Signal and Information Processing

The Accelerated ?-Leap Simulation Method for Biochemical Reaction Systems

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  • 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

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.

Cite this article

YI Na, ZHUANG Gang, WANG Yi-fei . The Accelerated ?-Leap Simulation Method for Biochemical Reaction Systems[J]. Journal of Applied Sciences, 2011 , 29(2) : 203 -208 . DOI: 10.3969/j.issn.0255-8297.2011.02.014

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