NEURONS v is different than mine
Posted: Sun Jun 28, 2020 5:54 pm
Hello,
I am in the process of replicating two models in the NEURON framework to extend them in certain ways. At first I wrote one of the models into a single mod file. I didn't use NEURONs built-n v (membrane voltage), I wrote my own differential equation to calculate membrane potential, and I didn't use any USEION statements. Once I ran that model, it worked well. I was able to replicate figures from the paper the original model had come from.
The next step was to break that single mod file up into individual mod files for each of the currents that went into calculating membrane potential. An example of one is shown below. I left out the INITIAL, ASSIGNED, etc blocks to be concise.
NEURON{
SUFFIX B_CaL
USEION CaL WRITE iCaL VALENCE 2
USEION Ca WRITE eCa VALENCE 2
}
BREAKPOINT{
tdCaL = (2.2 - (1.79 * exp( - (.00020292043084065876 * ( - 9.7 + v) * ( - 9.7 + v)))))
fCaLi = (1.0 / (1.0 + exp(((v - VfCaL) / kfCaL))))
dCaLi = (1.0 / (1.0 + exp(((VdCaL - v) / kdCaL))))
iCaL = (gmCaL * dCaL * f1CaL * f2CaL * (v - eCa))
SOLVE states METHOD cnexp
}
When writing these individual mod files I started to use NEURONs v to calculate membrane potential. I also started to use USEION statements to READ in the reversal potential for different currents that have the same ion. For example I also have a R-type calcium current and in that mod file, I would READ eCa in since I had already defined it in the first calcium current mod file (above).
When I ran a simulation with the separate mod files, using neuron's built-in voltage variable, my cells exhibited greater spike magnitude and frequency than when membrane potential was calculated using a differential equation I had in my original single mod file.
I thought that maybe the reversal potential was held fixed in the model I'm trying to replicate, and that by using the USEION statements to READ and WRITE reversal potential, their values might be changing throughout the simulation. So I commented out the USEION statements for reversal potential in each mod file and wrote the value of the reversal potential in the initial block. This had no effect.
I was wondering if there's something I'm missing that would cause such a difference in membrane potential between my single, big mod file, and the separate ones that calculate membrane potential using NEURONs v. Any help is greatly appreciated!
I am in the process of replicating two models in the NEURON framework to extend them in certain ways. At first I wrote one of the models into a single mod file. I didn't use NEURONs built-n v (membrane voltage), I wrote my own differential equation to calculate membrane potential, and I didn't use any USEION statements. Once I ran that model, it worked well. I was able to replicate figures from the paper the original model had come from.
The next step was to break that single mod file up into individual mod files for each of the currents that went into calculating membrane potential. An example of one is shown below. I left out the INITIAL, ASSIGNED, etc blocks to be concise.
NEURON{
SUFFIX B_CaL
USEION CaL WRITE iCaL VALENCE 2
USEION Ca WRITE eCa VALENCE 2
}
BREAKPOINT{
tdCaL = (2.2 - (1.79 * exp( - (.00020292043084065876 * ( - 9.7 + v) * ( - 9.7 + v)))))
fCaLi = (1.0 / (1.0 + exp(((v - VfCaL) / kfCaL))))
dCaLi = (1.0 / (1.0 + exp(((VdCaL - v) / kdCaL))))
iCaL = (gmCaL * dCaL * f1CaL * f2CaL * (v - eCa))
SOLVE states METHOD cnexp
}
When writing these individual mod files I started to use NEURONs v to calculate membrane potential. I also started to use USEION statements to READ in the reversal potential for different currents that have the same ion. For example I also have a R-type calcium current and in that mod file, I would READ eCa in since I had already defined it in the first calcium current mod file (above).
When I ran a simulation with the separate mod files, using neuron's built-in voltage variable, my cells exhibited greater spike magnitude and frequency than when membrane potential was calculated using a differential equation I had in my original single mod file.
I thought that maybe the reversal potential was held fixed in the model I'm trying to replicate, and that by using the USEION statements to READ and WRITE reversal potential, their values might be changing throughout the simulation. So I commented out the USEION statements for reversal potential in each mod file and wrote the value of the reversal potential in the initial block. This had no effect.
I was wondering if there's something I'm missing that would cause such a difference in membrane potential between my single, big mod file, and the separate ones that calculate membrane potential using NEURONs v. Any help is greatly appreciated!