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fig6a1-2.hoc
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/* fig6a1-2.hoc Driver Program for Midbrain Dopaminergic Neuron model */
/* The following command loads the standard run library functions into
* the simulator. These library functions are used to initialize the
* simulator, begin and end simulations, and plot variables during a
* simulation. */
timecon = 0
back= 1 /* 1 switch for running in the background */
sakmann=0
if(!back)load_file("nrngui.hoc")
verbose=0
v_init = -60
vcseries = 0
clamp = 0 /* switch for voltage clamp*/
restart = 0 /* switch for initializing from state.old */
tstart = 0
if(vcseries) tstop = 800 else tstop = 10000
if(clamp && !vcseries) tstop= 600
/*if(timecon) tstop = 100*/
if(timecon) tstop = 800
nsyn = 1 /* The number of synapses */
soma_len= 25.0 /*25*/
soma_diam= 15.0
ndend=4
nbranch=2
dend_diam= 1.5 /* 1.5 need to make dendrite taper */
prox_diam= 3.0 /* 3.0 need to make dendrite taper */
taper = 1.0
dend_len = 500.0
prox_len = 150.0
Dtmax = 1.0
Dt = 1.00
if(timecon) Dtmax = 1.0
dt = 5e-4 /*0.1 5e-9 */
if(timecon) dt = 0.01
nainit= 4.000
vsolder=v_init
vdolder=v_init
vsold=v_init
vdold=v_init
create dummy,soma, prox[ndend], dend[nbranch*ndend] /* Create all of the cell's sections */
global_ra = 400
forall Ra = global_ra
global_cm = 1.0
forall cm = global_cm
g_celsius = 35
celsius = g_celsius
forall ion_style("na_ion", 2,2,0,0,0)
access soma /* All default references are to soma */
objectvar syn[nsyn] /* Declare the object variables for
* the three synapses */
objectvar stim
objectvar vc
objref cvode
cvode = new CVode(1) /* 0 for clamp*/
x= cvode.active(1)
proc init_cell() {
/* First set all of the dimensions and insert the channels into each
* section. */
dummy{
L=1
d=1
}
soma {
nseg = 1 /* # of compartments */
diam = soma_diam /* Set the diameter of the soma (in um) */
L = soma_len /* Set the length of the soma (in um) */
{insert nadifl D_nadifl = 0.60 nainit_nadifl = 2.4 f_nadifl = 4.0}
{insert hh3 gnabar_hh3 = 5500.0e-6 gkabar_hh3 = 100.0e-6 gkhhbar_hh3 = 1000.0e-6
miv_hh3 = 44.6 htv1_hh3 = 39.0 hiv_hh3 = 66.8 htv2_hh3 = 59.0}
{insert pump ipumpmax_pump = 0.0036 km_pump = 10.0 }
{insert leak gkbar_leak = 18.0e-6 gnabar_leak = 9.5e-6
ggabaa_leak = 1000.0e-6 gcabar_leak = 0.6e-6 }
{insert cadifus fCa_cadifus = 0.005 cainit_cadifus = 0.000116 }
{insert calcha gcatbar_calcha = 1044.0e-6 gcanbar_calcha = 171.0e-6
gcalbar_calcha = 216.0e-6 gcahvabar_calcha = 0.0e-6}
{insert gkca gkbar_gkca = 900.0e-6 /*0.0e-6*/
ek_gkca = -100 km_gkca = 0.00019
n_gkca = 4.0}
{insert capump icapumpmax_capump = 0.0312 km_capump = 0.0005}
if (!clamp) {
istim = 0.0 /* 0.07 nA=70pA*/
stim = new MyIClamp(.5)
{stim.del = 0 stim.dur = 200000 stim.amp = 0.0
stim.amp2 = 0}
if(timecon) stim.dur = 600 /*(ms)*/
if (sakmann) stim.amp2 = -0.050
if(timecon) stim.amp2 = -0.020
