A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference

DOI10.1016/j.apm.2017.09.026zbMath1480.65348arXiv1610.06173OpenAlexW2532493691MaRDI QIDQ2295320

Dexuan Xie, Jinyong Ying

Publication date: 12 February 2020

Published in: Applied Mathematical Modelling (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1610.06173

zbMATH Keywords

finite element methodfinite difference methoddomain decompositionPoisson-Boltzmann equationbinding free energyelectrostatic solvation free energy

Mathematics Subject Classification ID

Multigrid methods; domain decomposition for boundary value problems involving PDEs (65N55) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Finite difference methods for boundary value problems involving PDEs (65N06) Packaged methods for numerical algorithms (65Y15)

Related Items (8)

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ Unnamed Item ⋮ HRW: Hybrid Residual and Weak Form Loss for Solving Elliptic Interface Problems with Neural Network ⋮ A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule ⋮ On the analysis and application of an ion size-modified Poisson-Boltzmann equation ⋮ A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models ⋮ An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model ⋮ A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule

Uses Software

• PETSc
• DOLFIN
• FEniCS
• SyFi
• APBS
• MIBPB
• PDB2PQR
• Python
• PBEQ-Solver
• SDPBS
• DelPhi Web Server
• SMPBS

Cites Work

• Unnamed Item
• A new box iterative method for a class of nonlinear interface problems with application in solving Poisson-Boltzmann equation
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• Numerical methods for the Poisson-Fermi equation in electrolytes
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Finite element approximation to a finite-size modified Poisson-Boltzmann equation
• Automated solution of differential equations by the finite element method. The FEniCS book
• Accurate evaluation of electrostatics for macromolecules in solution
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• High order matched interface and boundary method for elliptic equations with discontinuous coefficients and singular sources
• DOLFIN
• Continuum electrostatics for ionic solutions with non-uniform ionic sizes
• Some Nonoverlapping Domain Decomposition Methods
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications

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