A stabilized finite element method for the Poisson-Nernst-Planck equations in three-dimensional ion channel simulations

DOI10.1016/J.AML.2020.106652MaRDI QIDQ2006347zbMATH OpenOpenAlexFDO

Authors Qin Wang, Hongliang Li, Linbo Zhang, Benzhuo Lu

Publication date 8 October 2020

Published in Applied Mathematics Letters (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.aml.2020.106652

zbMATH Keywords

stabilized finite element methodPoisson-Nernst-PlanckSUPGinterior penalty

Mathematics Subject Classification ID

Finite difference methods applied to problems in optics and electromagnetic theory (78M20) PDEs in connection with optics and electromagnetic theory (35Q60) Finite difference methods for initial value and initial-boundary value problems involving PDEs (65M06) Finite element, Rayleigh-Ritz and Galerkin methods for initial value and initial-boundary value problems involving PDEs (65M60) Finite element, Galerkin and related methods applied to problems in optics and electromagnetic theory (78M10) Electrochemistry (78A57)

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Cites work

• A finite volume scheme for Nernst-Planck-Poisson systems with ion size and solvation effects
• A parallel algorithm for adaptive local refinement of tetrahedral meshes using bisection
• Edge stabilization for Galerkin approximations of convection-diffusion-reaction problems
• Efficient and qualified mesh generation for Gaussian molecular surface using adaptive partition and piecewise polynomial approximation
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• Stabilized finite element methods to simulate the conductances of ion channels
• Streamline upwind/Petrov-Galerkin formulations for convection dominated flows with particular emphasis on the incompressible Navier-Stokes equations
• Theory of the flow of electrons and holes in Germanium and other semiconductors

Cited in

(21)

• Adaptive and iterative methods for simulations of nanopores with the PNP-Stokes equations
• Positivity preserving finite difference methods for Poisson-Nernst-Planck equations with steric interactions: application to slit-shaped nanopore conductance
• A new block preconditioner and improved finite element solver of Poisson-Nernst-Planck equation
• A class of finite element methods with averaging techniques for solving the three-dimensional drift-diffusion model in semiconductor device simulations
• Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes. I: Finite element solutions
• A positivity-preserving and free energy dissipative hybrid scheme for the Poisson-Nernst-Planck equations on polygonal and polyhedral meshes
• A structure-preserving finite element discretization for the time-dependent Nernst-Planck equation
• Finite element model of charge transport across ionic channels
• A stabilized finite element method for modified Poisson-Nernst-Planck equations to determine ion flow through a nanopore
• An Effective Finite Element Iterative Solver for a Poisson--Nernst--Planck Ion Channel Model with Periodic Boundary Conditions
• Efficient generation of membrane and solvent tetrahedral meshes for ion channel finite element calculation
• Convergence and superconvergence analysis for a mass conservative, energy stable and linearized BDF2 scheme of the Poisson-Nernst-Planck equations
• A flux-based moving mesh method applied to solving the Poisson-Nernst-Planck equations
• Superconvergent gradient recovery for nonlinear Poisson-Nernst-Planck equations with applications to the ion channel problem
• Second-order Poisson-Nernst-Planck solver for ion transport
• Stabilized finite element methods to simulate the conductances of ion channels
• A Poisson-Nernst-Planck single ion channel model and its effective finite element solver
• An inverse averaging finite element method for solving the size-modified Poisson-Nernst-Planck equations in ion channel simulations
• Error estimates for the finite element method of the Navier-Stokes-Poisson-Nernst-Planck equations
• A stabilized finite element method for the numerical simulation of multi-ion transport in electrochemical systems
• Positive and Conservative Characteristic Block-Centered Finite Difference Methods for Convection Dominated Diffusion Equations

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