DISCRETE STOCHASTIC SIMULATION METHODS FOR CHEMICALLY REACTING SYSTEMS

TitleDISCRETE STOCHASTIC SIMULATION METHODS FOR CHEMICALLY REACTING SYSTEMS
Publication TypeBook Chapter
Year of Publication2009
AuthorsCao, Y., and D. C. Samuels
Book TitleMETHODS IN ENZYMOLOGY: COMPUTER METHODS, VOL 454, PT A
Series TitleMETHODS IN ENZYMOLOGY
Volume454
Series VolumePart A
Pagination115-140
PublisherELSEVIER ACADEMIC PRESS INC
City525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA
ISBN0076-6879
Abstract

{Discrete stochastic chemical kinetics describe the time evolution of a chemically reacting system by taking into account the fact that, in reality, chemical species are present with integer populations and exhibit some degree of randomness in their dynamical behavior. In recent years, with the development of new techniques to study biochemistry dynamics in a single cell, there are increasing studies using this approach to chemical kinetics in cellular systems, where the small copy number of some reactant species in the cell may lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. This chapter reviews the fundamental theory related to stochastic chemical kinetics and several simulation methods based on that theory. We focus on nonstiff biochemical systems and the two most important discrete stochastic simulation methods: Gillespie's stochastic simulation algorithm (SSA) and the tau-leaping method. Different implementation strategies of these two methods are discussed. Then we recommend a relatively simple and efficient strategy that combines the strengths of the two methods: the hybrid SSA/tau-leaping method. The implementation details of the hybrid strategy are given here and a related software package is introduced. Finally, the hybrid method is applied to simple biochemical systems as a demonstration of its application.}

DOI10.1016/S0076-6879(08)03805-6