Model of CA1 activity during working memory task (Spera et al. 2016)

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Accession:223962
"The cellular processes underlying individual differences in the Woring Memory Capacity (WMC) of humans are essentially unknown. Psychological experiments suggest that subjects with lower working memory capacity (LWMC), with respect to subjects with higher capacity (HWMC), take more time to recall items from a list because they search through a larger set of items and are much more susceptible to interference during retrieval. ... In this paper, we investigate the possible underlying mechanisms at the single neuron level by using a computational model of hippocampal CA1 pyramidal neurons, which have been suggested to be deeply involved in the recognition of specific items. ..."
Reference:
1 . Spera E, Migliore M, Unsworth N, Tegolo D (2016) On the cellular mechanisms underlying working memory capacity in humans Neural Network World 4:335-359
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Synapse;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Working memory;
Implementer(s):
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell;
/
SperaEtAl2016
readme.txt
distr.mod *
Gfluct.mod
h.mod *
kadist.mod *
kaprox.mod *
kdrca1.mod *
na3n.mod *
naxn.mod *
netstims.mod *
fixnseg.hoc *
geoc91662.hoc *
mosinit.hoc
obliqui91662.txt
simulation91662.hoc
                            
load_file("nrngui.hoc")
//use_mcell_ran4(1) // MUST be used on CINECA
cvode_active(0)

a1=0.1

b1=0.7

a1max=a1

b1max=b1

rap_a1=5
rap_b1=(b1/0.71)*5


numaxon=1
numsoma=1
numbasal=58
numapical=78
numtrunk=57
cont=26  // ******  number of obliques

last=12 //********  n-ple size
ns=26  //********  number of trunk comps with noise

sim4conf=102
double pin[cont]
double cond[cont]
double trunko[cont]
double dendo[cont]
double u2[last+3]
double u[last]

weight=80

xopen("geoc91662.hoc")             // geometry file
xopen("fixnseg.hoc")           

Rm = 28000
RmDend = Rm/1
RmSoma = Rm
RmAx = Rm

Cm    = 1
CmSoma= Cm
CmAx  = Cm
CmDend = Cm*1

RaAll= 150
RaSoma=150  
RaAx = 50

Vrest = -65
dt = 0.1
gna =  .025
AXONM = 5
gkdr = 0.01
celsius = 35.0  
KMULT =  0.03
KMULTP = 0.03
ghd=0.00005
nash=0

objref g, b,c, stim, vbox,vecchio,pc, args, args2, r,ennupla
objref  p, s[cont], rsyn[cont], nc[last], sref, blist[numtrunk],aplist,f[2*cont]
strdef dend, trunk


for i=0, numtrunk-1 {blist[i] = new Vector()}



args = new Vector()
args2 = new Vector()


aplist = new Vector(numapical)

forsec "axon" {insert pas e_pas=Vrest g_pas = 1/RmAx Ra=RaAx cm=CmAx}
forsec "soma" {insert pas e_pas=Vrest g_pas = 1/RmSoma Ra=RaSoma cm=CmSoma}
forsec "dendrite"{insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}
forsec "user5" {insert pas e_pas=Vrest g_pas = 1/RmDend Ra=RaAll cm=CmDend}

access soma
freq=50
geom_nseg()
tot=0
forall {tot=tot+nseg}

distance()
maxdist=0
forsec "user5" for(x) {if (distance(x)>maxdist) {maxdist=distance(x)}}
print "total # of segments (50Hz): ",tot, "  max path distance: ", maxdist


//*********mapping bifurcations******************


for i=0, numapical-1 apical_dendrite[i] {
	while (!issection("user5.*")) {
	//print "before  ", i, secname()
		sref = new SectionRef()
		access sref.parent
		sprint(dend, secname())
	}
	//print "apical ",i," ",dend
	for k=0, numtrunk-1 user5[k] {
		sprint(trunk,secname())
		x=strcmp(dend, trunk)
		if (x==0) {blist[k].append(i)aplist.x[i]=k}
	}
}

/*****************lettura da file********************/

vecchio = new File()
vecchio.ropen("obliqui91662.txt")

for i=0,cont-1 {
	trunko[i]=vecchio.scanvar()
	dendo[i]=vecchio.scanvar()
	pin[i]=vecchio.scanvar()
	cond[i]=vecchio.scanvar()
}

vecchio.close()



