load_file("stdlib.hoc")
load_file("ObliquePath.hoc")
objref cvode
cvode = new CVode()
cvode.active(0)
create axon[2]
objref SD, AXON, SA, Basal, Trunk, AIS, Trial
objref LM, RAD, RADt, LUC, PSA, PSB, ORI
create soma[1], apical[1], basal[1]
objref pl[150], opl[150]
objref netlist, s, ampasyn, f1, DEND, sapamp, somavec, sampvec
strdef str2
dt = 0.025
tstop = 1650// 1050 //1sec (first 50ms not counted)
steps_per_ms=40
Rm_soma=80000
Rm_end=400
Rm_dend = Rm_soma
Rm_axon = Rm_soma
rm_xhalf = 225
rm_slope = 30
/*Rm_soma=155000
Rm_end=95000
Rm_dend = Rm_soma
Rm_axon = Rm_soma
*/
Ra_soma=150
Ra_end=150
Ra_axon = Ra_soma
Ra_xhalf = 210
Ra_slope = 50
c_m = 1
cmsoma = c_m
cmdend = c_m*1.8
cmaxon = c_m
Vrest = -65
v_init = -65
celsius = 34.0
// uncomment/call find_epsp_amplitudes whenever u change any of the following parameters ..
//gna=0.008//0.005//0.005//0.0066//0.0033
//gkdr =0.006// 0.00167//0.000267//0.00167//0.058
gna=0.02
gkdr=0.0014
//gna=0
//gkdr=0
gexFac = 0.9
AISFactor=5
epsp_amp = 0.0025 //mV
objref ampa_filename
ampa_filename = new String()
gh=0//µS set to the value for which you'll be running withH.hoc and WithHfast.hoc
ghmax=20 //35 //40 //50 //60 //95
xhalf=250 //350 //250 //350
slopegrad=50//5
sprint(ampa_filename.s,"g_dist_withgh0_epspAmp_%f_calculated.txt",epsp_amp)
/********************************************************************/
Ek = -90
Ena = 55
Eh = -30
/********************************************************************/
//radial distance calculation
somax=2.497
somay=-13.006
somaz=11.12
double distances[200]
func raddist() {
distn0=distance(0)
distances[0]=0
sum=0
for i=1,n3d()-1 {
xx=(x3d(i)-x3d(i-1))*(x3d(i)-x3d(i-1))
yy=(y3d(i)-y3d(i-1))*(y3d(i)-y3d(i-1))
zz=(z3d(i)-z3d(i-1))*(z3d(i)-z3d(i-1))
sum=sum+sqrt(xx+yy+zz)
distances[i]=sum
}
xval=$1
// Amoung the various pt3d's find which one matches the distance of
// x closely
distn=distance(xval)
match=distn-distn0
matchptdist=100000
for i=0,n3d()-1 {
matptdist=(match-distances[i])*(match-distances[i])
if(matchptdist>matptdist){
matchptdist=matptdist
matchi=i
}
}
//print "Match for ", x, " is ", matchi, " XDIST ", match, " MATCH ", distances[matchi], " ERROR ", sqrt(matchptdist)
// Find the distance of the closely matched point to the somatic
// centroid and use that as the distance for this BPAP measurement
xx=(x3d(matchi)-somax)*(x3d(matchi)-somax)
yy=(y3d(matchi)-somay)*(y3d(matchi)-somay)
zz=(z3d(matchi)-somaz)*(z3d(matchi)-somaz)
return sqrt(xx+yy+zz)
}
/********************************************************************/
proc update_init(){
finitialize(v_init)
fcurrent()
forall {
for (x){
if (ismembrane("hd")||ismembrane("nas")||ismembrane("na3")||ismembrane("nax")) {
e_pas(x)=v(x)+(i_hd(x)+ina(x)+ik(x))/g_pas(x)
} else {
e_pas(x)=v(x)
}
}
}
}
/********************************************************************/
/**********************************************************************/
// Passive Conductances
proc setpassive(){
forall {
insert pas
e_pas = v_init
Ra=Ra_soma
}
forsec SD{ // For somato-dendritic compartments
cm=cmdend
g_pas=1/Rm_dend
}
forsec "soma" {
cm = cmsoma
g_pas=1/Rm_soma
}
forsec Trunk {
for (x) {
rdist=raddist(x)
rm = Rm_soma + (Rm_end - Rm_soma)/(1.0 + exp((rm_xhalf-rdist)/rm_slope))
Ra = Ra_soma + (Ra_end - Ra_soma)/(1.0 + exp((Ra_xhalf-rdist)/Ra_slope))
g_pas(x)=1/rm
}
}
for i=0,plcount {
seccount=0
forsec pl[i] {
if(!seccount){
trunk_pas=g_pas(1)
seccount=seccount+1
} else {
g_pas=trunk_pas
seccount=seccount+1
}
//print secname()
}
}
}
/**********************************************************************/
