A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

DOI10.3934/jimo.2018155zbMath1438.65289OpenAlexW2889718018WikidataQ128978489 ScholiaQ128978489MaRDI QIDQ2338479

Jinyong Ying, Jiao Li

Publication date: 21 November 2019

Published in: Journal of Industrial and Management Optimization (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.3934/jimo.2018155

zbMATH Keywords

finite element methodbiomolecular electrostaticsnonlocal modelimplicit continuum modelblock iteration method

Mathematics Subject Classification ID

PDEs in connection with optics and electromagnetic theory (35Q60) Biological applications of optics and electromagnetic theory (78A70) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Biochemistry, molecular biology (92C40) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Computational methods for problems pertaining to biology (92-08) Electro- and magnetostatics (78A30) Boltzmann equations (35Q20)

Related Items (2)

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ Unnamed Item

Uses Software

• DOLFIN
• Python

Cites Work

• Unnamed Item
• A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation
• Numerical methods for the Poisson-Fermi equation in electrolytes
• A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for protein in ionic solvent
• A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules
• A new numerical method for nonlocal electrostatics in biomolecular simulations
• On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics
• On the analysis and application of an ion size-modified Poisson-Boltzmann equation
• A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
• A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• DOLFIN
• Accurate PKa Computation Using Matched Interface and Boundary (MIB) Method Based Poisson-Boltzmann Solver
• Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent

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