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利用机器学习的增强采样

Enhanced Sampling with Machine Learning.

作者信息

Mehdi Shams, Smith Zachary, Herron Lukas, Zou Ziyue, Tiwary Pratyush

机构信息

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA; email:

Biophysics Program, University of Maryland, College Park, Maryland, USA.

出版信息

Annu Rev Phys Chem. 2024 Jun;75(1):347-370. doi: 10.1146/annurev-physchem-083122-125941. Epub 2024 Jun 14.

Abstract

Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe timescale limitations. To address this, enhanced sampling methods have been developed to improve the exploration of configurational space. However, implementing these methods is challenging and requires domain expertise. In recent years, integration of machine learning (ML) techniques into different domains has shown promise, prompting their adoption in enhanced sampling as well. Although ML is often employed in various fields primarily due to its data-driven nature, its integration with enhanced sampling is more natural with many common underlying synergies. This review explores the merging of ML and enhanced MD by presenting different shared viewpoints. It offers a comprehensive overview of this rapidly evolving field, which can be difficult to stay updated on. We highlight successful strategies such as dimensionality reduction, reinforcement learning, and flow-based methods. Finally, we discuss open problems at the exciting ML-enhanced MD interface.

摘要

分子动力学(MD)能够以出色的时空分辨率研究物理系统,但存在严重的时间尺度限制。为了解决这个问题,人们开发了增强采样方法来改善对构型空间的探索。然而,实施这些方法具有挑战性,需要领域专业知识。近年来,将机器学习(ML)技术集成到不同领域已显示出前景,这也促使其在增强采样中得到应用。尽管ML在各个领域的广泛应用主要是由于其数据驱动的特性,但它与增强采样的集成因许多共同的潜在协同作用而更加自然。本综述通过呈现不同的共同观点来探讨ML与增强MD的融合。它全面概述了这个快速发展的领域,该领域可能难以跟上最新进展。我们重点介绍了诸如降维、强化学习和基于流的方法等成功策略。最后,我们讨论了在令人兴奋的ML增强MD界面上的开放问题。

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