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https://hdl.handle.net/1822/42214
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Campo DC | Valor | Idioma |
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dc.contributor.author | Pérez-Rodríguez, G. | por |
dc.contributor.author | Pérez-Pérez, M. | por |
dc.contributor.author | Fdez-Riverola, F. | por |
dc.contributor.author | Lourenço, Anália Maria Garcia | por |
dc.date.accessioned | 2016-07-12T14:33:41Z | - |
dc.date.available | 2016-07-12T14:33:41Z | - |
dc.date.issued | 2016-07 | - |
dc.identifier.citation | Pérez-Rodríguez, G.; Pérez-Pérez, M.; Fdez-Riverola, F.; Lourenço, Anália, High performance computing for three-dimensional agent-based molecular models. Journal of Molecular Graphics and Modelling, 68, 68-77, 2016 | por |
dc.identifier.issn | 1093-3263 | por |
dc.identifier.uri | https://hdl.handle.net/1822/42214 | - |
dc.description.abstract | Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool. | por |
dc.description.sponsorship | This work was partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). The research leading to these results has received funding from the European Union’s Seventh Framework Programme FP7/REGPOT-2012-2013.1 under grant agreement n◦316265, BIOCAPS | por |
dc.language.iso | eng | por |
dc.publisher | Elsevier 1 | por |
dc.relation | info:eu-repo/grantAgreement/EC/FP7/316265/EU | por |
dc.rights | openAccess | por |
dc.subject | Cellular systems | por |
dc.subject | Agent-based modelling | por |
dc.subject | Three-dimensional model representation | por |
dc.subject | Individual molecule simulation | por |
dc.subject | Distributed computing | por |
dc.title | High performance computing for three-dimensional agent-based molecular models | por |
dc.type | article | - |
dc.peerreviewed | yes | por |
dc.relation.publisherversion | http://www.journals.elsevier.com/journal-of-molecular-graphics-and-modelling | por |
dc.comments | CEB39004 | por |
sdum.publicationstatus | info:eu-repo/semantics/publishedVersion | por |
oaire.citationStartPage | 68 | por |
oaire.citationEndPage | 77 | por |
oaire.citationConferencePlace | Netherlands | - |
oaire.citationTitle | Journal of Molecular Graphics and Modelling | por |
oaire.citationVolume | 68 | por |
dc.date.updated | 2016-07-10T11:45:38Z | - |
dc.identifier.doi | 10.1016/j.jmgm.2016.06.001 | por |
dc.identifier.pmid | 27372059 | por |
dc.subject.wos | Science & Technology | por |
sdum.journal | Journal of Molecular Graphics and Modelling | por |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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document_39004_1.pdf | 2,29 MB | Adobe PDF | Ver/Abrir |