Biophysically realistic neuron models for simulation of cortical stimulation (Aberra et al. 2018)

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Accession:241165
This archive instantiates the single-cell cortical models used in (Aberra et al. 2018) and sets up extracellular stimulation with either a point-current source, to simulate intracortical microstimulation (ICMS), or a uniform E-field distribution, with a monophasic, rectangular pulse waveform in both cases.
Reference:
1 . Aberra AS, Peterchev AV, Grill WM (2018) Biophysically realistic neuron models for simulation of cortical stimulation. J Neural Eng 15:066023 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon;
Brain Region(s)/Organism: Neocortex; Barrel cortex;
Cell Type(s): Myelinated neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Detailed Neuronal Models;
Implementer(s): Aberra, Aman [aman.aberra at duke.edu];
/*
* Assigns biophysical parameters to myelinated axon
* should have created SectionLists: Myelin_secList, Node_secList, UnMyelin_secList, iseg_secList, and axonal
* AUTHOR: Aman Aberra, Duke University
* CONTACT: aman.aberra@duke.edu
*/

proc myelin_biophys() { localobj axon_bp //iseg_secList,Node_secList,Myelin_seclist,Unmyelin_secList

	axon_bp = get_axon_biophys()
	forsec cell.somatic {
		cm=1 // uF/cm2 
	}
	forsec cell.apical {
		cm = 2 // uF/cm2 
	}
	forsec cell.basal {
		cm = 2 // uF/cm2 
	}
	forsec axonal {		// cell.axonal still not formed
		insert pas						
		e_pas = axon_bp.x[12] // usually -75 mV
		Ra = 100 // Ohm*cm
		cm = 1 // µF/cm2
		g_pas = axon_bp.x[13] // usually 3e-5 S/cm2		
	}	

	
	//forsec axonal {
	forsec Node_secList {					
		//insert Ca_HVA
		insert SKv3_1
		//insert SK_E2
		//insert CaDynamics_E2
		insert Nap_Et2
		insert K_Pst
		insert K_Tst
		//insert Ca_LVAst
		insert NaTa_t			
		//insert NaTa2_t
		for(x,0){
			if (ismembrane("NaTa_t")) gNaTa_tbar_NaTa_t(x) = 2*axon_bp.x[0] //2.5
			//if (ismembrane("NaTa2_t")) gNaTa2_tbar_NaTa2_t(x) = axon_bp.x[0] // New sodium channel for axon proper
			if (ismembrane("K_Tst")) gK_Tstbar_K_Tst(x) = axon_bp.x[1] //2
			if (ismembrane("CaDynamics_E2")) gamma_CaDynamics_E2(x) = axon_bp.x[2]
			if (ismembrane("Nap_Et2")) gNap_Et2bar_Nap_Et2(x) = axon_bp.x[3] 
			if (ismembrane("SK_E2")) gSK_E2bar_SK_E2(x) = axon_bp.x[4] 
			if (ismembrane("Ca_HVA")) gCa_HVAbar_Ca_HVA(x) = axon_bp.x[5]
			if (ismembrane("K_Pst")) gK_Pstbar_K_Pst(x) = axon_bp.x[6] //2
			if (ismembrane("SKv3_1")) gSKv3_1bar_SKv3_1(x) = axon_bp.x[7] //2
			if (ismembrane("CaDynamics_E2")) decay_CaDynamics_E2(x) = axon_bp.x[8]
			if (ismembrane("Ca_LVAst")) gCa_LVAstbar_Ca_LVAst(x) = axon_bp.x[9]
			if (ismembrane("Im")) gImbar_Im(x) = axon_bp.x[10] 
			if (ismembrane("Ca")) gCabar_Ca(x) = axon_bp.x[11]	
		}		
		// don't change e_pas or g_pas
		//g_pas = 3e-5 // 0.02 - Mainen 1995
		ena = 50
		ek = -85					
	}
	
	
	forsec Myelin_secList {		
		cm = 0.02	// Mainen 1996, 0.02 - Eyal 2014
		g_pas = 1/1.125e6 // 1/1.125e6 - Eyal 2014 
	}

	forsec Unmyelin_secList {	
		//insert Ca_HVA
		insert SKv3_1
		//insert SK_E2
		//insert CaDynamics_E2
		insert Nap_Et2
		insert K_Pst
		insert K_Tst
		//insert Ca_LVAst
		insert NaTa_t
		for (x,0) {
			if (ismembrane("NaTa_t")) gNaTa_tbar_NaTa_t(x) = axon_bp.x[0]
			if (ismembrane("K_Tst")) gK_Tstbar_K_Tst(x) = axon_bp.x[1]
			if (ismembrane("CaDynamics_E2")) gamma_CaDynamics_E2(x) = axon_bp.x[2]
			if (ismembrane("Nap_Et2")) gNap_Et2bar_Nap_Et2(x) = axon_bp.x[3] 
			if (ismembrane("SK_E2")) gSK_E2bar_SK_E2(x) = axon_bp.x[4] 
			if (ismembrane("Ca_HVA")) gCa_HVAbar_Ca_HVA(x) = axon_bp.x[5]
			if (ismembrane("K_Pst")) gK_Pstbar_K_Pst(x) = axon_bp.x[6]
			if (ismembrane("SKv3_1")) gSKv3_1bar_SKv3_1(x) = axon_bp.x[7]
			if (ismembrane("CaDynamics_E2")) decay_CaDynamics_E2(x) = axon_bp.x[8]
			if (ismembrane("Ca_LVAst")) gCa_LVAstbar_Ca_LVAst(x) = axon_bp.x[9]
			if (ismembrane("Im")) gImbar_Im(x) = axon_bp.x[10] 
			if (ismembrane("Ca")) gCabar_Ca(x) = axon_bp.x[11]
		}			
		ena = 50
		ek = -85
	}
	

}

// get conductances from original cell.axon[0], save to vector
obfunc get_axon_biophys() { localobj axon_bp
	axon_bp = new Vector(14)
	access cell.axon[0]		 	 	 				 	 	
	if (ismembrane("NaTa_t")) axon_bp.x[0] = gNaTa_tbar_NaTa_t
	if (ismembrane("K_Tst")) axon_bp.x[1] = gK_Tstbar_K_Tst
	if (ismembrane("CaDynamics_E2")) axon_bp.x[2] = gamma_CaDynamics_E2
	if (ismembrane("Nap_Et2")) axon_bp.x[3] = gNap_Et2bar_Nap_Et2
	if (ismembrane("SK_E2")) axon_bp.x[4] = gSK_E2bar_SK_E2
	if (ismembrane("Ca_HVA")) axon_bp.x[5] = gCa_HVAbar_Ca_HVA
	if (ismembrane("K_Pst")) axon_bp.x[6] = gK_Pstbar_K_Pst
	if (ismembrane("SKv3_1")) axon_bp.x[7] = gSKv3_1bar_SKv3_1
	if (ismembrane("CaDynamics_E2")) axon_bp.x[8] = decay_CaDynamics_E2
	if (ismembrane("Ca_LVAst")) axon_bp.x[9] = gCa_LVAstbar_Ca_LVAst
	if (ismembrane("Im")) axon_bp.x[10] = gImbar_Im
	if (ismembrane("Ca")) axon_bp.x[11] = gCabar_Ca
	axon_bp.x[12] = e_pas
	axon_bp.x[13] = g_pas
	return axon_bp	
}

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