Literature DB >> 20886924

Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

J W Mullinax1, W G Noid.   

Abstract

Coarse-grained (CG) models provide a computationally efficient means for investigating phenomena that remain beyond the scope of atomically detailed models. Although CG models are often parametrized to reproduce the results of atomistic simulations, it is highly desirable to determine accurate CG models from experimental data. Recently, we have introduced a generalized Yvon-Born-Green (g-YBG) theory for directly (i.e., noniteratively) determining variationally optimized CG potentials from structural correlation functions. In principle, these correlation functions can be determined from experiment. In the present work, we introduce a reference state potential into the g-YBG framework. The reference state defines a fixed contribution to the CG potential. The remaining terms in the potential are then determined, such that the combined potential provides an optimal approximation to the many-body potential of mean force. By specifying a fixed contribution to the potential, the reference state significantly reduces the computational complexity and structural information necessary for determining the remaining potentials. We also validate the quantitative accuracy of the proposed method and numerically demonstrate that the reference state provides a convenient framework for transferring CG potentials from neat liquids to more complex systems. The resulting CG model provides a surprisingly accurate description of the two- and three-particle solvation structures of a hydrophobic solute in methanol. This work represents a significant step in developing the g-YBG theory as a useful computational framework for determining accurate CG models from limited experimental data.

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Year:  2010        PMID: 20886924      PMCID: PMC3188631          DOI: 10.1063/1.3481574

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


  52 in total

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3.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems.

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Journal:  J Chem Phys       Date:  2008-10-14       Impact factor: 3.488

4.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.

Authors:  W G Noid; Pu Liu; Yanting Wang; Jhih-Wei Chu; Gary S Ayton; Sergei Izvekov; Hans C Andersen; Gregory A Voth
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

5.  Multiscale modeling of emergent materials: biological and soft matter.

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6.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures.

Authors:  Vinod Krishna; Will G Noid; Gregory A Voth
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

7.  Statistical potentials extracted from protein structures: how accurate are they?

Authors:  P D Thomas; K A Dill
Journal:  J Mol Biol       Date:  1996-03-29       Impact factor: 5.469

8.  Note on the free energy of transfer of fullerene C60 simulated by using classical potentials.

Authors:  Cleiton Maciel; Eudes E Fileti; Roberto Rivelino
Journal:  J Phys Chem B       Date:  2009-05-21       Impact factor: 2.991

9.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Gregory A Voth
Journal:  J Phys Chem B       Date:  2007-03-30       Impact factor: 2.991

10.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Vinod Krishna; Sergei Izvekov; Gregory A Voth; Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

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  3 in total

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Review 2.  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

3.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

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

  3 in total

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