你试过关机再开机吗?增强抽样的随机重置

IF 16.8 2区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Ofir Blumer, Barak Hirshberg
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引用次数: 0

摘要

分子动力学模拟广泛应用于化学、物理和生物学,提供了对原子细节复杂过程的定量洞察。然而,它们有限的几微秒时间尺度是描述生物分子构象转变和分子晶体多态性等现象的重大障碍。近年来,随机重置(即随机停止和重新启动模拟)作为一种强大的增强采样方法出现,该方法具有集体无变量、高度并行化和易于在现有分子动力学代码中实现的特点。重置加速了对罕见事件的采样,同时使对潜在过程的动态可观测值的推断成为可能。它可以作为一个独立的工具使用,也可以与其他增强的采样方法(如metaddynamics)结合使用,每种技术都可以弥补另一种技术的缺点。在这里,我们全面描述重置及其理论背景,回顾随机重置增强采样的最新进展,并为从业者提供指导性指导。本文分类如下:
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Have You Tried Turning It Off and On Again? Stochastic Resetting for Enhanced Sampling

Have You Tried Turning It Off and On Again? Stochastic Resetting for Enhanced Sampling

Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant obstacle in describing phenomena such as conformational transitions of biomolecules and polymorphism in molecular crystals. Recently, stochastic resetting, that is, randomly stopping and restarting the simulations, emerged as a powerful enhanced sampling approach, which is collective variable-free, highly parallelized, and easily implemented in existing molecular dynamics codes. Resetting expedites sampling rare events while enabling the inference of kinetic observables of the underlying process. It can be employed as a standalone tool or in combination with other enhanced sampling methods, such as Metadynamics, with each technique compensating for the drawbacks of the other. Here, we comprehensively describe resetting and its theoretical background, review recent developments in stochastic resetting for enhanced sampling, and provide instructive guidelines for practitioners.

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来源期刊
Wiley Interdisciplinary Reviews: Computational Molecular Science
Wiley Interdisciplinary Reviews: Computational Molecular Science CHEMISTRY, MULTIDISCIPLINARY-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
28.90
自引率
1.80%
发文量
52
审稿时长
6-12 weeks
期刊介绍: Computational molecular sciences harness the power of rigorous chemical and physical theories, employing computer-based modeling, specialized hardware, software development, algorithm design, and database management to explore and illuminate every facet of molecular sciences. These interdisciplinary approaches form a bridge between chemistry, biology, and materials sciences, establishing connections with adjacent application-driven fields in both chemistry and biology. WIREs Computational Molecular Science stands as a platform to comprehensively review and spotlight research from these dynamic and interconnected fields.
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