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观点:预测粗粒度模型的进展、挑战和见解。

Perspective: Advances, Challenges, and Insight for Predictive Coarse-Grained Models.

机构信息

Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

出版信息

J Phys Chem B. 2023 May 18;127(19):4174-4207. doi: 10.1021/acs.jpcb.2c08731. Epub 2023 May 7.

Abstract

By averaging over atomic details, coarse-grained (CG) models provide profound computational and conceptual advantages for studying soft materials. In particular, bottom-up approaches develop CG models based upon information obtained from atomically detailed models. At least in principle, a bottom-up model can reproduce all the properties of an atomically detailed model that are observable at the resolution of the CG model. Historically, bottom-up approaches have accurately modeled the structure of liquids, polymers, and other amorphous soft materials, but have provided lower structural fidelity for more complex biomolecular systems. Moreover, they have also been plagued by unpredictable transferability and a poor description of thermodynamic properties. Fortunately, recent studies have reported dramatic advances in addressing these prior limitations. This Perspective reviews this remarkable progress, while focusing on its foundation in the basic theory of coarse-graining. In particular, we describe recent insights and advances for treating the CG mapping, for modeling many-body interactions, for addressing the state-point dependence of effective potentials, and even for reproducing atomic observables that are beyond the resolution of the CG model. We also outline outstanding challenges and promising directions in the field. We anticipate that the synthesis of rigorous theory and modern computational tools will result in practical bottom-up methods that not only are accurate and transferable but also provide predictive insight for complex systems.

摘要

通过对原子细节进行平均处理,粗粒化 (CG) 模型为研究软物质提供了深远的计算和概念优势。特别是,自下而上的方法基于从原子细节模型中获得的信息来开发 CG 模型。至少从原则上讲,一个自下而上的模型可以再现 CG 模型分辨率下可观察到的原子细节模型的所有性质。从历史上看,自下而上的方法已经准确地模拟了液体、聚合物和其他无定形软物质的结构,但对于更复杂的生物分子系统,提供的结构保真度较低。此外,它们还受到不可预测的可转移性和热力学性质描述不佳的困扰。幸运的是,最近的研究报告称在解决这些先前的限制方面取得了显著进展。本观点回顾了这一显著进展,同时侧重于其在粗粒化基本理论中的基础。特别是,我们描述了最近在 CG 映射处理、多体相互作用建模、解决有效势能状态点依赖性以及甚至再现超出 CG 模型分辨率的原子可观测方面的见解和进展。我们还概述了该领域的突出挑战和有前途的方向。我们预计,严格理论和现代计算工具的综合将产生不仅准确且可转移,而且还能为复杂系统提供预测性见解的实用自下而上方法。

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