I browsered modeldb.science/135787 :
Title:
Intracortical synaptic potential modulation by presynaptic somatic potential (Shu et al. 2006, 2007)
References:
Shu Y, Duque A, Yu YG, McCormick DA. Properties of action potential
initiation in neocortical pyramidal cells: evidence from whole cell
axon recordings. Journal of Neurophysiology. 97: 746-760, (2007).
Shu Y, Hasenstaub A, Duque A, Yu Y, McCormick DA (2006) Modulation of
intracortical synaptic potentials by presynaptic somatic membrane
potential. Nature 441: 761-765.
I opened the Files tab which showed many mod files including:
ca.mod, cad.mod. caL3d.mod, capump.mod
I clicked on only the ca.mod file, then the small gray download arrow and downloaded it directly into desktop/ted/initspineneckcalcium folder.
I browsered modeldb.science/3670
Title:
Thalamic Reticular Network (Destexhe et al 1994)
Reference:
Destexhe A, Contreras D, Sejnowski TJ, Steriade M. (1994). A model of spindle rhythmicity in the isolated thalamic reticular nucleus. J Neurophysiol 72 [PubMed]
I opened the Files tab which showed only one calcium mod file:
capump.mod
I clicked on capump.mod file, and as above put it in the initspineneckcalcium folder.
I confirmed that ca.mod and capump.mod were in the folder.
In the hoc file initspineneckcalcium I looked in vain for a statement that inserts the cad calcium accumulation mechanism (cad), so that I could insert a statement changing the depth parameter to diam/2. I wonder if I am missing an objref statement. I decide to wait for class to garner more details on how to change mod file parameters.
I left clicked on Windows Terminal
at prompt I typed cd initspineneckcalcium, then nrnivmodl, and got:
nrnmech.dll was built successfully.
PS C:\Users\david\Desktop\ted\initspineneckcalcium>
I double-clicked on the folder, then double-clicked on the GUI icon
The familiar graphs and windows opened.
In Biophysics I inserted ca and cad (I saw cad but not capump as Ted had warned me)
into both the spine_head (kopf) and spine_neck.
I made current graphs of cai for both the spine_head and the neck
I Init&Run’d it. I checked View = plot.
https://docs.google.com/document/d/1K-M ... sp=sharing
I expected a baseline calcium concentration of .5-1 x10-4 mM until the first synaptic transmission at 5 ms, then a rapid peak, possibly 10-100 times higher, then a plateau for the 4 synaptic transmissions in the spine_head (kopf), then a return to baseline.
Instead I got a reasonable starting concentration of 1x10-4, but then it decays to zero even before the synaptic transmissions begin.
I am doubtful my failure to change the depth parameter of the calcium accumulation on the inner membrane explains this finding. How much calcium ion is diffused out into the dendrite and how much is pumped out channels along the neck membrane is uncertain. My spine_neck diameter is 0.3 mm, default for the mechanism is 2 mm.
I tried adding an AMPA.mod and an NMDA.mod to the spine_head (kopf) in case the ExpSyn and NetStim mechanisms do not include the ion concentration changes in the standard glutamatergic synaptic transmission parameters. But that made no difference.