多重时滞生化反应系统的MD-Leaping算法

doi:10.3969/j.issn.1007-2861.2013.01.015

上海大学学报(自然科学版) ›› 2013, Vol. 19 ›› Issue (1): 75-79.doi: 10.3969/j.issn.1007-2861.2013.01.015

多重时滞生化反应系统的MD-Leaping算法

庄刚, 衣娜, 答亮, 王翼飞

1. 上海大学理学院, 上海200444; 2. 中国科学院上海生物化学与细胞生物学研究所, 上海200031

收稿日期:2012-03-05 出版日期:2013-02-28 发布日期:2013-02-28
通讯作者: 王翼飞(1948—), 男, 教授, 博士生导师, 研究方向为生物信息学、智能化算法等. E-mail:yifei wang@staff.shu.edu.cn
作者简介:王翼飞(1948—), 男, 教授, 博士生导师, 研究方向为生物信息学、智能化算法等. E-mail: yifei wang@staff.shu.edu.cn
基金资助:
国家自然科学基金资助项目(30971480)

MD-Leaping Algorithm for Multi-delayed Biochemical Reaction Systems

ZHUANG Gang, YI Na, DA Liang, WANG Yi-fei

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:2012-03-05 Online:2013-02-28 Published:2013-02-28

摘要/Abstract

摘要： 针对多重时滞生化反应系统, 提出MD-Leaping模拟算法, 该算法能快速有效地刻画封闭系统中生化反应的进程和结果. 相较于D-Leaping算法, 针对单时滞反应建立以反应序列为主体的四元结构体, 该算法通过对多重时滞反应系统建立以不同时滞时间为主体的四元结构体, 使得在每一个跳跃时间步长内可以同时模拟多个生化反应, 提高了模拟速度. 该算法拓展D-Leaping算法, 并首次解决多重时滞生化反应系统的加速模拟问题. 通过对2个具体生化反应系统的模拟表明, 该算法可以广泛地应用于多重时滞生化反应系统, 并且与已有的多重时滞系统非跳跃方法(multi-delay stochastic simulation algorithm, MDSSA)相比, 其运行效率有显著提高.

关键词: MD-Leaping算法, 生化反应系统, 随机模拟算法, 多重时滞系统

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

中图分类号:

O 644

庄刚, 衣娜, 答亮, 王翼飞. 多重时滞生化反应系统的MD-Leaping算法[J]. 上海大学学报(自然科学版), 2013, 19(1): 75-79.

ZHUANG Gang, YI Na, DA Liang, WANG Yi-fei. MD-Leaping Algorithm for Multi-delayed Biochemical Reaction Systems[J]. Journal of Shanghai University（Natural Science Edition）, 2013, 19(1): 75-79.

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多重时滞生化反应系统的MD-Leaping算法

MD-Leaping Algorithm for Multi-delayed Biochemical Reaction Systems

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