Re: [ESPResSo-users] DPD

[Dr. Jens Smiatek]

Dear Dusan,

thanks for your interest.
You should use the constraint plane cell for the tunable slip boundaries in microchannels.
Maybe I miss your point, but:
If you want to perform some DPD simulations, there is no way around to use explicit solvent particles for dilute polymer solution simulations. Otherwise the method won't work.
Instead you can think of using the Lattice-Boltzmann method which is significantly faster (if you are purely interested in hydrodynamic interactions and not 'solvation' properties).
The situations changes if dense polymer melts are considered. Here, above a critical concentration, the monomers themselves can be considered as the surrounding environment such that DPD solvent particles can be safely ignored.

Best regards,
Jens

On 09/11/2014 03:51 PM, Dudo wrote:

Dear Jens,

thank you very much for the lead.

Well, so I've compiled in a feature for "TUNABLE_SLIP"

and I have set up interactions: inter $cid $idpolym tunable_slip $temperature $gamma_L $r_cut_L $timestep .....

I have turned the flag to 2: constraint cylinder center $cx $cy $cz axis $cnx $cny $cnz radius $crad length $clength direction $cdirection type $cid reflecting 2 .....

as Stefan suggested, and I'm trying with the parameters from your paper on polyelectrolytes J. Phys Chem B 2010..

Now I see you have used explicit solvent with density 3.75, while modelling a chain of 20 beads.

In my case this would mean zillions of solvent particles..

Well at the begining Chris asked me, why would I do add explicit particles - so.. is there a way around?

Kind regards,
Dusan

On Thu, Sep 11, 2014 at 12:41 PM, Dr. Jens Smiatek <address@hidden> wrote:

Dear Dusan,

here are some references where tunable-slip boundaries (already implemented in ESPResSo) for polyelectrolyte and colloidal electrophoresis as well as for Poiseuille/Couette flow and electroosmotic flow in nano/microchannels have been used.

If you have some questions with regard to the implementation, please don't hesitate to ask.

Best regards,
Jens

Tunable-slip boundaries for coarse-grained simulations of fluid flow

By: Smiatek, J.; Allen, M. P.; Schmid, F.

EUROPEAN PHYSICAL JOURNAL E  Volume: 26   Issue: 1-2   Pages: 115-122   Published: MAY 2008

Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study

By: Smiatek, Jens; Sega, Marcello; Holm, Christian; et al.

JOURNAL OF CHEMICAL PHYSICS  Volume: 130   Issue: 24     Article Number: 244702   Published: JUN 28 2009

Polyelectrolyte Electrophoresis in Nanochannels: A Dissipative Particle Dynamics Simulation

By: Smiatek, Jens; Schmid, Friederike

JOURNAL OF PHYSICAL CHEMISTRY B  Volume: 114   Issue: 19   Pages: 6266-6272   Published: MAY 20 2010

Mesoscopic simulations of electroosmotic flow and electrophoresis in nanochannels

By: Smiatek, Jens; Schmid, Friederike

COMPUTER PHYSICS COMMUNICATIONS  Volume: 182   Issue: 9   Special Issue: SI   Pages: 1941-1944   Published: SEP 2011

Anisotropic flow in striped superhydrophobic channels

By: Zhou, Jiajia; Belyaev, Aleksey V.; Schmid, Friederike; et al.

JOURNAL OF CHEMICAL PHYSICS  Volume: 136   Issue: 19     Article Number: 194706   Published: MAY 21 2012

Separation of Chiral Particles in Micro- or Nanofluidic Channels

By: Meinhardt, Sebastian; Smiatek, Jens; Eichhorn, Ralf; et al.

PHYSICAL REVIEW LETTERS  Volume: 108   Issue: 21     Article Number: 214504   Published: MAY 23 2012

Dielectric response of nanoscopic spherical colloids in alternating electric fields: a dissipative particle dynamics simulation

By: Zhou, Jiajia; Schmid, Friederike

JOURNAL OF PHYSICS-CONDENSED MATTER  Volume: 24   Issue: 46   Special Issue: SI     Article Number: 464112   Published: NOV 21 2012

AC-field-induced polarization for uncharged colloids in salt solution: A dissipative particle dynamics simulation

By: Zhou, Jiajia; Schmid, Friederike

EUROPEAN PHYSICAL JOURNAL E  Volume: 36   Issue: 4     Article Number: 33   Published: APR 2013

Effective slip-length tensor for a flow over weakly slipping stripes

By: Asmolov, Evgeny S.; Zhou, Jiajia; Schmid, Friederike; et al.

