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加速随机模拟化学反应系统的“最后所有可能的步进”方法 被引量:4

"Final All Possible Steps" Approach for Accelerating Stochastic Simulation of Coupled Chemical Reactions
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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. 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.
机构地区 上海大学数学系
出处 《应用数学和力学》 CSCD 北大核心 2008年第3期342-350,共9页 Applied Mathematics and Mechanics
基金 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)
关键词 “最后所有可能的步进”方法 随机模拟算法 化学反应系统 "final all possible steps" approach stochastic simulation algorithm chemically reacting system
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参考文献21

  • 1McAdams H H,Arkin A. Stochastic mechanisms in gene expression[J].Proc Natl Acad Sci U S A, 1997,94(3) :814-819.
  • 2Arkin 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.
  • 3Fedoroff N, Fontana W. Small numbers of large molecules[J]. Science,2002,297 (5584):1129-1130.
  • 4Van Kampen N G. Stochastic Process in Physics and Chemistry [M]. Amsterdam: North-Holland, 1981.
  • 5Gillespie 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.
  • 6Gillespie D T. Exact stochasic simulation of coupled chemical reactions[J]. J Chem Phys, 1977,81 (25) :2340-2361.
  • 7Gibson M, Bruck J. Efficient formlation of the stochastic simulation algorithm for chemically reacting systems[J]. J Chem Phys,2000,104(9):1876-1889.
  • 8McCollum 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.
  • 9Gillespie D T. Approximate accelerated stochastic simulation of chemically reacting systems[J]. J Chem Phys ,2001,115(4):1716-1733.
  • 10Gillespie D T, Petzold L R. Improved leap-size selection for accelerated stochastic simulation[J].J Chem Phys, 2003,119(16):8229-8234.

同被引文献34

  • 1GILLESPIE D T. A general method for numerically simulating the stochastic time evolution of cou- pled chemical reactions[J]. Journal of Computational Physics, 1976, 22(4): 403-434.
  • 2GILLESPIE D T. Exact stochastic simulation of cou- pled chemical reactions[J]. Journal of Physical Chem- istry, 1977, 81(25): 2340-2361.
  • 3GmsoN M A, BRUCK J. Efficient exact stochastic simulation of chemical systems with many species and many channels[J]. Journal of Physical Chem- istry, 2000, 104(9): 1876-1889.
  • 4CAO Yang, LI Hong, PETZOLD L. Efficient formulation of the stochastic simulation algorithm for chem- ically reacting systems[J]. The Journal of Chemical Physics, 2004, 121(9): 4059-4067.
  • 5CA! Xiaodong, WEN Ji. Efficient exact and K-skip methods for stochastic simulation of coupled chem- ical reactions[J]. The Journal of Chemical Physics, 2009, 131(6): 064108(1-10).
  • 6GILLESPIE D T. Approximate accelerated stochas- tic simulation of chemically reacting systems[J]. The Journal of Chemical Physics,2001, 115(4): 1716- 1733.
  • 7GILLESPIE D T, PETZOLD L R. Improved leap-size se- lection for accelerated stochastic simulation[J]. The Journal of Chemical Physics, 2003, 119(16): 8229- 8234.
  • 8CAO Yang, GILLESPIE D T, PETZOLD L R. Effi- cient step size selection for the τ-leaping simulation method[J]. The Journal of Chemical Physics, 2006, 124(4): 044109(1-11).
  • 9RATHINAM M, PETZOLD L R, CAO Yang, GILLESPIE D T. Stiffness in stochastic chemically reacting sys- tems: the implicit v-leaping method[J]. The Journal of Chemical Physics, 2003, 119(24): 12784-1-2794.
  • 10TIAN Tianhai, BURRAGE K. Binomial leap methods for simulating chemical kinetics[J]. The Journal of Chemical Physics, 2004, 121(21): 10356-10364.

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