Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

Handle URI:
http://hdl.handle.net/10754/597551
Title:
Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions
Authors:
Lipková, Jana; Zygalakis, Konstantinos C.; Chapman, S. Jonathan; Erban, Radek
Abstract:
A class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.
Citation:
Lipková J, Zygalakis KC, Chapman SJ, Erban R (2011) Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions. SIAM Journal on Applied Mathematics 71: 714–730. Available: http://dx.doi.org/10.1137/100794213.
Publisher:
Society for Industrial & Applied Mathematics (SIAM)
Journal:
SIAM Journal on Applied Mathematics
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
Jan-2011
DOI:
10.1137/100794213
Type:
Article
ISSN:
0036-1399; 1095-712X
Sponsors:
Received by the editors May 5, 2010; accepted for publication (in revised form) February 9, 2011; published electronically May 4, 2011. This publication is based on work (by J. Lipkova, K. Zygalakis, and R. Erban) supported by award KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). The 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 239870. R. Erban would also like to thank Somerville College, University of Oxford, for a Fulford Junior Research Fellowship.
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Full metadata record

DC FieldValue Language
dc.contributor.authorLipková, Janaen
dc.contributor.authorZygalakis, Konstantinos C.en
dc.contributor.authorChapman, S. Jonathanen
dc.contributor.authorErban, Radeken
dc.date.accessioned2016-02-25T12:41:54Zen
dc.date.available2016-02-25T12:41:54Zen
dc.date.issued2011-01en
dc.identifier.citationLipková J, Zygalakis KC, Chapman SJ, Erban R (2011) Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions. SIAM Journal on Applied Mathematics 71: 714–730. Available: http://dx.doi.org/10.1137/100794213.en
dc.identifier.issn0036-1399en
dc.identifier.issn1095-712Xen
dc.identifier.doi10.1137/100794213en
dc.identifier.urihttp://hdl.handle.net/10754/597551en
dc.description.abstractA class of Brownian dynamics algorithms for stochastic reaction-diffusion models which include reversible bimolecular reactions is presented and analyzed. The method is a generalization of the λ-bcȳ model for irreversible bimolecular reactions which was introduced in [R. Erban and S. J. Chapman, Phys. Biol., 6(2009), 046001]. The formulae relating the experimentally measurable quantities (reaction rate constants and diffusion constants) with the algorithm parameters are derived. The probability of geminate recombination is also investigated. © 2011 Society for Industrial and Applied Mathematics.en
dc.description.sponsorshipReceived by the editors May 5, 2010; accepted for publication (in revised form) February 9, 2011; published electronically May 4, 2011. This publication is based on work (by J. Lipkova, K. Zygalakis, and R. Erban) supported by award KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). The 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 239870. R. Erban would also like to thank Somerville College, University of Oxford, for a Fulford Junior Research Fellowship.en
dc.publisherSociety for Industrial & Applied Mathematics (SIAM)en
dc.subjectBrownian dynamicsen
dc.subjectReaction-diffusion problemsen
dc.subjectReversible bimolecular reactionsen
dc.subjectStochastic simulation algorithmsen
dc.titleAnalysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactionsen
dc.typeArticleen
dc.identifier.journalSIAM Journal on Applied Mathematicsen
dc.contributor.institutionCharles University in Prague, Prague, Czech Republicen
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdomen
kaust.grant.numberKUK-C1-013-04en
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