2016/09/08 by Ling Lin, Lin, Ling, Jianfeng Lu +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Chemical Physics (physics.chem-ph) #Complex Network Analysis Techniques #FOS: Physical sciences #Gene Regulatory Network Analysis #Mathematical Physics (math-ph) #Opinion Dynamics and Social Influence
paper · pdf · doi:10.48550/arxiv.1609.02511
openalex publication_date 2016/09/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Milestoning is a computational procedure that reduces the dynamics of complex systems to memoryless jumps between intermediates, or milestones, and only retains some information about the probability of these jumps and the time lags between them. Here we analyze a variant of this procedure, termed optimal milestoning, which relies on a specific choice of milestones to capture exactly some kinetic features of the original dynamical system. In particular, we prove that optimal milestoning permits the exact calculation of the mean first passage times (MFPT) between any two milestones. In so doing, we also analyze another variant of the method, called exact milestoning, which also permits the exact calculation of certain MFPTs, but at the price of retaining more information about the original system's dynamics. Finally, we discuss importance sampling strategies based on optimal and exact milestoning that can be used to bypass the simulation of the original system when estimating the statistical quantities used in these methods.