Detection of MOD files in rxd.Region 'o'

Extending NEURON to handle reaction-diffusion problems.

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malthe.nielsen
Posts: 1
Joined: Fri Dec 10, 2021 2:57 pm

Detection of MOD files in rxd.Region 'o'

Post by malthe.nielsen »

Hi

I'm trying to simulate ion accumulation/depletion and diffusion in the Frankenhauser Hodgkin space surrounding a dendrite. Here I want to investigate what happens in this space during intense activation of AMPA and NMDA.
My problem arises when I want my MOD files to communicate with my FH space. At first I defined my FH space as

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fh = rxd.Region(h.allsec(), nrn_region='o', geometry=rxd.Shell(lo=1.5, hi=2.0))
When running my script, there was no response, even if I upped the current going outwards. Meanwhile the concentration inside the dendrite declined in a fashion I would expect.
Then I tried scrapping my FH space and define a extracellular space with rxd.Extracellular, and with this modification the code worked as intended. I found a solution, but moving forwards it would be hard to use that solution with rxd.Extracellular
My main question is if it is even possible to treat a region 'o' as extracellular space and get MOD files to interact with it?
ramcdougal
Posts: 239
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: Detection of MOD files in rxd.Region 'o'

Post by ramcdougal »

We'll look into this. What you describe sounds like it should have worked.
ramcdougal
Posts: 239
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: Detection of MOD files in rxd.Region 'o'

Post by ramcdougal »

Try putting the Shell next to the dendrite... i.e. you want lo = 1

Code: Select all

fh = rxd.Region(h.allsec(), nrn_region='o', geometry=rxd.Shell(lo=1.0, hi=2.0))
The numbers here are in fractions of a radius not µm.
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