Literature DB >> 24028101

Electrostatic forces in the Poisson-Boltzmann systems.

Li Xiao1, Qin Cai, Xiang Ye, Jun Wang, Ray Luo.   

Abstract

Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.

Mesh:

Year:  2013        PMID: 24028101      PMCID: PMC3779268          DOI: 10.1063/1.4819471

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


  34 in total

Review 1.  Generalized born models of macromolecular solvation effects.

Authors:  D Bashford; D A Case
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

2.  Accelerated Poisson-Boltzmann calculations for static and dynamic systems.

Authors:  Ray Luo; Laurent David; Michael K Gilson
Journal:  J Comput Chem       Date:  2002-10       Impact factor: 3.376

3.  pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model.

Authors:  D Bashford; M Karplus
Journal:  Biochemistry       Date:  1990-11-06       Impact factor: 3.162

4.  Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method.

Authors:  Benzhuo Lu; Deqiang Zhang; J Andrew McCammon
Journal:  J Chem Phys       Date:  2005-06-01       Impact factor: 3.488

5.  A first-order system least-squares finite element method for the Poisson-Boltzmann equation.

Authors:  Stephen D Bond; Jehanzeb Hameed Chaudhry; Eric C Cyr; Luke N Olson
Journal:  J Comput Chem       Date:  2010-06       Impact factor: 3.376

6.  Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: size effects on ionic distributions and diffusion-reaction rates.

Authors:  Benzhuo Lu; Y C Zhou
Journal:  Biophys J       Date:  2011-05-18       Impact factor: 4.033

7.  Computation of molecular electrostatics with boundary element methods.

Authors:  J Liang; S Subramaniam
Journal:  Biophys J       Date:  1997-10       Impact factor: 4.033

8.  Boundary element solution of macromolecular electrostatics: interaction energy between two proteins.

Authors:  H X Zhou
Journal:  Biophys J       Date:  1993-08       Impact factor: 4.033

9.  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

10.  Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations.

Authors:  Jun Wang; Qin Cai; Ye Xiang; Ray Luo
Journal:  J Chem Theory Comput       Date:  2012-06-18       Impact factor: 6.006

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  12 in total

1.  Numerical interpretation of molecular surface field in dielectric modeling of solvation.

Authors:  Changhao Wang; Li Xiao; Ray Luo
Journal:  J Comput Chem       Date:  2017-03-20       Impact factor: 3.376

2.  Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

Authors:  Changhao Wang; Jun Wang; Qin Cai; Zhilin Li; Hong-Kai Zhao; Ray Luo
Journal:  Comput Theor Chem       Date:  2013-11-15       Impact factor: 1.926

3.  A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.

Authors:  Li Xiao; Qin Cai; Zhilin Li; Hongkai Zhao; Ray Luo
Journal:  Chem Phys Lett       Date:  2014-11-25       Impact factor: 2.328

4.  Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

Authors:  Li Xiao; Ray Luo
Journal:  J Chem Phys       Date:  2017-12-07       Impact factor: 3.488

5.  Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.

Authors:  Ruxi Qi; Ray Luo
Journal:  J Chem Inf Model       Date:  2018-12-31       Impact factor: 4.956

6.  DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.

Authors:  Lin Li; Arghya Chakravorty; Emil Alexov
Journal:  J Comput Chem       Date:  2017-01-28       Impact factor: 3.376

7.  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

8.  A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins.

Authors:  Li Xiao; Jianxiong Diao; D'Artagnan Greene; Junmei Wang; Ray Luo
Journal:  J Chem Theory Comput       Date:  2017-06-14       Impact factor: 6.006

9.  Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.

Authors:  Changhao Wang; Pengyu Ren; Ray Luo
Journal:  J Phys Chem B       Date:  2017-12-01       Impact factor: 2.991

10.  Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions.

Authors:  Li Xiao; Changhao Wang; Xiang Ye; Ray Luo
Journal:  J Phys Chem B       Date:  2016-05-20       Impact factor: 2.991

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