Subject: Monte Carlo for Diffusion - Summary

From: "Andrey Blizniuk" <[email-masked]>
Date: Mon, 24 Jun 1996 13:23:25 +0010

Dear Netters,

Thanks to everyone who responded to my question about
use of Monte Carlo for diffusion. Some people
asked about summary. I am sending them the copy
of this message.

(1)
Several people recommend to look at Monte Carlo Page
<http://www.cooper.edu/engineering/chemechem/monte.html>
Unfortunately, I couldn't find anything on the subject in there.
But I am still looking :-).

(2)
Mr. Mark J Biggs <[email-masked]>
sent following references on the diffusion in porous solids:

Abbasi et al., AIChE Journal V29, p617, 1983
Havlin and Ben Avraham, Adv in Physics, V36, 695, 1987.
Sahimi, J Chem Phys, V92, 5107, 1990
Gusev et al, J Chem Phys, V99, 2221, 1993
Nakano and Evans, J Chem Phys, V78, 2568, 1983
Evans et al, J Chem Phys, V72, 2967, 1980

Tomadakis and Sotirchos, J Chem Phys, V99, 9820, 1993
-----------------------, AIChE J, V39, 397, 1993
they have a few more papers in these Journals as well

Melkote and Jensen, AIChE J, V35, 1942, 1989.

(3)
Dr Kieran F Lim <[email-masked]>
sent the following comments:

Monte Carlo (MC) methods imply that the underlying maths has some 
random
event.  Brownian dynamics has the *assumption* that the solvent 
imparts
random forces to the molecule (substrate) of interest.  Molecular 
dynamics (MD)
incorporates both solvent and substrate motions and so there is 
nothing
random - ie non-MC method.  By including everything, the MD
calculation is much bigger - hence *many* (not most) prefer MC rather 
than MD.
the choice depends on the nature of the problem, the size of your 
system and
your computer resources.

(4)
While waiting for the reply from CCL I had a look at the Current
Contents. The following papers may be useful:

H. Gudbjartsson S. Patz "NMR Diffusion Simulation Based on
Conditional Random Walk", IEEE Transactions on Medical Imaging,
1995, 14, 636-642

P.A. Mahama, J.L. Linderman "A Monter Carlo Study of the
Dynamics of G-Protein Activation", Biophysical Journal, 1994,
67, 1345-1357.

Z. Hong-Dong, L. Jian-Ming, Y. Yu-Liang "Sample duplication
Method for Monte Carlo Simulation of Large Reaction-Diffusion
System", Science in China, Ser.B., 1994, 37, 385-394.

P. Gao "Computer Experiments for Surface Diffusion: The
Real Time in Monte Carlo Simulations", Physical Review Letters,
1994, 73, 2595-2598.

H. Breuer, W. Huber, F. Petruccione "Fast Monte Carlo algorithm
for nonequilibrium systems", Physical Review E, 1996, 4232-4235.

Sincerely,

Dr. Andrey Bliznyuk
Computational Molecular Biology and Drug Design Group
Division of Molecular Biology and Biochemistry
John Curtin School of Medical Research
Australian National University
PO Box 334, Canberra, ACT 2601
Australia
Email: [email-masked]
http://biocomp.anu.edu.au/~aab

---

From: TOPPER ROBERT <[email-masked]>
Date: Mon, 24 Jun 1996 11:58:00 -0400 (EDT)

Hi all,
I will put a copy of Andrew's summary on the
Molecular Monte Carlo home page. Just FYI.
best, robert

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Robert Q. Topper                       email:   [email-masked]
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