Study On The Accelerating Stochastic Simulation Algorithm For Biochemical Reaction System

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.The Representative Reaction Approach(RRA) opens up a new direction in the study of biochemical reaction system. Its main idea is that the reaction2Aâ†'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) 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 biochemical reaction system with delays. Numerical results demonstrate that compared with DSSA, our proposed algorithm is more efficient and practical in the biochemical reaction system with delays.Bayati proposed an accelerating stochastic simulation algorithm (D-leaping), when he considered delayed reaction and non-delayed reaction occur. The algorithm quickly and efficiently simulates biochemical reaction system with delays by establishing a quaternary structure. In actual operation, averaging over a great deal of simulations is needed for reliable statistical algorithm for simulating biochemical reaction system with delays. It’s called the DFAPS-leaping algorithm. The algorithm minimize the running time while preserving the accuracy, so it can improve the efficiency of algorithm. Numerical experiments show our proposed algorithm can be widely applied to a variety of biochemical reaction system and be more efficient than the existed algorithms.