Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011)

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Accession:138379
"Coordination of neocortical oscillations has been hypothesized to underlie the "binding" essential to cognitive function. However, the mechanisms that generate neocortical oscillations in physiological frequency bands remain unknown. We hypothesized that interlaminar relations in neocortex would provide multiple intermediate loops that would play particular roles in generating oscillations, adding different dynamics to the network. We simulated networks from sensory neocortex using 9 columns of event-driven rule-based neurons wired according to anatomical data and driven with random white-noise synaptic inputs. ..."
Reference:
1 . Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Oscillations; Synchronization; Laminar Connectivity;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic cell; Neocortex V1 L2/6 pyramidal intratelencephalic cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; Gaba; Glutamate;
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fdemo
readme.txt
intf6_.mod
misc.mod *
nstim.mod *
stats.mod *
vecst.mod
col.hoc
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc
finish_run.hoc
grvec.hoc *
init.hoc *
labels.hoc *
local.hoc *
misc.h
mosinit.hoc
network.hoc
nload.hoc
nqs.hoc *
nqsnet.hoc *
nrnoc.hoc *
params.hoc
python.hoc *
pywrap.hoc *
run.hoc
setup.hoc
simctrl.hoc *
spkts.hoc *
stats.hoc *
syncode.hoc *
xgetargs.hoc *
                            
// $Id: params.hoc,v 1.114 2011/02/10 20:24:02 samn Exp $

//* batch params
jrsvn_INTF6=1e3
jrsvd_INTF6=2e4

//* general params
declare("mytstop",3e3)
tstop = mytstop
v_init=1000 // so keep v's as set randomly

//* ARTC params
mg_INTF6=1.6
EAM_INTF6=65 // these are deviations above RMP
ENM_INTF6=90
EGA_INTF6=-15
seadsetting_INTF6 = 2 // fixed inter-cell weights

//* Declarations

dosetexvals=name_declared("wmatex")==0 // whether to set values in wmatex,ratex

sprint(tstr,"d[%d][%d]",CTYPi,STYPi)
declare("wmatex",tstr,"ratex",tstr) // weights,avg. rate of external inputs

declare("fih","o[1]","nstim","o[1]")
vseed_stats(223481)
rdm.MCellRan4(seed_stats)

declare("vsgrpp",new Vector(CTYPi)) //% X 100 of cells of a type to stim, used in stim,sgrcells
declare("vsgrsidx",new Vector(CTYPi)) //startind index of cell to stim when using topstim
declare("sgrdur",mytstop) //duration of stim
declare("inputseed",1234)
declare("sgrhzE",300,"sgrhzI",125,"sgrhzNM",50,"sgron",1,"sgrdel",0)
declare("sgrhzdel",0.2)//variance in sgrhz for an INTF6
declare("EXGain",15) // gain for external inputs
declare("lcstim",new List()) // list of CSTIM objects
declare("nqwmex",new NQS("ct","sy","w","rate")) // NQS passed to CSTIM init
{sprint(tstr,"d[%d]",numcols) declare("EIBalance",tstr)} // whether to balance rate of external E/I inputs
declare("usens",0) // whether to use NetStims in CSTIM

SCAHP=SCTH=1

//* setwmatex - set weights of external inputs to INTF6s
proc setwmatex () {  local ct,sy
  if(dosetexvals) {
    for ct=0,CTYPi-1 for sy=0,STYPi-1 wmatex[ct][sy]=0
    for ct=0,CTYPi-1 {
      ratex[ct][AM2]=sgrhzE
      ratex[ct][NM2]=sgrhzNM
      ratex[ct][GA2]=ratex[ct][GA]=sgrhzI
      if(IsLTS(ct)) {
        wmatex[ct][AM2] = 0.2
        wmatex[ct][NM2] = 0.025
        wmatex[ct][GA]=wmatex[ct][GA2]=0.125
      } else {
        wmatex[ct][NM2] = 0.05   
        wmatex[ct][AM2] = 0.25 
        wmatex[ct][GA]=wmatex[ct][GA2]=0.125
      }
      for sy=0,STYPi-1 wmatex[ct][sy] *= EXGain // apply gain control
    }    
  }
  nqwmex.clear()
  for ct=0,CTYPi-1 for sy=0,STYPi-1 if(wmatex[ct][sy]) nqwmex.append(ct,sy,wmatex[ct][sy],ratex[ct][sy])
}

