CA1 Pyramidal Neuron: slow Na+ inactivation (Migliore 1996)

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Accession:2937
Model files from the paper: M. Migliore, Modeling the attenuation and failure of action potentials in the dendrites of hippocampal neurons, Biophys. J. 71:2394-403 (1996). Please see the below readme file for installation and use instructions. Contact michele.migliore@pa.ibf.cnr.it if you have any questions about the implementation of the model.
Reference:
1 . Migliore M (1996) Modeling the attenuation and failure of action potentials in the dendrites of hippocampal neurons. Biophys J 71:2394-403 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Channel(s): I Na,t; I K; I M; I h;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Active Dendrites; Detailed Neuronal Models; Synaptic Integration;
Implementer(s): Migliore, Michele [Michele.Migliore at Yale.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; I Na,t; I K; I M; I h;
/* base.hoc  */
load_file("nrngui.hoc")
cvode.active(1)

dt=0.05
celsius=30
gna=0.02
gkdr=0.004
gkm=0.0005
gqbar=0.001
mid=1
dist=7
tstop=800

xopen("model.axon")

ropen("mod_ap.sod1d")
num_na_ap=fscan()
double sodium_ap[num_na_ap],coeff_ap[num_na_ap]
for i=0, num_na_ap-1 {
sodium_ap[i]=fscan()
}
ropen()

ropen("mod_ap.nosod1d")
no_num_na_ap=fscan()
double no_sodium_ap[no_num_na_ap]
for i=0, no_num_na_ap-1 {
no_sodium_ap[i]=fscan()
}
ropen()

access soma[0]
distance()

objref g, b
b = new VBox()
b.intercept(1)
g = new Graph()
xpanel("",1)
xbutton("run Fig.3 ", "run3()")
xbutton("run Fig.4bc ", "run4bc()")
xbutton("run Fig.4bd ", "run4bd()")
xpanel()
b.intercept(0)
b.map()

forall {insert pas e_pas=-65 g_pas=1/8000 cm=3.5 Ra=200}

for i=0,NumAxon-1 axon[i] {
	Ra=50
	insert namr ena=50
		gnabar_namr=gna*50 
                vhalf_namr=-55
                vhalfl_namr=-62
                vhalfn_namr=-35
                vvh_namr=55
	insert borgkdr ek=-91
		gkdrbar_borgkdr=gkdr
		vhalfn_borgkdr=-40
		vhalfl_borgkdr=-60
	insert borgkm  gkmbar_borgkm=gkm
	insert q gqbar_q=0
        }

for i=0,NumSoma-1 soma[i] { 
	insert namr ena=50
		gnabar_namr=gna
		vhalf_namr=-50
		vhalfl_namr=-57
		vhalfn_namr=-30
		vvh_namr=58
	insert borgkdr ek=-91
		gkdrbar_borgkdr=gkdr
		vhalfn_borgkdr=-40
		vhalfl_borgkdr=-60
	insert q gqbar_q=gqbar
 	}

for i=0,num_na_ap-1 apical[sodium_ap[i]] {
        insert namr ena=50
		b_namr=0
		gnabar_namr=gna
		vhalf_namr=-50
		vhalfl_namr=-57
		vhalfn_namr=-30
		vvh_namr=-58
	insert borgkdr ek=-91
		gkdrbar_borgkdr=gkdr
		vhalfn_borgkdr=-40
		vhalfl_borgkdr=-60
	insert q gqbar_q=gqbar
        }

for i=0,NumBasal-1 basal[i] {
	insert namr ena=50
		gnabar_namr=gna
		vhalfl_namr=-50
		vhalfl_namr=-57
		vhalfn_namr=-30
		vvh_namr=58
	insert borgkdr ek=-91
		gkdrbar_borgkdr=gkdr
		vhalfn_borgkdr=-40
		vhalfl_borgkdr=-60
	insert q gqbar_q=gqbar
        }


proc init() {
	t=0
        forall {v=-65}
	finitialize(v)
        fcurrent()
        forall {if (ismembrane("namr")) {e_pas=v+(Iq_q+Ir_namr+ina+ik)/g_pas} else {e_pas=v}}
	cvode.re_init()
	}

proc step() {
	fadvance()
	g.plot(t)
//	g.flush()
//	doNotify()
}

proc run() {
	init()
	t=0
	while(t<tstop) { step()}
}

proc run3() {
	tstop=800
	access apical[7]
        nstim=2
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 705, 70, 0.1)
	g.erase_all()
	g.size(0,tstop,-70,30)
	g.addvar("soma[0].v(0.5)",2,1, 2*tstop,0,2)
	g.addvar("apical[mid].v(0.25)",4,2,2*tstop,0,2)
	g.addvar("apical[dist].v(0.4)",3,2,2*tstop,0,2)
	g.color(2)
	g.label(0.2,0.05,"soma")
	g.color(4)
	g.label(0.4,0.05,"152um ")
	g.color(3)
	g.label(0.6,0.05,"410um ")
	g.xaxis(1)
	g.begin()
	printf ("running...")
	run()
	printf("done \n")
}

proc run4bc() {
	tstop=1600
	access apical[7]
	g.erase_all()
	g.size(0,tstop,-70,30)
	g.addvar("apical[dist].v(0.4)",3,1,2*tstop,0,2)
	g.addexpr("r_namr*30",3,1,2*tstop,0,2)
	g.color(1)
	g.label(0.25,0.5,"v 410um ")
	g.label(0.25,0.8,"r_namr ")
	g.xaxis(1)
	g.begin()
        nstim=2
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 655, 70, 0.1)
	tstop=750
	printf("running with 200ms delay...")
	run()
	printf("done \n")
	g.flush()
	doNotify()
	tstop=1050
	g.exec_menu("Keep Lines")
	g.addvar("apical[dist].v(0.4)",2,1,2*tstop,0,2)
	g.addexpr("r_namr*30",2,1,2*tstop,0,2)
	g.begin()
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 955, 70, 0.1)
	printf("running with 500ms delay...")
	run()
	printf("done \n")
	g.flush()
	doNotify()
	tstop=1250
	g.exec_menu("Keep Lines")
	g.addvar("apical[dist].v(0.4)",4,1,2*tstop,0,2)
	g.addexpr("r_namr*30",4,1,2*tstop,0,2)
	g.begin()
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 1155, 70, 0.1)
	printf("running with 750ms delay...")
	run()
	printf("done \n")
	tstop=1550
	g.exec_menu("Keep Lines")
	g.addvar("apical[dist].v(0.4)",1,1,2*tstop,0,2)
	g.addexpr("r_namr*30",1,1,2*tstop,0,2)
	g.begin()
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 1455, 70, 0.1)
	printf("running with 1000ms delay...")
	run()
	printf("done \n")
}

proc run4bd() {
	tstop=800
	access apical[7]
        nstim=3
        fstim(nstim)
        fstim(0, 0.4, 5, 450, 0.1)
        fstim(1, 0.4, 455, 250, -0.5)
        fstim(2, 0.4, 705, 70, 0.1)
	g.erase_all()
	g.size(0,tstop,-120,0)
	g.addvar("apical[dist].v(0.4)",3,1,2*tstop,0,2)
	g.xaxis(1)
	g.begin()
	printf ("running...")
	run()
	printf("done \n")
}



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