A constrained approach to multiscale stochastic simulation of chemically reacting systems

Handle URI:
http://hdl.handle.net/10754/597243
Title:
A constrained approach to multiscale stochastic simulation of chemically reacting systems
Authors:
Cotter, Simon L.; Zygalakis, Konstantinos C.; Kevrekidis, Ioannis G.; Erban, Radek
Abstract:
Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. © 2011 American Institute of Physics.
Citation:
Cotter SL, Zygalakis KC, Kevrekidis IG, Erban R (2011) A constrained approach to multiscale stochastic simulation of chemically reacting systems. J Chem Phys 135: 094102. Available: http://dx.doi.org/10.1063/1.3624333.
Publisher:
AIP Publishing
Journal:
The Journal of Chemical Physics
KAUST Grant Number:
KUK-C1-013-04
Issue Date:
2011
DOI:
10.1063/1.3624333
PubMed ID:
21913748
Type:
Article
ISSN:
0021-9606
Sponsors:
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 No. 239870. This publication was based on work supported in part by Award No. KUK-C1-013-04, made by King Abdullah University of Science and Technology (KAUST). The work of I.G.K. was partially supported by the US Department of Energy. Thanks also to Tomáš Vejchodský for useful conversations regarding the assembly and solution within the finite element method. RE 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.authorCotter, Simon L.en
dc.contributor.authorZygalakis, Konstantinos C.en
dc.contributor.authorKevrekidis, Ioannis G.en
dc.contributor.authorErban, Radeken
dc.date.accessioned2016-02-25T12:28:48Zen
dc.date.available2016-02-25T12:28:48Zen
dc.date.issued2011en
dc.identifier.citationCotter SL, Zygalakis KC, Kevrekidis IG, Erban R (2011) A constrained approach to multiscale stochastic simulation of chemically reacting systems. J Chem Phys 135: 094102. Available: http://dx.doi.org/10.1063/1.3624333.en
dc.identifier.issn0021-9606en
dc.identifier.pmid21913748en
dc.identifier.doi10.1063/1.3624333en
dc.identifier.urihttp://hdl.handle.net/10754/597243en
dc.description.abstractStochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems. © 2011 American Institute of Physics.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 King Abdullah University of Science and Technology (KAUST). The work of I.G.K. was partially supported by the US Department of Energy. Thanks also to Tomáš Vejchodský for useful conversations regarding the assembly and solution within the finite element method. RE would also like to thank Somerville College, University of Oxford, for a Fulford Junior Research Fellowship.en
dc.publisherAIP Publishingen
dc.titleA constrained approach to multiscale stochastic simulation of chemically reacting systemsen
dc.typeArticleen
dc.identifier.journalThe Journal of Chemical Physicsen
dc.contributor.institutionUniversity of Oxford, Oxford, United Kingdomen
dc.contributor.institutionPrinceton University, Princeton, United Statesen
kaust.grant.numberKUK-C1-013-04en

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