begintemplate Mousa2020
//"This is a simplified 6 compartment cell template for Mousa, 2020 Model"
public soma, iseg, dend1, dend2, dend3,dend0
public all, somatic, basal, AHIS
// load_file("nrngui.hoc") // Load Neuron
proc init() {
createCell()
subsets()
parameters()
//segments_numbers() //enabling this, would increase the nseg
}
// soma
//------
create soma
//
proc createCell(){
RM = 225/2.28 //change RM
v_init = -70
soma {
nseg = 1
L = 48.8
diam = 48.8
insert pas
g_pas= 1/RM
e_pas= v_init
Ra = 70
cm = 1
insert NafSmb1
gnabar_NafSmb1 = 0.105 // 0.06
th_NafSmb1 = 40
insert KdrSmb1
gkdrbar_KdrSmb1 = 0.2 //0.80048
insert CaSmb1
gkcabar_CaSmb1 = 0.0221 // instead of 0.02
gcanbar_CaSmb1 = 0.01
gcalbar_CaSmb1 = 0
amA_NafSmb1 = 17 //22 ->changed
bmA_NafSmb1 = 37 //46 ->changed
theta_h_NafSmb1 = 47
theta_n_KdrSmb1 = 20
thetamn_CaSmb1 = 14
thetahn_CaSmb1 = 32
f_CaSmb1 = 0.01
alpha_CaSmb1 = 1
kca_CaSmb1 = 8
kd_CaSmb1 = 0.0005
nexp_CaSmb1 = 1
}
// axon hillock
//--------------
// iseg {
// nseg = 1
// L = 20
// diam = 12.94999838
// insert pas
// g_pas= 1/225
// e_pas= v_init
// Ra = 70
// cm = 1
// // insert hb1
// // ghbar_hb1 = 0.001/7
// insert NafIsb1
// gnabar_NafIsb1 = 1.3392
// th_NafIsb1 = 40
// insert NapIsb1
// gnapbar_NapIsb1 = 3.2971e-5
// insert KdrIsb1
// gkbar_KdrIsb1 = 0.16552
// amA_NafIsb1 = 18
// bmA_NafIsb1 = 38
// theta_h_NafIsb1 = 47
// theta_n_KdrIsb1 = 20
// ampB_NapIsb1 = 30.4
// bmpB_NapIsb1 = 34.7
// }
// CaDen_Max = 0.000168 // for a peak of 12.29
// // Dendrites
// //-----------
// dend0 {
// insert info
// nseg = 1
// // L = 1625.55
// L = 1450.97
// diam = 42.2188 // Area 64%
// // diam(0:1) = 41.436:42.492
// insert pas
// g_pas= 1/11000
// e_pas= v_init
// Ra = 70
// cm = 1
// // insert hb1
// // ghbar_hb1 = 0.002/7
// }
// dend1 {
// insert info
// nseg = 1
// // L = 1625.55
// L = 1450.97
// diam = 42.2188 // Area 64%
// // diam(0:1) = 41.436:42.492
// insert pas
// g_pas= 1/11000
// e_pas= v_init
// Ra = 70
// cm = 1
// // insert hb1
// // ghbar_hb1 = 0.002/7
// }
// dend2 {
// insert info
// // L = 1581.58
// // diam(0:1) = 42.492:34.303
// L = 754.842 * 1.81
// diam = 36.4297 //Area 26%
// nseg = 1
// insert pas
// g_pas= 1/11000
// e_pas= v_init
// Ra = 70
// cm = 1
// // insert hb1
// // ghbar_hb1 = 0.002/7
// // insert Llvab1
// // gcaLlvabar_Llvab1 = 0.00016
// // theta_m_Llvab1 = -43
// // tau_m_Llvab1 = 60
// // kappa_m_Llvab1 = -6
// insert CaDen
// theta_m_CaDen = -43 // was 43 originally
// O_tau_CaDen = 10 // was 60 originally , 20 , 10 give better results
// O_tau2_CaDen = 50
// W_tau_d_CaDen = 1200 // was 1200 originally
// tailon_CaDen = 1 // 1 for on, 0 for off
// AmpRandG_CaDen = 0.5 // compensation for turning the RNG off
// gcabar_CaDen = CaDen_Max
// gkcabar_CaDen = CaDen_Max * 0.41
// Warm_Gear_CaDen = 1 // 1 is the default, increasing it, ramp-up the warm-up kinetics
// Warm_thresh_CaDen= 0.27
// }
// dend3 {
// // L = 3587.98
// // diam(0:1) = 34.303:0.53
// L = 1037.91 * 1.81
// diam = 10.1901 // area 10%
// nseg = 1
// insert info
// insert pas
// g_pas= 1/11000
// e_pas= v_init
// Ra = 70
// cm = 1
// // insert hb1
// // ghbar_hb1 = 0.002/7
// insert CaDen
// theta_m_CaDen = -43 // was 43 originally
// O_tau_CaDen = 10 // was 60 originally , 20 , 10 give better results
// O_tau2_CaDen = 50
// W_tau_d_CaDen = 1200 // was 1200 originally
// tailon_CaDen = 1 // 1 for on, 0 for off
// AmpRandG_CaDen = 0.5 // compensation for turning the RNG off
// gcabar_CaDen = CaDen_Max * 0.25
// gkcabar_CaDen = CaDen_Max * 0.41 * 0.25
// Warm_Gear_CaDen = 1 // 1 is the default, increasing it, ramp-up the warm-up kinetics
// Warm_thresh_CaDen= 0.27
// }
print "Soma-> One compartment cell created"
}
objref all, somatic, basal , AHIS
proc subsets() {
objref all, somatic, basal , AHIS
all = new SectionList()
soma all.append()
// iseg all.append()
// dend1 all.append()
// dend2 all.append()
// dend3 all.append()
// dend0 all.append()
somatic = new SectionList()
soma somatic.append()
// basal = new SectionList()
// dend1 basal.append()
// dend2 basal.append()
// dend3 basal.append()
// dend0 basal.append()
// AHIS = new SectionList()
// iseg AHIS.append()
}
proc parameters() {
celsius = 36 // Temperature at which simulations are performed
v_init = -70 // mV, resting membrane potential
}
proc uninsert_Active_channels() {
soma {
uninsert NafSmb1
uninsert KdrSmb1
uninsert CaSmb1
uninsert hb1
uninsert kv2_hh
}
// iseg {
// uninsert hb1
// uninsert NafIsb1
// uninsert NapIsb1
// uninsert KdrIsb1
// }
// forsec "den" {
// //uninsert CaDen
// }
print "Active channels has been removed from Soma , iseg , ah sections, please check the dendrites carefully"
}// End of Procedure
// Define nseg in every segment according to d_lambda
// for testing purposes.
external lambda_f
proc segments_numbers() {
D_LAMBDA = 0.1
forall { nseg = int((L/(D_LAMBDA*lambda_f(100))+0.9)/2)*2 + 1 }
} // End of Procedure
endtemplate Mousa2020