title: The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems.
abstract: The Inhomogeneous Stochastic Simulation Algorithm (ISSA) is a variant of the stochastic simulation algorithm in which the spatially inhomogeneous volume of the system is divided into homogeneous subvolumes, and the chemical reactions in those subvolumes are augmented by diffusive transfers of molecules between adjacent subvolumes. The ISSA can be prohibitively slow when the system is such that diffusive transfers occur much more frequently than chemical reactions. In this paper we present the Multinomial Simulation Algorithm (MSA), which is designed to, on the one hand, outperform the ISSA when diffusive transfer events outnumber reaction events, and on the other, to handle small reactant populations with greater accuracy than deterministic-stochastic hybrid algorithms. The MSA treats reactions in the usual ISSA fashion, but uses appropriately conditioned binomial random variables for representing the net numbers of molecules diffusing from any given subvolume to a neighbor within a prescribed distance. Simulation results illustrate the benefits of the algorithm.
authors.affiliation: Department of Computer Science, University of California, Santa Barbara, California 93106, USA. slampoud@cs.ucsb.edu
authors.forename: Sotiria
authors.initials: S
authors.lastname: Lampoudi
authors.forename: Dan T
authors.initials: DT
authors.lastname: Gillespie
authors.forename: Linda R
authors.initials: LR
authors.lastname: Petzold
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical