Pyramidal Neuron Deep: attenuation in dendrites (Stuart, Spruston 1998)

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Accession:3677
Stuart, G. and Spruston, N. Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. Journal of Neuroscience 18:3501-3510, 1998.
Reference:
1 . Stuart G, Spruston N (1998) Determinants of voltage attenuation in neocortical pyramidal neuron dendrites. J Neurosci 18:3501-10 [PubMed]
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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): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I h;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Parameter Fitting;
Implementer(s): Spruston, Nelson [Spruston at Northwestern.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I h;
double vrest[1091]
double vss[1091]
double peakv[1091], synint[1091]

proc init_params() {
	strdef somareadfile, dendreadfile
/*	somareadfile="ri18scs.asc" */
/*	dendreadfile="ri18dcs.asc" */
	somav="dend1[21].v(0.5)"     /* somatic recording site */
	dendv="dend1[183].v(0.01)"   /* dendritic recording site */
	if (syn>0) {
		dendv="dend1[184].v(0.5)" /* dendritic recording site for synaptics */
	}
	tuftv="dend1[235].v(0.5)"   /* dendritic recording site */
	basalv="dend1[866].v(0.5)"  /* distal end of basal beginning at 808 */
	/* initialize user-defined membrane parameters */
	celsius = 35
	global_ra=151   /* internal resistivity in ohm-cm */
	Cm=1.0          /* specific membrane capacitance in uF/cm^2 */
	Rm=23375        /* specific membrane resistivity in ohm-cm^2 */
 	Vleak=-76		/* leak reversal */
	Vrest=-76		/* resting potential */
	qblock=0		/* fraction of q current blocked by Cs */
	nablock=1       /* fraction of na current blocked by TTX */
	kblock=1        /* fraction of k current blocked */
	spinescale=2.0  /* scale total area to account for spines */
	areascale=1.30  /* scale total area by an additional factor */
	target=53.6     /* input resistance target in CsCl */
	/* attenuation is 0.485 in CsCl */
  /* init_pass2 (nonuniform Rm with no sag) */
	if (ipass>1) {
		global_ra=68.022
		rmsoma = 34963
		rmend = 5357
		rmhalfdis=405.84
		rmsteep=50
		Cm=1.5431
		areascale=1.0
		/* determined from fits of five free parameters with rmsteep=50 fixed */
	}
  /* init_pass1 with initq1 (uniform Rm and uniform gh) */
	if ((initq==1) && (qblock<1)) {
		print "uniform Rm and uniform gh"
		maxq=0.000072
		zeta_q=7.2
		a0_q=0.00034
		b0_q=a0_q
		Vleak=-76
	}
  /* init_pass2 with initq1 (nonuniform Rm and uniform gh) */
	if ((initq>1) && (ipass>1) && (qblock<1)) {
		print "nonuniform Rm and uniform gh"
		maxq=0.0000282
		Vleak=-76
		zeta_qq=7.2
		erevq_qq=-43
		vhalf_qq=-81
		a0_qq=0.00034  	/* this value gives taus similar to */
		b0_qq=a0_qq	/* Solmon & Nerbonne, but are too slow, */
				/* hence the very large qten */
		/* qten_qq=33 */
		qten_qq=23.5
	}
  /* init_pass2 with initq2 (nonuniform Rm and nonuniform gh */
 	if ((initq>0) && (ipass>1) && (qblock<1)) {
		print "nonuniform Rm and gh"
		qscale=0.0010001
		maxq=0.01996
		qhalfdis=438.52
		qsteep=50
		Vleak=-76
		zeta_qq=7.2
		erevq_qq=-43
		vhalf_qq=-81 /* was -81 a la Solmon and Nerbonne */
		a0_qq=0.00034  	/* this value gives taus similar to */
		b0_qq=a0_qq	/* Solmon & Nerbonne, but are too slow, */
				/* hence the very large qten */
		qten_qq=3.7963 /* was 7.263 for Vleak=-82 */
	}
}

proc init() { local dtsav
	finitialize(Vrest)
	fcurrent()
	finitialize()
	for i=0,1090 {
		vrest[i]=dend1[i].v(0.5)
	}
	ss_save()
	if (writeout>0) {
		somasimvec.record(&dend1[21].v(0.5))
		dendsimvec.record(&dend1[183].v(0.01))
		if (syn==1) {
			dendsimvec.record(&dend1[184].v(0.5))
			tuftsimvec.record(&dend1[235].v(0.5))
		}
		if (syn>1) {
			dendsimvec.record(&dend1[177].v(0.5))
			tuftsimvec.record(&dend1[235].v(0.5))
		}
	}
	if (qblock<1) {
		dtsav=dt
		dt=10
		t=1e6
		printf("initializing")
		for i=0,40 {
			printf(".")
			fadvance()
		}
		printf("\n")
		dt=dtsav
		finitialize()
		for i=0,1090 {
			vrest[i]=dend1[i].v(0.5)
		}
		ss_save()
	}
	t=0
}

proc advance() {
	fadvance()
	ss_subtract()
}

proc ss_save() {
	Vrestsoma=somaticv()
	Vrestdend=dendriticv()
	ss_subtract()
	for i=0,1090 {
		vss[i]=dend1[i].v(0.5)
	}
}

proc ss_subtract() {
	vsoma=somaticv()-Vrestsoma
	vdend=dendriticv()-Vrestdend
}

proc insert_pass() {
	print "Inserting passive membrane properties\n"
	forall {insert pas Ra=global_ra e_pas=Vleak}
}

proc insertq() {
	printf("Inserting sag conductance in all segments: %d pecent blocked\n",qblock*100)
	forall { insert qq gqbar_qq=0 }
}

proc init_pass1() {
	Cm=$1
	dendscale=spinescale*areascale
	somascale=areascale*1.0
	print "Initializing uniform passive membrane properties\n"
	forall { g_pas=1/(Rm/dendscale) cm=Cm*dendscale Ra=global_ra e_pas=Vleak}
	/* the following segments are NOT scaled for spines */
	/* these include the axon, soma, 1st 100 um of apical trunk, */
	/*  and the 1st 20 um of basals */
	/* the reconstructed axon */
	axon {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	soma {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	for i=0,13 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	/* the real soma */
	for i=14,27 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	/* the 1st 100 um of the apical trunk */
	for i=28,32 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=43,47 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=71,72 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	/* the 1st 20 um of the basals */
	for i=777,778 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=808,810 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=923,924 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=957,959 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=1006,1007 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=1055,1058 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=1059,1060 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
	for i=1067,1069 {
		dend1[i] {g_pas=1/(Rm/somascale) cm=Cm*somascale }
	}
}

proc init_pass2() {
	Cm=$1
	dendscale=spinescale*areascale
	somascale=areascale*1.0
	/* sigmoidal decrease in Rm from rmsoma to rmend */
	/* rmsoma and rmend, and rmhalfdis and rmsteep are set in init_params */
	/* differs from nurm3 in that function applies to basal dendrites also */
	maxdis=1113
	dis=0
	access dend1[21]
	area(0.5)
	distance()
	print "Initializing nonuniform passive membrane properties with nurm4\n"
	forall {g_pas=1/(rmsoma/dendscale) cm=Cm*dendscale Ra=global_ra e_pas=Vleak}
	for i=0,1090 {
		access dend1[i]
		dis=distance(0)
		rmpoint=rmend+(rmsoma-rmend)/(1+exp((dis-rmhalfdis)/rmsteep))
		dend1[i] {g_pas=1/(rmpoint/dendscale) }
	}
	/* the following segments are NOT scaled for spines */
	/* these include the axon, soma, 1st 100 um of apical trunk, */
	/*  and the 1st 20 um of basals */
	/* the reconstructed axon */
	axon { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	soma { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	for i=0,13 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	/* the real soma */
	for i=14,27 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	/* the 1st 100 um of the apical trunk */
	for i=28,32 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=43,47 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=71,72 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	/* the 1st 20 um of the basals */
	for i=777,778 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=808,810 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=923,924 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=957,959 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=1006,1007 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=1055,1058 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=1059,1060 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
	for i=1067,1069 {
		dend1[i] { g_pas=g_pas*somascale/dendscale cm=Cm*somascale/dendscale }
	}
}

proc initq1() {
	qten_qq=$1*10
	/* uniform sag conductance in all compartments */
	forall { gqbar_qq=maxq*dendscale*(1-qblock) }
	printf("Initializing uniform sag conductance in all segments\n")
	/* the reconstructed axon */
	axon { gqbar_qq=0}
	soma { gqbar_qq=maxq*somascale*(1-qblock)}
	for i=0,13 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock) }
	}
	/* the real soma */
	for i=14,27 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	/* the 1st 100 um of the apical trunk */
	for i=28,32 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=43,47 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=71,72 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	/* the 1st 20 um of the basals */
	for i=777,778 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=808,810 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=923,924 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=957,959 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=1006,1007 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=1055,1058 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=1059,1060 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
	for i=1067,1069 {
		dend1[i] { gqbar_qq=maxq*somascale*(1-qblock)}
	}
}

proc initq2() {
	qten_qq=$1
	/* scale up sag conductance as a sigmoidal function of distance from the soma */
	/* q=minq+(maxq-minq)/(1+exp((-dis-qhalfdis)/qsteep)) */
	/* minq=qscale*maxq */
	/* set maxq, qscale, and qhalfdis and qsteep in init_params */
	maxdis=1113
	minq=qscale*maxq
	dis=0
	access dend1[21]
	area(0.5)
	distance()
	printf("Initializing sag conductance in all segments with initq2\n")
	forall { gqbar_qq=0 }
	for i=0,1090 {
		access dend1[i]
		dis=distance(0)
		gqbar_qq=minq+(maxq-minq)/(1+exp(-(dis-qhalfdis)/qsteep))
		gqbar_qq=gqbar_qq*dendscale*(1-qblock)
	}
	/* the reconstructed axon */
	axon { gqbar_qq=0 }
	soma { gqbar_qq=0 }
	for i=0,13 {
		dend1[i] { gqbar_qq=0 }
	}
	/* the real soma */
	for i=14,27 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	/* the 1st 100 um of the apical trunk */
	for i=28,32 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=43,47 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=71,72 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	/* the 1st 20 um of the basals */
	for i=777,778 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=808,810 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=923,924 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=957,959 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=1006,1007 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=1055,1058 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=1059,1060 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
	for i=1067,1069 {
		dend1[i] { gqbar_qq=gqbar_qq*somascale/dendscale }
	}
}