Literature DB >> 21842924

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary.

Dezso Boda1, Douglas Henderson, Bob Eisenberg, Dirk Gillespie.   

Abstract

In the implicit solvent models of electrolytes (such as the primitive model (PM)), the ions are modeled as point charges in the centers of spheres (hard spheres in the case of the PM). The surfaces of the spheres are not polarizable which makes these models appropriate to use in computer simulations of electrolyte systems where these ions do not leave their host dielectrics. The same assumption makes them inappropriate in simulations where these ions cross dielectric boundaries because the interaction energy of the point charge with the polarization charge induced on the dielectric boundary diverges. In this paper, we propose a procedure to treat the passage of such ions through dielectric interfaces with an interpolation method. Inspired by the "bubble ion" model (in which the ion's surface is polarizable), we define a space-dependent effective dielectric coefficient, ε(eff)(r), for the ion that overlaps with the dielectric boundary. Then, we replace the "bubble ion" with a point charge that has an effective charge q/ε(eff)(r) and remove the portion of the dielectric boundary where the ion overlaps with it. We implement the interpolation procedure using the induced charge computation method [D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg, Phys. Rev. E 69, 046702 (2004)]. We analyze the various energy terms using a spherical ion passing through an infinite flat dielectric boundary as an example.

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Year:  2011        PMID: 21842924      PMCID: PMC3170393          DOI: 10.1063/1.3622857

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  20 in total

1.  Permeation of ions across the potassium channel: Brownian dynamics studies.

Authors:  S H Chung; T W Allen; M Hoyles; S Kuyucak
Journal:  Biophys J       Date:  1999-11       Impact factor: 4.033

2.  Electrostatic interaction between two charged dielectric spheres in contact

Authors: 
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-08

3.  Role of the dielectric constants of membrane proteins and channel water in ion permeation.

Authors:  Turgut Baştuğ; Serdar Kuyucak
Journal:  Biophys J       Date:  2003-05       Impact factor: 4.033

4.  Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems.

Authors:  Dezsö Boda; Dirk Gillespie; Wolfgang Nonner; Douglas Henderson; Bob Eisenberg
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-04-29

5.  An accurate and efficient empirical approach for calculating the dielectric self-energy and ion-ion pair potential in continuum models of biological ion channels.

Authors:  Mary Hongying Cheng; Rob D Coalson
Journal:  J Phys Chem B       Date:  2005-01-13       Impact factor: 2.991

6.  Dielectric saturation of the ion hydration shell and interaction between two double helices of DNA in mono- and multivalent electrolyte solutions: foundations of the epsilon-modified Poisson-Boltzmann theory.

Authors:  Sergei Gavryushov
Journal:  J Phys Chem B       Date:  2007-04-18       Impact factor: 2.991

7.  Combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel.

Authors:  Dezso Boda; Mónika Valiskó; Bob Eisenberg; Wolfgang Nonner; Douglas Henderson; Dirk Gillespie
Journal:  Phys Rev Lett       Date:  2007-04-17       Impact factor: 9.161

8.  The nonmonotonic concentration dependence of the mean activity coefficient of electrolytes is a result of a balance between solvation and ion-ion correlations.

Authors:  Julianna Vincze; Mónika Valiskó; Dezso Boda
Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

9.  Discretization of the induced-charge boundary integral equation.

Authors:  Jaydeep P Bardhan; Robert S Eisenberg; Dirk Gillespie
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-07-06

10.  Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion.

Authors:  Dezso Boda; Mónika Valiskó; Douglas Henderson; Bob Eisenberg; Dirk Gillespie; Wolfgang Nonner
Journal:  J Gen Physiol       Date:  2009-05       Impact factor: 4.086

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  1 in total

1.  Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations.

Authors:  Eva Csányi; Dezso Boda; Dirk Gillespie; Tamás Kristóf
Journal:  Biochim Biophys Acta       Date:  2011-11-04
  1 in total

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