PHYSICAL REVIEW E  Volume: 88   Issue: 2     Article Number: 023004   Published: AUG 8 2013

Computer simulations of charged colloids in alternating electric fields

By: Zhou, Jiajia; Schmid, Friederike

EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS  Volume: 222   Issue: 11   Pages: 2911-2922   Published: NOV 2013

Effective slippage on superhydrophobic trapezoidal grooves

By: Zhou, Jiajia; Asmolov, Evgeny S.; Schmid, Friederike; et al.

JOURNAL OF CHEMICAL PHYSICS  Volume: 139   Issue: 17     Article Number: 174708   Published: NOV 7 2013

On 09/11/2014 11:42 AM, Dudo wrote:

Hi Ulf,

thanks for replying. Some nice papers you've got there, I'm going to see if I find the solution in there.

Well, I'm not sure about the physical picture though. Of course, the picture is correct as for the conservation of energy,
but the periodic box now does not represent a sample of an infinite system, it's more like a limited amount of
solvent taking an infinite energy, what is not very physical.

Also, I very agree on the word 'pump'. The molecule really acts here like a pump, what is not the picture
I'd like to have.

I like the idea to dissipate the energy on the walls as Chris suggested, please, would I implement it with the
"thermostat inter_dpd ignore_fixed_particles 0"? Or should I make the boundary from additional particles? I'd like
to avoid explicit particles as possible, due to the size of the problem.

Thanks,
Dusan

On Wed, Sep 10, 2014 at 9:52 PM, Ulf Schiller <address@hidden> wrote:

On 09/10/2014 07:02 PM, Dudo wrote:
> On Wed, Sep 10, 2014 at 7:09 PM, Christoph Junghans <address@hidden
> <mailto:address@hidden>> wrote:
>
>     2014-09-10 9:08 GMT-06:00 Dudo <address@hidden
>     <mailto:address@hidden>>:
>     > Please,
>     >
>     > should I generate additional particles for using the DPD thermostat?
>     I don't really understand why you would do that. Can you give some
>     details about the problem you are studying?
>
> Hi Chris,
>
> well, what I would like to do is to drag a polymer molecule through media,
> with a constant velocity with respect to the media as possible.
> Hence, even if I fill the periodic box with a huge number of "solvent"
> bodies it would start moving as one phase after some time.
> So this is not the way.

But that is physical. Assuming you intend to drag the molecule by
applying a force, this will 'pump' momentum into the system which will
diffuse according to the viscosity of the medium. Unless you dissipate
momentum by some means (e.g. walls), the whole system will accelerate.
If you stop applying the force at some point, velocity gradients will
decay while total momentum of the system is conserved.

> What I would like to see coming from my simulation, is at first the
> molecule orienting with its lowest energy/lowest friction or
> hydrodynamic radius profile with respect to the direction of the
> movement through the media, with the molecule started re-shaping after a
> while..

This sounds like you intend to look at the response of the molecule to
an external flow. In that case, you need to decide first what kind of
flow you would like to impose. Simple examples might be uniform, linear
or parabolic flow profiles. However, if you are merely interested in the
mobility tensor of the molecule, you may be able extract it from
equilibrium simulations by means of linear response theorems (keep
finite size effects in mind for a periodic system).

Note that such properties have been studied extensively for various
kinds of polymers (linear chains, stars, rings), and you may want to
take a second look at the available literature.

Best wishes,
Ulf

--
Ulf D. Schiller
Centre for Computational Science
University College London
20 Gordon Street
London WC1H 0AJ
United Kingdom

http://ccs.chem.ucl.ac.uk/

--

____________________
Ing. Dusan Racko, PhD

https://www.researchgate.net/profile/Dusan_Racko
Polymer Institute of the Slovak Academy of Sciences
Dubravska cesta 3
845 41 Bratislava, Slovak Republic
tel: +421 2 3229 4321

-- 
================
Dr. Jens Smiatek

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart
Germany

Office: 1.032
Phone: +49-(0)711/685 63757
E-Mail: address@hidden

--

____________________
Ing. Dusan Racko, PhD

https://www.researchgate.net/profile/Dusan_Racko
Polymer Institute of the Slovak Academy of Sciences
Dubravska cesta 3
845 41 Bratislava, Slovak Republic
tel: +421 2 3229 4321

-- 
================
Dr. Jens Smiatek

Institute for Computational Physics
University of Stuttgart
Allmandring 3
70569 Stuttgart
Germany

Office: 1.032
Phone: +49-(0)711/685 63757
E-Mail: address@hidden