Subject: Re: CCL:MD & MC; Modelling of counterions effects in polyelectrolytes.

From: [email-masked] (Eberhard von Kitzing)
Date: Fri, 5 Aug 94 15:36:30 +0200

Dear netters,

I would like to provide a late resonse to this subject.

As long as only the structure of the DNA is considered the proposed
"tricks" to deal with counterions may work.

For instance if one is interested in the stability of the DNA molecule as a
function of ionic concentration more fancy methods have to be used. The
most simple one is the potential of mean force approach. Here only screened
electrostatic interactions are considered. At low ionic strength, the
electrostatic interaction would be screened by the Debye-Hueckel function.
At higher concentrations MSA or even more advanced potentials must be
introduced. By this means it is possible to calculate the B-Z transition as
a function of ionic concentration and ionic radii or the distributions of
ions around the molecule; see:

%0 Journal Article
%A Soumpasis, Dikeos Mario
%D 1984
%T Statistical mechanics of the B-Z transition of DNA: Contribution of
diffuse ionic interations
%J Proceedings of the National Academy of Sciences of the USA
%V 81
%P 5116-5120
%K DNA polymorphism, polyelectrolytes, diffuse ion cloud, free energy of
conformational stability, DNA B-Z transition, potential of mean force, MSA
approximation, mean spherical approximation, hypernetted chain equation,
Kirkwood superposition approximation

%0 Journal Article
%A Klement, Reinhard
%A Soumpasis, Dikeos Mario
%A Kitzing, Eberhard v.
%A Jovin, Thomas M.
%D 1990
%T Inclusion of ionic interactions in force field calculations of charged
biomolecules - DNA structural transitions
%J Biopolymers
%V 29
%P 1089-1103
%K force field, potential of mean force, pair correlation function, MSA
theory, mean sperical approximation, electrolyte theory, screened
interactions

%0 Journal Article
%A Klement, Reinhard
%A Soumpasis, Dikeos Mario
%A Jovin, Thomas M.
%D 1991
%T Computation of ionic destributions around charged biomolecular
structures: Results for right-handed and left-handed DNA
%J Proceedings of the National Academy of Sciences of the USA
%V 88
%P 4631-4635
%K force field, potential of mean force, pair correlation function, MSA
theory, mean sperical approximation, electrolyte theory, screened
interactions, counter ion cloud, radial distribution function

If one does not want to used potentials of mean force, Brownian dynamics
are required to get fairly the statistics of the ions:

%0 Journal Article
%A Cooper, Kim
%A Jakobsson, Eric
%A Wolynes, Peter
%D 1985
%T The Theory of Ion Transport through Membrane Channels
%J Progress in Biophysics and molecular Biology
%V 46
%P 51-96
%K Nernst-Planck equation, Fokker-Planck equation, Smoluchowski equation,
Kramer's equation, Eyring rate theory, ion-ion interaction, molecular
dynamics, Brownian dynamics
%O review

%0 Journal Article
%A Bek, S.
%A Jakobsson, E.
%D 1994
%T Brownian dynamics study of a multiply-occupied cation channel -
application to understanding permeation in potassium channels
%J Biophysical Journal
%V 66
%N 4
%P 1028-1038
%K squid giant-axons; gramicidin channels; continuum theory; ion channel;
k+ channel; membrane; diffusion; motion; model; pores;

-------------------------------------------------------------------------

Eberhard von Kitzing
Max-Planck-Institut fuer Medizische Forschung
Jahnstr. 29, D69120 Heidelberg, FRG

Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat)

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