Analysis of Brownian dynamics simulations of reversible bimolecular reactions

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SIAM Journal on Applied Mathematics, ISSN: 0036-1399, Vol: 71, Issue: 3, Page: 714-730

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Lipková, Jana; Zygalakis, Konstantinos C.; Chapman, S. Jonathan; Erban, Radek
Society for Industrial & Applied Mathematics (SIAM); Society for Industrial and Applied Mathematics
Mathematics; Brownian dynamics; Reaction-diffusion problems; Reversible bimolecular reactions; Stochastic simulation algorithms
article description
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.