parameter controlling the rate of influx of a species in multiple compartments

Extending NEURON to handle reaction-diffusion problems.

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Tuoma
Posts: 13
Joined: Mon Apr 23, 2018 6:59 am

parameter controlling the rate of influx of a species in multiple compartments

Post by Tuoma »

I'm trying to introduce RxD species and reactions into a set of compartments in a multicompartmental neuron model and give inputs to some of the species. I have a list of sections for which I'm creating the Rxd Region (after defining a cell model L5PC, in this case a regular Hay model) as

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seclist = [h.L5PC.apic[3],h.L5PC.apic[30],h.L5PC.apic[90]]
cyt = rxd.Region(seclist, name='cyt', nrn_region='i')
I divided it also into different regions as

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cyts = []
for iapic in [3,30,90]:
    cyts.append(rxd.Region([h.L5PC.apic[iapic]], name='cyt_apic'+str(iapic), nrn_region='i'))
Let's say I have a species gaba in my three compartments as follows:

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gaba = rxd.Species(cyt, name='gaba', charge=0, initial=0.0)
I then try to allow gabaergic input to one of the compartments, so I created parameters controlling the rate of gaba influx for each of them:

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gaba_flux_rates = []
reaction_gaba_fluxes = []
for icyt in range(0,len(seclist)):
  gaba_flux_rates.append(rxd.Parameter(cyts[icyt], initial=0))
  reaction_gaba_fluxes.append(rxd.Rate(gaba, gaba_flux_rates[icyt]))

Later I'd like to add events that alter the parameters gaba_flux_rates[icyt], but I'm already getting an error saying "Rates and Reactions with species defined on different regions are not currently supported." If I instead define just one gaba_flux_rate parameter for the whole cyt region and one corresponding Rate reaction, it compiles and runs. But then I cannot control the gaba rate at different compartments separately, instead the gaba flux is always the same to all compartments.

Any advice?
Tuoma
Posts: 13
Joined: Mon Apr 23, 2018 6:59 am

Re: parameter controlling the rate of influx of a species in multiple compartments

Post by Tuoma »

I think I resolved the issue. The problem seems to be that I first defined a "master" RxD region 'cyt' and then for each of the sections (already included in 'cyt') a separate miniregion cyts, and maybe that's what caused the error message "Rates and Reactions with species defined on different regions are not currently supported". My code seems to work when I dump the master region 'cyt'.
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