基于時間可逆性的動力學加速算法tRPS
時間：2023-12-29
Zhirong Liu*. Accelerating kinetics with time-reversal path sampling. Molecules 28 (24), 8147/1-12 (2023).
導讀: 熱力學和動力學是物理化學的兩個重要内容。一般而言，熱力學性質的模拟比動力學容易一些。基于玻爾茲曼分布以及其它的平衡統計規律，已經開發了各種有效的增強采樣方法來加快熱力學的分子模拟速度。與此相比，動力學和非平衡統計的加速模拟方法相對較少，效果也沒那麼理想。針對這個問題，我們基于微觀動力學過程的時間可逆對稱性，提出了一種稱為時間可逆路徑采樣（time-reversal path sampling，簡稱為tRPS）的方法，以實現分子模拟的動力學加速。
Abstract: In comparison to numerous enhanced sampling methods for equilibrium thermodynamics, accelerating simulations for kinetics and nonequilibrium statistics are relatively rare and less effective. Here we derive a time-reversal path sampling (tRPS) method based on the time reversibility to accelerate simulations for determining the transition rates between free-energy basins. It converts the difficult up-hill path sampling into an easy down-hill problem. The method is easy to implement, i.e., forward and backward shooting simulations with opposite initial velocities are conducted from random initial conformations within a transition-state region until they reach the basin minima, which are then assembled to give the distribution of transition paths efficiently. The effects of tRPS are demonstrated by comparison with direct simulations on protein folding and unfolding, where tRPS is shown to give results consistent with direct simulations and increase the efficiency by up to five orders of magnitude. The approach is generally applicable to stochastic processes with microscopic reversibility, no matter whether the variables are continuous or discrete.
