Longitudinal diffusion with NEURON

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rc05ej06
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Longitudinal diffusion with NEURON

Post by rc05ej06 » Tue Jul 31, 2007 3:25 am

Hi,
I don't know how correct my question is, however...
Is it possible to use only LONGITUDINAL_DIFFUSION mechanism, without the accompanying radial diffusion. I think for my purposes it will be enough to consider exchange of molecules between different sections/segments, but I don't understand how to describe this mech. within NMODL.
Thanks for your help.

ted
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Post by ted » Tue Jul 31, 2007 10:06 am

The answer is yes. Just eliminate radial discretization.

But before you even bother with it, think carefully about longitudinal diffusion. Like all
diffusion, it is driven by concentration gradient. What in your model will generate a
sufficiently steep concentration gradient as to cause significant longitudinal flux? Membrane
potential has a very shallow spatial gradient, and so do most assumed ion channel
distributions. Surface/volume ratio also changes slowly, except in the near vicinity of the
soma and spine necks. Pumps, buffers, and sequestration by organelles seem likely to be
more important than longitudinal diffusion.

That said, it remains an empirical question, so go ahead. Make sure that your longitudinal
spatial grid is sufficiently fine--diffusion requires a much larger nseg than electrical signaling
does.

rc05ej06
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Post by rc05ej06 » Tue Jul 31, 2007 10:46 am

Thank you !!!
Also, (another probably un-related question) - is there something like "break" statement that can be used in "FROM...TO" structure of NMODL? I would like to save computational time and not to check all the sequence when I can avoid it.
Thanks again.

ted
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Post by ted » Tue Jul 31, 2007 1:17 pm

Not as far as I know. FROM...TO...WITH... is for proper maintenance of rate tables, to
help ensure accuracy. If one had a mod file that used tables, why would one ever want to
defeat accuracy?

suffa
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Re: Longitudinal diffusion with NEURON

Post by suffa » Fri Mar 11, 2016 8:29 am

Hi,

it seems that Longitudinal Diffusion implemented in NEURON is proportional to the concentration gradient, i.e., it is given by the Fick's law. But for charged particles the Nernts-Planck electrodiffusion equation seemed to be more appropriate since diffusing particles are charged and also moved according to the gradient of electrical potential in space. Still many modelers (not only NEURON users) are using Fick's law to model longitudinal and radial diffusion of ions in the intra/extracellular space. Could you please give some hint why Fick's law is applicable in such case?

ted
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Re: Longitudinal diffusion with NEURON

Post by ted » Fri Mar 11, 2016 11:36 am

In most cases electrical potential gradients are very shallow compared to concentratonn gradients, and diffusion accounts for most flux.

--Ted

suffa
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Re: Longitudinal diffusion with NEURON

Post by suffa » Tue Mar 22, 2016 3:41 am

Thank you, Ted!

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