Accessing the current between extracellular layers

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TimKamsma
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Accessing the current between extracellular layers

Post by TimKamsma » Tue Jun 04, 2019 4:47 am

Hello,

I am working on a model with two extracellular layers, where I would like to somehow control the current between the first and second extracellular layer in order to also have channel mechanisms there. Is there some way to make NMODL mechanisms write current which is then modelled as current between these two extracellular layers instead of between the standard cable and the first layer? Or is there perhaps some other way to achieve the same effect?

Thank you in advance.

ted
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Re: Accessing the current between extracellular layers

Post by ted » Tue Jun 04, 2019 1:58 pm

No.

Are you trying to create a model of interactions between a neuron and other cells that lie adjacent to it?

TimKamsma
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Re: Accessing the current between extracellular layers

Post by TimKamsma » Thu Jun 06, 2019 5:03 am

Dear Ted,

Thank you for your answer!
Yes that is what I am trying to do. The second extracellular layer corresponds to the intracellular space of a different cell which directly neighbours the modelled axon for a long stretch.

ted
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Re: Accessing the current between extracellular layers

Post by ted » Thu Jun 06, 2019 10:16 am

Then you may need to represent exchange between each cell and a shared extracellular space, and/or direct exchange between cells (e.g. through gap junctions). This can be done with special mechanisms implemented in NMODL, or by using NEURON's reaction-diffusion (rxd) module. Both approaches have their own strengths and weaknesses. rxd's particular advantage is in maintaining conceptual clarity, that is, ensuring that there is a close match between your conceptual model (hypothesis) and its implementation in computational form. I'll refer this to Adam Newton and Robert McDougal for their input.

ramcdougal
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Re: Accessing the current between extracellular layers

Post by ramcdougal » Thu Jun 06, 2019 10:25 am

Are you trying to simulate ephaptic coupling or extracellular diffusion of ion concentrations in the extracellular space?

There are currently at least two models in ModelDB that use NEURON for ephaptic coupling: http://identifiers.org/modeldb/3676 and http://identifiers.org/modeldb/240957

(The rxd module does not directly support ephaptic coupling.)

The basics of simulating extracellular diffusion in NEURON are introduced in this tutorial page: https://neuron.yale.edu/neuron/docs/ext ... -diffusion

TimKamsma
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Re: Accessing the current between extracellular layers

Post by TimKamsma » Fri Jun 07, 2019 5:04 pm

Thank you for your replies, however the cables represent the axon core, periaxonal space and inner myelin region. Therefore I fear that crxd or ephaptic coupling aren't applicable.
Would it however be possible to let an NMODL mechanism read and use vext[0] and vext[1]? It doesn't seem to recognize vext[1] and gives of an error when I try to introduce it in an NMODL file.

ted
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Re: Accessing the current between extracellular layers

Post by ted » Sun Jun 09, 2019 9:21 am

Without more specific information about your hypothesis, it is difficult to advise you how to build a computational model that is a close match to that hypothesis. After all, you know most about your hypothesis and something (much? little?) about NEURON, but we know a lot about NEURON and almost nothing about your hypothesis. Consequently we're playing "guess what you're thinking," and the risk is that the discussion will get lost in a tangle of implementational details instead of producing useful suggestions. We'll need to know more about what you have in mind (i.e. what aspects of biology do you need to represent in your model, and why). You might prefer to do that in a private email exchange. My address is
ted dot carnevale
and ramcdougal's is
robert dot mcdougal
both at yale dot edu

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