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Journal of Shanghai University >

2013 , Vol. 19 >Issue 1: 75 - 79

DOI: https://doi.org/10.3969/j.issn.1007-2861.2013.01.015

Mathematics.Physics and Chemistry

MD-Leaping Algorithm for Multi-delayed Biochemical Reaction Systems

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  • 1. College of Sciences, Shanghai University, Shanghai 200444, China;
    2. Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China

Received date: 2012-03-05

  Online published: 2013-02-28

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Abstract

To simulate multi-delayed biochemical reaction systems, an MD-Leaping algorithm is proposed to efficiently analyze the process of biochemical reaction in closed systems. In contrast to the D-Leaping algorithm in which the quadruple structure is based on a single delay reaction, a new quadruple structure is built by different time-delay for the multi-delayed reactions. Several reactions can be simulated simultaneously in a time leap, leading to significant increase of the simulation speed. The proposed algorithm extends the D-Leaping method and speeds simulation of multi-delayed biochemical reaction system. Results of two specific biochemical reaction systems show effectiveness of the algorithm for multi-delayed biochemical reaction systems and the mprovement in speed compared to the multi-delay stochastic simulation algorithm (MDSSA) of multi-delayed systems.

Key words： biochemical reaction system; MDLeaping algorithm; stochastic simulation algorithm; multi-delayed stochastic system

Cite this article

ZHUANG Gang, YI Na, DA Liang, WANG Yi-fei . MD-Leaping Algorithm for Multi-delayed Biochemical Reaction Systems[J]. Journal of Shanghai University, 2013 , 19(1) : 75 -79 . DOI: 10.3969/j.issn.1007-2861.2013.01.015

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