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dc.contributor.authorFlegg, M. B.
dc.contributor.authorChapman, S. J.
dc.contributor.authorErban, R.
dc.date.accessioned2016-02-28T06:33:34Z
dc.date.available2016-02-28T06:33:34Z
dc.date.issued2011-10-19
dc.identifier.citationFlegg MB, Chapman SJ, Erban R (2011) The two-regime method for optimizing stochastic reaction-diffusion simulations. Journal of The Royal Society Interface 9: 859–868. Available: http://dx.doi.org/10.1098/rsif.2011.0574.
dc.identifier.issn1742-5689
dc.identifier.issn1742-5662
dc.identifier.pmid22012973
dc.identifier.doi10.1098/rsif.2011.0574
dc.identifier.urihttp://hdl.handle.net/10754/599972
dc.description.abstractSpatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models. Often microscopic detail is only required in a small region (e.g. close to the cell membrane). Currently, the best way to achieve microscopic detail is to use a resource-intensive simulation over the whole domain. We develop the two-regime method (TRM) in which a molecular-based algorithm is used where desired and a compartment-based approach is used elsewhere. We present easy-to-implement coupling conditions which ensure that the TRM results have the same accuracy as a detailed molecular-based model in the whole simulation domain. Therefore, the TRM combines strengths of previously developed stochastic reaction-diffusion software to efficiently explore the behaviour of biological models. Illustrative examples and the mathematical justification of the TRM are also presented.
dc.description.sponsorshipThe research leading to these results has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 239870. This publication was based on work supported in part by award no. KUK-C1-013-04, made by the King Abdullah University of Science and Technology (KAUST). R.E. would also like to thank Somerville College, University of Oxford, for a Fulford Junior Research Fellowship.
dc.publisherThe Royal Society
dc.subjectHybrid algorithm
dc.subjectMulti-scale simulation
dc.subjectReaction-diffusion processes
dc.subjectStochastic modelling
dc.subject.meshStochastic Processes
dc.subject.meshModels, Theoretical
dc.subject.meshComputer Simulation
dc.titleThe two-regime method for optimizing stochastic reaction-diffusion simulations
dc.typeArticle
dc.identifier.journalJournal of The Royal Society Interface
dc.identifier.pmcidPMC3306650
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdom
kaust.grant.numberKUK-C1-013-04


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