An adaptive algorithm for simulation of stochastic reaction-diffusion processes
- Division of Scientific Computing, Department of Information Technology, Uppsala University, P.O. Box 337, SE-75105 Uppsala (Sweden)
We propose an adaptive hybrid method suitable for stochastic simulation of diffusion dominated reaction-diffusion processes. For such systems, simulation of the diffusion requires the predominant part of the computing time. In order to reduce the computational work, the diffusion in parts of the domain is treated macroscopically, in other parts with the tau-leap method and in the remaining parts with Gillespie's stochastic simulation algorithm (SSA) as implemented in the next subvolume method (NSM). The chemical reactions are handled by SSA everywhere in the computational domain. A trajectory of the process is advanced in time by an operator splitting technique and the timesteps are chosen adaptively. The spatial adaptation is based on estimates of the errors in the tau-leap method and the macroscopic diffusion. The accuracy and efficiency of the method are demonstrated in examples from molecular biology where the domain is discretized by unstructured meshes.
- OSTI ID:
- 21333922
- Journal Information:
- Journal of Computational Physics, Journal Name: Journal of Computational Physics Journal Issue: 2 Vol. 229; ISSN JCTPAH; ISSN 0021-9991
- Country of Publication:
- United States
- Language:
- English
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