/********************  fine  **********************/


tstop=30

for z=0, cont-1 {
	s[z] = new NetStims(.5)
	s[z].interval=0.2
	s[z].number = 1
	s[z].start=10
	s[z].noise=0
	s[z].seed(987651119)
	rsyn[z] = new Exp2Syn(0.5)
	rsyn[z].tau1 = 0.4
	rsyn[z].tau2 = 1
	rsyn.e=0
	
}

user5[13] {		// *************cell dependent
	stim= new IClamp(0)
	stim.amp=0
	stim.dur=tstop
	stim.del=0
}

forsec "axon" {   
                insert nax gbar_nax=gna * AXONM	sh_nax=nash
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP*1
}

forsec "soma" {   
		insert hd ghdbar_hd=ghd	vhalfl_hd=-73
                insert na3 ar_na3=1 sh_na3=nash gbar_na3=gna
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP
		insert ds
}

for i=0, numbasal-1 dendrite[i] {
		insert hd ghdbar_hd=ghd	vhalfl_hd=-73
                insert na3 ar_na3=1 gbar_na3=gna sh_na3=nash
                insert kdr gkdrbar_kdr=gkdr
                insert kap gkabar_kap = KMULTP
}
                

forsec "user5" {
	insert hd ghdbar_hd=ghd
        insert na3 ar_na3=1 gbar_na3=gna sh_na3=nash
        insert kdr gkdrbar_kdr=gkdr
	insert kap gkabar_kap=0
	insert kad gkabar_kad=0
	for (x,0) { 
		xdist = distance(x)
               	ghdbar_hd(x) = ghd*(1+3*xdist/100)
               		if (xdist > 100){
						vhalfl_hd=-81
                    	gkabar_kad(x) = KMULT*(1+xdist/100)
               		} else {
						vhalfl_hd=-73
                    	gkabar_kap(x) = KMULTP*(1+xdist/100)
        			}
	}
}

for i=0, numapical-1 apical_dendrite[i] {
	insert hd 
        insert na3 ar_na3=1 gbar_na3=gna sh_na3=nash
        insert kdr gkdrbar_kdr=gkdr
	insert kap
	insert kad
		gkabar_kad = 1*user5[aplist.x[i]].gkabar_kad(1)
		gkabar_kap = 1*user5[aplist.x[i]].gkabar_kap(1)
		vhalfl_hd = user5[aplist.x[i]].vhalfl_hd
       	ghdbar_hd = user5[aplist.x[i]].ghdbar_hd(1)
}

proc init() {

	t=0
    forall {
    	v=Vrest
    	if (ismembrane("nax") || ismembrane("na3")) {ena=55}
       	if (ismembrane("kdr") || ismembrane("kap") || ismembrane("kad")) {ek=-90}
       	if (ismembrane("hd") ) {ehd_hd=-30}
	}
	finitialize(Vrest)
    fcurrent()

    forall {
		for (x) {
			if (ismembrane("na3")||ismembrane("nax")){e_pas(x)=v(x)+(ina(x)+ik(x))/g_pas(x)}
			if (ismembrane("hd")) {e_pas(x)=e_pas(x)+i_hd(x)/g_pas(x)}
		}
	}
	cvode.re_init()
	cvode.event(tstop)
	access soma
	//g.begin()
	flag=0
	
}


proc advance() {
	fadvance()
	if (vmax_ds(.5)>0) {t=tstop flag=1}
	//g.plot(t)
	//g.flush()
	//p.flush()
	doNotify()
}


func superrun() {local id, numprove, c, k, seme1, seme2, seme3

	a1=$o2.x[0]
	b1=$o2.x[1]
	stim.amp=$o2.x[2]
    
	k=$3
	c=$4
	seme1=(k*sim4conf+c)*31530
	seme2=(k*sim4conf+c)*22210
	seme3=(k*sim4conf+c)*18230

	print "seme1", seme1
	print "seme2", seme2
	print "seme3", seme3

	for kk=0, ns user5[kk] {  // cell-dependent
	f[kk] = new Gfluct2(0.5)
	f[kk].g_e0 = a1
	f[kk].g_i0 = b1
	f[kk].std_e = a1/rap_a1
	f[kk].std_i = b1/rap_b1
	f[kk].new_seed(seme1)
	print " noise #",kk, " at ",secname()
	}
	
