fig2A.hoc

load_file("nrngui.hoc")
cvode_active(1)

numaxon=1
numsoma=1
numbasal=52
numapical=70
numtrunk=49

xopen("geo5038804.hoc")             // geometry file
xopen("fixnseg.hoc")           

Rm = 28000
RmDend = Rm
RmSoma = Rm
RmAx = Rm

Cm    = 1
CmSoma= Cm
CmAx  = Cm
CmDend = Cm

RaAll= 150
RaSoma=150  
RaAx = 50

Vrest = -65
dt = 0.1
gna =  .025
AXONM = 5
gkdr = 0.01
celsius = 35.0  
KMULT =  0.03
KMULTP = 0.03
ghd=0.00005

objref g, b,c, stim, distrx, distry, cdistry, p

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"{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
geom_nseg()
tot=0
forall {tot=tot+nseg}
distance()

tstop=20

b = new VBox()
b.intercept(1)
g = new Graph()
g.size(0,tstop,-70,30)
g.addvar("soma.v(0.5)",1,1,2*tstop,0,2)
g.xaxis(1)
c = new Graph()
c.size(0,740,0,100)
c.xaxis(1)
c.exec_menu("10% Zoom out")
c.color(1)
c.label(0.4,0.8," peak AP")
xpanel("")
xbutton("runm ", "runm()")
xpanel()
b.intercept(0)
b.map()

p = new PlotShape()
p.exec_menu("Shape Plot")
p.size(-194.658,304.758,-223.667,609.667)
p.variable("v")
p.show(0)

rel=0.5
soma {
stim= new IClamp(rel)
stim.amp=2.5
stim.dur=1.5
stim.del=1
}

forsec "axon" {   
                insert nax gbar_nax=gna * AXONM
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP
}

forsec "soma" {   
		insert hd ghdbar_hd=ghd	vhalfl_hd=-73
                insert na3 gbar_na3=gna
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP
}

for i=0, numbasal-1 dendrite[i] {
		insert hd ghdbar_hd=ghd vhalfl_hd=-73
                insert na3 gbar_na3=gna
                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)
               				}
		}
}
                
forsec "apical_dendrite" {
	insert ds
		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) 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)
               				}
		}
}

forsec "user5" {
	insert ds
		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) 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)
               				}
		}
}

proc init() {
	t=0
        forall {
        v=Vrest
        if (ismembrane("nax") || ismembrane("na3")) {ena=55}
        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()
}

proc runp() {
stdinit()
continuerun(tstop)

	distrx=new Vector()
	distry=new Vector()
	forsec "apical_dendrite" {
		for (x) if (x>0 && x<1) {
			if (diam>=0.) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	distry.mark(c,distrx,"O",3,3,2)

	distrx=new Vector()
	distry=new Vector()
	forsec "user5" {
		for (x) if (x>0 && x<1) {
			if (diam>=0) {
			distrx.append(distance(x)) 
			distry.append(vmax_ds(x)-Vrest)
			}
		}
	}
	distry.mark(c,distrx,"t",5,$1,1)
	c.flush()
	doNotify()

}

proc runm() {
runp(1)
}