Computer Methods for Ordinary Differential Equations and Differential-Algebraic Equations
Computer Methods for Ordinary Differential Equations and Differential-Algebraic Equations
Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques
BioSimWare: a software for the modeling, simulation and analysis of biological systems
CMC'10 Proceedings of the 11th international conference on Membrane computing
Design and development of software tools for Bio-PEPA
Winter Simulation Conference
The Propagation Approach for Computing Biochemical Reaction Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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This chapter reviews the theory of stochastic chemical kinetics and several simulation methods that are based on that theory. An effort is made to delineate the logical connections among the major elements of the theory, such as the chemical master equation, the stochastic simulation algorithm, tau-leaping, the chemical Langevin equation, the chemical Fokker-Planck equation, and the deterministic reaction rate equation. Focused presentations are given of two approximate simulation strategies that aim to improve simulation efficiency for systems with "multiscale" complications of the kind that are often encountered in cellular systems: The first, explicit tau-leaping, deals with systems that have a wide range of molecular populations. The second, the slow-scale stochastic simulation algorithm, is designed for systems that have a wide range of reaction rates. The latter procedure is shown to provide a stochastic generalization of the Michaelis-Menten analysis of the enzyme-substrate reaction set.