A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications

DOI10.2478/mlbmb-2014-0006zbMath1347.92006OpenAlexW2093640145MaRDI QIDQ5890948

Jinyong Ying, Yi Jiang, Dexuan Xie

Publication date: 12 October 2016

Published in: Molecular Based Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.2478/mlbmb-2014-0006

zbMATH Keywords

finite element methodfinite difference methodPoisson-Boltzmann equationelectrostatic potentialcontinuum electrostatics

Mathematics Subject Classification ID

Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Biochemistry, molecular biology (92C40) Biophysics (92C05) Finite difference methods for boundary value problems involving PDEs (65N06)

Related Items (5)

A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation ⋮ A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule ⋮ SDPBS web server for calculation of electrostatics of ionic solvated biomolecules ⋮ On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics ⋮ A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference

Uses Software

• DOLFIN
• APBS
• PBEQ-Solver

Cites Work

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• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Automated solution of differential equations by the finite element method. The FEniCS book
• Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
• A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation
• On the approximation of singular source terms in differential equations
• Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation
• Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
• The Mathematical Theory of Finite Element Methods

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