load_file("nrngui.hoc")
cvode_active(1)
objref g,p,k,vbox,stim,syn,nc,si,param,apct, apco
Dtaper=1 // setting the initial morphological parameters
Ddend=1
lc=1
Dtrunk=1
ed=0.3 // synapse position in the oblique
ed1=0.15 // recording position in the trunk
weight=.3 // starting synaptic strenght
delta=.05 // increase in synaptic strenght on each simulation
ns=100 // nseg for each compartment
param = new File()
RmDend = 28000
CmDend = 1
RaAll= 150
Vrest = -65
dt = 0.1
gna =0.025
gkdr =0.01
celsius = 35.0
KMULT =0.03
KMULTP =0.03
ghd =0.00005
tstop = 20
create dend[3] // creates 3 dendrites
connect dend[1](0), dend[0](0.5) // connecting the trunk with the branch point
connect dend[2](0), dend[1](1) // connecting the branch point with the oblique dendrite
dend[0] {nseg = ns diam=1 L = 240 insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}
dend[1] {nseg = ns diam=1 L = lc insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}
dend[2] {nseg = ns diam=1 L = 120 insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}
g = new Graph() // vtrunk graph
g.size(0,tstop,-70,30)
g.addvar("dend[0].v(ed1)",1,1,tstop,0,2)
g.label(0.75,0.75,"time (ms)")
g.label(0,0.95,"vtrunk (mV)")
p = new PlotShape() //Shape plot
p.exec_menu("Shape Plot")
p.variable("v")
p.show(0)
p.label(0.6,0.7,"Regular branches")
k = new Graph() // Fig. 6, inset
k.size(0.1,0.4,0,20)
k.label(0.15,0.7,"AP")
k.label(0.15,0.25,"d-spike",2, 1, 0.1, 0.1, 9)
k.label(0.05,0.95,"threshold (nS)")
k.label(0.7,0.15,"d_dend/d_trunk")
// k.label(0.7,0.95,"FIG. 1E, inset")
access dend[0]
distance()
forsec "dend" { //Ion channels
insert hd ghdbar_hd=ghd
insert na3 gbar_na3=gna
insert kdr gkdrbar_kdr=gkdr
insert kap gkabar_kap=0
insert kad gkabar_kad=0
for (x,0) { xdist = distance(x)
ghdbar_hd(x) = ghd*(1+3*xdist/100)
if (xdist > 100){
vhalfl_hd=-81
gkabar_kad(x) = KMULT*(1+xdist/100)
} else {
vhalfl_hd=-73
gkabar_kap(x) = KMULTP*(1+xdist/100)
}
}
}
proc init() {
t=0
forall {
insert ds
v=Vrest
if (ismembrane("nax") || ismembrane("na3")) {ena=55}
if (ismembrane("kdr") || ismembrane("kap") || ismembrane("kad")) {ek=-90}
if (ismembrane("hd") ) {ehd_hd=-30}
for (x,0) { xdist = distance(x)
if (xdist > 100){
vhalfl_hd=-81
gkabar_kad(x) = KMULT*(1+xdist/100)
} else {
vhalfl_hd=-73
gkabar_kap(x) = KMULTP*(1+xdist/100)
}
}
}
finitialize(Vrest)
fcurrent()
forall {
for (x) {
if (ismembrane("na3")||ismembrane("nax")){e_pas(x)=v(x)+(ina(x)+ik(x))/g_pas(x)}
if (ismembrane("hd")) {e_pas(x)=e_pas(x)+i_hd(x)/g_pas(x)}
}
}
cvode.re_init()
cvode.event(tstop)
g.begin()
}
proc advance() {
fadvance()
g.plot(t)
g.flush()
p.flush()
k.flush()
doNotify()
}
forsec "dend[2]"{
objectvar syn // putting a synapse in the oblique
syn = new Exp2Syn(ed)
syn.e=0
syn.tau1 = 0.5
syn.tau2 = 3
si= new NetStimm(ed)
si.interval=0
si.number = 1
si.start=1
si.noise=0
}
param.ropen("morph.txt") //opens the file with the branch morphological parameters
proc run_simulation() {
while(!param.eof()){
branch=branch+1
Ddend= param.scanvar()
lc= param.scanvar()
Dtaper= param.scanvar()
Dtrunk= param.scanvar()
dend[0] {diam(0:1)=Dtrunk:Dtrunk}
dend[1] {diam(0:1)=Dtaper:Ddend L = lc}
dend[2] {diam(0:1)=Ddend:Ddend}
define_shape()
dend[0] apct = new APCount(ed1) //AP count in the trunk
apct.thresh=-20
dend[2] apco = new APCount(ed) //AP count in the oblique
apco.thresh=-40
dend[2] syn.loc(ed)
a=0
while(weight<20 && apct.n<1){ // increases the syn weight until 20 nS or until there is an AP
weight=weight+delta
nc = new NetCon(si,syn,0,0,weight*1.e-3)
run()
if (apco.n > 0){
a=a+1
if (a==1){
loc=weight
delta=.25
k.mark(Ddend/Dtrunk, loc, "o",4,9,4)
}
}
if (apct.n > 0){
print "branch",branch,"; d_dend/d_trunk",Ddend/Dtrunk,"; dspike(nS) ",loc,"; AP(nS) ",weight
k.mark(Ddend/Dtrunk, weight, "o",7,1,2)
}
}
weight=.15
if(apct.n<1){
print branch, ";", Ddend/Dtrunk, ";", loc, ";", "noAP"
}
}
}
xpanel("Run simulation")
xbutton("Run simulation (takes 2 1/2 hours)","run_simulation()")
xpanel()
