Adding a Rate to an Ion based on the flux of another Reaction function

Extending NEURON to handle reaction-diffusion problems.

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jetlim
Posts: 2
Joined: Wed Oct 21, 2020 9:53 am

Adding a Rate to an Ion based on the flux of another Reaction function

Post by jetlim »

Hello,

I am currently working on inserting pump mechanisms, specifically the Na-K ATPase, into a very simple neuron in order to map out the dynamics of the pump before we move to insert the mechanism into a more complex neuron.

Thus far, I have accomplished this by using the MultiCompartmentReaction function, but I have an interesting problem where the rate scheme that I am using is based purely on the concentrations of internal and external Na (as a form of simplification). This means that thus far, only the sodium concentrations are being affected by MultiCompartmentReaction, while the potassium is left out. This should be easy to fix because I could simply apply the molecular ratio of the Na-K exchange, but unfortunately I am unable to find a means to extract the sodium current of the MultiCompartmentReaction.

We are expecting other forms of Na-based exchange pumps such as Na-Ca to be involved in the larger model, so I also can't use ina as the basis. I'd really appreciate for any advice on this matter!
adamjhn
Posts: 46
Joined: Tue Apr 18, 2017 10:05 am

Re: Adding a Rate to an Ion based on the flux of another Reaction function

Post by adamjhn »

Hi,

If I have understood your question, you have something like;

Code: Select all

pump_current_na = rxd.MultiCompartmentReaction(nai, nao, 3.0*pump,
                                               mass_action=False, membrane=mem,
                                               membrane_flux=True)
Where `nai` and `nai` are rxd Species on an intracellular and extracellular region and `pump` is the rate of the Na/K-pump, that only depends on `nai` and `mem` is the membrane region.

To add a potassium current to the model you can add a second MultiCompartmentReaction reaction;

Code: Select all

pump_current_k = rxd.MultiCompartmentReaction(ki, ko, -2.0*pump,
                                               mass_action=False, membrane=mem,
                                               Membrane_flux=True)
Where `ki` and `ko` are rxd Species on an intracellular and extracellular regions.

Or you could specify a single MultiCompartmentReaction to produce both currents;

Code: Select all

pump = rxd.MultiCompartmentReaction(3*nai + 2*ko, 3*nao + 2*ki, pump,
                                               mass_action=False, membrane=mem,
                                               membrane_flux=True)
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