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dc.contributor.authorFlegg, M. B.*
dc.contributor.authorChapman, S. J.*
dc.contributor.authorErban, R.*
dc.date.accessioned2016-02-28T06:33:34Zen
dc.date.available2016-02-28T06:33:34Zen
dc.date.issued2011-10-19en
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.en
dc.identifier.issn1742-5689en
dc.identifier.issn1742-5662en
dc.identifier.pmid22012973en
dc.identifier.doi10.1098/rsif.2011.0574en
dc.identifier.urihttp://hdl.handle.net/10754/599972en
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.en
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.en
dc.publisherThe Royal Societyen
dc.subjectHybrid algorithmen
dc.subjectMulti-scale simulationen
dc.subjectReaction-diffusion processesen
dc.subjectStochastic modellingen
dc.subject.meshStochastic Processesen
dc.subject.meshModels, Theoreticalen
dc.subject.meshComputer Simulationen
dc.titleThe two-regime method for optimizing stochastic reaction-diffusion simulationsen
dc.typeArticleen
dc.identifier.journalJournal of The Royal Society Interfaceen
dc.identifier.pmcidPMC3306650en
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdom*
kaust.grant.numberKUK-C1-013-04en


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