A question about units
Posted: Thu Dec 01, 2016 3:52 pm
Hello all,
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:
Here, mu is unitless dopaminergic modulation, gbar is maximal conductance of the KIR channel in mS/cm2, n is the state variable (I believe also unitless), and v and ek are membrane voltage and channel reversal potential in milivolts, respectively.
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
I've found on this page that Faraday's is taken as
Since Wikipedia sais that F=96485.33289(59) C mol−1, I was wondering is the mol-1 assumed in NEURON's definition of F? Because if I assume that it is, then calculation to get units of GHK equation written in the code correctly comes to coulomb/litre.
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
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:
Code: Select all
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
Code: Select all
FARADAY = (faraday) (kilocoulombs)
Code: Select all
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