/* ____________ CELL SET-UP PROCEEDURE _____________ */
strdef sectype
objref CAN_temp, CAL_temp, CAT_temp, KAD_temp, KAP_temp, NA_temp
//RTH>> set distance ref
soma distance()
// Set passive membrane properties
Rm_trunk = 36900 // Non-oblique dendritic specific membrane resistance.")
Rm_non_trunk = 36900 // Apical oblique specific membrane resistance.")
Rm_basal = 46000 // Basal specific membrane resistance.")
Rm_tip = 36900 // Tip specific membrane resistance.")
Rm_soma = 20000 // Somatic specific membrane resistance.")
Rm_axon = 28000 // Axonal specific membrane resistance. ")
Ra_basal = 150 // Basal specific axial resistance.")
Ra_trunk = 150 // Somatic specific axial resistance.")
Ra_non_trunk = 150 // Somatic specific axial resistance.")
Ra_soma = 150 // Somatic specific axial resistance.")
Ra_tip = 150 // Apical tip specific axial resistance.")
Ra_axon = 50 // Axonal specific axial resistance. ")
Cm_default = 1 // Default specific capacitance.")
Cm_axon = Cm_default // Axonal specific capacitance. ")
Cm_soma = 1 // Somatic specific capacitance. ")
Cm_soma = 1.5 // Somatic specific capacitance. ")
Cm_trunk = 1.192 // Trunk specific capacitance.")
Cm_trunk = 1.5 // Trunk specific capacitance.")
Cm_non_trunk = 1.192 // Oblique specific capacitance.")
Cm_non_trunk = 1.5 // Oblique specific capacitance.")
Cm_basal = 1.144 // Basal specific capacitance.")
Cm_tip = 1.192 // Apical tip specific capacitance.")
// SEVERELY affects experiment results
celsius = 34 // Temperature of slice.")
//NDB >>>> $o1.xopen_library("Terrence","cut-sections")
// cut_sections(maximum_segment_length)
maximum_segment_length=75
forall {
nseg=1+int(L/maximum_segment_length)
}
//<<<< NDB
//ORIG>>// make 3-d mapping of cell sections
//NDB >>>> $o1.xopen_library("Terrence","map-segments-to-3d")
// map_segments_to_3d()
forall {
insert d3
i=0
x_d3(0)=x3d(0)
y_d3(0)=y3d(0)
z_d3(0)=z3d(0)
for (x) if (x > 0 && x < 1) {
while (arc3d(i)/L < x) { i += 1 }
D=arc3d(i) - arc3d(i-1)
if (D <= 0) {
printf("\t\t * %s had a D < 0\n", secname())
}
alpha = (x*L - arc3d(i-1))/D
x_d3(x)=x3d(i-1) + (x3d(i) - x3d(i-1))*alpha
y_d3(x)=y3d(i-1) + (y3d(i) - y3d(i-1))*alpha
z_d3(x)=z3d(i-1) + (z3d(i) - z3d(i-1))*alpha
}
x_d3(1)=x3d(n3d()-1)
y_d3(1)=y3d(n3d()-1)
z_d3(1)=z3d(n3d()-1)
}
//NDB <<<<
//ORIG>>// prepare to make a graph with cell configuration
//NDB >>>> $o1.tmpo2=new Shape()
objref tmpo2
tmpo2=new Shape()
//NDB <<<<
//ORIG>>// Set initial conductance values
soma_caL =0.00006
soma_car =0.00003
gsomacar =0.00008
soma_caLH =0.0001 // 0.00017
soma_caT =0.0003
soma_km=0*0.001
potNa=50
mykca_init =0.9*1.5*0.03 //0.03 flag
soma_kca =0.7*4.5*0.0001//0.003 flag
soma_kap =7*0.0005
soma_hbar =1.8e-6
soma_kad =7*0.0005
gna=1.2*0.035 // 0.035
gkdr=2.2*0.015 //flag
gkd=0.005
gnadend=0.015
gkdrdend=2.2*0.015 //flag
gnanotrunk=0*0.01 // 0.035
gkdrnotrunk=2.2*0.015
AXKdr=1
AXNa=1
//v_init=-70
//ORIG>>// Start inserting mechanisms in cell
sectype ="soma"
forsec "soma" {
insert na3
insert kdr
gbar_na3=gna
gkdrbar_kdr=gkdr
ena = potNa
insert nap //flag
gnabar_nap = 0*.5*0.000014
K_nap = 4.5
vhalf_nap = -60.4
insert pas // leak conductance
g_pas = 1/Rm_soma
e_pas = -70
Ra = Ra_soma
cm= Cm_soma
insert h // h current
gbar_h = soma_hbar
K_h = 8.8
vhalf_h = -82
insert kap // proximal A current
gkabar_kap = soma_kap
ek = -80
insert km // m-type potassium current
gbar_km = soma_km
ek = -80
insert cal // HVA Ca++-L type current
gcalbar_cal = 0.1*soma_caL
insert cat // LVA Ca++-T type current
gcatbar_cat = soma_caT
//insert somacar // HVAm Ca++-R type current
//gcabar_somacar = gsomacar
insert car // HVAm Ca++-R type current
gcabar_car = gsomacar
insert kca // K(Ca) mAHP potassium type current
cac_kca=0.00075 //0.0005
gbar_kca = 0.5*soma_kca
insert mykca // K(Ca) fAHP potassium type current
