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

DOI10.1016/J.APM.2017.09.026zbMATH Open1480.65348arXiv1610.06173OpenAlexW2532493691MaRDI QIDQ2295320FDOQ2295320

Authors: Jinyong Ying, Dexuan Xie 

Publication date: 12 February 2020

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

Abstract: The size-modified Poisson-Boltzmann equation (SMPBE) is one important variant of the popular dielectric model, the Poisson-Boltzmann equation (PBE), to reflect ionic size effects in the prediction of electrostatics for a biomolecule in an ionic solvent. In this paper, a new SMPBE hybrid solver is developed using a solution decomposition, the Schwartz's overlapped domain decomposition, finite element, and finite difference. It is then programmed as a software package in C, Fortran, and Python based on the state-of-the-art finite element library DOLFIN from the FEniCS project. This software package is well validated on a Born ball model with analytical solution and a dipole model with a known physical properties. Numerical results on six proteins with different net charges demonstrate its high performance. Finally, this new SMPBE hybrid solver is shown to be numerically stable and convergent in the calculation of electrostatic solvation free energy for 216 biomolecules and binding free energy for a DNA-drug complex.

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

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zbMATH Keywords

domain decompositionfinite difference methodfinite element methodPoisson-Boltzmann equationbinding free energyelectrostatic solvation free energy

Mathematics Subject Classification ID

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

Cites Work

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

Cited In (13)

• New finite element iterative methods for solving a nonuniform ionic size modified Poisson-Boltzmann equation
• HRW: Hybrid Residual and Weak Form Loss for Solving Elliptic Interface Problems with Neural Network
• A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation
• Finite volume element method for predicting electrostatics of a biomolecule immersed in an ionic solvent
• A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule
• A simple and efficient technique to accelerate the computation of a nonlocal dielectric model for electrostatics of biomolecule
• SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
• On the analysis and application of an ion size-modified Poisson-Boltzmann equation
• A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
• A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
• An effective minimization protocol for solving a size-modified Poisson-Boltzmann equation for biomolecule in ionic solvent
• An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model
• A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach

Uses Software

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

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