State and location dependence of action potential metabolic cost (Hallermann et al., 2012)

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Accession:144526
With this model of a layer 5 pyramidal neuron the state and location dependence of the ATP usage and the metabolic efficiency of action potentials can be analyzed. Model parameters were constrained by direct subcellular recordings at dendritic, somatic and axonal compartments.
Reference:
1 . Hallermann S, de Kock CP, Stuart GJ, Kole MH (2012) State and location dependence of action potential metabolic cost in cortical pyramidal neurons Nat Neurosci. 15(7):1007-14 [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: Neocortex;
Cell Type(s): Neocortex V1 L6 pyramidal corticothalamic cell;
Channel(s): I Na,t; I K;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Action Potentials;
Implementer(s): Hallermann, Stefan [hallermann at medizin.uni-leipzig.de]; Kole, Maarten [m.kole at nin.knaw.nl];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic cell; I Na,t; I K;
/
HallermannEtAl2012
readme.txt *
Cad.mod *
CaH.mod *
CaT.mod *
charge.mod *
h.mod *
Kca.mod *
Kv.mod *
Kv1_axonal.mod *
Kv7.mod *
na8st.mod
nax8st.mod
28_04_10_num19.hoc *
all_28_04_10_num19.ses *
Cell parameters.hoc
charge.hoc *
mosinit.hoc *
                            
objref ff
proc ch() { local i,j,fac, pos, chAll,chDe,chAp,chSo,chCol,chAis,chMy,chNo, chAllA,chDeA,chApA,chSoA,chColA,chAisA,chMyA,chNoA


	//all
	chAll=0
	chAllA=0
	ff=new File()
	ff.wopen("exportOverlAll.tmp")
	forall {
		for j=1,nseg {
			ff.printf("%e\n",overl_charge_(j/nseg))
			pos=0.5/nseg+(j-1)/nseg
			chAll = chAll + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
			chAllA = chAllA + area(pos)
		}
	}
	ff.close()

	//dend
	chDe=0
	chDeA=0
	ff=new File()
	ff.wopen("exportOverlDend.tmp")
	for i=0,dendNum-1 {
		dend[i] {
			for j=1,nseg {
				ff.printf("%e\n",overl_charge_(j/nseg))
				pos=0.5/nseg+(j-1)/nseg
				chDe = chDe + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
				chDeA = chDeA + area(pos)
			}
		}
	}
	ff.close()


	//apic
	chAp=0
	chApA=0
	ff=new File()
	ff.wopen("exportOverlApic.tmp")
	for i=0,apicNum-1 {
		apic[i] {
			for j=1,nseg {
				ff.printf("%e\n",overl_charge_(j/nseg))
				pos=0.5/nseg+(j-1)/nseg
				chAp = chAp + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
				chApA = chApA + area(pos)	
			}
		}
	}
	ff.close()

	//soma
	chSo=0
	chSoA=0
	ff=new File()
	ff.wopen("exportOverlSoma.tmp")
	soma {
		for j=1,nseg {
			ff.printf("%e\n",overl_charge_(j/nseg))
			pos=0.5/nseg+(j-1)/nseg
			chSo = chSo + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
			chSoA = chSoA + area(pos)
		}
	}
	ff.close()

	//collaterals
	chCol=0
	chColA=0
	ff=new File()
	ff.wopen("exportOverlAxon.tmp")
	for i=1,axonNum-1 {					//axon[0] is AIS
		axon[i] {
			for j=1,nseg {
				ff.printf("%e\n",overl_charge_(j/nseg))
				pos=0.5/nseg+(j-1)/nseg
				chCol = chCol + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
				chColA = chColA + area(pos)
			}
		}
	}
	ff.close()

	//ais
	chAis=0
	chAisA=0
	ff=new File()
	ff.wopen("exportOverlAxon.tmp")
	axon[0] {
		for j=1,nseg {
			ff.printf("%e\n",overl_charge_(j/nseg))
			pos=0.5/nseg+(j-1)/nseg
			chAis = chAis + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
			chAisA = chAisA + area(pos)
		}
	}
	ff.close()



	//myelin
	chMy=0
	chMyA=0
	ff=new File()
	ff.wopen("exportOverlMyelin.tmp")
	for i=0,myNum-1 {
		my[i] {
			for j=1,nseg {
				ff.printf("%e\n",overl_charge_(j/nseg))
				pos=0.5/nseg+(j-1)/nseg
				chMy = chMy + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
				chMyA = chMyA + area(pos)
			}
		}
	}
	ff.close()