if(timecon) stim.del = 100
} else {
vc = new SEClamp(.5)
if(!vcseries) vc.amp1 = -60.0 else vc.amp1 = -130
vc.dur1 = 50
vc.amp2 = -30.0
vc.dur2 = 350
vc.amp3 = -60.0
vc.dur3 = 201
}
pt3dclear()
pt3dadd(0,0,0,soma_diam)
pt3dadd(soma_len,0,0,soma_diam)
}
for i = 0, ndend-1 prox[i] {
nseg = 1 /* # of compartments */
L = prox_len /* Set the length of the dendrite (in um) */
{insert nadifl D_nadifl = 0.60 nainit_nadifl = 3.0 f_nadifl = 1.0}
{insert hh3 gnabar_hh3 = 5500.0e-6 gkabar_hh3 = 300.0e-6 gkhhbar_hh3 = 1000.0e-6
miv_hh3 = 34.6 htv1_hh3 = 29.0 hiv_hh3 = 56.8 htv2_hh3 = 49.0}
{insert pump ipumpmax_pump = 0.0072 km_pump = 10.0}
{insert leak gkbar_leak = 18.0e-6 gnabar_leak = 9.5e-6
ggabaa_leak = 100.0e-6 gcabar_leak = 0.0e-6 }
{insert nmda Pbar_nmda = 1.5e-6 }
{insert ampa gampa_ampa = 0.0e-6 gampak_ampa = 0.0e-6 ek_ampa = -100.0 ratio = 1}
forall cm = global_cm
forall Ra = global_ra
g_celsius = 35
}
for i = 0, nbranch*ndend - 1 dend[i] {
nseg = 1 /* # of compartments */
L = dend_len - prox_len /* Set the length of the dendrite (in um) */
{insert nadifl D_nadifl = 0.60 nainit_nadifl = 4.59 f_nadifl = 1.0}
{insert hh3 gnabar_hh3 = 5500.0e-6 gkabar_hh3 = 1000.0e-6 gkhhbar_hh3 = 1000e-6
miv_hh3 = 26.6 htv1_hh3 = 21 hiv_hh3 = 48.8 htv2_hh3 = 41.0}
{insert pump ipumpmax_pump = 0.009 km_pump = 10.0}
{insert leak gkbar_leak = 18.0e-6 gnabar_leak = 9.5e-6
ggabaa_leak = 100.0e-6 gcabar_leak = 0.0e-6 }
{insert nmda Pbar_nmda = 1.5e-6}
{insert ampa gampa_ampa = 0.0e-6 gampak_ampa = 0.0e-6 ek_ampa = -100.0 ratio = 1}
forall cm = global_cm
forall Ra = global_ra
g_celsius = 35
}
/* Next we construct the topology by connecting each of the sections
* together. */
connect soma(0),dummy(1)
connect prox[0](0),soma(0)
connect prox[1](0), soma(1)
connect prox[2](0), soma(0.5)
connect prox[3](0), soma(0.5)
for j = 0, ndend-1 {
for i = 0, nbranch-1 {
connect dend[j+i*ndend](0), prox[j](1)}}
dummy{
pt3dclear()
pt3dadd(0.5*soma_len,0,1,1)
pt3dadd(0.5*soma_len,0,0,1)
}
prox[0]{
pt3dclear()
pt3dadd(0,0,0,prox_diam)
pt3dadd(-prox_len,0,0,prox_diam)
}
dend[0]{
pt3dclear()
pt3dadd(-prox_len,0,0,dend_diam)
pt3dadd(-dend_len,0,0,dend_diam/taper)
}
if(nbranch==2) dend[4]{
pt3dclear()
pt3dadd(-prox_len,0,0,dend_diam)
pt3dadd(-prox_len,dend_len-prox_len,0,dend_diam/taper)
}
prox[1]{
pt3dclear()
pt3dadd(soma_len,0,0,prox_diam)
pt3dadd(soma_len+prox_len,0,0,prox_diam)
}
dend[1]{
pt3dclear()
pt3dadd(soma_len+prox_len,0,0,dend_diam)
pt3dadd(soma_len+dend_len,0,0,dend_diam/taper)
}
if(nbranch==2) dend[5]{
pt3dclear()
pt3dadd(soma_len+prox_len,0,0,dend_diam)
pt3dadd(soma_len+prox_len,prox_len-dend_len,0,dend_diam/taper)
}
prox[2]{
pt3dclear()
pt3dadd(0,soma_diam/2,0,prox_diam)
pt3dadd(0,(soma_diam/2 + prox_len),0,prox_diam)
}
dend[2]{
pt3dclear()
pt3dadd(0,(soma_diam/2 + prox_len),0,dend_diam)
pt3dadd(0,soma_diam/2 + dend_len,0,dend_diam/taper)
}
if(nbranch==2) dend[6]{
pt3dclear()