// Active Conductances
proc setactive () {
forall{
insert na3
gbar_na3= gna
insert kdr
gkdrbar_kdr=gkdr
insert hd
ghdbar_hd=gh vhalfl_hd=-82
tfactor_hd=1
}
forsec AXON{
gbar_na3= 0
gkdrbar_kdr=0
ghdbar_hd=0
}
forsec "apical"{
insert nas
gbar_nas = gna //has a slow "s" factor
gbar_na3 = 0 //since this was added forall, remove from apical section
}
forsec AIS {
gbar_na3= 0
insert nax
gbar_nax = gna*AISFactor
gkdrbar_kdr=gkdr
ghdbar_hd=0
}
forall{
if(ismembrane("hd")){
ehd_hd=-30
}
if(ismembrane("na3") || ismembrane("nas") || ismembrane("nax")){
ena=55
}
if(ismembrane("kdr")){
ek=-90
}
}
}
/********************************************************************/
proc gh_gradient(){
forsec Trunk { // Trunk
for (x) {
xdist=raddist(x)
ghdbar_hd(x) = gh*(1+ghmax/(1+exp(-(xdist-xhalf)/slopegrad)))
if (xdist > 100){
if (xdist>300) {
ndist=300
} else { // 100 <= xdist <= 300
ndist=xdist
}
vhalfl_hd(x)=-82-8*(ndist-100)/200
} else { // xdist < 100
vhalfl_hd(x)=-82
}
}
}
for i=0,plcount { // Apical obliques
seccount=0
forsec pl[i] {
if(!seccount){ // The first section is the trunk
trunk_h=ghdbar_hd(1)
trunk_vhalf=vhalfl_hd(1)
seccount=seccount+1
} else {
ghdbar_hd=trunk_h
vhalfl_hd=trunk_vhalf
seccount=seccount+1
}
//print secname()
}
}
forsec "soma" {
ghdbar_hd=gh vhalfl_hd=-82
}
forsec Basal {
ghdbar_hd=gh vhalfl_hd=-82
}
forall if (ismembrane("hd") ) ehd_hd = Eh
}
/**********************************************************************/
proc load_3dcell() {
// $s1 filename
forall delete_section()
xopen($s1)
access soma[2] //define origin for distance calculation
distance()
SD = new SectionList() //Somato-dendritic section
SA = new SectionList() // Somato-axonic section
Trunk = new SectionList() //Trunk
Basal = new SectionList() //Basal
Trial = new SectionList()
forsec "soma" {
SD.append()
SA.append()
}
forsec "basal" {
SD.append()
Basal.append()
}
forsec "apical"{
SD.append()
SA.append()
}
// Trunk.
soma[0] Trunk.append()
apical[0] Trunk.append()
apical[4] Trunk.append()
apical[6] Trunk.append()
apical[14] Trunk.append()
apical[15] Trunk.append()
apical[16] Trunk.append()
apical[22] Trunk.append()
apical[23] Trunk.append()
apical[25] Trunk.append()
apical[26] Trunk.append()
apical[27] Trunk.append()
apical[41] Trunk.append()
apical[42] Trunk.append()
apical[46] Trunk.append()
apical[48] Trunk.append()
apical[56] Trunk.append()
apical[58] Trunk.append()
apical[60] Trunk.append()
apical[62] Trunk.append()
apical[64] Trunk.append()
apical[65] Trunk.append()
apical[69] Trunk.append()
apical[71] Trunk.append()
apical[81] Trunk.append()
apical[83] Trunk.append()
apical[95] Trunk.append()
apical[103] Trunk.append()
apical[104] Trunk.append()
soma[0] Trial.append()
apical[58] Trial.append() // 196 µm
apical[64] Trial.append() // 242 µm
apical[69] Trial.append() // 300 µm
apical[103] Trial.append() // 420 µm
load_file("oblique-paths.hoc")
setpassive() //before setting the nseg
// The lambda constraint
totcomp=0
forall{
nseg=int((L/(0.1*lambda_f(100))+0.9)/2)*2+1
totcomp=totcomp+nseg
}
print "totcomp = ",totcomp
init_cell() //calls setpassive()
DEND = new SectionList()
forsec "apical"{
xdist=raddist(1)
if(xdist<300 && xdist > 50){
DEND.append()
}
}
}
/**********************************************************************/
// For cell number n123 on the DSArchive, converted with CVAPP to give
// HOC file, the following definition holds. This is the same as Poirazi et
// al. have used in Neuron, 2003. The argument is that the subtree seems
// so long to be a dendrite, and the cell does not have a specific axon.
