English

应用科学学报 >

2011 , Vol. 29 >Issue 2: 203 - 208

DOI: https://doi.org/10.3969/j.issn.0255-8297.2011.02.014

信号与信息处理

生化反应系统的加速t-Leap模拟算法

展开
  • 上海大学数学系，上海200444
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

收稿日期: 2010-10-07

  修回日期: 2011-01-12

  网络出版日期: 2011-03-23

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

收起

The Accelerated ?-Leap Simulation Method for Biochemical Reaction Systems

Expand
  • Department of Mathematics, Shanghai University, Shanghai 200444, China
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

Received date: 2010-10-07

  Revised date: 2011-01-12

  Online published: 2011-03-23

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

Fold

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

本文引用格式

衣娜， 庄刚， 王翼飞 . 生化反应系统的加速t-Leap模拟算法[J]. 应用科学学报, 2011 , 29(2) : 203 -208 . DOI: 10.3969/j.issn.0255-8297.2011.02.014

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

Options
文章导航

/

〈 〉