init_ring.hoc

// This script runs simulation of loop of pyramidal cells
// connected by gap junctions in axonal section 21, at distance 2296 um from soma
// one gap junction is set weak to break loop symmetry and induce reentrant oscillations

load_file ("nrngui.hoc")
load_file("cellTemplate.hoc")
load_file("gapjunction.hoc")

tstop = 25
ncells = 9
gj_conductance = 3e-3 //[mcS]
weakgj_conductance = 1.3e-3 //[mcS]
axonal_section = 21 // axonal section used
section_pos1 = 0.45 // position within section1
section_pos2 = 0.55 // position within section2

objectvar cells, gaps

proc mkloop(){ local i localobj cell_, gap_
// $1 - length of loop
   cells = new List()
   gaps = new List()
   for i=0,$1-1{
     cell_ = new pyramidal()
	 cells.append(cell_)
   }
   for i=0,$1-1{
    gap_ = new gapjunction(cells.object(i), axonal_section, cells.object((i+1)%$1), axonal_section, gj_conductance, section_pos1, section_pos2)
	gap_.setcells(i,(i+1)%$1)
	gaps.append(gap_)
   }
}

proc setpositions(){ local i, x, y
  for i = 0,cells.count()-1{
      x = 1000*cos(2*PI*i/cells.count())
	  y = 1000*sin(2*PI*i/cells.count())
	  cells.object(i).position(x,y,0)
	  cells.object(i).setgid(i+1)
  }
}

// adds steady current to soma (hyperpolarizing)
// $1 is the current in nA, "-" for hyperpolarizing, "+" for depolarizing
proc setcurrentbias(){ local i, area_soma localobj cell_
 cell_ = new pyramidal() //create a generic cell
 cell_.soma { area_soma = PI*diam*L*1e-8 } // unts converted [mcm2->cm2], area_soma is the area of a soma membrane
 for i = 0,cells.count-1{
   cells.object(i).soma {
      insert bias
	  amp_bias = -$1*1e-6/area_soma //note conversion [nA->mA] by 1e-6 and change of sign
    }
  }
}

// sets all conductances to 0 except HH: fast Na+ and K+(DR)
// this function is used to have only Na(F) and K(DR) conductances and a minimum loop length (9)
// a model with Na(F), K(DR), K(A) and K(M) requires a loop of 40 cells
proc setaxonalchannelsHH(){ local i
 for i = 0,cells.count-1{
	forsec cells.object(i).axonal {	gbar_ka = gbar_km = 0 } 
 }
}

mkloop(ncells)
setpositions()
setcurrentbias(-0.1) // electrode current, [nA]
setaxonalchannelsHH()

// set one gap junction weak
gaps.object(0).setg(weakgj_conductance)

objectvar pulse
cells.object(0).soma pulse = new Ipulse1(0.5)
pulse.amp = 1
pulse.del = 2
pulse.num = 1
pulse.ton = pulse.toff = 1

access cells.object(0).soma
xopen("ringGUI.ses")