A single column thalamocortical network model (Traub et al 2005)

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Accession:45539
To better understand population phenomena in thalamocortical neuronal ensembles, we have constructed a preliminary network model with 3,560 multicompartment neurons (containing soma, branching dendrites, and a portion of axon). Types of neurons included superficial pyramids (with regular spiking [RS] and fast rhythmic bursting [FRB] firing behaviors); RS spiny stellates; fast spiking (FS) interneurons, with basket-type and axoaxonic types of connectivity, and located in superficial and deep cortical layers; low threshold spiking (LTS) interneurons, that contacted principal cell dendrites; deep pyramids, that could have RS or intrinsic bursting (IB) firing behaviors, and endowed either with non-tufted apical dendrites or with long tufted apical dendrites; thalamocortical relay (TCR) cells; and nucleus reticularis (nRT) cells. To the extent possible, both electrophysiology and synaptic connectivity were based on published data, although many arbitrary choices were necessary.
References:
1 . Traub RD, Contreras D, Cunningham MO, Murray H, LeBeau FE, Roopun A, Bibbig A, Wilent WB, Higley MJ, Whittington MA (2005) Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J Neurophysiol 93:2194-232 [PubMed]
2 . Traub RD, Contreras D, Whittington MA (2005) Combined experimental/simulation studies of cellular and network mechanisms of epileptogenesis in vitro and in vivo. J Clin Neurophysiol 22:330-42 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex; Thalamus;
Cell Type(s): Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; FORTRAN;
Model Concept(s): Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Simplified Models; Epilepsy; Sleep; Spindles;
Implementer(s): Traub, Roger D ;
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell; Thalamus reticular nucleus GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 L6 pyramidal corticalthalamic GLU cell; GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I Calcium; I A, slow;
Files displayed below are from the implementation
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nrntraub
mod
alphasyndiffeq.mod *
alphasynkin.mod *
alphasynkint.mod *
ampa.mod *
ar.mod *
cad.mod *
cal.mod *
cat.mod *
cat_a.mod *
gabaa.mod *
iclamp_const.mod *
k2.mod *
ka.mod *
ka_ib.mod *
kahp.mod *
kahp_deeppyr.mod *
kahp_slower.mod *
kc.mod *
kc_fast.mod *
kdr.mod *
kdr_fs.mod *
km.mod *
naf.mod *
naf_tcr.mod *
naf2.mod *
nap.mod *
napf.mod *
napf_spinstell.mod *
napf_tcr.mod *
par_ggap.mod *
pulsesyn.mod *
rampsyn.mod *
rand.mod *
ri.mod *
traub_nmda.mod *
                            
TITLE Sodium persistent current for RD Traub et al 2003, 2005

COMMENT

	This persistent sodium current is based on the activation
	permissive quantity, m, from the transient sodium channel. -TMM
	modified from an
	Implementation by Maciej Lazarewicz 2003 (mlazarew@seas.upenn.edu)
	fastNashift init to 0 and removed from arg modification Tom Morse 3/8/2006
	(for Traub et al 2005)
	The difference between napf and napf_tcr is that napf_tcr has a single power
	of m in ina_napf_tcr where as napf has the third power of m in ina_napf
ENDCOMMENT

INDEPENDENT { t FROM 0 TO 1 WITH 1 (ms) }

UNITS { 
	(mV) = (millivolt) 
	(mA) = (milliamp) 
} 
NEURON { 
	SUFFIX napf_tcr
	USEION na READ ena WRITE ina
	RANGE gbar, ina,m, df, fastNa_shift, a, b, c, d, minf, mtau
}
PARAMETER { 
	fastNa_shift = 7 (mV)
	a = 0 (1)
	b = 0 (1)
	c = 0 (1)
	d = 0 (1)
	gbar = 0.0 	   (mho/cm2)
	v (mV) ena 		   (mV)  
} 
ASSIGNED { 
	ina 		   (mA/cm2) 
	minf 	   (1)
	mtau 	   (ms)
	df	(mV)
} 
STATE {
	m
}
BREAKPOINT { 
	SOLVE states METHOD cnexp
	ina = gbar * m * ( v - ena ) 
	df = v - ena
} 
INITIAL { 
	settables( v )
	m = minf
	m = 0
} 
DERIVATIVE states { 
	settables( v ) 
	m' = ( minf - m ) / mtau 
}

UNITSOFF 

PROCEDURE settables(v1(mV)) {

	TABLE minf, mtau  FROM -120 TO 40 WITH 641

	minf  = 1 / ( 1 + exp( ( - ( v1 + fastNa_shift ) - 38 ) / 10 ) )
	if( ( v1 + fastNa_shift ) < -30.0 ) {
		mtau = 0.025 + 0.14 * exp( ( ( v1 + fastNa_shift ) + 30 ) / 10 )
	} else {
		mtau = 0.02 + a + (0.145+ b) * exp( ( - ( v1 + fastNa_shift +d ) - 30 ) / (10+c) ) 
	}

}

UNITSON

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