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];
/* -----------------------------------------------
    Data Recording
-------------------------------------------------*/

/* Vectors Recording as Running  */
objref rec_soma, rec_hill, rec_ais[10], rec_nakeaxon[9], rec_node0, rec_mat, rec_time, rec_k[100], rec_k_soma[10], rec_ik[100], rec_ik_soma[10], rec_kca_soma, rec_km_soma
objref curr_sum_vec, ik_list
proc record_basic(){
    // soma
    rec_soma= new Vector()
    rec_soma.record(&soma.v(0.5))
    for i=0,9{
        rec_k_soma[i]= new Vector()
        rec_k_soma[i].record(&soma.gk_kv(.1*i))
        rec_ik_soma[i]= new Vector()
        rec_ik_soma[i].record(&soma.ik(.1*i))
    }
    rec_km_soma= new Vector()
    rec_km_soma.record(&soma.gk_km(0.5))
    rec_kca_soma= new Vector()
    rec_kca_soma.record(&soma.gk_kca(0.5))

    // hill
    rec_hill= new Vector()
    rec_hill.record(&hill.v(.5))
    // ais
    for i=0,9 {
      rec_ais[i]= new Vector()
      rec_ais[i].record(&ais[i].v(.5))
      }
    for i=0,9 {
        for j=0,9 {
          x = i*10+j
          rec_k[x]= new Vector()
          rec_k[x].record(&ais[i].gk_kv(.1*j))
          rec_ik[x]= new Vector()
          rec_ik[x].record(&ais[i].ik(.1*j))
        }
      }
    // nakeaxon
    for i=1,9 {
      rec_nakeaxon[i-1]= new Vector()
      rec_nakeaxon[i-1].record(&nakeaxon.v(i*0.1))
      }
    // node
    rec_node0= new Vector() 
    rec_node0.record(&node[0].v(.5))
    // time
    rec_time = new Vector()
    rec_time.record(&t)
  }

 proc normalize_k_vects(){
  for i=0,9{
    for j=0,9{
        x = i*10+j
        rec_k[x].div(ais[i].gbar_kv(.1*j))
    }
    rec_k_soma.div(soma.gbar_kv(.1*i))
  }

  rec_kca_soma.div(soma.gbar_kca(.5))
  rec_km_soma.div(soma.gbar_km(.5))
}

proc sum_k_vects(){
  for i=0,9 {
    for j=1,9 {
      x = i*10+j
      rec_k[i*10].add(rec_k[i*10+j])
      rec_ik[i*10].add(rec_ik[i*10+j])
    }
  }
}

/* Save to File */
objref f
proc save_basic() {
  normalize_k_vects() // turn conductances into percentages
  sum_k_vects()

  rec_mat= new Matrix()
  rec_mat.resize(rec_soma.size(),66)
  // Set Matrix Column Values
  rec_mat.setcol(0,rec_soma)
  rec_mat.setcol(1,rec_hill)
  for i=0,9 {
    rec_mat.setcol(i+2,rec_ais[i])
  }
  for i=1,9 {
    rec_mat.setcol(i+11, rec_nakeaxon[i-1])
  }
  rec_mat.setcol(21,rec_node0)
  rec_mat.setcol(22,rec_time)
  for i=0,9 {
    rec_mat.setcol(23+i,rec_k[i*10])
  }
  for i=0,9 {
    rec_mat.setcol(33+i,rec_k_soma[i])
  }
  for i=0,9 {
    rec_mat.setcol(43+i,rec_ik_soma[i])
  }
  for i=0,9 {
    rec_mat.setcol(53+i,rec_ik[i*10])
  }
  rec_mat.setcol(63,rec_kca_soma)
  rec_mat.setcol(64,rec_km_soma)
  rec_mat.setcol(65,curr_sum_vec)

