Computational model of cerebellar tDCS (Zhang et al., 2021)

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Accession:267189
This archive contains models used in (Zhang et al. 2021) and simulates Purkinje cell, granule cell, and deep cerebellar neuron activities under cerebellar tDCS (transcranial direct current stimulation).
Reference:
1 . Zhang X, Hancock R, Santaniello S (2021) Transcranial Direct Current Stimulation of Cerebellum Alters Spiking Precision in Cerebellar Cortex: A Modeling Study of Cellular Responses. PLoS Comp Biol 17(12):e1009609 [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: Cerebellum;
Cell Type(s): Cerebellum Purkinje GABA cell; Cerebellum interneuron granule GLU cell; Cerebellum deep nucleus neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s):
Implementer(s):
Search NeuronDB for information about:  Cerebellum Purkinje GABA cell; Cerebellum interneuron granule GLU cell;
// Template of the Purkinje cell model, Masoli et al.,2015
// Masoli S, Solinas S, D'Angelo E (2015) Action potential processing in a detailed Purkinje cell model reveals a critical role for axonal compartmentalization. Front Cell Neurosci 9:47
// Modified to include dendritic voltage shift for simulation of calcium bursts under tDCS
load_file("nrngui.hoc")
load_file("PC_param.hoc")

// Soma
create soma
soma {
	nseg = 1
	diam = 29.8
	cm = 0.77
	L =  29.8
	Ra = 122

	insert Leak
	e_Leak = eleak
	gmax_Leak = LeakSoma

	insert Cav3_1
	pcabar_Cav3_1 = Cav3_1Soma

	insert Cav2_1
	pcabar_Cav2_1 = Cav2_1Soma

	insert HCN1
	gbar_HCN1 = HCNSoma
	eh = -34.4

	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Soma
	ena = 60

	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Soma
	ek = -88

	insert Kv1_1
	gbar_Kv1_1 = Kv1_1Soma

	insert Cav3_2
	gcabar_Cav3_2 = Cav3_2Soma

	insert Kca3_1
	gkbar_Kca3_1 = Kca3_1Soma

	insert Cav3_3
	pcabar_Cav3_3 = Cav3_3Soma

	insert Kir2_3
	gkbar_Kir2_3 = PC_KirSoma

	insert Kca1_1
	gbar_Kca1_1 = Kca1_1Soma

	insert Kca2_2
	gkbar_Kca2_2 = Kca2_2Soma

	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.000267 + 0.0167* exp(-(diam)/0.722) + 0.0028* exp(-(diam)/4)

	TotalPump_cdp5 = 5e-8

	pt3dclear()
	pt3dadd(0.0, 0, 0.0, 29.8)
	pt3dadd(0.0, 29.8, 0.0, 29.8)

	ion_style("ca_ion", 1, 1, 0, 1, 0) 
	eca = 137.52625 
	cai = cai0_ca_ion
	cao = cao0_ca_ion
}

// Dendrites
load_file("createDendrites.hoc")
objref alldend, Sdend, Mdend, Ldend
alldend = new SectionList()
Sdend = new SectionList()
Mdend = new SectionList()
Ldend = new SectionList()
forsec "dend*" {alldend.append() }
load_file("locateDendrites.hoc")
load_file("connectDendrites.hoc")

forsec alldend {
	Ra = 122
	
	insert Leak
	e_Leak = eleak

	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Dend

	insert Kca1_1
	gbar_Kca1_1 = Kca1_1Dend

	insert Kv4_3
	gkbar_Kv4_3 = Kv4_3Dend

	insert Kv1_1
	gbar_Kv1_1 = Kv1_1Dend

	insert Kv1_5
	gKur_Kv1_5 = Kv1_5Dend

	insert Kv3_3
	gbar_Kv3_3 = Kv3_3Dend

	insert Cav3_3
	pcabar_Cav3_3 = Cav3_3Dend

	insert HCN1
	gbar_HCN1 = HCNDend
	eh = -34.4
		
	TotalPump_cdp5 = 2e-8
}

forsec Mdend {
	insert Cav3_2
	gcabar_Cav3_2 = Cav3_2Dend

	insert Kca3_1 
	gkbar_Kca3_1 = Kca3_1Dend

	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Dend

	insert Kca2_2 
	gkbar_Kca2_2 = Kca2_2Dend

	insert Kir2_3
	gkbar_Kir2_3 = PC_KirDend
}

forsec Ldend {
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Dend
	ena = 60
	ek = -88

