Dentate gyrus (Morgan et al. 2007, 2008, Santhakumar et al. 2005, Dyhrfjeld-Johnsen et al. 2007)

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Accession:124513
This model was implemented by Rob Morgan in the Soltesz lab at UC Irvine. It is a scaleable model of the rat dentate gyrus including four cell types. This model runs in serial (on a single processor) and has been published at the size of 50,000 granule cells (with proportional numbers of the other cells).
References:
1 . Santhakumar V, Aradi I, Soltesz I (2005) Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol 93:437-53 [PubMed]
2 . Dyhrfjeld-Johnsen J, Santhakumar V, Morgan RJ, Huerta R, Tsimring L, Soltesz I (2007) Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. J Neurophysiol 97:1566-87 [PubMed]
3 . Morgan RJ, Soltesz I (2008) Nonrandom connectivity of the epileptic dentate gyrus predicts a major role for neuronal hubs in seizures. Proc Natl Acad Sci U S A 105:6179-84 [PubMed]
4 . Morgan RJ, Santhakumar V, Soltesz I (2007) Modeling the dentate gyrus. Prog Brain Res 163:639-58 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Dentate gyrus;
Cell Type(s): Dentate gyrus granule cell; Dentate gyrus mossy cell; Dentate gyrus basket cell; Dentate gyrus hilar cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Epilepsy;
Implementer(s): Bezaire, Marianne [mariannejcase at gmail.com]; Morgan, Robert [polomav at gmail.com];
Search NeuronDB for information about:  Dentate gyrus granule cell;
Files displayed below are from the implementation
/
dentate_gyrus
500net
README.html
bgka.mod *
CaBK.mod
ccanl.mod *
Gfluct2.mod
gskch.mod *
hyperde3.mod *
ichan2.mod *
inhsyn.mod
LcaMig.mod *
nca.mod
ppsyn.mod
tca.mod *
50knet.hoc
bcdist.hoc
bcell.bcell
bcell.gcell
bcell.hcell *
bcell.mcell
gcdist.hoc
gcell.bcell
gcell.gcell
gcell.hcell
gcell.mcell
hcdist.hoc
hcell.bcell
hcell.gcell
hcell.hcell *
hcell.mcell
mcdist.hoc
mcell.bcell
mcell.gcell
mcell.hcell
mcell.mcell
mosinit.hoc
parameters.dat
pbc.hoc
pgc.hoc
phc.hoc
pmc.hoc
run50knet.bash
screenshot.jpg
                            
TITLE l-calcium channel
: l-type calcium channel


UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)
	(molar) = (1/liter)
	(mM) = (millimolar)
	FARADAY = 96520 (coul)
	R = 8.3134 (joule/degC)
	KTOMV = .0853 (mV/degC)
}

PARAMETER {
	v (mV)
	celsius 	(degC)
	glcabar		 (mho/cm2)
	ki=.001 (mM)
	cai (mM)
	cao (mM)
        tfa=1
}


NEURON {
	SUFFIX lca
	USEION lca READ elca WRITE ilca VALENCE 2
	USEION ca READ cai, cao VALENCE 2 
        RANGE glcabar, cai, ilca, elca
        GLOBAL minf,matu
}

STATE {
	m
}

ASSIGNED {
	ilca (mA/cm2)
        glca (mho/cm2)
        minf
        matu   (ms)
	elca (mV)   

}

INITIAL {
	rate(v)
	m = minf
	VERBATIM
	cai=_ion_cai;
	ENDVERBATIM
}

BREAKPOINT {
	SOLVE state METHOD cnexp
	glca = glcabar*m*m*h2(cai)
	ilca = glca*ghk(v,cai,cao)

}

FUNCTION h2(cai(mM)) {
	h2 = ki/(ki+cai)
}


FUNCTION ghk(v(mV), ci(mM), co(mM)) (mV) {
        LOCAL nu,f

        f = KTF(celsius)/2
        nu = v/f
        ghk=-f*(1. - (ci/co)*exp(nu))*efun(nu)
}

FUNCTION KTF(celsius (DegC)) (mV) {
        KTF = ((25./293.15)*(celsius + 273.15))
}


FUNCTION efun(z) {
	if (fabs(z) < 1e-4) {
		efun = 1 - z/2
	}else{
		efun = z/(exp(z) - 1)
	}
}

FUNCTION alp(v(mV)) (1/ms) {
	TABLE FROM -150 TO 150 WITH 200
	alp = 15.69*(-1.0*v+81.5)/(exp((-1.0*v+81.5)/10.0)-1.0)
}

FUNCTION bet(v(mV)) (1/ms) {
	TABLE FROM -150 TO 150 WITH 200
	bet = 0.29*exp(-v/10.86)
}

DERIVATIVE state {  
        rate(v)
        m' = (minf - m)/matu
}

PROCEDURE rate(v (mV)) { :callable from hoc
        LOCAL a
        a = alp(v)
        matu = 1/(tfa*(a + bet(v)))
        minf = tfa*a*matu
}
 



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