Model reduction-based initialization methods for solving the Poisson-Nernst-Plank equations in three-dimensional ion channel simulations

doi:10.1016/j.jcp.2020.109627

CSpace

	Model reduction-based initialization methods for solving the Poisson-Nernst-Plank equations in three-dimensional ion channel simulations
	Zhang, Qianru 1,2; Gui, Sheng 1,2; Li, Hongliang 3,4; Lu, Benzhuo 1,2
	2020-10-15
发表期刊	JOURNAL OF COMPUTATIONAL PHYSICS
ISSN	0021-9991
卷号	419 页码:18
摘要	The Poisson-Nernst-Planck (PNP) model is frequently-used in simulating ion transport through ion channel systems. Due to the nonlinearity and coupling of PNP model, choosing appropriate initial values is crucial to obtaining a convergent result or accelerating the convergence rate of finite element solution, especially for large channel systems. Continuation is an effective and commonly adopted strategy to provide good initial guesses for the solution procedure. However, this method needs multiple times to solve the whole system at different conditions. We utilize a reduced model describing a near or partial-equilibrium state as an approximation of the original PNP system (describing a non-equilibrium process in general). Based on the reduced model, we design three initialization methods for the solution of PNP equations under general conditions. These methods provide the initial guess of the PNP system by solving a specifically designed Poisson-Boltzmann-like model, Smoluchowski-Poisson-Boltzmann-like model, and linear approximation model. Simulations of potassium channels 1BL8 and 2JK4 demonstrate that these methods can effectively reduce the number of Gummel iteration steps and the total CPU time in the solution of the PNP equations, and especially do not need the continuation approach anymore. The reason is that these initial guesses can approximate the PNP solution well in the channel region. Besides, our numerical experiments demonstrate that as one of the initialization methods, the linear approximation method can even produce very close results such as current-voltage curves to that from the PNP model when the membrane potential is not high. (C) 2020 Elsevier Inc. All rights reserved.
关键词	Reduced model Poisson-Nernst-Planck Smoluchowski-Poisson-Boltzmann Initialization Linear approximation of PNP model Finite element method
DOI	10.1016/j.jcp.2020.109627
收录类别	SCI
语种	英语
资助项目	Science Challenge Program[TZ2016003-1] ; National Key Research and Development Program of Ministry of Science and Technology[2016YFB0201304] ; China NSF[21573274] ; China NSF[11771435]
WOS研究方向	Computer Science ; Physics
WOS类目	Computer Science, Interdisciplinary Applications ; Physics, Mathematical
WOS记录号	WOS:000629857800007
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/58361
专题	中国科学院数学与系统科学研究院
通讯作者	Li, Hongliang; Lu, Benzhuo
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, State Key Lab Sci & Engn Comp, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 3.Sichuan Normal Univ, Dept Math, Chengdu 610066, Peoples R China 4.China Acad Engn Phys, Inst Elect Engn, Mianyang 621900, Sichuan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Qianru,Gui, Sheng,Li, Hongliang,et al. Model reduction-based initialization methods for solving the Poisson-Nernst-Plank equations in three-dimensional ion channel simulations[J]. JOURNAL OF COMPUTATIONAL PHYSICS,2020,419:18.
APA	Zhang, Qianru,Gui, Sheng,Li, Hongliang,&Lu, Benzhuo.(2020).Model reduction-based initialization methods for solving the Poisson-Nernst-Plank equations in three-dimensional ion channel simulations.JOURNAL OF COMPUTATIONAL PHYSICS,419,18.
MLA	Zhang, Qianru,et al."Model reduction-based initialization methods for solving the Poisson-Nernst-Plank equations in three-dimensional ion channel simulations".JOURNAL OF COMPUTATIONAL PHYSICS 419(2020):18.