Efficient Generation of Membrane and Solvent Tetrahedral Meshes for Ion Channel Finite Element Calculation
Year: 2022
Author: Zhen Chao, Sheng Gui, Benzhuo Lu, Dexuan Xie
International Journal of Numerical Analysis and Modeling, Vol. 19 (2022), Iss. 6 : pp. 887–906
Abstract
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 shapes. Currently, an ion channel mesh generation software package developed in Lu’s research group is the only one available in the public domain. To significantly improve its mesh quality and computer performance, in this paper, new numerical schemes for generating membrane and solvent meshes are presented and implemented in Python, resulting in a new ion channel mesh generation software package. Numerical results are then reported to demonstrate the efficiency of the new numerical schemes and the quality of meshes generated by the new package for ion channel proteins with ion channel pores having different geometric complexities.
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Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/2022-IJNAM-21038
International Journal of Numerical Analysis and Modeling, Vol. 19 (2022), Iss. 6 : pp. 887–906
Published online: 2022-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 20
Keywords: Finite element method Poisson-Nernst-Planck equations ion channel membrane mesh generation tetrahedral mesh.