Can rxd.Rate() intrinsically keep track of currents?

Extending NEURON to handle reaction-diffusion problems.

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duytanph
Posts: 16
Joined: Wed Jul 10, 2019 5:03 pm

Can rxd.Rate() intrinsically keep track of currents?

Post by duytanph »

Hello,

I wanted to ask if it is possible for rxd to keep track of currents that arise from the movement of ions from one compartment to another. For example, if there was an rxd.Rate() that defined a mechanism for calcium influx (extracellular to intracellular), would the movement of these calcium ions affect the membrane potential of the cell (and also the Nernst potential, eca, since the concentration gradient is changing)? Or is NMODL the only way to get these currents "recognized" by NEURON?

I tried creating a python script that includes a single section placed in an extracellular space that defines ion x with a specified initial 'i' and 'o' concentration. I then defined a constant rxd.Rate() of ion x. I plotted the voltage (_ref_v) of the section and there was no change in the membrane potential as a result of the rxd.Rate(). I thought that rxd would handle this naturally since the rxd.Species() function allows you to define the charge of the ion. Please let me know if I'm missing something. Appreciate the help!
adamjhn
Posts: 54
Joined: Tue Apr 18, 2017 10:05 am

Re: Can rxd.Rate() intrinsically keep track of currents?

Post by adamjhn »

Sorry for the late reply. RxD will keep track of concentrations and update Nernst potentials of the `rxd.Species` in your model. It can also generate currents, but only when a charge carrier movers across a membrane, which can be defined with a `rxd.MultiCompartmentReaction`.

Here is an example of two cells with Hodgkin-Huxley channels, in both RxD keeps track of concentrations. In one the currents are defined by NEURON's hh mechanism, in the other the currents are defined by MultiCompartmentReactions.
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