A finite element iterative solver for a PNP ion channel model with Neumann boundary condition and membrane surface charge

DOI10.1016/J.JCP.2020.109915OpenAlexW3093414199MaRDI QIDQ2123871

Zhen Chao, Dexuan Xie

Publication date: 14 April 2022

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

Full work available at URL: https://doi.org/10.1016/j.jcp.2020.109915

zbMATH Keywords

finite element methodNeumann boundary conditionelectrostaticsPoisson-Nernst-Planck equationsion channelmembrane surface charge

Mathematics Subject Classification ID

Biology and other natural sciences (92-XX) Statistical mechanics, structure of matter (82-XX)

Related Items (4)

A Poisson-Nernst-Planck single ion channel model and its effective finite element solver ⋮ Unnamed Item ⋮ An efficient finite element solver for a nonuniform size-modified Poisson-Nernst-Planck ion channel model ⋮ An efficient finite element iterative method for solving a nonuniform size modified Poisson-Boltzmann ion channel model

Uses Software

• FEniCS
• PNPSIC

Cites Work

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• A local approximation of fundamental measure theory incorporated into three dimensional Poisson-Nernst-Planck equations to account for hard sphere repulsion among ions
• Stabilized finite element methods to simulate the conductances of ion channels
• New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
• Second-order Poisson-Nernst-Planck solver for ion transport
• Automated solution of differential equations by the finite element method. The FEniCS book
• Energetically stable discretizations for charge transport and electrokinetic models
• A linearized local conservative mixed finite element method for Poisson-Nernst-Planck equations
• Accurate evaluation of electrostatics for macromolecules in solution
• Preconditioners for nonsymmetric indefinite linear systems
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• Analysis of the Mean Field Free Energy Functional of Electrolyte Solution with Nonhomogenous Boundary Conditions and the Generalized PB/PNP Equations with Inhomogeneous Dielectric Permittivity
• Variational Multiscale Models for Charge Transport
• An Effective Finite Element Iterative Solver for a Poisson--Nernst--Planck Ion Channel Model with Periodic Boundary Conditions
• The Mathematical Theory of Finite Element Methods

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