Propagation of AP using ion-specific currents

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leanne
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Propagation of AP using ion-specific currents

Post by leanne » Wed Apr 18, 2018 4:01 am

I've got a question about linking two models with different characteristics. The first one is a model of a myelinated fibre that is based on the McIntyre motor neuron, with a double cable structure implemented using the extracellular mechanism (https://senselab.med.yale.edu/modeldb/s ... model=3810). The second one is an unmyelinated fibre that has a periaxonal space where ions accumulate. This means that the second model uses ion-specific dynamics and updates the nernst potentials after each time step (by writing nai, nao, ki and ko), whereas the McIntyre model uses a nonspecific current.

I have two questions about linking these models:

1. I understand that NEURON calculates the propagation of the action potential using the discretized cable equation, but I do not see how this relates to specific ions. What happens with the ion-specific currents in the second model? How does NEURON calculate diffusion of ions within the axon (and the periaxonal space)?

2. Would it cause problems if I link these two models? I'm assuming that something strange would happen with the sudden transition from non-specific currents to ion-specific currents, but as far as I can see everything looks quite normal.

ted
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Re: Propagation of AP using ion-specific currents

Post by ted » Wed Apr 18, 2018 11:16 am

I understand that NEURON calculates the propagation of the action potential using the discretized cable equation, but I do not see how this relates to specific ions. What happens with the ion-specific currents in the second model? How does NEURON calculate diffusion of ions within the axon (and the periaxonal space)?
NEURON doesn't simulate diffusion or even ion accumulation unless you tell it how to. That's what ion accumulation mechanisms are for (mechanisms that WRITE ionic concentrations). An ion accumulation mechanism must explicitly define the equations that relate ionic currents to ionic concentrations, and ionic concentration gradients to fluxes between adjacent compartments. You'll find examples in chapter 9 of The NEURON Book. Also see examples 6, 8, and 9 in
http://www.neuron.yale.edu/neuron/stati ... odl400.pdf
(be sure to read this too http://www.neuron.yale.edu/neuron/stati ... rrata.html)
RxD provides an alternative way to specify ion accumulation and diffusion, but again, it is up to the modeler to specify which species accumulate etc..
Would it cause problems if I link these two models?
What do you mean by "link"?

leanne
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Joined: Wed Oct 18, 2017 5:15 am

Re: Propagation of AP using ion-specific currents

Post by leanne » Thu Apr 19, 2018 4:41 am

Thank you for your quick reply Ted!

I am writing ionic concentrations (nai, nao, ki and ko) in my model, but only locally. My first question, whether longitudinal diffusion of ions happens automatically, was well answered by the documents you attached (it doesn't).

With my second question about linking models I meant that I want to connect two branches, of which the first one writes ion concentrations based on ionic currents and the second one doesn't. I was wondering if this would cause any problems in "flows" of ions from one branch to the other one. As I didn't insert any longitudinal diffusion statement, I'm guessing the answer is no because neighbouring segments will not be influenced by the local updating of the ion concentrations.

ted
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Re: Propagation of AP using ion-specific currents

Post by ted » Thu Apr 19, 2018 10:56 am

My first question, whether longitudinal diffusion of ions happens automatically, was well answered by the documents you attached
Two of the principles that have guided the design and implementation of NEURON are:
1. The properties and phenomena that are represented in a model should be entirely up to the person who creates the model.
2. The utility of a model depends not only on what its creator has included in it, but also on what has been omitted. Simpler is usually better, not only because complexity is a barrier to understanding, but also because insights derived from simple models are usually more generalizable than insights obtained from complex models. Think of "the canonical Newtonian chicken": a 10 cm diameter sphere that weighs 1000 g and moves along a straight path at a velocity of 100 cm/s.
With my second question about linking models . . . I'm guessing the answer is no because neighbouring segments will not be influenced by the local updating of the ion concentrations.
Correct.

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