I am interested in a model of striatal medium spiny neuron proposed in the paper by Gruber et al. 2003. I have found a NEURON implementation on ModelDB, but going through the files I've encountered a problem with how units of ion channel variables are implemented in the simulation. Since I would like to change ion channel parameters later on, I would like to understand what are the proper ranges for the units. Also, a disclaimer, I'm a total beginner in NEURON.
There are two main questions that are confusing me. The first is in the file kir2.mod, in the section BREAKPOINT:
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BREAKPOINT {
SOLVE states METHOD cnexp
g = mu*(0.001)*gbar*n
ik = g*(v - ek)
i = (1000)*ik
}
What confuses me is why was g, which in ASSIGNED block is given the units in mho/cm2, not simply declared in mS/cm2 right from the start? Also, what was the purpose of introducing current ik, which is just i but in mA/cm2?
The second question concerns CaL channel. In the UNITS section, Faraday's constant is defined as
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FARADAY = (faraday) (kilocoulombs)
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faraday \= 9.652+4 coul
The good news is that during the very long time it took to write this post and double-check all the units, definitions, and conversions between the paper and the code, I actually found answers to most of the other problems that have been bothering me for a while now.
Best regards,
Marko