Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks.

ABSTRACT: The biochemical reaction networks include elementary reactions differing by many orders of magnitude in the numbers of molecules involved. The kinetics of reactions involving small numbers of molecules can be studied by exact stochastic simulation. This approach is not practical for the simulation of metabolic processes because of the computational cost of accounting for individual molecular collisions. We present the "maximal time step method," a novel approach combining the Gibson and Bruck algorithm with the Gillespie tau-leap method. This algorithm allows stochastic simulation of systems composed of both intensive metabolic reactions and regulatory processes involving small numbers of molecules. The method is applied to the simulation of glucose, lactose, and glycerol metabolism in Esc

SUBMITTER: Puchalka J 

PROVIDER: S-EPMC1303974 | biostudies-literature | 2004 Mar

REPOSITORIES: biostudies-literature