A flux-jump preserved gradient recovery technique for accurately predicting the electrostatic field of an immersed biomolecule

DOI10.1016/j.jcp.2019.06.049zbMath1452.78030OpenAlexW2955951027WikidataQ127566264 ScholiaQ127566264MaRDI QIDQ2222411

Benzhuo Lu, Jinyong Ying, Jiao Li

Publication date: 27 January 2021

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jcp.2019.06.049

zbMATH Keywords

electrostatic fieldflux preservinggradient recovery techniqueimplicit continuum modeltotal electrostatic force

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Biophysics (92C05) Motion of charged particles (78A35) Electro- and magnetostatics (78A30)

Related Items (5)

A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation ⋮ Unnamed Item ⋮ Diagonal quasi-Newton methods via least change updating principle with weighted Frobenius norm ⋮ Superconvergent gradient recovery for nonlinear Poisson-Nernst-Planck equations with applications to the ion channel problem ⋮ INN: interfaced neural networks as an accessible meshless approach for solving interface PDE problems

Uses Software

• FEniCS
• SyFi
• MIBPB
• AFMPB
• SDPBS
• DelPhi Web Server

Cites Work

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• Continuum electrostatics for ionic solutions with non-uniform ionic sizes
• Minimization of Electrostatic Free Energy and the Poisson–Boltzmann Equation for Molecular Solvation with Implicit Solvent
• The superconvergent patch recovery anda posteriori error estimates. Part 1: The recovery technique
• Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation
• Gradient Recovery for Elliptic Interface Problem: I. Body-Fitted Mesh
• A New Finite Element Gradient Recovery Method: Superconvergence Property
• The Mathematical Theory of Finite Element Methods
• AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

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