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record conductance of soma

Posted: Tue Oct 10, 2017 6:35 pm
by pfortier
I can record the voltage of the soma, soma.v(0.5), but can I record the conductance, soma.g(0.5), to view how the conductance changes with all the opening and closing of voltage-gated and ligand-gated membrane channels?


Re: record conductance of soma

Posted: Tue Oct 10, 2017 7:10 pm
by ted
Assuming that the soma is a single compartment, and that all ion channels in the soma are associated with "density mechanisms" (AKA "distributed mechanisms")--

You need to add up the conductances associated with each kind of active and passive ion channel that is present in the soma. Each active ion channel mechanism must actually calculate the conductance associated with the current that it generates, and make that conductance available as a RANGE variable; this means you may have to revise some of the mod files you are using.

The easiest thing to do is just record the time course of each active ionic conductance to its own Vector during the simulation, then do an elementwise addition of the Vectors after the simulation ends, and finally add the conductances of any passive channels. The result will have density units (S/cm2). If you also need to add the conductance of a point process (who knows, your model might have one highly localized ion channel implemented as a point process) then you'll want to those add that too, but remember that its conductance will be in uS so you'll first have to convert to S/cm2 (divide its Vector's elements by the soma's area in um2, then multiply by 1e8).