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Review Article

Enhanced sampling in molecular dynamics simulations and their latest applications—A review

Wenhui Shen1,2,§Tong Zhou1,2,§Xinghua Shi1,2( )
Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
University of Chinese Academy of Sciences, Beijing 100049, China

§ Wenhui Shen and Tong Zhou contributed equally to this work.

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Abstract

Molecular dynamics (MD) simulations are capable of reproducing dynamic evolution at the molecular scale, but are limited by temporal scales. Enhanced sampling has emerged as a powerful tool to improve sampling efficiency, thereby extending the simulation timescales of a range of simulation studies in materials, chemistry, biology, nanoscience, and related fields. Here, we provide a systematic overview of established enhanced sampling methods and clarify the principles and interconnections between these methods. Furthermore, we categorically elaborate on the state-of-the-art applications of enhanced sampling in the last five years. Through these exemplified applications, we discuss the unique advantages of this technique, showing the prospects and challenges for its future development. This review could help researchers in different fields gain a comprehensive understanding of the enhanced sampling technique, and jointly facilitate its application and advancement.

Graphical Abstract

Enhanced sampling technology enables molecular dynamics simulations to surpass time scale limitations, offering atomic-level information on thermodynamics and kinetics. Its applications span various research areas, including, but not limited to, ligand binding, protein folding, and phase transitions.

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Nano Research
Pages 13474-13497

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Cite this article:
Shen W, Zhou T, Shi X. Enhanced sampling in molecular dynamics simulations and their latest applications—A review. Nano Research, 2023, 16(12): 13474-13497. https://doi.org/10.1007/s12274-023-6311-9
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Received: 27 September 2023
Revised: 01 November 2023
Accepted: 02 November 2023
Published: 02 December 2023
© Tsinghua University Press 2023