Add term to RxD solution.

Extending NEURON to handle reaction-diffusion problems.

Moderators: hines, wwlytton, ramcdougal

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ahmed.hamzah
Posts: 37
Joined: Thu Jun 07, 2018 10:57 am

Add term to RxD solution.

Post by ahmed.hamzah » Fri Sep 07, 2018 5:43 pm

Hi everyone

I am working in RxD to find Na and k concentration inside axon, I know that RxD equation consists many terms:
\[\frac{\partial u}{\partial t} = d \nabla^2 u + f(u, t)\]
but I would like to add a new term to the right side, I know that the first term on the left side of the equation above " d \nabla^2 u" is one term of Nernst-Planck flux. I would like to add the other term of Nernst-Planck flux to the RxD equation. Can anyone help me please?

ahmed.hamzah
Posts: 37
Joined: Thu Jun 07, 2018 10:57 am

Re: Add term to RxD solution.

Post by ahmed.hamzah » Wed Sep 12, 2018 11:58 am

Can anyone help me please ? is there answer to my question ?

ramcdougal
Posts: 149
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Medicine

Re: Add term to RxD solution.

Post by ramcdougal » Fri Sep 14, 2018 10:59 am

The bad news: The reaction-diffusion module rxd currently only directly supports reactions and diffusions. So you could add arbitrary local kinetics, but you'd have to modify the source to add the type of dynamics you describe.

The good news: besides storing parameters, all of the changes would be confined to neuron.rxd.species.section1d.Section1d._setup_diffusion_matrix which ought to be cleaned up anyways. There's a little complexity based on the use of algebraic/0-volume/conservation-of-mass nodes at section boundaries, but basically it would be a matter of setting the right entries in the Jacobian matrix g.

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