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BREAKPOINT {
SOLVE states METHOD cnexp
rates(v)
ica = gca*inf_m*(v-RT/(2F)*log(cao0/cai))
i = gsyn*s*(v - Esyn)
}
DERIVATIVE states {
s' = -s/tau_s
}
NET_RECEIVE (weight (microsiemens)) {
s=1
}
PROCEDURE rates(v (mV)) {
inf_m = (1/2)*(1+tanh((v-theta_m)/sig_m))
}
I'm having some difficulty understanding how this mechanism relates to anything that might be interesting to model. inf_m is an instantaneous function of membrane potential, and so is ica. There is also some other i that is governed by a conductance that is forced to the value gsyn whenever an input event arrives, regardless of the weight of that event, and then decays monoexponentially back toward 0. These are the features that you want?
I then set up a kinetic scheme for calcium diffusion with the following code:
You're using a different mechanism for this, right? A density mechanism, not a point process, right?
I realize that my ica is a point process (and so the ica*PI*diam/(2*FARADY) is likely flawed)
Why would it be? Presumably this mechanism has a
USEION ca READ cai, ica WRITE cai
statement in its NEURON block, and declares
ica (mA/cm2)
in its ASSIGNED block. In any section that has a mechanism with a USEION ca statement, NEURON automatically creates a ca_ion mechanism that takes care of gathering all calcium currents, whether written by density mechanisms or point processes, and reconciling their units. So you really shouldn't have to do anything special about the fact that one mechanism is a point process and the other is a density mechanism.
At rest I expect the dendrite to reach an equilibrium where the majority of the pipe has calcium concentrations close to or at 50 nM and at and around the site of the synapse the calcium concentrations are slightly elevated. However this is not the case when I run the simulation. The calcium continues accumulated and never seems to stop. I usually stop simulations after 100 seconds (10^5 ms) when the internal calcium becomes absurdly high (in the molar range).
The first thing to do is to debug your calcium accumulation mechanism. Put it into a section all by itself, with no other mechanisms that WRITE ica, and see what happens when you run a simulation.