加速随机模拟化学反应系统的“最后所有可能的步进”方法

周文; 彭新俊; 刘祥; 闫正楼; 王翼飞

加速随机模拟化学反应系统的“最后所有可能的步进”方法

1.
上海大学数学系,上海 200444;
安徽师范大学数学与计算机科学学院,安徽芜湖 241000

基金项目: 国家自然科学基金资助项目(30571059);国家高技术研究发展(S63)计划资助项目(AA0272190)

详细信息

作者简介:
周文(1980- ),女,安徽人,讲师,博士生(E-mail:zhouww83@shu.edu.cn);王翼飞(1948- ),男,教授(联系人.Tel:+86-21-66134331;E-mail:yifei_wang@staff.shu.edu.cn).

中图分类号: O644；O242.1
计量
- 文章访问数: 2384
- HTML全文浏览量: 98
- PDF下载量: 726
- 被引次数: 0
出版历程
- 收稿日期: 2007-08-03
- 修回日期: 2008-01-29
- 刊出日期: 2008-03-15

“Final All Possible Steps” Approach for Accelerating Stochastic Simulation of Coupled Chemical Reactions

1.
Department of Mathematics, Shanghai University, Shanghai 200444, P. R. China;
Department of Mathematics, Anhui Normal University, Wuhu 241000, P. R. China

摘要

摘要: 提出了一种改进的模拟化学反应系统的加速方法,称为“最后所有可能的步进”（FAPS）方法．此方法不仅可以用较少的模拟次数得到整个运行过程中任何时刻物种的统计特性,而且还可以与leap算法相结合,有效地进行大规模的化学反应系统的模拟．数值模拟的结果表明提出的方法可以广泛地应用于多种化学反应系统,并且与已有的方法相比其运行效率有显著的改进．
- “最后所有可能的步进”方法 /
- 随机模拟算法 /
- 化学反应系统
Abstract: A modified accelerated stochastic simulation method for chemically reacting systems, called the "final all possible steps" (FAPS) method is developed. The reliable statistics of all species were obtained in any time during the time course with fewer simulation times. Moreover, the FAPS method can be incorporated into the leap methods, which makes the simulation of larger systems more efficient. Numerical results indicate that the proposed methods can be applied to a wide range of chemically reacting systems with a high-precision level and a significant improvement can be obtained on efficiency over the existed methods.
- “final all possible steps” approach /
- stochastic simulation algorithm /
- chemically reacting system

HTML全文

参考文献(21)

[1]	McAdams H H,Arkin A.Stochastic mechanisms in gene expression[J].Proc Natl Acad Sci U S A,1997,94(3):814-819. doi: 10.1073/pnas.94.3.814
[2]	Arkin A,Ross J,McAdams H H.Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected E coli cells[J].Genetics,1998,149(4):1633-1648.
[3]	Fedoroff N,Fontana W. Small numbers of large molecules[J].Science,2002,297(5584):1129-1130. doi: 10.1126/science.1075988
[4]	Van Kampen N G.Stochastic Process in Physics and Chemistry[M].Amsterdam:North-Holland,1981.
[5]	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
[6]	Gillespie D T. Exact stochastic simulation of coupled chemical reactions[J].J Chem Phys,1977,81(25):2340-2361. doi: 10.1021/j100540a008
[7]	Gibson M, Bruck J. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems[J].J Chem Phys,2000,104(9):1876-1889. doi: 10.1021/jp993732q
[8]	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
[9]	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
[10]	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
[11]	Rathinam M,Petzold L R,Cao Y,et al.Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method[J].J Chem Phys,2003,119(24):12784-12794. doi: 10.1063/1.1627296
[12]	Tian T, Burrage K.Binomial leap methods for simulating stochastic chemical kinetics[J].J Chem Phys,2004,121(21):10356-10364. doi: 10.1063/1.1810475
[13]	Chatterjee A, Vlachos D G, Katsoulakis M A.Binomial distribution based τ-leap accelerated stochastic simulation[J].J Chem Phys,2005,122(2): 024112. doi: 10.1063/1.1833357
[14]	Peng X J, Zhou W,Wang Y F. Efficient binomial leap method for simulating chemical kinetics[J].J Chem Phys,2007,126(22):1-9.
[15]	Cai X D, Xu Z Y.K-leap method for accelerating stochastic simulation of coupled chemical reactions[J].J Chem Phys,2007,126(7):1.
[16]	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
[17]	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
[18]	Cao Y, Petzold L R.Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems[J].J Comput Phys,2006,212(1):6-24. doi: 10.1016/j.jcp.2005.06.012
[19]	Cao Y, Li H,Petzold L R. Efficient exact stochastic simulation algorithm for chemically reacting systems[J].J Comput Phys,2004,121(9):4059-4067.
[20]	Cao Y, Gillespie D T,Petzold L R. Avoiding negative populations in explicit poisson tau-leaping[J].J Chem Phys,2005,123(5):054104. doi: 10.1063/1.1992473
[21]	Lipshtat A.“All possible steps” approach to the accelerated use of Gillespie's algorithm[J].J Chem Phys,2007,126(18):184103. doi: 10.1063/1.2730507

施引文献

资源附件(0)

访问统计

计量

文章访问数: 2384
HTML全文浏览量: 98
PDF下载量: 726
被引次数: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

留言板

加速随机模拟化学反应系统的“最后所有可能的步进”方法

作者简介:
周文(1980- ),女,安徽人,讲师,博士生(E-mail:zhouww83@shu.edu.cn);王翼飞(1948- ),男,教授(联系人.Tel:+86-21-66134331;E-mail:yifei_wang@staff.shu.edu.cn).

计量

“Final All Possible Steps” Approach for Accelerating Stochastic Simulation of Coupled Chemical Reactions

计量

目录

留言板

加速随机模拟化学反应系统的“最后所有可能的步进”方法

作者简介: 周文(1980- ),女,安徽人,讲师,博士生(E-mail:zhouww83@shu.edu.cn);王翼飞(1948- ),男,教授(联系人.Tel:+86-21-66134331;E-mail:yifei_wang@staff.shu.edu.cn).

计量

出版历程

“Final All Possible Steps” Approach for Accelerating Stochastic Simulation of Coupled Chemical Reactions

计量

出版历程

目录

作者简介:
周文(1980- ),女,安徽人,讲师,博士生(E-mail:zhouww83@shu.edu.cn);王翼飞(1948- ),男,教授(联系人.Tel:+86-21-66134331;E-mail:yifei_wang@staff.shu.edu.cn).