gkbar_mykca = 5.5*mykca_init
insert cad // calcium pump/buffering mechanism
taur_cad=20
//insert cabalan // calcium pump/buffering mechanism
tmpo2.color(2)
}
//ORIG>> Configure Axon
sectype="axon"
forsec axon_sec_list {
insert nax
gbar_nax=gna*AXNa
insert kdr
gkdrbar_kdr=gkdr*AXKdr
ena = potNa
insert pas // leak conductance
g_pas = 1/Rm_axon
e_pas = -70
Ra = Ra_axon
cm = Cm_axon
insert km // m-type potassium current
gbar_km = 3*soma_km
ek = -80
insert kap // proximal A current
gkabar_kap = soma_kap
ek = -80
}
//ORIG>> Configure apical trunk
forsec apical_trunk_list {
//ORIG>>// apical_h_insert_sig($o1) // Inserting h-current
//NDF>>> apical_caR_caLH_insert($o1) // Inserting Ca++ R-type and Ca++ L-type currents
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist=distance(x)
insert car
gcabar_car(x) = 0.1*soma_car
insert calH
if (xdist > 50) {
gcalbar_calH(x) = 2*soma_caLH //4.6*soma_caLH
} else {
gcalbar_calH(x) = 0.1*soma_caLH //0.1*soma_caLH
}
}
//<<<NDF
//NDF>>> apical_caT_insert($o1) // Inserting Ca++ T-type current
caT_distal_maxfactor = 4 //ORIG>> maximum cond. factor in dendrites
caT_distal_distance = 350 //ORIG>> distance in dendrites for maximum cond.
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist = distance(x)
fr = xdist/caT_distal_distance
insert cat
if (xdist < 100) {
gcatbar_cat(x) = 0
} else {
gcatbar_cat(x) = caT_distal_maxfactor*soma_caT*fr
}
}
//<<<NDF
//NDF>>> apical_kca_insert($o1) // Inserting K(Ca) sAHP and mAHP potassium currents
kca_distal_maxfactor = 1 //ORIG>> maximum cond. factor in dendrites
//ORIG>>// kca_distal_maxfactor = 0 //maximum cond. factor in dendrites
kca_distal_distance = 200 //ORIG>> distance in dendrites for maximum cond.
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist = distance(x)
fr = xdist/kca_distal_distance
insert cad // calsium pump/buffering mechanism
taur_cad=20
insert kca // slow AHP K++ current
cac_kca=0.00075 //0.0005
insert mykca // medium AHP K++ current
if (xdist < kca_distal_distance && xdist > 50) {
gbar_kca(x) = 5*soma_kca
gkbar_mykca = 2*mykca_init
} else {
gbar_kca(x) = 0.5*soma_kca
gkbar_mykca = 0.5*mykca_init
}
}
//<<<NDF
//ORIG>>// A_insert($o1) // Inserting A-current
insert h
insert kap
insert kad
for (x){
xdist = distance(x)
if (xdist>500) {xdist=500}
gbar_h(x) = soma_hbar*(1+3*xdist/100)
if (xdist > 100){
if (xdist>300) {ndist=300} else {ndist=xdist}
vhalf_h(x)=-81-8*(ndist-100)/200
gkabar_kad(x) = soma_kad*(1+xdist/100)
gkabar_kap(x)=0
} else {
vhalf_h(x)=-81
gkabar_kap(x) = soma_kap*(1+xdist/100)
gkabar_kad(x)=0
}
}
insert na3
gbar_na3=gnadend
insert nap //flag
gnabar_nap = 0*.5*0.000014
K_nap = 4.5
vhalf_nap = -60.4
insert kdr
gkdrbar_kdr=gkdr
ena = potNa
insert km // m-type potassium current
gbar_km = soma_km
ek = -80
insert pas // leak conductance
g_pas = 1/Rm_trunk
g_pas = 1/Rm_soma //flag
e_pas = -70
Ra = Ra_trunk
cm = Cm_trunk
//ORIG>>>// Rm_sigmoid($o1) // configure Rm along apical trunk
//ORIG>>>// Ra_sigmoid($o1) // configure Ra along apical trunk
tmpo2.color(4)
}
// Configure the apical-non-trunk section: insert basic mechanisms
sectype = "apical non-trunk"
forsec apical_non_trunk_list {
//ORIG>>// apical_h_insert_sig($o1) // Inserting h-current
//NDF>>> apical_caR_caLH_insert($o1) // Inserting Ca++ R-type and Ca++ L-type currents
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist=distance(x)
insert car
gcabar_car(x) = 0.1*soma_car
insert calH
if (xdist > 50) {
gcalbar_calH(x) = 2*soma_caLH //4.6*soma_caLH
} else {
gcalbar_calH(x) = 0.1*soma_caLH //0.1*soma_caLH
}
}
//<<<NDF
//NDF>>> apical_caT_insert($o1) // Inserting Ca++ T-type current
caT_distal_maxfactor = 4 // ORIG>> maximum cond. factor in dendrites")
caT_distal_distance = 350 // ORIG>> distance in dendrites for maximum cond.")
