title: The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.
abstract: We have developed a computational framework for accurate and efficient simulation of stochastic spatially inhomogeneous biochemical systems. The new computational method employs a fractional step hybrid strategy. A novel formulation of the finite state projection (FSP) method, called the diffusive FSP method, is introduced for the efficient and accurate simulation of diffusive transport. Reactions are handled by the stochastic simulation algorithm.
authors.affiliation: Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA. bdrawert@cs.ucsb.edu
authors.forename: Brian
authors.initials: B
authors.lastname: Drawert
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Lawson
authors.forename: Linda
authors.initials: L
authors.lastname: Petzold
authors.forename: Mustafa
authors.initials: M
authors.lastname: Khammash
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D007700:Kinetics; D008390:Markov Chains; D008954:Models, Biological; D008956:Models, Chemical