L-leaping:Accelerating the Stochastic Simulation of Chemically Reacting Systems
-
摘要: 提出了随机模拟化学反应系统的加速L-leap算法,该算法根据leap条件确定具有最大倾向函数的反应通道的反应次数,并利用二项分布随机数生成其它反应通道在当前leap时间区间内的反应次数.L-leap算法可更好地满足leap条件.数值模拟实验表明该算法能取得更好的模拟性能.Abstract: Presented here is an L-leap method for accelerating stochastic simulation of well stirred chemically reacting systems,in which the number of reactions occurring of a reaction channel with the largest propensity function is calculated from the leap condition and the numbers of reactions occurring of the other reaction channels are generated by using binomial random variables during a leap.The L-leap method can better satisfy the leap condition.Numerical simulation results indicate that the L-Leap method can obtain better perfor mance than established methods.
-
[1] Ideker T, Galitski T,Hood L.A new approach to decoding life: systems biology[J].Annu Tev Genom Human Genet,2001,2(1):343-372. doi: 10.1146/annurev.genom.2.1.343 [2] Fedoroff N, Fontana W. Genetic networks: Small numbers of big molecules[J].Science,2002,297(5584):1129-1131. doi: 10.1126/science.1075988 [3] Gillespie D T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions[J].J Comput Phys,1976,22(4):403-434. doi: 10.1016/0021-9991(76)90041-3 [4] Gillespie D T. Exact stochastic simulation of coupled chemical reactions[J].J Chem Phys,1977,81(25):2340- 2361. doi: 10.1021/j100540a008 [5] Gibson M, Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels[J].J Chem Phys,2000,104(9):1876-1889. doi: 10.1021/jp993732q [6] Cao Y, Li H, Petzold L R.Efficient formulation of the stochastic simulation algorithm for chemically reacting systems[J].J Comput Phys,2004,121(9):4059-4067. [7] McCollum J M,Peterson G D,Cox C D,et al. The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior[J].Comput Biol Chem,2006,30(1):39-49. doi: 10.1016/j.compbiolchem.2005.10.007 [8] Gillespie D T.Approximate accelerated stochastic simulation of chemically reacting systems[J].J Chem Phys,2001,115(4):1716-1733. doi: 10.1063/1.1378322 [9] Chatterjee A, Vlachos D G, Katsoulakis M A. Binomial distribution based tau-leap accelerated stochastic simulation[J].J Chem Phys,2005,122(2):024112. doi: 10.1063/1.1833357 [10] Auger A, Chatelain P,Koumoutsakos P.R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps[J].J Chem Phys,2006,125(8):084103. doi: 10.1063/1.2218339 [11] Cai X D, Xu Z Y.K-leap method for accelerating stochastic simulation of coupled chemical reactions[J].J Chem Phys,2007,126(7):074102. doi: 10.1063/1.2436869 [12] Gillespie D T,Petzold L R.Improved leap-size selection for accelerated stochastic simulation[J].J Chem Phys,2003,119(16):8229-8234. doi: 10.1063/1.1613254 [13] Cao Y, Gillespie D T,Petzold L R. Avoiding negative populations in explicit tau leaping method[J].J Chem Phys,2005,123(5):054104-054112. doi: 10.1063/1.1992473 [14] Cao Y, Gillespie D T,Petzold L R. Efficient step size selection for the tau-leaping simulation method[J].J Chem Phys,2006,124(4):044109. doi: 10.1063/1.2159468
点击查看大图
计量
- 文章访问数: 2148
- HTML全文浏览量: 49
- PDF下载量: 791
- 被引次数: 0