Stochastic layer V pyramidal neuron: interpulse interval coding and noise (Singh & Levy 2017)

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Accession:237594
Layer V pyramidal neuron with stochastic Na channels. Supports evidence for interpulse interval coding and has very detailed AIS with Nav1.2 and Nav1.6 channels.
Reference:
1 . Singh C, Levy WB (2017) A consensus layer V pyramidal neuron can sustain interpulse-interval coding. PLoS One 12:e0180839 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation;
Implementer(s): Singh, Chandan [chandan_singh at berkeley.edu];
// Initialize GUI
objref p
p=new PWManager()

t_stop_temp = tstop
dt_temp = dt
xopen("$(NEURONHOME)/lib/hoc/noload.hoc")
tstop = t_stop_temp
dt = dt_temp
nrnmainmenu()

// Initialize Model

objref somatodendritic, dendritic


/* Global */
  celsius   = 37
  v_init = -70
  
/* Passive membrane */
  ra        = 150  // decrease ad to decrease of soma vth variability, increase axon's vth variability
  global_ra = ra
  rm        = 30000   // g_pas=1/rm
  c_m       = 0.5
  cm_myelin = 0.02
  g_pas_node = 0.02

/* Active channels */
  // Nav
  Ena = 60
  gna12_soma = 80
  gna12_dend = 80 
  gna12_ais_max = 3200   // Nav1.2 
  gna16_ais_max = 3200   // Nav1.6
  gna16_nakeaxon= 300    
  gna12_myelin=20       // Nav1.2 at myelins
  gna16_node = 3200     // Nav1.6 at node

  // usetable
  usetable=0
  usetable_na=0
  usetable_na12=0
  usetable_na16=0
  usetable_kca=0
  usetable_km=0
  usetable_kv=0

  vhalf_na12 = -30
  vhalf_na16 = -43
  vhalf_na = -30
  vhalf_na12_stoch = -30
  vhalf_na16_stoch = -43
  vhalf_na_stoch = -30
  
  // Kv
  Ek = -90  
  gkv_soma = 20
  gkv_dend = 10 
  gkv_axon = 1000
  
  // Km
  gkm = .3
  gkm_soma = gkm
  
  // Kca
  gkca = 3
  gkca_soma = gkca
  
  // Ca
  Eca=140
  gca = .3
  gca_soma = gca

  // gamma
  gamma_na =  gamma
  gamma_na12 = gamma
  gamma_na16 = gamma
  gamma_na_stoch = gamma
  gamma_na12_stoch = gamma
  gamma_na16_stoch = gamma

// ------------------------------------------------
//    Cell Geometry
// ------------------------------------------------
 

/* Clean up */  
  forall delete_section()

/* Soma and Dendrites */
  load_file("morphology/soma_dendrites.hoc")

  // build a sectionlist for soma and dendrites
  somatodendritic = new SectionList()
  forall {
    if (L/nseg>40) {
      nseg = L/40 + 1 
    }    // make sure no segments exceed 40 uM length. Note, soma.nseg remains 10.
    somatodendritic.append()  // soma and dendrites are all included
  }

    
  // build a sectionlist for dendrites only
  dendritic = new SectionList()
  forsec somatodendritic dendritic.append()
  soma  dendritic.remove()     // remove soma for pure dendritic sectionlist

/* Axon */
  axonOnSoma=1
  load_file ("morphology/axon.hoc")
  create_axon()

  
/* Spines */
  aspiny = 0  // 0 for spiny
  if (!aspiny) {
    load_file ("morphology/spines.hoc")
    add_spines(dendritic,spine_dens)
  }
  
  distance(0,axonOnSoma)  // set the point where axon seated on soma as the origin

// ----------------------------------------------------
//  Insert Density Mechanisms
// ----------------------------------------------------

load_file ("density_mechs.hoc")

// Install passive membrane properties
install_passive()  
printf("stoch,%d\n",stoch)
// Install active channels
if(stoch==0){
    install_channels()
}
if(stoch==1){
    install_channels_stoch()
}
    
  
// -----------------------------------------------------------
//  Experiments: Insert Point Processes or Something Else
// -----------------------------------------------------------


xopen("recording.hoc")
// Call the Session "hu_all"
xopen ("sess.ses")

/* Where Ini */
xopen("inject_soma.hoc")