A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models

DOI10.1137/18M119553XzbMATH Open1414.65041arXiv1807.05384OpenAlexW2963536931MaRDI QIDQ4631997FDOQ4631997

Benjamin Stamm, Chaoyu Quan, Yvon Maday

Publication date: 25 April 2019

Published in: SIAM Journal on Scientific Computing (Search for Journal in Brave)

Abstract: In this paper, a domain decomposition method for the Poisson-Boltzmann (PB) solvation model that is widely used in computational chemistry is proposed. This method, called ddLPB for short, solves the linear Poisson-Boltzmann (LPB) equation defined in $mathbb{R}^3$ using the van der Waals cavity as the solute cavity. The Schwarz domain decomposition method is used to formulate local problems by decomposing the cavity into overlapping balls and only solving a set of coupled sub-equations in balls. A series of numerical experiments is presented to test the robustness and the efficiency of this method including the comparisons with some existing methods. We observe exponential convergence of the solvation energy with respect to the number of degrees of freedom which allows this method to reach the required level of accuracy when coupling with quantum mechanical descriptions of the solute.

Full work available at URL: https://arxiv.org/abs/1807.05384

zbMATH Keywords

domain decomposition methodPoisson-Boltzmann equationimplicit solvation modelspherical harmonic approximation

Mathematics Subject Classification ID

Multigrid methods; domain decomposition for boundary value problems involving PDEs (65N55) Boltzmann equations (35Q20) PDEs in connection with optics and electromagnetic theory (35Q60) Spectral, collocation and related methods for boundary value problems involving PDEs (65N35)

Cites Work

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Cited In (9)

• Title not available (Why is that?)
• A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
• Efficient calculation of fully resolved electrostatics around large biomolecules
• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
• A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
• Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format
• Title not available (Why is that?)
• A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
• Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery

Uses Software

• APBS
• MIBPB
• AFMPB
• PAFMPB
• SDPBS
• SMPBS
• tabipb
• DelPhi

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