  print "open:",v_str
  f = new File()  //savdata is a file pointer
  f.wopen(v_str)  //open a file with a defined name to save data
  f.printf(" soma   hill   ais0    ais1    ais2    ais3    ais4    ais5    ais6    ais7    ais8    ais9   nake0.1    nake0.2    nake0.3    nake0.4    nake0.5    nake0.6    nake0.7    nake0.8    nake0.9    node[0]    t   k0  k1  k2  k3  k4  k5  k6  k7  k8  k9 k0_s k1_s    k2_s    k3_s    k4_s    k5_s    k6_s    k7_s    k8_s    k9_s     ik0_s  ik1_s   ik2_s   ik3_s   ik4_s   ik5_s   ik6_s   ik7_s   ik8_s   ik9_s   ik0 ik1 ik2 ik3 ik4 ik5 ik6 ik7 ik8 ik9 soma_km    soma_kca ik_sum\n")
  f.printf("delay= %f\n",del)
  f.printf("intensity= %f\n",intensity)
  f.printf("dur= %f\n",dur)
  rec_mat.fprint(f," %g")
  f.close()
  
  printf("Traces saved.\n")
}


///////////////// chans ///////////////////
/* Vectors Recording as Running  */
objref rec_12_ais[100],rec_16_ais[100], rec_soma_chans[10], rec_mat_chans
proc recordV_chans(){
  for i=0,9 {
    for j=0,9 {
      x = i*10+j
      rec_12_ais[x]= new Vector()
      rec_16_ais[x]= new Vector()
      rec_12_ais[x].record(&ais[i].m3h0_na12_stoch(.1*j))
      rec_16_ais[x].record(&ais[i].m3h0_na16_stoch(.1*j))
    }
    rec_soma_chans[i] = new Vector()
    rec_soma_chans[i].record(&soma.m3h0_na_stoch(.1*i))
  }
}

proc sum_vects(){
  for i=0,9{
    for j=1,9{
        rec_12_ais[i*10].add(rec_12_ais[i*10+j])
        rec_16_ais[i*10].add(rec_16_ais[i*10+j])
    }
  }
  for i=1,9{
    rec_soma_chans[0].add(rec_soma_chans[i])
  }
}

/* Save to File */
objref f_chans
proc saveV_chans() {
  print "opening:",chans_str
  sum_vects()
  rec_mat_chans= new Matrix()
  rec_mat_chans.resize(rec_12_ais.size(),21)
  for i=0,9 {
    rec_mat_chans.setcol(i,rec_12_ais[i*10])
    }
  for i=0,9 {
    rec_mat_chans.setcol(i+10, rec_16_ais[i*10])
  }
  rec_mat_chans.setcol(20, rec_soma_chans[0])
  f_chans = new File()  //savdata is a file pointer
  f_chans.wopen(chans_str)  //open a file with a defined name to save data
  f_chans.printf(" 12_0   12_1   12_2   12_3   12_4   12_5   12_6   12_7   12_8   12_9   16_0   16_1   16_2   16_3   16_4   16_5   16_6   16_7   16_8   16_9    soma_chans\n")
  f_chans.printf("delay= %f\n",del)
  rec_mat_chans.fprint(f_chans," %g")
  f_chans.close()
  print "saved to: ",chans_str
}


obfunc record_all_ik() { localobj tmpvec, tmplist
  tmplist = new List()
  forall{
      for (x,0) {
        tmpvec = new Vector()
        tmpvec.record(&ik(x))
        tmplist.append(tmpvec)
      }
  }
  return tmplist
}

proc sum_and_save_all_ik(){ localobj l
    T = ik_list.o(0).size()
    num_secs = ik_list.count()
    curr_sum_vec = new Vector(T)
    curr_sum_vec.fill(0)
    sec = 0
    forall{
        for(x,0){
            surface_area_mult = area(x)/100
            for i=0,T-1{
                curr_sum_vec.x[i] +=ik_list.o(sec).x[i] *surface_area_mult
            }
            sec += 1
        }
    }
//    print "sec ",sec," ",num_secs
}