[Camino-users] Unexpected Monte Carlo Diffusion Simulations

Thu Sep 18 12:17:49 PDT 2014

Hi David.

I don't  really have an explanation for the weird behavior of the radial
diffusivity. Can you tell us the set of radius and separation values that
you used in your experiments? I would like to visualize the trajectories of
the spins in each simulation.

Another thing, in your graphic, what's the meaning of "icvf"? I'm not
familiar with the concept.

Best!

2014

-09-16 10:34 GMT-05:00 Slater David <David.Slater at chuv.ch>:

>  Hi everyone,
>
>
>
> I’ve been working with the Camino Monte Carlo diffusion simulator. To
> check things were working correctly I tried some simple tests of diffusion
> around hexagonally packed cylinders. Spins were placed only in the
> extracellular space by using the ‘extra’ option. However even with these
> simple tests I’ve got some unexpected results.
>
>
>
> I created a number of substrates with different axon radii while keeping
> the ratio of cylinder separation to axon radius constant. In this way we
> scale up and down the characteristic length scales of the system while
> keeping the intra- and extra-cellular volume fractions constant.
>
>
>
> By applying the same scheme to each substrate with (Δ-δ/3)=30ms we would
> expect radial diffusivity to approach free diffusivity in systems with very
> large length scales (i.e. relatively few membrane interactions) while
> radial diffusivity should approximate theoretical tortuosity model
> predictions in systems with very small characteristic length scales.
>
>
>
> In fact what we find from the simulations is that radial diffusivity can
> go *up* as the axon radius and axonal spacing go *down*. See the attached
> figure. This seems physically implausible to me: how is it that
> extracellular diffusivity can increase in systems with more membranes per
> unit length?
>
>
>
> Here are example commands that I used to create the .traj files and to
> generate the synthetic measurements:
>
>
>
> datasynth -walkers 200000 -tmax 5000 -p 0 -voxels 1 -initial extra
> -duration 0.04 -diffusivity 17E-10 -substrate cylinder -packing hex
> -cylinderrad 9.01E-07 -cylindersep 2.22E-06 -trajfile
> ic60_diam1p8E-06_extra_hex_dura40ms.traj
>
>
>
> scan -trajfile ic60_diam1p8E-06_extra_hex_dura40ms.traj -schemefile
> J30_DELTA30.scheme2 | float2txt >
> ic60_diam1p8E-06_extra_hex_dura40ms_J30_DELTA30.txt
>
>
>
> I have also attached the .scheme2 file that was used.
>
>
>
> What might be leading to these unexpected results? Do you have any
> suggestions for where I might be going wrong?
>
>
>
> Any help or suggestions will be greatly appreciated.
>
>
>
> Thanks,
>
> David
>
> _______________________________________________
> Camino-users mailing list
> Camino-users at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/camino-users
>
>

J

.

 R.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/camino-users/attachments/20140918/3ec09f19/attachment.html>