In modeldb.science I found several calcium models written for NEURON
Excellent.
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"Spine neck plasticity controls postsynaptic calcium signals" (Grunditz et al. 2008)
That's an interesting paper.
at the c> typed cd then nrnivmodl and it worked
It's great when things work the way they should.
I used the GUI and the Biophysics menu to insert my first test, cadiffus.mod into the neck. I added a Graph for calcium current and ran it.
Very good.
Time for a small digression about cadiffus.mod
In an NMODL definition of a mechanism, the NEURON block contains some important declarations, like what ionic concentrations, concentrations, and equilibrium potentials are used by the mechanism. In cadiffus.mod this statement
USEION ca READ cai, ica WRITE cai
means that the cadiffus mechanism will get these values from NEURON's main computational engine:
cai which is intracellular calcium concentration
ica which is net transmembrane calcium current
and that it will calculate a new value for cai and return that to NEURON's main computational engine.
The cadiffus mechanism implements both radial and longitudinal diffusion; note all the statements that involve calcium exchange between adjacent "annuli," and the LONGITUDINAL_DIFFUSION statement in the KINETIC block.
My Graph for calcium current shows a steady current for the 50ms of stimulation.
I see a graph that plots the time course of two variables: neck.cai(0.5) and something else called "i". neck.cai(0.5) is the intracellular calcium concentration of the compartment that contains the middle of the neck section. From the graph the value of neck.cai(0.5) is not apparent--is it very close to 0, so that it lies on top of the x axis? or is it very close to 4, but hidden by the thick blue line, which plots the time course of i? The way to be sure is to plot neck.cai(0.5) by itself i.e. in its own graph.
And what does i signify? It's not calcium current; that would be called neck.ica(0.5). My guess is that i was a user-defined hoc variable that was used as an index of some sort, e.g. in a loop that does some task several times.
Should diffusion be in the spine head as well?
You could do that by inserting cadiffus into the spine head, but it isn't going to have a significant effect on simulation results.
Can I assume that the ExpSyn activation includes AMPA and NMDA receptor?
ExpSyn generates a NONSPECIFIC_CURRENT which, as you might guess, is not attributed to any particular ion. Grunditz et al. used synaptic mechanisms defined by ampa.mod, and nmda.mod, both of which generate NONSPECIFIC_CURRENTs. For some reason they also use a mechanism called canmda.mod to account for calcium current generated by activation of NMDA receptors. I'm not sure why they thought it was necessary to do that; maybe they explain why in their paper.
Are the voltage-gated ca++ channels only in the postsynaptic density or also in the neck?
I'm not sure what the latest experimental findings have shown, but would assume that they are present everywhere except in the postsynaptic density. In your models there won't be any, anywhere, unless you insert some somewhere.