Literature DB >> 20228879

Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates.

Bo Li1, Benzhuo Lu, Zhongming Wang, J Andrew McCammon.   

Abstract

We study a reduced Poisson-Nernst-Planck (PNP) system for a charged spherical solute immersed in a solvent with multiple ionic or molecular species that are electrostatically neutralized in the far field. Some of these species are assumed to be in equilibrium. The concentrations of such species are described by the Boltzmann distributions that are further linearized. Others are assumed to be reactive, meaning that their concentrations vanish when in contact with the charged solute. We present both semi-analytical solutions and numerical iterative solutions to the underlying reduced PNP system, and calculate the reaction rate for the reactive species. We give a rigorous analysis on the convergence of our simple iteration algorithm. Our numerical results show the strong dependence of the reaction rates of the reactive species on the magnitude of its far field concentration as well as on the ionic strength of all the chemical species. We also find non-monotonicity of electrostatic potential in certain parameter regimes. The results for the reactive system and those for the non-reactive system are compared to show the significant differences between the two cases. Our approach provides a means of solving a PNP system which in general does not have a closed-form solution even with a special geometrical symmetry. Our findings can also be used to test other numerical methods in large-scale computational modeling of electro-diffusion in biological systems.

Entities:  

Year:  2010        PMID: 20228879      PMCID: PMC2835320          DOI: 10.1016/j.physa.2009.12.024

Source DB:  PubMed          Journal:  Physica A        ISSN: 0378-4371            Impact factor:   3.263


  15 in total

1.  Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on gramicidin A channel conductance.

Authors:  A E Cárdenas; R D Coalson; M G Kurnikova
Journal:  Biophys J       Date:  2000-07       Impact factor: 4.033

2.  Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics.

Authors:  B Corry; S Kuyucak; S H Chung
Journal:  Biophys J       Date:  2000-05       Impact factor: 4.033

3.  Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory.

Authors:  Sergei Yu Noskov; Wonpil Im; Benoît Roux
Journal:  Biophys J       Date:  2004-10       Impact factor: 4.033

4.  Application of the Poisson-Nernst-Planck theory with space-dependent diffusion coefficients to KcsA.

Authors:  Simone Furini; Francesco Zerbetto; Silvio Cavalcanti
Journal:  Biophys J       Date:  2006-07-28       Impact factor: 4.033

5.  Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.

Authors:  Benzhuo Lu; Y C Zhou; Gary A Huber; Stephen D Bond; Michael J Holst; J Andrew McCammon
Journal:  J Chem Phys       Date:  2007-10-07       Impact factor: 3.488

Review 6.  Theoretical and computational models of biological ion channels.

Authors:  Benoît Roux; Toby Allen; Simon Bernèche; Wonpil Im
Journal:  Q Rev Biophys       Date:  2004-02       Impact factor: 5.318

7.  Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier.

Authors:  Courtney L Lopreore; Thomas M Bartol; Jay S Coggan; Daniel X Keller; Gina E Sosinsky; Mark H Ellisman; Terrence J Sejnowski
Journal:  Biophys J       Date:  2008-06-13       Impact factor: 4.033

8.  A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel.

Authors:  M G Kurnikova; R D Coalson; P Graf; A Nitzan
Journal:  Biophys J       Date:  1999-02       Impact factor: 4.033

Review 9.  Computing the field in proteins and channels.

Authors:  R S Eisenberg
Journal:  J Membr Biol       Date:  1996-03       Impact factor: 1.843

10.  Kinetics of diffusion-controlled enzymatic reactions with charged substrates.

Authors:  Benzhuo Lu; J Andrew McCammon
Journal:  PMC Biophys       Date:  2010-01-18
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  4 in total

1.  Poisson-Boltzmann-Nernst-Planck model.

Authors:  Qiong Zheng; Guo-Wei Wei
Journal:  J Chem Phys       Date:  2011-05-21       Impact factor: 3.488

2.  Multiscale Multiphysics and Multidomain Models I: Basic Theory.

Authors:  Guo-Wei Wei
Journal:  J Theor Comput Chem       Date:  2013-12       Impact factor: 0.939

3.  Progress in developing Poisson-Boltzmann equation solvers.

Authors:  Chuan Li; Lin Li; Marharyta Petukh; Emil Alexov
Journal:  Mol Based Math Biol       Date:  2013-03-01

4.  Variational multiscale models for charge transport.

Authors:  Guo-Wei Wei; Qiong Zheng; Zhan Chen; Kelin Xia
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2012-11-08       Impact factor: 10.780

  4 in total

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