/****************************************************************
Used in CA1Models/MiglioreNew2/
cleaned up from Model.hoc. Has been tested to be correct
Jan.9 2005
Load a cell's morphology file and then load Type I biophysical model
****************************************************************/
/*--------------------playing random seed----------------*/
MODELTYPE = 0
use_mcell_ran4(1)
lowindex = 1001
mcell_ran4_init(lowindex)
highindex = 1
tstop = 250
print "---------------------------Type I Model-----------------------------"
//flag for wether or not to use NMDA-R: 0 for without NMDA-R, 1 for with NMDA-R
//this flag will be used in subsequent hoc files: NregNsyn.hoc, Nregsyn.hoc etc
NMDAFLAG = 0
if (NMDAFLAG == 0) { //only AMPA-R
wtAmpa = 1
wtNmda = 0
} else { //NMDAFLAG = 1, with both AMPA-R, NMDA-R
wtAmpa = 0.8
wtNmda = 0.2
}
xopen("./c20466.hoc") // geometry file
soma area(0.5) //make sure diam reflects 3d points
//USER5MAX, APIDENDMAX, BASDENDMAX are set in cell's hoc file
TOTALDEND = USER5MAX + APIDENDMAX + BASDENDMAX + 3 //"3": counting start at 0
objref dend[TOTALDEND]
/****************************************************************************
Grouping dendritic sections together in an array dend, later for being used to
randomly put synapses on the proximal apical, distal apical and basal dendrite
*****************************************************************************/
index = 0
forsec "dendrite" { //this will includes both dendrites and apical-dendrites
dend[index] = new SectionRef()
index += 1
}
forsec "user5" {
dend[index] = new SectionRef()
index += 1
} //now index = USER5MAX + 1
//quadratic function fitting result A and B are set in cell's hoc file
A = A0
B = B0
//synapse rise and decay time constants
TAU1=0.2 //ms
TAU2=10 //ms
dist=1
rel=0.1
Rm = 28000 //unit: Ohm-cm^2
RmDend = Rm/1
RmSoma = Rm
RmAx = Rm
Cm = 1
CmSoma= Cm
CmAx = Cm
CmDend = Cm*1
RaAll= 50 //unit: Ohm-cm
RaSoma=50
RaAx = 50
Vrest = -65
gna = .02 //increasing Na+ channel density instead of decreasing KMULT from 0.025 to 0.015
AXONM = 2
gkdr = 0.01
celsius = 35.0
KMULT = 0.025 //was 0.025
KMULTP = 0.025 //was 0.025
gcan=0.0//005
gcal=0.0//005
gcat=0.0//005
ghd=0.00005
nash=0
forsec "axon" {
insert pas e_pas=Vrest g_pas = 1/RmAx Ra=RaAx cm=CmAx
}
forsec "soma" {
insert pas e_pas=Vrest g_pas = 1/RmSoma Ra=RaSoma cm=CmSoma
}
forsec "dendrite" { //acidentally includes both dendrte and apical_dendrite, i.e. basal & oblique api.
insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend
}
forsec "user5" {
insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend
}
access soma
freq=50
load_file("fixnseg.hoc")
geom_nseg()
tot=0
forall {tot=tot+nseg}
distance()
maxdist=0
forsec "user5" for(x) {if (distance(x)>maxdist) {maxdist=distance(x)}}
printf ("total # of segments (%g hz): %g \t max path distance: %g\n", freq, tot, maxdist)
/****************************************************************************************
The following two lines of declaration are to match up ModelTypeC.hoc mapping bifurcation.
They are not used in ModelTypeI.hoc & ModelPassive.hoc
****************************************************************************************/
objref outfile, sref, blist[USER5MAX+1], aplist
strdef dend2, trunk
forsec "axon" {
insert nax gbar_nax=gna * AXONM sh_nax=nash
insert kdr gkdrbar_kdr=gkdr
//insert pas e_pas=Vrest g_pas = 1/RmAx Ra=RaAx cm=CmAx
insert kap gkabar_kap = KMULTP*0.2
}
forsec "soma" {
insert hd ghdbar_hd=ghd vhalfl_hd=-73
insert na3 ar_na3=1 sh_na3=nash gbar_na3=gna
insert kdr gkdrbar_kdr=gkdr
insert kap gkabar_kap = KMULTP
//insert pas e_pas=Vrest g_pas = 1/RmSoma Ra=RaSoma cm=CmSoma
}
/*---------------------setting up apical oblique dendrite channel kinetics--------*/
for (i=0; i<= APIDENDMAX; i += 1) {
access apical_dendrite[i] {
insert ds
if (diam>0.35) {factor=1} else {factor=1}
insert hd ghdbar_hd=ghd
insert na3 ar_na3=1 gbar_na3=gna*factor sh_na3=nash
insert kdr gkdrbar_kdr=gkdr*factor
insert kap gkabar_kap=0
insert kad gkabar_kad=0
for (x) if (x>0 && x<1) { xdist = distance(x)
ghdbar_hd(x) = factor*ghd*(1+3*xdist/100)
if (xdist > 100){
vhalfl_hd=-81
gkabar_kad(x) = factor*KMULT*(1+xdist/100)
} else {
vhalfl_hd=-73
gkabar_kap(x) = factor*KMULTP*(1+xdist/100)
}
}
}
}
/*---------------------setting up basal dendrite channel kinetics--------*/
for (i=0; i <= BASDENDMAX; i += 1) {
access dendrite[i] {
if (diam>0.35) {factor=1} else {factor=1}
insert hd ghdbar_hd=ghd
insert na3 ar_na3=1 gbar_na3=gna*factor sh_na3=nash
insert kdr gkdrbar_kdr=gkdr*factor
insert kap gkabar_kap=0
insert kad gkabar_kad=0
for (x) if (x>0 && x<1) { xdist = distance(x)
ghdbar_hd(x) = factor*ghd*(1+3*xdist/100)
if (xdist > 100){
vhalfl_hd=-81
gkabar_kad(x) = factor*KMULT*(1+xdist/100)
} else {
vhalfl_hd=-73
gkabar_kap(x) = factor*KMULTP*(1+xdist/100)
}
}
}
}
/*----------------------------setting up main trunk channel kinetics-------------*/
forsec "user5" { // the main trunk
insert ds
// if (diam>0.5) {
insert hd ghdbar_hd=ghd
insert na3 ar_na3=1 gbar_na3=gna sh_na3=nash
insert kdr gkdrbar_kdr=gkdr
insert kap gkabar_kap=0
insert kad gkabar_kad=0
for (x) if (x>0 && x<1) { 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)
}
}
// }
}
//correct the default section name
access soma
objref pw
pw = new PWManager()
pw.landscape(1)
proc init() {
t=0
forall {
v=Vrest
if (ismembrane("nax") || ismembrane("na3")) {ena=55}
//if (ismembrane("na3")) {ar_na3 = 0.6}
if (ismembrane("kdr") || ismembrane("kap") || ismembrane("kad")) {ek=-90}
if (ismembrane("hd") ) {ehd_hd=-30}
}
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)
access soma
// g.begin()
}
proc advance() {
fadvance()
// g.plot(t)
// g.flush()
// p.flush()
// doNotify()
}