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Re: [ESPResSo-users] Simulation of a polyelectrolytes system.

From: Owen Hickey
Subject: Re: [ESPResSo-users] Simulation of a polyelectrolytes system.
Date: Thu, 1 Sep 2011 12:29:17 -0400


Using the electrohydrodynamics featuer in Espresso you only have
control of the relative speed of beads to the lattice-Boltzmann fluid.
 Essentially by switching the way monomers are coupled to the
lattice-Boltzmann fluid it forces the monomer velocity to be muE
greater than the surrounding fluid velocity.  Thus you can control the
mobility multiplied by the electric field, the Smoluchowski slip
velocity, but I do not think this method will work given the
hypothesis put forth in your article.

I have read your work on collapse of DNA in an AC electric field.  In
your work you hypothesize that the reason for the collapse has to do
with polarization of the counterion cloud.  This would not be achieved
by using the electrohydrodynamics feature in Espresso and instead you
need to use explicit ions.  This can be done by adding explicit
charges to both the monomers which make up the polymer, counterions
and an appropriate density of salt ions (all just Lennard-Jones beads
with a charge).  Long ranged electrostatic calculations would then
need to be performed using P3M, ELC or one of the other algorithms
contained in Espresso.  Then in order to add the effect of an electric
field you would use the external force feature which simply places a
force on individual beads.  I believe currently it is only implemented
for a constant force on particles but I am guessing it wouldn't be too
hard to change it such that the external force varies with time.

Hope that helps,

On Thu, Sep 1, 2011 at 11:40 AM, Chunda Zhou <address@hidden> wrote:
> Dear Dr. Holm,
> I am a graduate student in biophysics. We conduct a series experiments which
> show DNA collapses under A.C. electric field.  ( Collapse of DNA in ac
> Electric Fields, in the attachment. )
> We are now using general ESPResSo to simulate. But according to the mail
> list, in the general ESPResSo could only set the velocity for all the
> charged particles as one value muE. In your paper Mesoscale modelling of
> polyelectrolyte electrophoresis, you have measured the relation between
> velocities and electric field with ESPResSo. I think you are the only person
> who can do this. Could you please show us more information on this?
> Best wishes,
> Chunda Zhou
> Department of Physics
> 919-995-5631

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