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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
Source PublicationBIOPHYSICAL JOURNAL
ISSN0006-3495
Volume100Issue:10Pages:2475-2485
AbstractThe 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.
DOI10.1016/j.bpj.2011.03.059
Language英语
Funding ProjectChinese Academy of Sciences ; State Key Laboratory of Scientific and Engineering Computing ; National Science Foundation of China (NSFC)[10971218] ; Colorado State University
WOS Research AreaBiophysics
WOS SubjectBiophysics
WOS IDWOS:000290830900019
PublisherCELL PRESS
Citation statistics
Cited Times:62[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/12692
Collection计算数学与科学工程计算研究所
Affiliation1.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
Recommended Citation
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.
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