The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.
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.
Drawert
Brian
B
Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA. bdrawert@cs.ucsb.edu
Lawson
Michael J
MJ
Petzold
Linda
L
Khammash
Mustafa
M
D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D007700:Kinetics; D008390:Markov Chains; D008954:Models, Biological; D008956:Models, Chemical