><idno type="halRef">Journal of Computational Chemistry, Wiley, 2011, 32 (13), pp.2924-35. <10.1002/jcc.21861></idno></publicationStmt><seriesStmt><idno type="stamp" n="UNIV-PARIS7">Université Denis Diderot - Paris VII</idno><idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno><idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno><idno type="stamp" n="UNIV-GRENOBLE1" p="UGA">Université Joseph Fourier - Grenoble I</idno><idno type="stamp" n="UNIV-PMF_GRENOBLE" p="UGA">Université Pierre-Mendès-France - Grenoble II</idno><idno type="stamp" n="UNIV-ORLEANS">Université d'Orléans</idno><idno type="stamp" n="INPL">Institut National Polytechnique de Lorraine</idno><idno type="stamp" n="ENSI-BOURGES">Ecole Nationale Supérieure d'Ingénieurs de Bourges</idno><idno type="stamp" n="INPG" p="UGA">Institut polytechnique de Grenoble</idno><idno type="stamp" n="INRIA-RHA">INRIA Grenoble - Rhône-Alpes</idno><idno type="stamp" n="LORIA2">Publications du LORIA</idno><idno type="stamp" n="INRIA-NANCY-GRAND-EST">INRIA Nancy - Grand Est</idno><idno type="stamp" n="LORIA-ACGI" p="LORIA">Algorithmique, calcul, image et géométrie</idno><idno type="stamp" n="LORIA-TALC" p="LORIA">Traitement automatique des langues et des connaissances</idno><idno type="stamp" n="LORIA">LORIA - 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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.</abstract></profileDesc></hal></record>Pour manipuler ce document sous Unix (Dilib)
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