Analysis of Brownian Dynamics Simulations of Reversible Bimolecular Reactions

Lipková, Jana; Zygalakis, Konstantinos C.; Chapman, S. Jonathan; Erban, Radek

Type

Article

Authors

Lipková, Jana
Zygalakis, Konstantinos C.
Chapman, S. Jonathan
Erban, Radek

KAUST Grant Number

KUK-C1-013-04

Date

2011-01

Permanent link to this record

http://hdl.handle.net/10754/597551

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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.

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.