where to declare cai and cao ?
Posted: Sun Nov 24, 2019 10:54 pm
Dear all,
My question is somehow related to the Pascal's question viewtopic.php?f=16&t=4084 because, it seems, I stumbled to a similar problems.
I'm trying to play around with Iavarone's model, which uses the same old Destexhe's code https://senselab.med.yale.edu/ModelDB/S ... 881#tabs-1. At least in two modules for low and high threshold calcium currents read inner and outer calcium concentrations (cai, cao) and compute the GHK equation. These two global segment's variables are listed in the parameters block:
Note that someone tried to adjust these parameters and even set inner calcium concentration into different values for different calcium currents.
However, it seems, NEURON ignores these values:
Do I understand correctly, that cai and cao should be in ASSIGNED block without any values attached and all default settings should be done in a compartment? Something like this in hoc
or python
It isn't clear to me whether should I set ion style for calcium ion and if I should, which style should I choose?
My question is somehow related to the Pascal's question viewtopic.php?f=16&t=4084 because, it seems, I stumbled to a similar problems.
I'm trying to play around with Iavarone's model, which uses the same old Destexhe's code https://senselab.med.yale.edu/ModelDB/S ... 881#tabs-1. At least in two modules for low and high threshold calcium currents read inner and outer calcium concentrations (cai, cao) and compute the GHK equation. These two global segment's variables are listed in the parameters block:
Code: Select all
:from TC_iL.mod
PARAMETER {
v (mV)
celsius (degC)
dt (ms)
cai = 0.5E-4 (mM) : Value from Amarillo et al., J Neurophysiol, 2014
cao = 2 (mM)
pcabar= 1e-4 (cm/s)
}
:from TC_ITGHK_Des98.mod
PARAMETER {
v (mV)
:celsius = 36 (degC)
celsius (degC) : EI
pcabar =.2e-3 (cm/s) : Maximum Permeability
shift = 2 (mV) : corresponds to 2mM ext Ca++
actshift = 0 (mV) : shift of activation curve (towards hyperpol)
cai = 2.4e-4 (mM) : adjusted for eca=120 mV
cao = 2 (mM)
qm = 2.5 : Amarillo et al., J Neurophysiol, 2014
qh = 2.5 : Amarillo et al., J Neurophysiol, 2014
}
However, it seems, NEURON ignores these values:
Code: Select all
nocmodl" TC_ITGHK_Des98
Translating TC_ITGHK_Des98.mod into TC_ITGHK_Des98.c
Warning: Default 2 of PARAMETER cao will be ignored and set by NEURON.
Warning: Default 0.00024 of PARAMETER cai will be ignored and set by NEURON.
Thread Safe
Code: Select all
soma cai = 2.4e-4 // default variable adjusted for eca=120 mV
soma cao = 2
Code: Select all
soma(0.5).cai = 2.4e-4 # default variable adjusted for eca=120 mV
soma(0.5).cao = 2