On the analysis and application of an ion size-modified Poisson-Boltzmann equation

被引：48
|
作者：
Li, Jiao [1 ]
Ying, Jinyong [2 ]
Xie, Dexuan [3 ]
机构：
[1] Changsha Univ Sci & Technol, Sch Math & Stat, Hunan Prov Key Lab Math Modeling & Anal Engn, Changsha 410114, Hunan, Peoples R China
[2] Cent S Univ, Sch Math & Stat, Changsha 410083, Hunan, Peoples R China
[3] Univ Wisconsin, Dept Math Sci, Milwaukee, WI 53211 USA
来源：
NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS | 2019年 / 47卷
基金：
中国国家自然科学基金; 美国国家科学基金会;
关键词：
Size-modified Poisson-Boltzmann equation; Electrostatic free energy; PDE-constrained variational methods; Electric double layer; FINITE-ELEMENT; BIOMOLECULAR ELECTROSTATICS; DECOMPOSITION; MINIMIZATION; PROTEIN; ATMOSPHERE;
D O I：
10.1016/j.nonrwa.2018.10.011
中图分类号：
O29 [应用数学];
学科分类号：
070104 ;
摘要：
In this paper, an improved electrostatic free energy functional is presented as an extension of the one proposed in Xie and Li (2015) to reflect ion size effects. It is then shown to have a unique minimizer, resulting in the solution existence and uniqueness of one commonly-used ion size-modified Poisson-Boltzmann equation (SMPBE). As for applications, SMPBE is used to calculate the electrostatic solvation free energy with the new derived well-defined formula and simulate an electric double layer numerically to demonstrate the advantage of SMPBE over the classic Poisson-Boltzmann equation in the prediction of ionic concentrations. (C) 2018 Elsevier Ltd. All rights reserved.
引用
收藏
页码：188 / 203
页数：16
相关论文
共 50 条
  • [1] Sensitivities to parameterization in the size-modified Poisson-Boltzmann equation
    Harris, Robert C.
    Boschitsch, Alexander H.
    Fenley, Marcia O.
    JOURNAL OF CHEMICAL PHYSICS, 2014, 140 (07):
  • [2] Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers
    Wang, Nuo
    Zhou, Shenggao
    Kekenes-Huskey, Peter M.
    Li, Bo
    McCammon, J. Andrew
    JOURNAL OF PHYSICAL CHEMISTRY B, 2014, 118 (51): : 14827 - 14832
  • [3] Comparing the Predictions of the Nonlinear Poisson-Boltzmann Equation and the Ion Size-Modified Poisson-Boltzmann Equation for a Low-Dielectric Charged Spherical Cavity in an Aqueous Salt Solution
    Silalahi, Alexander R. J.
    Boschitsch, Alexander H.
    Harris, Robert C.
    Fenley, Marcia O.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (12) : 3631 - 3639
  • [4] Formulation of a new and simple nonuniform size-modified poisson-boltzmann description
    Boschitsch, Alexander H.
    Danilov, Pavel V.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2012, 33 (11) : 1152 - 1164
  • [5] A size-modified poisson-boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel
    Xie, Dexuan
    Audi, Said H.
    Dash, Ranjan K.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2020, 41 (03) : 218 - 230
  • [6] Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT
    Ringe, Stefan
    Oberhofer, Harald
    Hille, Christoph
    Matera, Sebastian
    Reuter, Karsten
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2016, 12 (08) : 4052 - 4066
  • [7] NEW FINITE ELEMENT ITERATIVE METHODS FOR SOLVING A NONUNIFORM IONIC SIZE MODIFIED POISSON-BOLTZMANN EQUATION
    Xie, Dexuan
    INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING, 2017, 14 (4-5) : 688 - 711
  • [8] VDAC Solvation Free Energy Calculation by a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model
    Jemison, Liam
    Stahl, Matthew
    Dash, Ranjan K.
    Xie, Dexuan
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2025, 46 (01)
  • [9] Finite Element Approximation to a Finite-Size Modified Poisson-Boltzmann Equation
    Chaudhry, Jehanzeb Hameed
    Bond, Stephen D.
    Olson, Luke N.
    JOURNAL OF SCIENTIFIC COMPUTING, 2011, 47 (03) : 347 - 364
  • [10] SMPBS: Web Server for Computing Biomolecular Electrostatics Using Finite Element Solvers of Size Modified Poisson-Boltzmann Equation
    Xie, Yang
    Ying, Jinyong
    Xie, Dexuan
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2017, 38 (08) : 541 - 552
12345