title: Abstract Next Subvolume Method: a logical process-based approach for spatial stochastic simulation of chemical reactions.
abstract: The spatial stochastic simulation of biochemical systems requires significant calculation efforts. Parallel discrete-event simulation is a promising approach to accelerate the execution of simulation runs. However, achievable speedup depends on the parallelism inherent in the model. One of our goals is to explore this degree of parallelism in the Next Subvolume Method type simulations. Therefore we introduce the Abstract Next Subvolume Method, in which we decouple the model representation from the sequential simulation algorithms, and prove that state trajectories generated by its executions statistically accord with those generated by the Next Subvolume Method. The experimental performance analysis shows that optimistic synchronization algorithms, together with careful controls over the speculative execution, are necessary to achieve considerable speedup and scalability in parallel spatial stochastic simulation of chemical reactions. Our proposed method facilitates a flexible incorporation of different synchronization algorithms, and can be used to select the proper synchronization algorithm to achieve the efficient parallel simulation of chemical reactions.
authors.affiliation: School of Computer Science, National University of Defense Technology, 410073 Changsha, PR China. wangbing@nudt.edu.cn
authors.forename: Bing
authors.initials: B
authors.lastname: Wang
authors.forename: Bonan
authors.initials: B
authors.lastname: Hou
authors.forename: Fei
authors.initials: F
authors.lastname: Xing
authors.forename: Yiping
authors.initials: Y
authors.lastname: Yao
mesh_terms: D000465:Algorithms; D002621:Chemistry / Q000379:methods*; D019295:Computational Biology; D003198:Computer Simulation; D013269:Stochastic Processes