	eca = 137.52625
	cai = cai0_ca_ion
	cao = cao0_ca_ion
	ion_style("ca_ion", 1, 1, 0, 1, 0)
}

load_file("CmParams.hoc")
load_file("loadExtraParams.hoc")

// Axon AIS. First section after the soma
create axonAIS
axonAIS {
	nseg = 1
	diam = 0.97 
	cm = 0.77
	L = 17
	Ra = 122
	
	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6AIS
	ena = 75
	
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Ais
	
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1AIS
	
	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4AIS
	ek = -88
	
	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003

	TotalPump_cdp5 = 5e-8
	
	
	ion_style("ca_ion", 1, 1, 0, 1, 0) 
	eca = 137.52625
	cai = cai0_ca_ion
	cao = cao0_ca_ion
}

// AISK	
create axonAISK
axonAISK {
	nseg = 1
	diam = 0.97 
	cm = 0.77
	L = 4 
	Ra = 122
	
	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	
	insert Kv1_1
	gbar_Kv1_1 = Kv1_1AisK
	ek = -88

}
// First Myelination
create axonmyelin
axonmyelin {
	nseg = 1
	diam = 0.73
	L = 100

	insert pas 
	e_pas = -63 
	g_pas = 5.60e-9 
	cm = 1.87e-11
	Ra = 122
}
	
// First Node of Ranvier
create axonNOR
axonNOR {	
	nseg = 1
	diam = 0.73 
	cm = 0.77
	L = 4 
	Ra = 122
	
	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Nor
	ena = 60

	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Nor
	ek = -88
	    
	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003
		
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Nor
	  
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Nor
	
	TotalPump_cdp5 = 5e-7
}
	
// second part of the axon
create axonmyelin2
axonmyelin2 {
	nseg = 1
	diam = 0.73
	L = 100 
	
	insert pas 
	e_pas = -63 
	g_pas = 5.60e-9 
	cm = 1.87e-11 
	Ra = 122
}
	
// Second Node of Ranvier	
create axonNOR2
axonNOR2 {
	nseg = 1
	diam = 0.73 
	cm = 0.77
	L = 4 
	Ra = 122
	
	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Nor2
	ena = 60

	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Nor2
	ek = -88

	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003
	
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Nor2
	  
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Nor2
	
	TotalPump_cdp5 = 5e-7
}

// Third part of the axon
create axonmyelin3
axonmyelin3 {
	nseg = 1
	diam = 0.73
	L = 100 
	
	insert pas 
	e_pas = -63 
	g_pas = 5.60e-9 
	cm = 1.87e-11 
	Ra = 122
}
	
// Third Node of Ranvier
create axonNOR3
axonNOR3 {
	nseg = 1
	diam = 0.73 
	cm = 0.77
	L = 4 
	Ra = 122
	
	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Nor3
	ena = 60

	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Nor3
	ek = -88
	
	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003
	
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Nor3
	  
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Nor3
	
	TotalPump_cdp5 = 5e-7
}
	
// Third part of the axon
create axonmyelin4
axonmyelin4 {
	nseg = 1
	diam = 0.73
	L = 100 
	
	insert pas 
	e_pas = -63 
	g_pas = 5.60e-9 
	cm = 1.87e-11 
	Ra = 122
}

// Collateral.
create axoncoll
axoncoll {
	nseg = 1
	diam = 0.6
	L = 100
	Ra = 122

