title: Efficient exact and K-skip methods for stochastic simulation of coupled chemical reactions.
abstract: Gillespie's direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao et al., J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K-skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K-skip method can save 20%-30% and 70%-80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K-skip method provide almost the same simulation accuracy as the ODM.
authors.affiliation: Department of Electrical and Computer Engineering, University of Miami, Coral Gables, Florida 33124, USA. x.cai@miami.edu
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Cai
authors.forename: Ji
authors.initials: J
authors.lastname: Wen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D019281:Dimerization; D015870:Gene Expression; D007763:Lac Operon; D026901:Membrane Transport Proteins / Q000235:genetics; D008956:Models, Chemical; D013269:Stochastic Processes
chemical_list: D026901:Membrane Transport Proteins; C021499:lactose permease