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist=distance(x)
fr = xdist/caT_distal_distance
insert cat
if (xdist < 100) {
gcatbar_cat(x) = 0
} else {
gcatbar_cat(x) = caT_distal_maxfactor*soma_caT*fr
}
}
//<<<NDF
//NDF>>> apical_kca_insert($o1) // Inserting K(Ca) sAHP and mAHP potassium currents
kca_distal_maxfactor = 1 // ORIG>> maximum cond. factor in dendrites")
// ORIG>>//kca_distal_maxfactor = 0 // maximum cond. factor in dendrites
kca_distal_distance = 200 // ORIG>> distance in dendrites for maximum cond.")
for (x) {
xdist = find_vector_distance_precise(secname(),x)
xdist=distance(x)
fr = xdist/kca_distal_distance
insert cad // calsium pump/buffering mechanism
taur_cad=20
insert kca // slow AHP K++ current
cac_kca=0.00075 //0.0005
insert mykca // medium AHP K++ current
if (xdist < kca_distal_distance && xdist > 50) {
gbar_kca(x) = 5*soma_kca
gkbar_mykca = 2*mykca_init
} else {
gbar_kca(x) = 0.5*soma_kca
gkbar_mykca = 0.5*mykca_init
}
}
//<<<NDF
//ORIG>>// A_insert($o1) // Inserting A-current
insert h
insert kap
insert kad
for (x){
xdist = distance(x)
if (xdist>500) {xdist=500}
gbar_h(x) = soma_hbar*(1+3*xdist/100)
if (xdist > 100){
if (xdist>300) {ndist=300} else {ndist=xdist}
vhalf_h(x)=-81-8*(ndist-100)/200
gkabar_kad(x) = soma_kad*(1+xdist/100)
gkabar_kap(x) = 0
} else {
vhalf_h(x)=-81
gkabar_kap(x) = soma_kap*(1+xdist/100)
gkabar_kad(x) = 0
}
}
insert na3
gbar_na3 = gnadend
insert nap //flag
gnabar_nap = 0*.5*0.000014
K_nap = 4.5
vhalf_nap = -60.4
insert kdr
gkdrbar_kdr = gkdr
ena = potNa
insert km // m-type potassium current
gbar_km = soma_km
ek = -80
insert pas // passive properties
g_pas = 1/Rm_non_trunk
e_pas = -70
Ra = Ra_non_trunk
cm = Cm_non_trunk
//ORIG>>//Rm_sigmoid($o1) // configure Rm along apical trunk
//ORIG>>//Ra_sigmoid($o1) // configure Ra along apical trunk
tmpo2.color(3)
}
//ORIG>>//khoblique_peri_decay($o1) // Configure the apical oblique dendrites
// Configure the basal dendrites
sectype = "basal tree"
forsec basal_tree_list {
insert na3dend
insert nap
gnabar_nap = 0*.5*0.000014 //flag
K_nap = 4.5
vhalf_nap = -60.4
insert kap
gkabar_kap = 0.0025036
insert h
gbar_h = soma_hbar
//ORIG>>//ek = -80
insert kdr
gbar_na3dend=gnadend
gkdrbar_kdr=gkdrdend
ena = potNa
insert pas // passive properties
g_pas = 6.458e-05 // 1/Rm_basal
e_pas = -70
Ra = Ra_basal
cm = Cm_basal
//ORIG>>// Ra_sigmoid($o1) // configure Ra
tmpo2.color(5)
}
//ORIG>>//khbasal_fixed($o1) // Configure basal dendrites
forsec "soma" { g_pas= 1/Rm_soma} // force Rm at all soma sections
//ORIG>>// forall if (ismembrane("kdr") ) {
//ORIG>>// ek = -77 //-77
//ORIG>>// }
forall if(ismembrane("ca_ion")) {
eca =140
ion_style("ca_ion",0,1,0,0,0)
vshift_ca = 0
}
//ORIG>>// Print a postcript file in the generic directory with the cell configuration
//NTB>>> sprint(tmp_str2, "%s/configure_sections.eps", $o1.generic_dir)
// $o1.tmpo2.printfile($o1.tmp_str2)
tmpo2.printfile("experiment/configure_sections.eps")
//<<<NTB
//NTB>>> econ.xopen_library("Terrence","current-balance")
//ORIG>>//current_balance(v_init)
//<<<NTB
//ORIG>>//Carmen's change previous origin was at 0 end of apical dendrite[65]
soma distance()
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