• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法,用中文像聊天一样搜索,搜遍4000万医学文献。AI智能推荐,让科研检索更轻松。

立即免费搜索

文件翻译

保留排版,准确专业,支持PDF/Word/PPT等文件格式,支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述,25分钟生成高质量综述,智能提取关键信息,辅助科研写作。

立即免费体验

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.

DOI:10.1021/acs.jpcb.2c08731
PMID:37149781
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。

相似文献

1
Perspective: Advances, Challenges, and Insight for Predictive Coarse-Grained Models.观点:预测粗粒度模型的进展、挑战和见解。
J Phys Chem B. 2023 May 18;127(19):4174-4207. doi: 10.1021/acs.jpcb.2c08731. Epub 2023 May 7.
2
Van der Waals Perspective on Coarse-Graining: Progress toward Solving Representability and Transferability Problems.范德华观点下的粗粒化:解决代表性和可转移性问题的进展。
Acc Chem Res. 2016 Dec 20;49(12):2832-2840. doi: 10.1021/acs.accounts.6b00498. Epub 2016 Dec 8.
3
Rigorous Progress in Coarse-Graining.粗粒化方面的严格进展。
Annu Rev Phys Chem. 2024 Jun;75(1):21-45. doi: 10.1146/annurev-physchem-062123-010821.
4
Perspective: Coarse-grained models for biomolecular systems.观点:生物分子系统的粗粒度模型。
J Chem Phys. 2013 Sep 7;139(9):090901. doi: 10.1063/1.4818908.
5
Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids.能够精确描述分子液体的结构、压力和压缩性的自下而上粗粒度模型。
J Chem Phys. 2015 Dec 28;143(24):243148. doi: 10.1063/1.4937383.
6
A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy.基于相对熵的温度传递粗粒化模型的微正则路径方法。
J Chem Phys. 2021 Sep 7;155(9):094102. doi: 10.1063/5.0057104.
7
Temperature and Phase Transferable Bottom-up Coarse-Grained Models.温度和相转移的自下而上的粗粒化模型。
J Chem Theory Comput. 2020 Nov 10;16(11):6823-6842. doi: 10.1021/acs.jctc.0c00832. Epub 2020 Oct 19.
8
Bottom-up coarse-grained models for external fields and interfaces.用于外场和界面的自下而上的粗粒度模型。
J Chem Phys. 2020 Dec 14;153(22):224103. doi: 10.1063/5.0030103.
9
Phase Equilibria Modeling with Systematically Coarse-Grained Models-A Comparative Study on State Point Transferability.相平衡建模与系统粗粒化模型——关于状态点可转移性的比较研究。
J Phys Chem B. 2019 Jan 17;123(2):504-515. doi: 10.1021/acs.jpcb.8b07320. Epub 2019 Jan 8.
10
Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids.分子液体的粗粒度模型的准确性、可转移性和效率。
J Phys Chem B. 2018 Nov 15;122(45):10257-10278. doi: 10.1021/acs.jpcb.8b06687. Epub 2018 Sep 22.

引用本文的文献

1
PROFET Predicts Continuous Gene Expression Dynamics from scRNA-seq Data to Elucidate Heterogeneity of Cancer Treatment Responses.PROFET从单细胞RNA测序数据预测连续基因表达动态,以阐明癌症治疗反应的异质性。
bioRxiv. 2025 Jul 3:2025.06.27.662030. doi: 10.1101/2025.06.27.662030.
2
Microtubules in Martini: Parameterizing a heterogeneous elastic-network towards a mechanically accurate microtubule.《马提尼中的微管:针对机械精确的微管对异质弹性网络进行参数化》
PNAS Nexus. 2025 Jun 21;4(7):pgaf202. doi: 10.1093/pnasnexus/pgaf202. eCollection 2025 Jul.
3
MSBack: Multiscale Backmapping of Highly Coarse-Grained Proteins Using Constrained Diffusion.
MSBack:使用约束扩散对高度粗粒度蛋白质进行多尺度反向映射
J Chem Theory Comput. 2025 Jun 24;21(12):6184-6193. doi: 10.1021/acs.jctc.5c00459. Epub 2025 Jun 1.
4
A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes.一种用于大型分子复合物精确粗粒化的自下而上与数据驱动相结合的机器学习方法。
J Chem Theory Comput. 2025 May 13;21(9):4846-4854. doi: 10.1021/acs.jctc.5c00063. Epub 2025 Apr 16.
5
CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions.CG 微笑式:一种适用于多分辨率分子表示的通用线性表示法。
J Chem Inf Model. 2025 Apr 14;65(7):3405-3419. doi: 10.1021/acs.jcim.5c00064. Epub 2025 Mar 24.
6
Understanding the coarse-grained free energy landscape of phospholipids and their phase separation.理解磷脂的粗粒度自由能景观及其相分离。
Biophys J. 2025 Feb 18;124(4):620-636. doi: 10.1016/j.bpj.2024.12.030. Epub 2024 Dec 31.
7
Force-Field Benchmark for Polydimethylsiloxane: Density, Heat Capacity, Isothermal Compressibility, Viscosity and Thermal Conductivity.聚二甲基硅氧烷的力场基准:密度、热容、等温压缩率、粘度和热导率
J Phys Chem B. 2025 Feb 13;129(6):1864-1873. doi: 10.1021/acs.jpcb.4c08471. Epub 2025 Feb 2.
8
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.脂质介导的活性药物成分递送建模的计算方法
Mol Pharm. 2025 Mar 3;22(3):1110-1141. doi: 10.1021/acs.molpharmaceut.4c00744. Epub 2025 Jan 29.
9
Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.使用多肽链的UNRES粗粒度模型实现时间平均约束
J Chem Theory Comput. 2025 Feb 11;21(3):1476-1493. doi: 10.1021/acs.jctc.4c01504. Epub 2025 Jan 24.
10
Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.使用图神经网络的粗粒度力场中的热力学可转移性。
J Chem Theory Comput. 2024 Dec 10;20(23):10524-10539. doi: 10.1021/acs.jctc.4c00788. Epub 2024 Nov 23.