Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics

被引:399
作者
Haseltine, EL [1 ]
Rawlings, JB [1 ]
机构
[1] Univ Wisconsin, Dept Chem Engn, Madison, WI 53706 USA
关键词
D O I
10.1063/1.1505860
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
Exact methods are available for the simulation of isothermal, well-mixed stochastic chemical kinetics. As increasingly complex physical systems are modeled, however, these methods become difficult to solve because the computational burden scales with the number of reaction events. This paper addresses one aspect of this problem: the case in which reacting species fluctuate by different orders of magnitude. By partitioning the system into subsets of "fast" and "slow" reactions, it is possible to bound the computational load by approximating "fast" reactions either deterministically or as Langevin equations. This paper provides a theoretical background for such approximations and outlines strategies for computing these approximations. Two motivating examples drawn from the fields of particle technology and biotechnology illustrate the accuracy and computational efficiency of these approximations. (C) 2002 American Institute of Physics.
引用
收藏
页码:6959 / 6969
页数:11
相关论文
共 21 条
[1]  
[Anonymous], 1992, Markov Processes: An Introduction to Physical Scientists
[2]  
Arkin A, 1998, GENETICS, V149, P1633
[3]  
Gard T.C., 1988, INTRO STOCHASTIC DIF
[4]  
Gardiner C.W., 1990, HDB STOCHASTIC METHO
[5]   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
[6]   GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) :403-434
[7]   Approximate accelerated stochastic simulation of chemically reacting systems [J].
Gillespie, DT .
JOURNAL OF CHEMICAL PHYSICS, 2001, 115 (04) :1716-1733
[8]   The chemical Langevin equation [J].
Gillespie, DT .
JOURNAL OF CHEMICAL PHYSICS, 2000, 113 (01) :297-306
[9]   EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS [J].
GILLESPIE, DT .
JOURNAL OF PHYSICAL CHEMISTRY, 1977, 81 (25) :2340-2361
[10]   A RIGOROUS DERIVATION OF THE CHEMICAL MASTER EQUATION [J].
GILLESPIE, DT .
PHYSICA A, 1992, 188 (1-3) :404-425