EFFICIENT GENERATION OF MEMBRANE AND SOLVENT TETRAHEDRAL MESHES FOR ION CHANNEL FINITE ELEMENT CALCULATION

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	EFFICIENT GENERATION OF MEMBRANE AND SOLVENT TETRAHEDRAL MESHES FOR ION CHANNEL FINITE ELEMENT CALCULATION
	Chao, Zhen ; Gui, Sheng ; Lu, Benzhuo ; Xie, Dexuan
	2022
发表期刊	INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING
ISSN	1705-5105
卷号	19 期号:6 页码:887-906
摘要	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.
关键词	Finite element method Poisson-Nernst-Planck equations ion channel membrane mesh generation tetrahedral mesh
收录类别	SCI
语种	英语
资助项目	Simons Foundation, USA[711776] ; National Natural Science Foundation of China[11771435] ; National Natural Science Foundation of China[22073110] ; 2021 AMS-Simons Travel Grant, USA
WOS研究方向	Mathematics
WOS类目	Mathematics, Applied ; Mathematics
WOS记录号	WOS:000850154200008
出版者	ISCI-INST SCIENTIFIC COMPUTING & INFORMATION
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/60990
专题	中国科学院数学与系统科学研究院
通讯作者	Xie, Dexuan
作者单位	1.Univ Michigan, Dept Math, Ann Arbor, MI 48109 USA 2.Chinese Acad Sci, Acad Math & Syst Sci, Inst Syst Sci, Key Lab Syst & Control,LSEC,NCMIS, Beijing 100190, Peoples R China 3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Chao, Zhen,Gui, Sheng,Lu, Benzhuo,et al. EFFICIENT GENERATION OF MEMBRANE AND SOLVENT TETRAHEDRAL MESHES FOR ION CHANNEL FINITE ELEMENT CALCULATION[J]. INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING,2022,19(6):887-906.
APA	Chao, Zhen,Gui, Sheng,Lu, Benzhuo,&Xie, Dexuan.(2022).EFFICIENT GENERATION OF MEMBRANE AND SOLVENT TETRAHEDRAL MESHES FOR ION CHANNEL FINITE ELEMENT CALCULATION.INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING,19(6),887-906.
MLA	Chao, Zhen,et al."EFFICIENT GENERATION OF MEMBRANE AND SOLVENT TETRAHEDRAL MESHES FOR ION CHANNEL FINITE ELEMENT CALCULATION".INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING 19.6(2022):887-906.