The Mathematical Institute, University of Oxford, Eprints Archive

The Two Regime method for optimizing stochastic reaction-diffusion simulations

Flegg, M. B. and Chapman, S. J. and Erban, R. (2011) The Two Regime method for optimizing stochastic reaction-diffusion simulations. Proceedings of the National Academy of Sciences . (Submitted)

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Abstract

The computer simulation of stochastic reaction-diffusion processes in biology is often done using either compartment-based (spatially discretized) simulations or molecular-based (Brownian dynamics) approaches. Compartment-based approaches can yield quick and accurate mesoscopic results but lack the level of detail that is characteristic of the more computationally intensive molecular-based models. Often microscopic detail is only required in a small region but currently the best way to achieve this detail is to use a resource intensive model over the whole domain. We introduce the Two Regime Method (TRM) in which a molecular-based algorithm is used in part of the computational domain and a compartment-based approach is used elsewhere in the computational domain. We apply the TRM to two test problems including a model from developmental biology. We thereby show that the TRM is accurate and subsequently may be used to inspect both mesoscopic and microscopic detail of reaction diffusion simulations according to the demands of the modeller.

Item Type:Article
Subjects:D - G > General
Research Groups:Oxford Centre for Collaborative Applied Mathematics
ID Code:1388
Deposited By:Peter Hudston
Deposited On:08 Sep 2011 07:51
Last Modified:09 Feb 2012 14:02

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