Literature DB >> 22938246

Systematic coarse-graining of potential energy landscapes and dynamics in liquids.

M Scott Shell1.   

Abstract

Recent efforts have shown that the dynamic properties of a wide class of liquids can be mapped onto semi-universal scaling laws and constitutive relations that are motivated by thermodynamic analyses of much simpler models. In particular, it has been found that many systems exhibit dynamics whose behavior in state space closely follows that of soft-sphere particles interacting through an inverse power repulsion. In the present work, we show that a recently developed coarse-graining theory provides a natural way to understand how arbitrary liquids can be mapped onto effective soft-sphere models and hence how one might potentially be able to extract underlying dynamical scaling laws. The theory is based on the relative entropy, an information metric that quantifies how well a soft-sphere approximation to a liquid's multidimensional potential energy landscape performs. We show that optimization of the relative entropy not only enables one to extract effective soft-sphere potentials that suggest an inherent scaling of thermodynamic and dynamic properties in temperature-density space, but that also has rather interesting connections to excess entropy based theories of liquid dynamics. We apply the approach to a binary mixture of Lennard-Jones particles, and show that it gives effective soft-sphere scaling laws that well-describe the behavior of the diffusion constants. Our results suggest that the relative entropy formalism may be useful for "perturbative" type theories of dynamics, offering a general strategy for systematically connecting complex energy landscapes to simpler reference ones with better understood dynamic behavior.

Entities:  

Year:  2012        PMID: 22938246     DOI: 10.1063/1.4746391

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

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Authors:  Christopher M Baker; Robert B Best
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2.  Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation.

Authors:  Cesar Calero-Rubio; Bradford Paik; Xinqiao Jia; Kristi L Kiick; Christopher J Roberts
Journal:  Biophys Chem       Date:  2016-07-22       Impact factor: 2.352

3.  Communication: Adaptive boundaries in multiscale simulations.

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Review 4.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

5.  Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.

Authors:  Patrick Diggins; Changjiang Liu; Markus Deserno; Raffaello Potestio
Journal:  J Chem Theory Comput       Date:  2018-12-14       Impact factor: 6.006

6.  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

7.  An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.

Authors:  Marco Giulini; Roberto Menichetti; M Scott Shell; Raffaello Potestio
Journal:  J Chem Theory Comput       Date:  2020-10-27       Impact factor: 6.006

8.  A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.

Authors:  Roberto Menichetti; Marco Giulini; Raffaello Potestio
Journal:  Eur Phys J B       Date:  2021-10-12       Impact factor: 1.500

  8 in total

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