pt3dadd(0,(soma_diam/2 + prox_len),0,dend_diam)
pt3dadd(dend_len-prox_len,soma_diam/2 + prox_len,0,dend_diam/taper)
}
prox[3]{
pt3dclear()
pt3dadd(0,-soma_diam/2,0,prox_diam)
pt3dadd(0,(-soma_diam/2 - prox_len),0,prox_diam)
}
dend[3]{
pt3dclear()
pt3dadd(0,-soma_diam/2 - prox_len,0,dend_diam)
pt3dadd(0,-soma_diam/2 - dend_len,0,dend_diam/taper)
}
if(nbranch==2) dend[7]{
pt3dclear()
pt3dadd(0,-soma_diam/2 - prox_len,0,dend_diam)
pt3dadd(prox_len-dend_len,-soma_diam/2 - prox_len,0,dend_diam/taper)
}
}
topology()
init_cell() /* Call the function to initialize our
* cell. */
objref ss,f1,f2
ss = new SaveState()
f1 = new File()
f2 = new File()
proc init() {local i
if(!restart){
finitialize(v_init)
fcurrent()
}
if(restart){
f1.ropen("state.old")
ss.fread(f1)
f1.close
finitialize(v_init)
ss.restore()
t=tstart
if(cvode.active()){
cvode.re_init()
} else {
fcurrent()
}
frecord_init()
}
t = tstart
}
/*proc continuerun() {local rt
eventcount=0
eventslow=1
stoprun = 0
startsw()
while(t < $1 && stoprun == 0) {
step()
rt = stopsw()
if (rt > realtime) {
realtime = rt
fastflushPlot()
doNotify()
if (realtime == 2 && eventcount > 50) {
eventslow = int(eventcount/50) + 1
}
eventcount = 0
}else{
eventcount = eventcount + 1
if ((eventcount%eventslow) == 0) {
doEvents()
}
}
}
f2.wopen("state.new")
ss.save()
ss.fwrite(f2)
f2.close
flushPlot()
}*/
init()
/*startsw()
flushPlot()*/
if(back){
if(!clamp ||verbose) {print t,soma.v(0.5),dend[1].v(0.99),soma.nai(0.5), dend[1].nai(0.99),soma.cai(0.5),dend[1].inapump_pump(0.99), dend[1].inmda_nmda(0.99)}
if(clamp && !vcseries && !verbose) print t,vc.i,soma.cai(0.5),soma.v(0.5)
if(vcseries) j= 10 else j = 0
for i = 0, j { if (vcseries) vc.amp1 = vc.amp1 + 10}
if(vcseries) init()
next = t + Dt
flag1=0
flag2=0
hold = 0
while (t<tstop){
vsolder=vsold
vdolder=vdold
vsold=soma.v(0.5)
vdold=dend[1].v(0.99)
fadvance()
if(!clamp||verbose){
if((vsolder<vsold &&soma.v(0.5) <vsold)||(vsolder>vsold && soma.v(0.5)>vsold)||(vdolder<vdold &&dend[1].v(0.99) <vdold)|| (vdolder>vdold && dend[1].v(0.99)>vdold)) {
vsolder=soma.v(0.5)
vdolder=dend[1].v(0.99)
print t,soma.v(0.5),dend[1].v(0.99),soma.nai(0.5), dend[1].nai(0.99),soma.cai(0.5), dend[1].inapump_pump(0.99),dend[1].inmda_nmda(0.99)
next = t + Dt
flag2=1
hold=dt
soma.v(0.5)=vsolder
dend[1].v(0.99)=vdolder
}
}
if(t>=next){
Dt = 100*dt
if(Dt>Dtmax) Dt = Dtmax
if (Dt<.1) Dt = .1
next = t + Dt
if(!clamp||verbose) print t,soma.v(0.5),dend[1].v(0.99),soma.nai(0.5), dend[1].nai(0.99),soma.cai(0.5), dend[1].inapump_pump(0.99),dend[1].inmda_nmda(0.99)
if(clamp && !vcseries && !verbose) print t,vc.i,soma.cai(0.5),soma.v(0.5)
}
}
if(vcseries) print vc.amp1,vc.i
f2.wopen("state.new")
ss.save()
ss.fwrite(f2)
f2.close
} else{ if(clamp) {xopen("clamp.ses")} else {xopen("new.ses")}
forall Ra = global_ra
forall cm = global_cm
prox{ forall cm = global_cm}
dend{ forall cm = global_cm}
celsius = g_celsius
}