Literature DB >> 23853423

Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force.

Hsiao-Bing Cheng1, Li-Tien Cheng, Bo Li.   

Abstract

A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends non-trivially that of the Coulomb-field approximation which serves as a basis of the widely used generalized Born model of molecular electrostatics. The electrostatic free energy determines the dielectric boundary force that in turn influences crucially the molecular conformation, stability, and dynamics. An explicit formula of such forces with the Yukawa-field approximation is obtained using local coordinates and shape differentiation.

Entities:  

Keywords:  Molecular solvation; Yukawa-field approximation; electrostatic free energy; shape derivative

Year:  2011        PMID: 23853423      PMCID: PMC3709021          DOI: 10.1088/0951-7715/24/11/011

Source DB:  PubMed          Journal:  Nonlinearity        ISSN: 0951-7715


  23 in total

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Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

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Review 3.  Improving implicit solvent simulations: a Poisson-centric view.

Authors:  Nathan A Baker
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

4.  Application of the level-set method to the implicit solvation of nonpolar molecules.

Authors:  Li-Tien Cheng; Joachim Dzubiella; J Andrew McCammon; Bo Li
Journal:  J Chem Phys       Date:  2007-08-28       Impact factor: 3.488

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Journal:  Annu Rev Biophys Biophys Chem       Date:  1990

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7.  Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach.

Authors:  Shenggao Zhou; Zhongming Wang; Bo Li
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-08-01

8.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect.

Authors:  T J Richmond
Journal:  J Mol Biol       Date:  1984-09-05       Impact factor: 5.469

9.  Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules.

Authors:  Li-Tien Cheng; Yang Xie; Joachim Dzubiella; J Andrew McCammon; Jianwei Che; Bo Li
Journal:  J Chem Theory Comput       Date:  2009-02-10       Impact factor: 6.006

10.  Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.

Authors:  Li-Tien Cheng; Zhongming Wang; Piotr Setny; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2009-10-14       Impact factor: 3.488

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  10 in total

1.  A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Authors:  Hui Sun; Jiayi Wen; Yanxiang Zhao; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

2.  Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.

Authors:  Bo Li; Yanxiang Zhao
Journal:  SIAM J Appl Math       Date:  2013       Impact factor: 2.080

3.  Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach.

Authors:  Bo Li; Xiaoliang Cheng; Zhengfang Zhang
Journal:  SIAM J Appl Math       Date:  2011       Impact factor: 2.080

4.  DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT.

Authors:  B O Li; Yuan Liu
Journal:  SIAM J Appl Math       Date:  2015-09-15       Impact factor: 2.080

5.  Motion of a Cylindrical Dielectric Boundary.

Authors:  Li-Tien Cheng; Bo Li; Michael White; Shenggao Zhou
Journal:  SIAM J Appl Math       Date:  2013       Impact factor: 2.080

6.  LS-VISM: A software package for analysis of biomolecular solvation.

Authors:  Shenggao Zhou; Li-Tien Cheng; Hui Sun; Jianwei Che; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Comput Chem       Date:  2015-03-12       Impact factor: 3.376

7.  Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation.

Authors:  Zhongming Wang; Jianwei Che; Li-Tien Cheng; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2011-12-19       Impact factor: 6.006

8.  Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation.

Authors:  Zuojun Guo; Bo Li; Joachim Dzubiella; Li-Tien Cheng; J Andrew McCammon; Jianwei Che
Journal:  J Chem Theory Comput       Date:  2013-01-29       Impact factor: 6.006

9.  Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|

Authors:  Shenggao Zhou; Kathleen E Rogers; César Augusto F de Oliveira; Riccardo Baron; Li-Tien Cheng; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Chem Theory Comput       Date:  2013-08-01       Impact factor: 6.006

10.  Heterogeneous Hydration of p53/MDM2 Complex.

Authors:  Zuojun Guo; Bo Li; Joachim Dzubiella; Li-Tien Cheng; J Andrew McCammon; Jianwei Che
Journal:  J Chem Theory Comput       Date:  2014-01-31       Impact factor: 6.006

  10 in total

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