A Convergent Reaction-Diffusion Master Equation

DOI10.1063/1.4816377arXiv1211.6772WikidataQ46588804 ScholiaQ46588804MaRDI QIDQ6237576FDOQ6237576

Publication date: 28 November 2012

Abstract: The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME is often interpreted as an approximation to spatially-continuous models in which molecules move by Brownian motion and react by one of several mechanisms when sufficiently close. In the limit that the lattice spacing approaches zero, in two or more dimensions, the RDME has been shown to lose bimolecular reactions. The RDME is therefore not a convergent approximation to any spatially-continuous model that incorporates bimolecular reactions. In this work we derive a new convergent RDME (CRDME) by finite volume discretization of a spatially-continuous stochastic reaction-diffusion model popularized by Doi. We demonstrate the numerical convergence of reaction time statistics associated with the CRDME. For sufficiently large lattice spacings or slow bimolecular reaction rates, we also show the reaction time statistics of the CRDME may be approximated by those from the RDME. The original RDME may therefore be interpreted as an approximation to the CRDME in several asymptotic limits.

Mathematics Subject Classification ID

Finite volume methods for initial value and initial-boundary value problems involving PDEs (65M08) Probabilistic methods, particle methods, etc. for initial value and initial-boundary value problems involving PDEs (65M75) Computational methods for problems pertaining to biology (92-08)

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