Pass ._ref_concentration to pc.source_var()?

Extending NEURON to handle reaction-diffusion problems.

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itaru
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Pass ._ref_concentration to pc.source_var()?

Post by itaru »

Is this supported? I'd like to pass calcium ion concentration info of astrocytes to neighboring pyramidal cells.
ted
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Re: Pass ._ref_concentration to pc.source_var()?

Post by ted »

What are you trying to represent? Calcium-dependent release of neurotransmitters or other substances from astrocytes? Effects on neighboring neurons could be accomplished with a POINTER in an NMODL file for a density or point process mechanism in the affected neuron sections. Another way would be to use an NMODL- or rxd-implemented mechanism in the astrocyte(s) that generates an efflux of the released substance and calculates the resulting extracellular concentration of the substance, then have another mechanism in the affected neuron sections that uses that concentration to modulate channel conductances or production of second messengers. If you want more specific hints, you'll have to provide more information about what you have in mind.
itaru
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Re: Pass ._ref_concentration to pc.source_var()?

Post by itaru »

Hi Ted,
I'm trying to pass an astrocyte's Ca2+ concentration (which is modeled by RxD) to the neighboring pyramidal cells and interneurons via point process synapses that inhibit and excite the two types describing the cai to i conversion equations as described Ma et al. 2013.

As I also want to build a network of the above three, so I was wondering for now, in ParallellContext it is always required to convert
the node to the corresponding segment then pass it to source_var().
ted
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Re: Pass ._ref_concentration to pc.source_var()?

Post by ted »

Ma et al. 2013
Presumably you're referring to Tang et al. 2013 in PLoS One, DOI: 10.1371/journal.pone.0080324. Since you're already using rxd, it will be most natural to follow my second suggestion
rxd-implemented mechanism in the astrocyte(s) that generates an efflux of the released substance and calculates the resulting extracellular concentration of the substance, then have another mechanism in the affected neuron sections . . .
itaru
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Re: Pass ._ref_concentration to pc.source_var()?

Post by itaru »

Hi Ted,
Yes that's the paper I was trying to refer. I'll try your second suggestion and see it works well within my Python script.

Thanks,
Itaru.
ramcdougal
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Re: Pass ._ref_concentration to pc.source_var()?

Post by ramcdougal »

If you got an error or unexpected result with source_var, can you please post it here?

That should just work.
itaru
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Re: Pass ._ref_concentration to pc.source_var()?

Post by itaru »

I get this:

Code: Select all

NEURON: Pointer to src is not in the currently accessed section <Astrocyte.Astrocyte object at 0x15037d447ac0>.soma
 near line 0
 ^
        ParallelContext[0].source_var(..., 2000)
Traceback (most recent call last):
  File "ringtest.py", line 232, in <module>
    settings.pc.source_var(ca[cyt].nodes[100]._ref_concentration, i + 2000, sec=seg.soma)
RuntimeError: hocobj_call error

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