Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems

Journal Article · Fri Jul 01 00:00:00 EDT 2005 · Journal of Computational Physics

DOI:https://doi.org/10.1016/j.jcp.2004.12.014· OSTI ID:20687239

Yang, Cao ^[1]; Gillespie, Dan ^[2]; Petzold, Linda ^[1]

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1. Department of Computer Science, University of California Santa Barbara, Santa Barbara, CA 93106 (United States)
2. Dan T. Gillespie Consulting (United States)

In this paper, we introduce a multiscale stochastic simulation algorithm (MSSA) which makes use of Gillespie's stochastic simulation algorithm (SSA) together with a new stochastic formulation of the partial equilibrium assumption (PEA). This method is much more efficient than SSA alone. It works even with a very small population of fast species. Implementation details are discussed, and an application to the modeling of the heat shock response of E. Coli is presented which demonstrates the excellent efficiency and accuracy obtained with the new method.

• OSTI ID: 20687239
• Journal Information: Journal of Computational Physics, Vol. 206, Issue 2; Other Information: DOI: 10.1016/j.jcp.2004.12.014; PII: S0021-9991(04)00518-2; Copyright (c) 2005 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA); ISSN 0021-9991
• Country of Publication: United States
• Language: English

Related Subjects

71 CLASSICAL AND QUANTUM MECHANICS
GENERAL PHYSICS
ALGORITHMS
CHEMICAL REACTION KINETICS
EFFICIENCY
EQUILIBRIUM
SIMULATION
STOCHASTIC PROCESSES