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

被引：48

作者：

Drawert, Brian ^{[1
]}

Lawson, Michael J. ^{[2
]}

Petzold, Linda ^{[1
]}

Khammash, Mustafa ^{[3
]}

机构：

[1] Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA

[2] Univ Calif Santa Barbara, Dept Biomol Sci & Engn, Santa Barbara, CA 93106 USA

[3] Univ Calif Santa Barbara, Dept Mech Engn, Santa Barbara, CA 93106 USA

来源：

JOURNAL OF CHEMICAL PHYSICS | 2010年 / 132卷 / 07期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

biochemistry; biodiffusion; molecular biophysics; proteins; reaction-diffusion systems; stochastic processes; CHEMICAL-REACTIONS; ESCHERICHIA-COLI; GENE-EXPRESSION; SYSTEMS; CELL;

D O I：

10.1063/1.3310809

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页数：12

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