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从自适应分辨率到开放系统的分子动力学

From adaptive resolution to molecular dynamics of open systems.

作者信息

Cortes-Huerto Robinson, Praprotnik Matej, Kremer Kurt, Delle Site Luigi

机构信息

Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.

Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.

出版信息

Eur Phys J B. 2021;94(9):189. doi: 10.1140/epjb/s10051-021-00193-w. Epub 2021 Sep 23.

DOI:10.1140/epjb/s10051-021-00193-w
PMID:34720711
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8547219/
Abstract

ABSTRACT

We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

摘要

摘要

我们在讨论自适应分辨率模拟方法(AdResS)基本原理并介绍其当前数值和理论进展的基础上,对该方法进行了概述。针对软物质、化学物理和凝聚态物理等相关系统的应用实例,说明了该方法在实际应用中的优点和局限性,从而明确了未来数值和理论进一步发展所面临的挑战。

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3
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