	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	 
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Axoncoll
	ena = 60

	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Axoncoll
	ek = -88
	
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Axoncoll
	  
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Axoncoll
	
	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003
		
	TotalPump_cdp5 = 5e-7
	
	
	ion_style("ca_ion", 1, 1, 0, 1, 0) 
	eca = 137.52625
	cai = cai0_ca_ion
	cao = cao0_ca_ion
}
        
// Collateral second part
create axoncoll2
axoncoll2 {
	nseg = 1
	diam = 0.6
	L = 100
	Ra = 122

	insert Leak
	e_Leak = eleak
	gmax_Leak = 0.0003
	 
	insert Nav1_6
	gbar_Nav1_6 = Nav1_6Axoncoll
	ena = 60


	insert Kv3_4
	gkbar_Kv3_4 = Kv3_4Axoncoll
	ek = -88
	
	insert cdp5
	Nannuli_cdp5 = 0.326 + (1.94 * (diam)) + (0.289*(diam)*(diam)) - ((3.33e-2)*(diam)*(diam)*(diam)) + ((1.55e-3)*(diam)*(diam)*(diam)*(diam)) - (2.55e-5*(diam)*(diam)*(diam)*(diam)*(diam))
	Buffnull2_cdp5 = 64.2 - 57.3* exp(-(diam)/1.4)
	rf3_cdp5 = 0.162 - 0.106* exp(-(diam)/2.29)
	rf4_cdp5 = 0.003
	
	insert Cav3_1 
	pcabar_Cav3_1 = Cav3_1Axoncoll
	  
	insert Cav2_1 
	pcabar_Cav2_1 = Cav2_1Axoncoll
	
	TotalPump_cdp5 = 5e-7
	
        
	ion_style("ca_ion", 1, 1, 0, 1, 0) 
	eca = 137.52625
	cai = cai0_ca_ion
	cao = cao0_ca_ion
}
	  
// Connections of the axon	  
	connect axonAIS(1), soma(0)
	connect axonAISK(1), axonAIS(0)
	connect axonmyelin(1), axonAISK(0)		
	connect axonNOR(1), axonmyelin(0)
	connect axonmyelin2(1), axonNOR(0)
	connect axonNOR2(1), axonmyelin2(0)
	connect axonmyelin3(1), axonNOR2(0)
	connect axonNOR3(1), axonmyelin3(0)
	connect axonmyelin4(1), axonNOR3(0)
	
	
	connect axoncoll(1), axonNOR2(0)
	connect axoncoll2(1), axoncoll(0)
	
objref f_Vshifts
f_Vshifts = new File()
f_Vshifts.ropen("Vshifts_all_dend.txt")
tDCSvshift = f_Vshifts.scanvar() // for soma (skipped)

objref strobj_dend
strobj_dend = new StringFunctions()

forall{
	strdef tmpname
	tmpname = secname()
	index_dend = strobj_dend.substr(tmpname,"dend")
	if (index_dend>=0) {
		tDCSvshift = f_Vshifts.scanvar() // Read and apply voltage shift to every dendritic compartment
		vshift_Kv1_1 = tDCSvshift
		vshift_Kv1_5 = tDCSvshift
		vshift_Kv3_3 = tDCSvshift
		vshift_Kv4_3 = tDCSvshift
		vshift_Kca1_1 = tDCSvshift
		vshift_Cav2_1 = tDCSvshift	
		vshift_Cav3_3 = tDCSvshift
		vshift_HCN1 = tDCSvshift
		vshift_Leak = tDCSvshift
		if (diam>3.5) {
			vshift_Kir2_3 = tDCSvshift
			vshift_Kca2_2 = tDCSvshift
			vshift_Kca3_1 = tDCSvshift	
			vshift_Cav3_1 = tDCSvshift
			vshift_Cav3_2 = tDCSvshift
		}
		if (diam>8) {
			vshift_Nav1_6 = tDCSvshift
		}
	}
}
f_Vshifts.close()

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