//* RSparams - setup regular spiking excitatory cells
proc RSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,E2,E4,E5R,E5B,E6) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)
      
      xo.ahpwt=1
      xo.tauahp=400
      xo.RMP= -65
      xo.VTH= -40 
      xo.refrac=  50
      xo.Vblock= -25
      
      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      
      xo.tauRR = 8 
      xo.RRWght = .75 
    }
  }
}

//* LTSparams - setup low-threshold spiking interneurons
proc LTSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,I2L,I4L,I5L,I6L) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)  
      xo.ahpwt=0.5
      xo.refrac= 10
      xo.tauahp=50
      xo.Vblock=-10    
      xo.RMP = -65
      xo.VTH= -47

      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      
      xo.tauRR = 1.5
      xo.RRWght = 0.25
    }
  }
}

//* FSparams - setup fast spiking interneurons
proc FSparams () { local ii,jj localobj xo,co
  for ltr(co,lcol) for case(&ii,I2,I2C,I4,I5,I6,I6C) if(co.numc[ii]>0) {
    for jj=co.ix[ii],co.ixe[ii] { xo=co.ce.o(jj)    
      xo.ahpwt=0.5
      xo.refrac= 10
      xo.tauahp=50
      xo.Vblock=-10    
      xo.RMP = -63
      xo.VTH= -40

      xo.tauGA  = 10
      xo.tauGA2 = 20
      xo.tauAM2 = 20
      xo.tauNM2 = 300
      
      xo.tauRR = 1.5
      xo.RRWght = 0.25
    }
  }
}

//* setNMParams(col,celltype,mg0 factor,maxnmc) 
proc setNMParams () { local ct,mgf,maxnmc,idx localobj col,ce
  col=$o1 ce=col.ce ct=$2 mgf=$3 maxnmc=$4
  for idx=col.ix[ct],col.ixe[ct] {
    ce.o(idx).mg0 = 3.57 * mgf
    ce.o(idx).maxnmc = maxnmc
  }
}

//* setNMIParams(col[,mg0 factor,maxnmc])
proc setNMI () { local mgf,maxnmc,ct localobj col
  col=$o1
  if(numarg()>1) mgf=$2 else mgf=1 
  if(numarg()>2) maxnmc=$3 else maxnmc=1
  for ct=0,CTYPi-1 if(ice(ct)) setNMParams(col,ct,mgf,maxnmc)
}

//* schizon - turn on schizo params
proc schizon () { local c,ct
  for c=0,numcols-1 {
    setNMI(col[c],0.75,0.75)
    setNMParams(col[c],E4,1.25,1.25)
    for case(&ct,E2,E5R,E5B) setNMParams(col[c],ct,0.75,0.9)
  }
}
//* schizon - turn off schizo params
proc schizoff () { local c,ct
  for c=0,numcols-1 {
    setNMI(col[c],1,1)
    setNMParams(col[c],E4,1,1)
    for case(&ct,E2,E5R,E5B) setNMParams(col[c],ct,1,1)
  }
}


proc rewt () {} // nothing needs to be done since copy directly into wd0[][][]

//* setcstim - set external inputs to COLUMNs using CSTIM
proc setcstim () { local i,seed
  for i=0,lcol.count-1 {
    if(dbgcols)seed=inputseed else seed=(i+1)*inputseed
    lcstim.append(new CSTIM(lcol.o(i),seed,sgrdur,sgrhzdel,EIBalance[i],usens))
    lcstim.o(lcstim.count-1).setwm(nqwmex)
    lcstim.o(lcstim.count-1).setspks()
  }
  print "set external inputs"
}

//* function calls

setwmatex()

{RSparams() LTSparams() FSparams()}

if (!jcn) rjinet() //means no jitcon

if(disinhib) inhiboff()

setcstim()