	//node
	chNo=0
	chNoA=0
	ff=new File()
	ff.wopen("exportOverlNode.tmp")
	for i=0,nodeNum-1 {
		node[i]  {
			for j=1,nseg {
				ff.printf("%e\n",overl_charge_(j/nseg))
				pos=0.5/nseg+(j-1)/nseg
				chNo = chNo + area(pos)*na_ch_charge_(pos)	//mA/cm^2 * um^2
				chNoA = chNoA + area(pos)
			}
		}
	}
	ff.close()


	
	fac=-10^-3*10^4*10^-12*dt*10^-3*6.24*10^18*(1/3)
		// (current (mA) / area (cm^2) ) * area (um^2) * dt in ms   
		//	10^-3          10^4           10^-12        10^-3
		//                         => A*s
		//and:
		//     A*s * number of elementary charges per Coulomb * 3 Na per 1 ATP
		//                   6.24*10^18=1/e=1/1.6*10^19              1/3


	
	printf("--------------------------------------------------------------------------------------\n")
	printf("The Na influx was analyzed from %f to %f ms\n",tStart_charge_,tEnd_charge_)
	printf("Required ATP molecules to pump Na ions out:\n")
	printf("Total: %e\n",fac*chAll)
	printf("Soma: %e\n",fac*chSo)
	printf("Basal dendrite: %e\n",fac*chDe)
	printf("Apical dendrite: %e\n",fac*chAp)
	printf("Axon Initial Segment: %e\n",fac*chAis)
	printf("Axon collaterals: %e\n",fac*chCol)
	printf("Myelin: %e\n",fac*chMy)
	printf("Node: %e\n",fac*chNo)
	printf("--------------------------------------------------------------------------------------\n")
	printf("--------------------------------------------------------------------------------------\n")
	printf("Required ATP molecules to pump Na ions out per um^2:\n")
	printf("Total: %e\n",fac*chAll/chAllA)
	printf("Soma: %e\n",fac*chSo/chSoA)
	printf("Basal dendrite: %e\n",fac*chDe/chDeA)
	printf("Apical dendrite: %e\n",fac*chAp/chApA)
	printf("Axon Initial Segment: %e\n",fac*chAis/chAisA)
	printf("Axon collaterals: %e\n",fac*chCol/chColA)
	printf("Myelin: %e\n",fac*chMy/chMyA)
	printf("Node: %e\n",fac*chNo/chNoA)
	printf("--------------------------------------------------------------------------------------\n")
	printf("Total area (um^2): %e\n",chAllA)
	printf("Soma area (um^2): %e\n",chSoA)
	printf("--------------------------------------------------------------------------------------\n")

	


	//export
	ff=new File()
	ff.wopen("exportChargeNames.tmp")

	ff.printf("%s\n","Total:")
	ff.printf("%s\n","Soma:")
	ff.printf("%s\n","Basal dendrite:")
	ff.printf("%s\n","Apical dendrite:")
	ff.printf("%s\n","Axon Initial Segment: ")
	ff.printf("%s\n","Axon collaterals: ")
	ff.printf("%s\n","Myelin:")
	ff.printf("%s\n","Node: ")

	ff.printf("%s\n","TotalA:")
	ff.printf("%s\n","SomaA:")
	ff.printf("%s\n","Basal dendriteA:")
	ff.printf("%s\n","Apical dendriteA:")
	ff.printf("%s\n","Axon Initial SegmentA: ")
	ff.printf("%s\n","Axon collateralsA: ")
	ff.printf("%s\n","MyelinA:")
	ff.printf("%s\n","NodeA: ")

	ff.close()


	ff=new File()
	ff.wopen("exportChargeValues.tmp")

	ff.printf("%e\n",fac*chAll)
	ff.printf("%e\n",fac*chSo)
	ff.printf("%e\n",fac*chDe)
	ff.printf("%e\n",fac*chAp)
	ff.printf("%e\n",fac*chAis)
	ff.printf("%e\n",fac*chCol)
	ff.printf("%e\n",fac*chMy)
	ff.printf("%e\n",fac*chNo)

	ff.printf("%e\n",fac*chAll/chAllA)
	ff.printf("%e\n",fac*chSo/chSoA)
	ff.printf("%e\n",fac*chDe/chDeA)
	ff.printf("%e\n",fac*chAp/chApA)
	ff.printf("%e\n",fac*chAis/chAisA)
	ff.printf("%e\n",fac*chCol/chColA)
	ff.printf("%e\n",fac*chMy/chMyA)
	ff.printf("%e\n",fac*chNo/chNoA)


	ff.close()

}

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