	

	
	print k,c
	objref ennupla
	numprove=0
	id = hoc_ac_
	ennupla= new Vector()
	flag=0
	// definiamo ennupla 
	for c=0, cont-1 {
	ennupla.append(c)
	}
	aux=cont
	// print "seme", seme3
	r= new Random()
	r.MCellRan4(seme3)
	for c=0, last-1 {
	ind=r.discunif(0, aux-1)
	cond[ennupla.x[ind]]=80
	aux=aux-1
	print ennupla.x(ind)
	ennupla.remove(ind)
	}
	print "\n"
	for c=0, cont-last-1 {
	cond[ennupla.x(c)]=0
	print ennupla.x(c)

	}
	ennupla.resize(0)

	r= new Random(seme2)
        r.MCellRan4(seme2)

	while(0==0){ 
	numprove=numprove+1
	for c=0, cont-1 {
	ennupla.append(c)
	}
	aux=cont
	// print " \n"
	for c=0, last-1 {
	ind=r.discunif(0, aux-1)
	//print "indice ",ind
	u[c]=ennupla.x[ind]
	u2[c]=dendo[u[c]]
	nc[c] = new NetCon(s[u[c]],rsyn[u[c]],0,0,cond[u[c]]*1.e-3)
	apical_dendrite[u2[c]] rsyn[u[c]].loc(0.5)
	ennupla.remove(ind)
	aux=aux-1
	 
	//print u[c]
	}
	// print " \n"
	ennupla.resize(0)	
			
	// print f[2].g_e0
	run()
	//print numprove*0.025-0.5 ," s "
	if (flag==1) { print "ha sparato dopo",numprove,"prove" spikec=1}
	if(numprove>3600){print "piu di 3600 prove" flag=1 spikec=0}
	
 	}
	pc.post(id, $o2,numprove,seme1,seme2,seme3)
	
	return id
	
}


pc = new ParallelContext()
pc.runworker()


for yy=0, last-1 {u[yy]=0}

order=0
conto=0

print "Begin Simulation"
print "Contesto = ",stim.amp

objref aa1, bb1, aamp 
aa1 = new Vector()
bb1 = new Vector()
aamp = new Vector()
//ennupla = new Vector()

aa1.append(0.02)
//aa1.append(0.25,0.38,0.5,1,2.5,5,7.5)
bb1.append(0.02)

//bb1.append(0.5,0.75,1,2,5,10,15)
//aamp.append(0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5)
contex = 0
proc loop() { local k, first, ind, c
	k=$1
	c=$2
	args.resize(0)      
	args.append(aa1.x[nsim]*a1max)
	args.append(bb1.x[nsim]*b1max)
	args.append(contex)
	pc.submit("superrun", order, args,k,c)
	order=order+1
		
}

for nsim=0, aa1.size()-1 {
	for z=1,sim4conf{
	loop(nsim,z)	    
	}
}

objref outfile, outfile2
outfile = new File()
outfile2 = new File() 

strdef name, name2


total=0

while ((id = pc.working) != 0) {
	pc.take(id)
	args2 = pc.upkvec
	m  = pc.upkscalar
	seme1=pc.upkscalar
	seme2=pc.upkscalar
	seme3=pc.upkscalar
	
	//	args2.printf()
	total = total +1

//	printf("%d configurazioni ", m)
		//for y=0, last-1 {printf(" %g ", args2.x[y])}
//	printf("noise ex %g inh %g context %g semerum %d semeennupla %d \n",args2.x[0]/a1max,args2.x[1]/b1max, args2.x[2],seme1,seme2)
		//write n-uples
	
	
	
	
sprint(name,"le%dple-%dobl-%gecc-%gini-b%g-%d.txt",last,cont,args2.x[0]/a1max,args2.x[1]/b1max,b1max,sim4conf)
	     
sprint(name2,"le%dple-%dobl-%gecc-%gini-b%g-solotempi-%d.txt",last,cont,args2.x[0]/a1max,args2.x[1]/b1max,b1max,sim4conf)	

	outfile.aopen(name)
	outfile.printf(" %d configurazioni ",m)
	args2.printf(outfile, " %g ")	
	outfile.printf(" seme r seme e semel %d %d %d",seme1,seme2,seme3)
	outfile.close()
	
        outfile2.aopen(name2)	
        outfile2.printf(" %d   	%d \n",m,seme1)
        outfile2.close()
}

pc.done


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