A posteriori analysis and efficient refinement strategies for the Poisson-Boltzmann equation

DOI10.1137/17M1119846zbMATH Open1397.65236arXiv1702.05196OpenAlexW2595392941MaRDI QIDQ4582844FDOQ4582844

Authors: Jehanzeb Hameed Chaudhry 

Publication date: 24 August 2018

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

Abstract: The Poisson-Boltzmann equation (PBE) models the electrostatic interactions of charged bodies such as molecules and proteins in an electrolyte solvent. The PBE is a challenging equation to solve numerically due to the presence of singularities, discontinuous coefficients and boundary conditions. Hence, there is often large error in the numerical solution of the PBE that needs to be quantified. In this work, we use adjoint based a posteriori analysis to accurately quantify the error in an important quantity of interest, the solvation free energy, for the finite element solution of the PBE. We identify various sources of error and propose novel refinement strategies based on a posteriori error estimates.

Full work available at URL: https://arxiv.org/abs/1702.05196

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zbMATH Keywords

finite element methodadjoint operatormesh refinementa posteriori error estimationPoisson-Boltzmann equation

Mathematics Subject Classification ID

Boltzmann equations (35Q20) PDEs in connection with optics and electromagnetic theory (35Q60) Error bounds for boundary value problems involving PDEs (65N15) Finite element, Rayleigh-Ritz and Galerkin methods for boundary value problems involving PDEs (65N30) Mesh generation, refinement, and adaptive methods for boundary value problems involving PDEs (65N50) Computational methods for problems pertaining to biology (92-08)

Cites Work

• DOLFIN: automated finite element computing
• Automated solution of differential equations by the finite element method. The FEniCS book
• Adaptive numerical treatment of elliptic systems on manifolds
• A posteriori error estimation in finite element analysis
• Title not available (Why is that?)
• Title not available (Why is that?)
• An optimal control approach to a posteriori error estimation in finite element methods
• A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method
• A Convergent Adaptive Algorithm for Poisson’s Equation
• A Posteriori Error Bounds and Global Error Control for Approximation of Ordinary Differential Equations
• Title not available (Why is that?)
• Adjoint equations and perturbation algorithms in nonlinear problems
• Generalized Green's Functions and the Effective Domain of Influence
• A posteriori error estimation and adaptive mesh refinement for a multiscale operator decomposition approach to fluid-solid heat transfer
• The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
• Title not available (Why is that?)
• Title not available (Why is that?)
• Adjoint methods for PDEs: a posteriori error analysis and postprocessing by duality
• Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
• Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
• Estimating the error of numerical solutions of systems of reaction-diffusion equations
• A mortar finite element approximation for the linear Poisson-Boltzmann equation
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• A weighted adaptive least-squares finite element method for the Poisson-Boltzmann equation
• Error estimates for multiscale operator decomposition for multiphysics models
• Quantification of errors for operator-split advection-diffusion calculations
• A posteriori analysis and adaptive error control for multiscale operator decomposition solution of elliptic systems. I: Triangular systems
• Finite element approximation to a finite-size modified Poisson-Boltzmann equation
• A posteriori error analysis for finite element methods with projection operators as applied to explicit time integration techniques
• A posteriori error analysis of IMEX multi-step time integration methods for advection-diffusion-reaction equations
• A posteriori error analysis of two-stage computation methods with application to efficient discretization and the parareal algorithm
• A posteriori error estimates for the solution of variational inverse problems

Cited In (6)

• \textit{A posteriori} error estimation for the spectral deferred correction method
• Error estimation and uncertainty quantification for first time to a threshold value
• Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
• A reduced basis method for the nonlinear Poisson-Boltzmann equation
• Error estimation for the time to a threshold value in evolutionary partial differential equations
• A posteriori error analysis for Schwarz overlapping domain decomposition methods

Uses Software

• DOLFIN
• FEniCS
• APBS
• SG

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