tailieunhanh - Báo cáo hóa học: " Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems"

Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành hóa học dành cho các bạn yêu hóa học tham khảo đề tài: Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems | Xu and Cai EURASIP Journal on Bioinformatics and Systems Biology 2011 2011 4 http content 2011 1 4 s EURASIP Journal on Bioinformatics and Systems Biology a SpringerOpen Journal RESEARCH Open Access Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems Zhouyi Xu and Xiaodong Cai Abstract The weighted stochastic simulation algorithm wSSA recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for efficient estimation of the probability of rare events in biochemical reaction systems. In this paper we first apply the importance sampling technique to the next reaction method NRM of the stochastic simulation algorithm and develop a weighted NRM wNRM . We then develop a systematic method for selecting the values of importance sampling parameters which can be applied to both the wSSA and the wNRM. Numerical results demonstrate that our parameter selection method can substantially improve the performance of the wSSA and the wNRM in terms of simulation efficiency and accuracy. 1 Introduction Biochemical reaction systems in living cells exhibit significant stochastic fluctuations due to a small number of molecules involved in processes such as the transcription and translation of genes 1 . A number of exact 2-7 or approximate simulation algorithms 8-19 have been developed for simulating the stochastic dynamics of such systems. Recent research shows that some rare events occurring in biochemical reaction system with an extremely small probability within a specified limited time can have profound and sometimes devastating effects 20 21 . Hence it is important that computational simulation and analysis of systems with critical rare events can efficiently capture such rare events. However the existing exact simulation methods such as Gillespie s exact SSA 2 3 often require prohibitive .