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.
Longitudinal diffusion with NEURON
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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.
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.
Re: Longitudinal diffusion with NEURON
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?
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?
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Re: Longitudinal diffusion with NEURON
In most cases electrical potential gradients are very shallow compared to concentratonn gradients, and diffusion accounts for most flux.
--Ted
--Ted
Re: Longitudinal diffusion with NEURON
Thank you, Ted!