Journal
JOURNAL OF COMPUTATIONAL PHYSICS
Volume 274, Issue -, Pages 524-549Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jcp.2014.06.025
Keywords
Spatial stochastic simulation; Reaction-diffusion; Time dependent propensity
Funding
- NSF [DMS-1001012, CNS-0960316]
- NIH [ROIEB014877]
- US Army Research Office [W911NF-10-2-0114]
- Institute for Collaborative Biotechnologies from the US Army Research Office [W911NF-09-D-0001]
- DOE [DE-SC0008975]
- UCSB Center for Scientific Computing from the CNSI, MRL: an NSF MRSEC [DMR-1121053]
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [1001012] Funding Source: National Science Foundation
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The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. (C) 2014 Elsevier Inc. All rights reserved.
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