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应用科学学报 ›› 2011, Vol. 29 ›› Issue (2): 203-208.doi: 10.3969/j.issn.0255-8297.2011.02.014

• 信号与信息处理 • 上一篇    下一篇

生化反应系统的加速t-Leap模拟算法

衣娜， 庄刚， 王翼飞   

  1. 上海大学数学系，上海200444
  • 收稿日期:2010-10-07 修回日期:2011-01-12 出版日期:2011-03-23 发布日期:2011-03-23
  • 作者简介:王翼飞，教授，博导，研究方向：计算分子生物学，E-mail: yifei_wang@staff.shu.edu.cn
  • 基金资助:

    国家自然科学基金（No.30971480）；国家科技重大专项基金(No.2009ZX09103-686)；上海市教委重点学科建设项目基金(No.J50101)；上海市重点学科建设项目基金(No.S30104)资助

The Accelerated ?-Leap Simulation Method for Biochemical Reaction Systems

YI Na, ZHUANG Gang, WANG Yi-fei   

  1. Department of Mathematics, Shanghai University, Shanghai 200444, China
  • Received:2010-10-07 Revised:2011-01-12 Online:2011-03-23 Published:2011-03-23
  • About author:王翼飞，教授，博导，研究方向：计算分子生物学，E-mail: yifei_wang@staff.shu.edu.cn
  • Supported by:

    国家自然科学基金（No.30971480）；国家科技重大专项基金(No.2009ZX09103-686)；上海市教委重点学科建设项目基金(No.J50101)；上海市重点学科建设项目基金(No.S30104)资助

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摘要：

该文重新定义了临界反应，以更合理地界定可能出现负分子组分的反应. 在此基础上提出了加速? -leap算法，使系统中某些反应物数目较少时也可以采用? -leap方法进行模拟，同时提高了模拟速度. 以两个生化反应系统模型为例，分别用精确的随机模拟算法、修正? -leap算法和加速? -leap算法进行模拟运算，结果表明加速? -leap算法在保证精度的同时能有效提高模拟速度.

关键词: 步长选择策略, 临界反应, t-leap算法, 随机模拟算法, 生化反应系统

Abstract:

This paper redefines critical reaction. It is more reasonable to demarcate reactions which may have negative reactants. Based on the definition, the accelerated ? -leap algorithm is proposed. Even if the number of some species in biochemical systems is small, the ? -leap algorithm is adaptive. This algorithm also increases the speed of simulation. The accurate stochastic simulation algorithm (SSA) algorithm, an improved ? -leap algorithm and the present accelerated algorithm are compared in two biochemical reaction models. Numerical results demonstrate that the proposed method is faster under the same simulation precision.

Key words: step size selection strategy, critical reaction,  t -leap method, stochastic simulation algorithm, biochemical reaction system

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