Literature DB >> 31319036

Understanding Missing Entropy in Coarse-Grained Systems: Addressing Issues of Representability and Transferability.

Jaehyeok Jin1, Alexander J Pak1, Gregory A Voth1.   

Abstract

Coarse-grained (CG) models facilitate efficient simulation of complex systems by integrating out the atomic, or fine-grained (FG), degrees of freedom. Systematically derived CG models from FG simulations often attempt to approximate the CG potential of mean force (PMF), an inherently multidimensional and many-body quantity, using additive pairwise contributions. However, they currently lack fundamental principles that enable their extensible use across different thermodynamic state points, i.e., transferability. In this work, we investigate the explicit energy-entropy decomposition of the CG PMF as a means to construct transferable CG models. In particular, despite its high-dimensional nature, we find for liquid systems that the entropic component to the CG PMF can similarly be represented using additive pairwise contributions, which we show is highly coupled to the CG configurational entropy. This approach formally connects the missing entropy that is lost due to the CG representation, i.e., translational, rotational, and vibrational modes associated with the missing degrees of freedom, to the CG entropy. By design, the present framework imparts transferable CG interactions across different temperatures due to the explicit definition of an additive entropic contribution. Furthermore, we demonstrate that transferability across composition state points, such as between bulk liquids and their mixtures, is also achieved by designing combining rules to approximate cross-interactions from bulk CG PMFs. Using the predicted CG model for liquid mixtures, structural correlations of the fitted CG model were found to corroborate a high-fidelity combining rule. Our findings elucidate the physical nature and compact representation of CG entropy and suggest a new approach for overcoming the transferability problem. We expect that this approach will further extend the current view of CG modeling into predictive multiscale modeling.

Entities:  

Year:  2019        PMID: 31319036      PMCID: PMC6782054          DOI: 10.1021/acs.jpclett.9b01228

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  51 in total

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Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

6.  On the representability problem and the physical meaning of coarse-grained models.

Authors:  Jacob W Wagner; James F Dama; Aleksander E P Durumeric; Gregory A Voth
Journal:  J Chem Phys       Date:  2016-07-28       Impact factor: 3.488

Review 7.  Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back.

Authors:  Florian Müller-Plathe
Journal:  Chemphyschem       Date:  2002-09-16       Impact factor: 3.102

8.  A multiscale coarse-graining method for biomolecular systems.

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Journal:  J Phys Chem B       Date:  2005-02-24       Impact factor: 2.991

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10.  Solvent Free Ionic Solution Models from Multiscale Coarse-Graining.

Authors:  Zhen Cao; James F Dama; Lanyuan Lu; Gregory A Voth
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Review 2.  Bottom-up Coarse-Graining: Principles and Perspectives.

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4.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

Authors:  Jaehyeok Jin; Alexander J Pak; Yining Han; Gregory A Voth
Journal:  J Chem Phys       Date:  2021-01-28       Impact factor: 3.488

5.  Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction.

Authors:  Sergiy Markutsya; Austin Haley; Mark S Gordon
Journal:  ACS Omega       Date:  2022-07-12

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Authors:  Marco Giulini; Roberto Menichetti; M Scott Shell; Raffaello Potestio
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  6 in total

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