A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)

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Accession:150288
1000 Cell Lateral Amygdala model for investigation of plasticity and memory storage during Pavlovian Conditioning.
Reference:
1 . Kim D, Paré D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala. Learn Mem 20:421-30 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell; Synapse; Dendrite;
Brain Region(s)/Organism: Amygdala;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; Hodgkin-Huxley neuron;
Channel(s): I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump;
Gap Junctions:
Receptor(s): AMPA; NMDA; Gaba; Dopaminergic Receptor;
Gene(s):
Transmitter(s): Dopamine; Norephinephrine;
Simulation Environment: NEURON;
Model Concept(s): Synaptic Plasticity; Short-term Synaptic Plasticity; Long-term Synaptic Plasticity; Learning; Neuromodulation;
Implementer(s): Kim, Dongbeom [dk258 at mail.missouri.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA3 pyramidal GLU cell; AMPA; NMDA; Gaba; Dopaminergic Receptor; I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump; Dopamine; Norephinephrine;
/
KimEtAl2013
README.txt
bg2inter.mod
bg2pyr.mod
ca.mod *
cadyn.mod
cal2.mod *
capool.mod *
function_TMonitor.mod *
h.mod *
im.mod
interD2pyrD_STFD.mod
interD2pyrDDA_STFD.mod
interD2pyrDDANE_STFD.mod
interD2pyrDNE_STFD.mod
interD2pyrV_STFD.mod
interD2pyrVDA_STFD.mod
interV2pyrD_STFD.mod
interV2pyrDDA_STFD.mod
interV2pyrDDANE_STFD.mod
interV2pyrDNE_STFD.mod
interV2pyrV_STFD.mod
interV2pyrVDA_STFD.mod
kadist.mod *
kaprox.mod
kdrca1.mod
kdrca1DA.mod
kdrinter.mod *
leak.mod *
leakDA.mod *
leakinter.mod *
na3.mod
na3DA.mod
nainter.mod *
pyrD2interD_STFD.mod
pyrD2interV_STFD.mod
pyrD2pyrD_STFD.mod
pyrD2pyrDDA_STFD.mod
pyrD2pyrV_STFD.mod
pyrD2pyrVDA_STFD.mod
pyrV2interD_STFD.mod
pyrV2interV_STFD.mod
pyrV2pyrD_STFD.mod
pyrV2pyrDDA_STFD.mod
pyrV2pyrV_STFD.mod
pyrV2pyrVDA_STFD.mod
sahp.mod
sahpNE.mod
shock2interD.mod
shock2interV.mod
shock2pyrD.mod
shock2pyrV.mod
tone2interD.mod
tone2interDNE.mod
tone2interV.mod
tone2interVNE.mod
tone2pyrD.mod
tone2pyrD_LAdv.mod
tone2pyrDNE.mod
tone2pyrDNE_LAdv.mod
tone2pyrV.mod
tone2pyrV_LAdd.mod
tone2pyrVNE.mod
tone2pyrVNE_LAdd.mod
BgGen.hoc
Cell_list.txt
Cell_type.txt
function_ConnectInternal.hoc
function_ConnectTwoCells.hoc
function_NetStimOR.hoc *
function_TimeMonitor.hoc *
function_ToneGen.hoc
function_ToneSignalGen_Ctx.hoc
function_ToneSignalGen_Th.hoc
interneuron_template.hoc
LA_model_main_file.hoc
LAcells_template.hoc
NM.txt
shock2Idd.txt
shock2Idv.txt
shock2LAdd.txt
shock2LAdv.txt
shockcondi.hoc
Syn_Matrix.txt
tone2Idd.txt
tone2Idd2.txt
tone2Idv.txt
tone2Idv2.txt
tone2LAdd.txt
tone2LAdd2.txt
tone2LAdv.txt
tone2LAdv2.txt
                            
:  iC   fast Ca2+/V-dependent K+ channel

NEURON {
	SUFFIX sAHPNE
	USEION k READ ek WRITE ik
	USEION cas READ casi VALENCE 2 
        RANGE ik, gk, gsAHPbar
}

UNITS {
        (mM) = (milli/liter)
	(mA) = (milliamp)
	(mV) = (millivolt)
}

PARAMETER {
	tone_period = 4000  
	NE_period = 500
	NE_start = 64000 : 36000		   : NE beta-R(Low Affinity) Norepinephrine Effect after 1 conditioning trials (9*4000 = 36000)
	NE_stop = 96000
	NE_t1 = 0.9 : 0.9           : Amount(%) of NE effect
	NE_ext1 = 196000
	NE_ext2 = 212000	
	
	NE_period2 = 100
	NE_start2 = 36000		   : NE beta-R(Low Affinity) Norepinephrine Effect after 0 conditioning trials (8*4000 = 32000)
	NE_t2 = 0.7           : Amount(%) of NE effect	
	
	gsAHPbar= 2.318144e-05 : 0.0001	(mho/cm2) : 
}

ASSIGNED {
	v (mV)
	ek (mV)
	casi (mM)
	ik (mA/cm2)
	cinf 
	ctau (ms)
	gk (mho/cm2)
}

STATE {
	c
}

BREAKPOINT {
	SOLVE states METHOD cnexp
	gk = gsAHPbar*c       
	ik = gk*(v-ek)*NE1(t)*NE2(t)
}

INITIAL {
	rate(v,casi)
	c = cinf
}

DERIVATIVE states {
        rate(v,casi)
	c' = (cinf-c)/ctau
}

UNITSOFF


FUNCTION calf(v (mV), casi (mM)) (/ms) { LOCAL vs, va
	UNITSOFF
	vs=10*log10(1000*casi)
	calf = 0.0048/exp(-0.5*(vs-35))
	UNITSON
}

FUNCTION cbet(v (mV), casi (mM))(/ms) { LOCAL vs, vb 
	UNITSOFF
	  vs=10*log10(1000*casi)
	  cbet = 0.012/exp(0.2*(vs+100))
	UNITSON
}

UNITSON

PROCEDURE rate(v (mV), casi (mM)) {LOCAL  csum, ca, cb
	UNITSOFF
	ca=calf(v, casi) 
	cb=cbet(v, casi)		
	csum = ca+cb
	cinf = ca/csum
	ctau = 48
	UNITSON
}

FUNCTION NE1(t) {
	    if (t >= NE_start && t <= NE_stop){ 									: During conditioning
			if ((t/tone_period-floor(t/tone_period)) >= (1-NE_period/tone_period)) {NE1 = NE_t1}
			else if ((t/tone_period-floor(t/tone_period)) == 0) {NE1 = NE_t1}
			else {NE1 = 1}}
		else if (t >= NE_ext1 && t <= NE_ext2){								    : During 4trials of Extinction
			if ((t/tone_period-floor(t/tone_period)) >= (1-NE_period/tone_period)) {NE1 = NE_t1}
			else if ((t/tone_period-floor(t/tone_period)) == 0) {NE1 = NE_t1}
			else {NE1 = 1}}		
		else  {NE1 = 1}
	}
FUNCTION NE2(t) {
	    if (t >= NE_start2 && t <= NE_stop){
			if((t/tone_period-floor(t/tone_period)) >= (1-NE_period2/tone_period)) {NE2 = NE_t2}
			else if ((t/tone_period-floor(t/tone_period)) == 0) {NE2 = NE_t2}
			else  {NE2 = 1}}
		else  {NE2 = 1}
	}	

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