• Corpus ID: 246016542

Efficient Generation of Membrane and Solvent Tetrahedral Meshes for Ion Channel Finite Element Calculation

  title={Efficient Generation of Membrane and Solvent Tetrahedral Meshes for Ion Channel Finite Element Calculation},
  author={Zhen Chao and Sheng Gui and Benzhuo Lu and Dexuan Xie},
A finite element solution of an ion channel dielectric continuum model such as Poisson-Boltzmann equation (PBE) and a system of Poisson-Nernst-Planck equations (PNP) requires tetrahedral meshes for an ion channel protein region, a membrane region, and an ionic solvent region as well as an interface fitted irregular tetrahedral mesh of a simulation box domain. However, generating these meshes is very difficult and highly technical due to the related three regions having very complex geometrical… 


A software platform for continuum modeling of ion channels based on unstructured mesh
This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane.
Membrane-Channel Protein System Mesh Construction for Finite Element Simulations
This method of constructing the volume meshes of the membrane-channel protein system for finite element simulation of ion channels is presented, and is shown to be robust because of its independence of the pore structure of the ion channels.
An Efficient Finite Element Iterative Method for Solving a Nonuniform Size Modified Poisson-Boltzmann Ion Channel Model
Numerical results for a voltage-dependent anion channel (VDAC) in a mixture of four ionic species demonstrate a fast convergence rate of the damped two-block iterative method, the high performance of the software package, and the importance of considering nonuniform ion sizes.
An improved Poisson‐Nernst‐Planck ion channel model and numerical studies on effects of boundary conditions, membrane charges, and bulk concentrations
An improved Poisson-Nernst-Planck ion channel (PNPic) model is presented, along with its effective finite element solver and software package for an ion channel protein in a solution of multiple ionic species and results indicate that the cation selectivity property of gA occurs within a central portion of ion channel pore, insensitively to any change of boundary value condition, membrane charge, or bulk concentration.
TMSmesh: A Robust Method for Molecular Surface Mesh Generation Using a Trace Technique.
  • Minxin Chen, B. Lu
  • Computer Science
    Journal of chemical theory and computation
  • 2011
TMSmesh has a linear complexity with respect to the number of atoms and is shown to be capable of handling molecules consisting of more than one million atoms, which is usually difficult for the existing methods for surface generation used in molecular visualization and geometry analysis.
The Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation
This article apparently gives the first rigorous convergence result for a numerical discretization technique for the nonlinear Poisson-Boltzmann equation with delta distribution sources, and it introduces the first provably convergent adaptive method for the equation.
Efficient and Qualified Mesh Generation for Gaussian Molecular Surface Using Adaptive Partition and Piecewise Polynomial Approximation
New algorithms to greatly improve the meshing efficiency and qualities are presented, and implemented into a new program version, TMSmesh 2.0.
PNP equations with steric effects: a model of ion flow through channels.
Steric PNP combines atomic and macroscales in a computable formulation that allows the calculation of the macroscopic effects of changes in atomic scale structures studied very extensively in channology and molecular biology.