Improved leap-size selection for accelerated stochastic simulation

被引:252
作者
Gillespie, DT [1 ]
Petzold, LR
机构
[1] Dan T Gillespie Consulting, Castaic, CA 91384 USA
[2] Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA
关键词
D O I
10.1063/1.1613254
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
In numerically simulating the time evolution of a well-stirred chemically reacting system, the recently introduced "tau-leaping" procedure attempts to accelerate the exact stochastic simulation algorithm by using a special Poisson approximation to leap over sequences of noncritical reaction events. Presented here is an improved procedure for determining the maximum leap size for a specified degree of accuracy. (C) 2003 American Institute of Physics.
引用
收藏
页码:8229 / 8234
页数:6
相关论文
共 9 条
[1]  
[Anonymous], 1986, NUMERICAL RECIPES C
[2]  
Arkin A, 1998, GENETICS, V149, P1633
[3]   Modelling cellular behaviour [J].
Endy, D ;
Brent, R .
NATURE, 2001, 409 (6818) :391-395
[4]   Efficient exact stochastic simulation of chemical systems with many species and many channels [J].
Gibson, MA ;
Bruck, J .
JOURNAL OF PHYSICAL CHEMISTRY A, 2000, 104 (09) :1876-1889
[5]   GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) :403-434
[6]   Approximate accelerated stochastic simulation of chemically reacting systems [J].
Gillespie, DT .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (04) :1716-1733
[7]   EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF PHYSICAL CHEMISTRY, 1977, 81 (25) :2340-2361
[8]   Stochastic mechanisms in gene expression [J].
McAdams, HH ;
Arkin, A .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (03) :814-819
[9]  
RATHINAM M, IN PRESS J CHEM PHYS