Article,
Logarithmic Direct Method for discrete stochastic simulation of chemically reacting systems
(July 2006)
Abstract
In biological systems formed by living cells, the small populations of some reactant species can result in dynamical behavior which cannot be captured by the traditional reaction rate equations. In that case, a more accurate simulation can be obtained by using the machinery of Markov process theory, specifically the Stochastic Simulation Algorithm (SSA). Since for re-alistic, practical biochemical systems the simulation by the SSA carries a high computational cost, several formulations have been proposed to increase the efficiency of this algorithm. In this paper we propose a highly efficient formulation of SSA, with computational complexity that is independent of the ordering of the reactions.
