Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates

doi:10.1016/j.bpj.2011.03.059

	Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates
	Lu, Benzhuo1 ; Zhou, Y. C.2
	2011-05-18
发表期刊	BIOPHYSICAL JOURNAL
ISSN	0006-3495
卷号	100 期号:10 页码:2475-2485
摘要	The effects of finite particle size on electrostatics, density profiles, and diffusion have been a long existing topic in the study of ionic solution. The previous size-modified Poisson-Boltzmann and Poisson-Nernst-Planck models are revisited in this article. In contrast to many previous works that can only treat particle species with a single uniform size or two sizes, we generalize the Borukhov model to obtain a size-modified Poisson-Nernst-Planck (SMPNP) model that is able to treat nonuniform particle sizes. The numerical tractability of the model is demonstrated as well. The main contributions of this study are as follows. 1), We show that an (arbitrarily) size-modified PB model is indeed implied by the SMPNP equations under certain boundary/interface conditions, and can be reproduced through numerical solutions of the SMPNP. 2), The size effects in the SMPNP effectively reduce the densities of highly concentrated counterions around the biomolecule. 3), The SMPNP is applied to the diffusion-reaction process for the first time, to our knowledge. In the case of low substrate density near the enzyme reactive site, it is observed that the rate coefficients predicted by SMPNP model are considerably larger than those by the PNP model, suggesting both ions and substrates are subject to finite size effects. 4), An accurate finite element method and a convergent Gummel iteration are developed for the numerical solution of the completely coupled nonlinear system of SMPNP equations.
DOI	10.1016/j.bpj.2011.03.059
语种	英语
资助项目	Chinese Academy of Sciences ; State Key Laboratory of Scientific and Engineering Computing ; National Science Foundation of China (NSFC)[10971218] ; Colorado State University
WOS研究方向	Biophysics
WOS类目	Biophysics
WOS记录号	WOS:000290830900019
出版者	CELL PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/12692
专题	计算数学与科学工程计算研究所
通讯作者	Lu, Benzhuo
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, State Key Lab Sci & Engn Comp, Inst Computat Math & Sci Engn Comp, Beijing, Peoples R China 2.Colorado State Univ, Dept Math, Ft Collins, CO 80523 USA
推荐引用方式 GB/T 7714	Lu, Benzhuo,Zhou, Y. C.. Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates[J]. BIOPHYSICAL JOURNAL,2011,100(10):2475-2485.
APA	Lu, Benzhuo,&Zhou, Y. C..(2011).Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates.BIOPHYSICAL JOURNAL,100(10),2475-2485.
MLA	Lu, Benzhuo,et al."Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes II: Size Effects on Ionic Distributions and Diffusion-Reaction Rates".BIOPHYSICAL JOURNAL 100.10(2011):2475-2485.