// PARAMETER FILE FOR NEURON 'block' : mitral cell model under
// conditions of TEA and TTX block
// Author : Upi Bhalla
// Mar 29 1991
// Highly detailed model of mit cell with experimental averages for
// cell geometry.
// Format of file :
// x,y,z,dia are in microns, all other units are SI (Meter Kilogram Second Amp)
// In polar mode 'r' is in microns, theta and phi in degrees
// Control line options start with a '*'
// The format for each compartment parameter line is :
//name parent r theta phi d ch dens ...
//in polar mode, and in cartesian mode :
//name parent x y z d ch dens ...
// Coordinate mode
*cartesian
*relative
// Specifying constants
*set_global EREST_ACT -0.065
///// Aditya translated Davison's Bhalla and Bower adapted 7 compartment model from Neuron into Genesis.
///// Davison's model has pseudo compartments interleaved within proper compartments soma, prim, glom and dend.
///// pseudo compartments have only Ra and negligible Cm and Rm.
// #print self.Rs2d # 5154639 Ohms
// #print self.Rs2p # 18281535.6 Ohms
// #print self.Rp2g # 17064846 Ohms
// Ra = RA l / (pi r^2) = RA / (pi r^2), Rm = RM / (2 pi r l), Cm = CM * (2 pi r l)
///// proper compartments have only Rm and Cm, negligible Ra.
///// But cannot set Ra, Rm, Cm values to less than 1e-15, hence CM = 1e-3. However, 1e-15 leads to numerical error accumulation so set reasonable values
///// This is done to ensure no difference between symmetric and asymmetric compartments.
*set_global RA 1e-4
*set_global CM 0.01
*set_global RM 10
//soma none 100 0 0 16 LCa3_mit_usb 40 K_mit_usb 28 KA_bsg_yka 58.7 Ca_mit_conc 5.2e-6 Kca_mit_usb 142 Na_mit_usb 1532 K2_mit_usb 1956
//LCa3_mit_usb causes a 15ms current transient with voltage clamp in mitral cell (Ca ionic channels might cause part of observed 'IPSC'.) - fig 2A left of Isaacson & Westbrook 1998.
//To remove double spikes, the fast first one of which does not propagate into the soma, can increase KA to 587 or LCa3 to 400.
soma none 100 0 0 16 LCa3_mit_usb 40 K_mit_usb 28 KA_bsg_yka 58.7 Ca_mit_conc 5.2e-6 Kca_mit_usb 142 Na_mit_usb 1532 K2_mit_usb 1956
*set_global RM 1e5
*set_global CM 1e-3
// set such that Rs2p # 18281535.6 Ohms
*set_global RA 57.433089
s2p soma 1 0 0 2
*set_global RA 1e-4
*set_global CM 0.01
*set_global RM 10
//prim s2p 100 0 0 104 LCa3_mit_usb 22 K_mit_usb 17.4 K2_mit_usb 12.3 Na_mit_usb 13.4
// fast and full propagation along primary dendrite:
prim s2p 100 0 0 104 LCa3_mit_usb 10 K_mit_usb 17.4 K2_mit_usb 123 Na_mit_usb 134
*set_global RM 1e5
*set_global CM 1e-3
// set such that Rs2p # 17064846 Ohms
*set_global RA 53.6107495
p2g prim 1 0 0 2
*set_global RA 1e-4
*set_global CM 0.01
*set_global RM 10
// original bhalla and bower model had K_mit_usb as 28, but Davison used 200 as he says glom is too excitable. I also use 200.
//glom p2g 100 0 0 26.7 LCa3_mit_usb 95 K_mit_usb 28
glom p2g 100 0 0 26.7 LCa3_mit_usb 95 K_mit_usb 200
// I put below values to make mitral fire more and so that glom is less excitable - however it makes mitral double spike methinks.
//glom p2g 100 0 0 26.7 LCa3_mit_usb 20 K2_mit_usb 123 Na_mit_usb 134
*set_global RM 1e5
*set_global CM 1e-3
// set such that Rs2p # 5154639 Ohms - use this Ra and the dia and len of dend below to get RA. Don't use this pseudo segment's dia and len
//*set_global RA 16.193762
// RA was too large, the lateral dendrite was not responding fast enough - too long time constant. See Margie et al 2000.
// Break lateral dendrite into two compartments
*set_global RA 16
s2d soma 1 0 0 2
// after splitting into two, the electrotonic lengths have changed now.
*set_global RA 1e-4
*set_global CM 0.01
*set_global RM 10
// Using Ra above and l and dia for dend below to get RA + using RM and dia of dend, lambda = 600microns. So electrotonic L of dend = 1/6.
// Compare with lambda of Upi's cell which is 1600 microns, and typical dendrite length is 850microns, hence L=0.5.
// Unlike BBmit1993, Davison doesn't have these LCa3_mit_usb and K_mit_usb in the dendrite!
//dend s2d 100 0 0 170.9 LCa3_mit_usb 4 K_mit_usb 8.5 K2_mit_usb 226 Na_mit_usb 330
dend s2d 100 0 0 170.9 LCa3_mit_usb 4 K_mit_usb 8.5 K2_mit_usb 226 Na_mit_usb 330
*set_global RM 1e5
*set_global CM 1e-3
// set such that Rs2p # 5154639 Ohms - use this Ra and the dia and len of dend below to get RA. Don't use this pseudo segment's dia and len
//*set_global RA 16.193762
// RA was too large, the lateral dendrite was not responding fast enough - too long time constant. See Margie et al 2000.
// Break lateral dendrite into two compartments
*set_global RA 8
//s2d2 dend 1 0 0 2
*set_global RA 1e-4
*set_global CM 0.01
*set_global RM 10
// Unlike BBmit1993, Davison doesn't have these LCa3_mit_usb and K_mit_usb in the dendrite!
//dend2 s2d2 50 0 0 170.9 LCa3_mit_usb 4 K_mit_usb 8.5 K2_mit_usb 226 Na_mit_usb 330
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