论文标题
结晶模拟的集体变量 - 从早期发展到最近的进步
Collective Variables for Crystallization Simulations -- from Early Developments to Recent Advances
论文作者
论文摘要
结晶是在材料科学,生物学和环境中具有相关性的最重要的物理化学过程之一。已经做出了数十年的实验和理论努力,以理解这种基本的对称性过渡。尽管实验提供了平衡结构和晶体的形状,但它们仅限于揭示分子聚集的方式以形成晶体核,随后转化为散装晶体。计算机模拟(主要是分子动力学)可以在结晶事件的早期阶段提供此类微观细节。结晶是一个罕见的事件,发生在时间尺度上比典型的平衡MD模拟可以采样的时间要长得多。通过使用增强的采样(ES)仿真,可以轻松规避这种MD方法的采样不足。 ES方法通过应用偏差潜力来增强系统缓慢自由度的波动,称为集体变量(CVS),从而在短时间内将系统从一个状态转变为另一个状态。 ES方法中最关键的部分是找到通常需要直觉和多个反复试验步骤的合适的简历。多年来,已经开发并应用了大量的CVS在结晶研究中。在这篇综述中,我们简要概述了已在ES模拟中开发和使用的CVS,以研究熔体或溶液的结晶。这些CV可以主要分为四种类型:(i)基于球形粒子,(ii)基于分子模板,(iii)基于物理属性的基于物理属性,以及(iv)从维度降低技术获得的CVS。我们介绍了基于上下文的简历演变,讨论当前的挑战,并提出了未来的方向,以进一步开发有效的CVS来研究复杂系统的结晶。
Crystallization is one of the most important physicochemical processes which has relevance in material science, biology, and the environment. Decades of experimental and theoretical efforts have been made to understand this fundamental symmetry-breaking transition. While experiments provide equilibrium structures and shapes of crystals, they are limited to unraveling how molecules aggregate to form crystal nuclei that subsequently transform into bulk crystals. Computer simulations, mainly molecular dynamics (MD), can provide such microscopic details during the early stage of a crystallization event. Crystallization is a rare event that takes place in timescales much longer than a typical equilibrium MD simulation can sample. This inadequate sampling of the MD method can be easily circumvented by the use of enhanced sampling (ES) simulations. An ES method enhances the fluctuations of a system's slow degrees of freedom, called collective variables (CVs), by applying a bias potential, and thereby transforms the system from one state to the other within a short timescale. The most crucial part of an ES method is to find suitable CVs which often needs intuition and several trial-and-error optimization steps. Over the years, a plethora of CVs has been developed and applied in the study of crystallization. In this review, we provide a brief overview of CVs that have been developed and used in ES simulations to study crystallization from melt or solution. These CVs can be categorized mainly into four types: (i) spherical particle-based, (ii) molecular template-based, (iii) physical property-based, and (iv) CVs obtained from dimensionality reduction techniques. We present the context-based evolution of CVs, discuss the current challenges, and propose future directions to further develop effective CVs for the study of crystallization of complex systems.