Literature DB >> 26877556

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

B O Li1, Yuan Liu2.   

Abstract

A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.

Entities:  

Keywords:  Poisson–Boltzmann theory; diffused solute-solvent interface; matched asymptotic analysis; sharp-interface limit; variational implicit-solvent model

Year:  2015        PMID: 26877556      PMCID: PMC4752183          DOI: 10.1137/15M100701X

Source DB:  PubMed          Journal:  SIAM J Appl Math        ISSN: 0036-1399            Impact factor:   2.080


  26 in total

1.  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

2.  Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation.

Authors:  Yanxiang Zhao; Yuen-Yick Kwan; Jianwei Che; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2013-07-14       Impact factor: 3.488

3.  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

4.  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

5.  Computational model for cell morphodynamics.

Authors:  Danying Shao; Wouter-Jan Rappel; Herbert Levine
Journal:  Phys Rev Lett       Date:  2010-09-02       Impact factor: 9.161

6.  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

7.  Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies.

Authors:  Qin Cai; Xiang Ye; Jun Wang; Ray Luo
Journal:  Chem Phys Lett       Date:  2011-10       Impact factor: 2.328

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

Authors:  Hsiao-Bing Cheng; Li-Tien Cheng; Bo Li
Journal:  Nonlinearity       Date:  2011-11

9.  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

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

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  1 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

  1 in total

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