Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.
Computer simulations have become an invaluable tool to study the sometimes counterintuitive temporal dynamics of (bio-)chemical systems. In particular, stochastic simulation methods have attracted increasing interest recently. In contrast to the well-known deterministic approach based on ordinary differential equations, they can capture effects that occur due to the underlying discreteness of the systems and random fluctuations in molecular numbers. Numerous stochastic, approximate stochastic and hybrid simulation methods have been proposed in the literature. In this article, they are systematically reviewed in order to guide the researcher and help her find the appropriate method for a specific problem.
Pahle
Jürgen
J
Bioquant/Institute of Zoology, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany. juergen.pahle@bioquant.uni-heidelberg.de
D000465:Algorithms; D003198:Computer Simulation; D008954:Models, Biological; D009010:Monte Carlo Method; D012984:Software; D013269:Stochastic Processes