Den 2018-12-10 kl. 21:57, skrev Kevin Boyd:
Hi,
If you're reporting a diffusion coefficient, they're probably looking for
you to justify that you're out of the short-time subdiffusive regime. My
experience is in bilayer simulations, where the MSD hits that regime
typically in the time lag range of ~10-20 ns.
For a qualitative estimate of whether you've reached the long timescale
limit, you don't need a log-log plot, you can just eyeball when the MSD
goes linear, and (again in my experience) that's generally sufficient. A
log-log plot may make it easier to see, or catch some subtler trends.
Maybe take a look at "Non-brownian diffusion in lipid membranes:
experiments and simulations", by Metzler, Jeon, and Cherstvy, particularly
some of the later figures look at the extent of subdiffusion with log-log
plots.
https://www.sciencedirect.com/science/article/pii/S0005273616300219
Thanks!
Kevin
On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel <sp...@xray.bmc.uu.se>
wrote:
Hi,
unusual request, but here goes. I am dealing with a referee to one of my
papers who is asking for a mean square displacement plots:
"a log-log plot of the MSD vs. time, from which one could judge whether
the long-time limit subject to multiple collisions and obstructions is
actually reached."
Any clue what the referee is looking for? References?
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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