委员会指导下的分子转变速率估算

IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL Journal of Chemical Theory and Computation Pub Date : 2024-10-17 DOI:10.1021/acs.jctc.4c00997
Andrew R. Mitchell, Grant M. Rotskoff
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引用次数: 0

摘要

一个物理系统的构型发生反应或从一种态过渡到另一种态的概率,可以用委顿函数来量化。该函数包含有关过渡路径的丰富而详细的机理信息,但要对委顿函数进行全面参数化,需要构建一个高维函数,这在一般情况下是一项极具挑战性的任务。最近,利用神经网络作为解决高维偏微分方程的一种手段(通常称为 "物理信息 "机器学习)的努力,将委顿器纳入了计算范围。在此,我们以半群方法为基础来学习委顿器,并评估其在预测过渡率等动态量方面的实用性。我们的研究表明,对目标函数的仔细重构和改进的自适应采样策略可以提供高度精确的连带器表征。此外,通过直接应用希尔关系,我们还证明了这些委顿器能为分子系统提供精确的过渡率。
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Committor Guided Estimates of Molecular Transition Rates
The probability that a configuration of a physical system reacts, or transitions from one metastable state to another, is quantified by the committor function. This function contains richly detailed mechanistic information about transition pathways, but a full parametrization of the committor requires the construction of a high-dimensional function, a generically challenging task. Recent efforts to leverage neural networks as a means to solve high-dimensional partial differential equations, often called “physics-informed” machine learning, have brought the committor into computational reach. Here, we build on the semigroup approach to learning the committor and assess its utility for predicting dynamical quantities such as transition rates. We show that a careful reframing of the objective function and improved adaptive sampling strategies provide highly accurate representations of the committor. Furthermore, by directly applying the Hill relation, we show that these committors provide accurate transition rates for molecular systems.
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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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