生化反应系统中减速随机模拟算法的研究.pdfVIP

Study on the accelerating stochastic simulation algorithm for biochemical reaction system Abstract All activities of life are the basis of cell, cell activities constitute a set of precise and complex reaction networks. So studying the interaction of chemical reaction networks has become an important subject in the study of biochemical reaction system. In order to study the dynamics characteristics of complex chemical reaction, we need to model and simulate the biochemical reaction system. Because the cell of chemical reaction have randomness and discreteness,we need make random model. The Representative Reaction Approach(RRA) opens up a new direction in the study of biochemical reaction system. Its main idea is that the reaction 2A￫B representats all reactions of the biochemical reaction system. The Final All Possible Step RRA(FAPS RRA) based on RRA in is proposedthis paper. The algorithm changes the date collection of RRA. Our proposed algorithm can minimize the running time while preserving the accuracy. So it can improve efficiency of the RRA. The result reveals our proposed algorithm is more effective than RRA. Delay is a common phenomenon in the biochemical reaction system. For example, gene transcription and mRNA translation do not occur immediately but occur after a period of time . Exact stochastic simulation algorithm with delay(DSSA) which was proposed by Barrio and Cai et al solve these biochemical reaction system with delays. Because DSSA can only simulate every reaction event once, the reaction rate is too low. We expand on an existed RRA in this paper and propose a DRRA for stochastic simulation of