// There is a catch, though, if the morphology is closely scanned, then
// basal dendrites would branch from these axonal segments - which
// may be fine given the amount of ambiguity one has while tracing!
proc addaxon() {
AXON = new SectionList()
AIS = new SectionList() // Axonal initial segment
for i = 30,34 basal[i] {
AXON.append()
Basal.remove()
}
for i = 18,22 basal[i] {
AXON.append()
AIS.append()
Basal.remove()
}
forsec AXON {
e_pas=v_init
g_pas = 1/Rm_axon
Ra=Ra_axon
cm=cmaxon
}
}
/********************************************************************/
proc init_cell() {
setpassive()
addaxon()
setactive()
gh_gradient() //sets the gh gradient
access soma[2] // Reinitializing distance origin
distance()
finitialize(v_init)
fcurrent()
forall {
for (x) {
if (ismembrane("hd")||ismembrane("nas")||ismembrane("na3")||ismembrane("nax")) {
e_pas(x)=v(x)+(i_hd(x)+ina(x)+ik(x))/g_pas(x)
} else {
e_pas(x)=v(x)
}
}
}
}
/********************************************************************/
load_3dcell("n123.hoc") //calls setpassive()
/*****************************************************************/
proc find_epsp_amplitudes() { //always call this function whenever any parameter is changed to ensure correct gex values are used
nmdaamparat=0.25
atrise=2.0
atau=3
ntrise=5
ntau=50
netlist=new List()
tstop=40
Gstart=1e-5
Gend=1
wopen(ampa_filename.s)
soma[2] s = new NetStim(0.5)
s.interval=1 // ms (mean) time between spikes
s.number=1 // (average) number of spikes
s.start=2 // ms (mean) start time of first spike
s.noise=0 // range 0 to 1. Fractional randomness.
access soma[2]
distance()
forsec DEND {
for (x) {
if (x!=0 && x!=1){
xdist=raddist(x)
// fprint("%f\n", xdist)
G=Gstart
// ampasyn=new AMPA(x)
// ampasyn.TRise=atrise
// ampasyn.tau=atau
print secname(), " ", x, " ", xdist //distance(x)
ampasyn=new Exp2Syn(x)
ampasyn.e=0
ampasyn.tau1=0.1
ampasyn.tau2=5
netlist.append(new NetCon(s,ampasyn,1,0,0))
while(G<=Gend){
// ampasyn.gmax=G
netlist.remove_all()
netlist.append(new NetCon(s,ampasyn,1,0,G))
finitialize(v_init)
fcurrent()
MAX=-70
while (t <tstop){
fadvance()
if(soma[2].v(0.5)>MAX) {
MAX=soma[2].v(0.5)
}
}
if(MAX>(Vrest+epsp_amp)) {
fprint("%f\n", G)
print G ," ", MAX
//update_init()
break
}
//print G ," ", MAX
G=G+1e-5
}
if(G>=Gend){
print secname(), " ", x, " ", distance(x), "-1"
// fprint("-1\n")
}
}
}
}
wopen()
}
find_epsp_amplitudes()
/*****************************************************************/
///****************************************************************/
objref g_ampa,f1,f2
g_ampa= new Vector(220)
f1=new File()
f1.ropen(ampa_filename.s)
g_ampa.scanf(f1) //reading into vector
f1.close()
f2=new File()
f2.wopen("Calculated_EpspAmp.txt")
proc calc_epsp_amplitudes() {
netlist=new List()
tstop=40
soma[2] s = new NetStim(0.5)
s.interval=1 // ms (mean) time between spikes
s.number=1 // (average) number of spikes
s.start=2 // ms (mean) start time of first spike
s.noise=0 // range 0 to 1. Fractional randomness.
access soma[2]
distance()
count = 0
forsec DEND {
for (x) {
if (x!=0 && x!=1){
xdist=raddist(x)
// fprint("%f\n", xdist)
G=g_ampa.x[count]/gexFac
ampasyn=new Exp2Syn(x)
ampasyn.e=0
ampasyn.tau1=0.1
ampasyn.tau2=5
netlist.append(new NetCon(s,ampasyn,1,0,0))
netlist.remove_all()
netlist.append(new NetCon(s,ampasyn,1,0,G))
finitialize(v_init)
fcurrent()
MAX=-80
while (t <tstop){
fadvance()
if(soma[2].v(0.5)>MAX) {
MAX=soma[2].v(0.5)
}
}
f2.printf("%f\n", (MAX-Vrest))
// print xdist ," ", MAX-Vrest
// print xdist
count += 1
} //end of if()
} //end for(x)
} //end forsec DEND
print count
wopen()
}
//calc_epsp_amplitudes()
///****************************************************************/