The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation

The Journal of Chemical Physics
Brian DrawertM Khammash

Abstract

We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.

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Citations

May 3, 2012·BMC Bioinformatics·Bernie J DaigleJarad Niemi
Jun 1, 2014·Journal of Computational Physics·Andreas HellanderLinda Petzold
Mar 22, 2013·The Journal of Chemical Physics·Basil Bayati
May 10, 2013·The Journal of Chemical Physics·Daniel T GillespieLinda Petzold
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