makeIons.hoc

///////////////////////////////////////////////////////////////////////////////
// makeIons.hoc: creates ions for the model
///////////////////////////////////////////////////////////////////////////////

//////////////////// procedure definitions ////////////////////////////////////

//-----------------------------------------------------------------------------
// setIonParameters()
//-----------------------------------------------------------------------------
// sets the ion parameters for each segment inserting mechanisms given in mod files

proc setIonParameters() {

  // set the soma parameters
  forsec somatic {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_soma
    	g_pas = gl_soma
  }

  // set the proximal apical dendrite parameters
  forsec proximal {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_prox
    	g_pas = gl_prox
  }

  // set the middle apical dendrite parameters
  forsec middle {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion

    insert pas
    	e_pas = el_mid
    	g_pas = gl_mid
  }

  // set the distal apical dendrite parameters
  forsec distal {

    // insert the ion mechanisms
    insert k_ion
    insert na_ion
    insert hco3_ion
    insert cl_ion
    insert ca_ion     

    insert pas
    	e_pas = el_dist
    	g_pas = gl_dist
  }
}


//////////////////// procedure calls /////////////////////////////////////


// register the new ions with NEURON
forall{
  cltype      = ion_register("cl",-1)
  hco3type    = ion_register("hco3",-1)
  catype      = ion_register("ca",2)
}

//set the ion parameters throughout the cell
setIonParameters()

// tell neuron how to treat them during the simulation
                            //ion_style("name", c_style, e_style, einit, eadvance, cinit)
                             // c_style-concentration: [0, 1, 2, 3] (UNUSED, PARAMETER, ASSIGNED, STATE)
                              // e_style - reversal pot: [0, 1, 2, 3] (UNUSED, PARAMETER, ASSIGNED, STATE)
                              // einit: [0, 1] (If 1 then reversal potential computed by Nernst equation on call to finitialize() using values of concentrations.)
                              // eadvance: [0, 1] (If 1 then reversal potential computed every call to fadvance() using the values of the concentrations)
                              //cinit: [0, 1] (If 1 then a call to finitialize() sets the concentrations to the values of the global initial concentrations. eg. nai set to nai0_na_ion and nao set to nao0_na_ion.)
forall {

	kstyle      = ion_style("k_ion",1,2,1,0,1)            // k, na, hco3 all parameters; set and forget
	nastyle     = ion_style("na_ion",1,2,1,0,1)           // cl is a state variable
	clstyle     = ion_style("cl_ion",3,2,1,1,1)
	hco3style   = ion_style("hco3_ion",1,2,1,0,1)
	castyle     = ion_style("ca_ion",3,2,1,0,1)
}

forall {
	ki = ki0_k_ion        
	ko = ko0_k_ion        
	nai = nai0_na_ion      
	nao = nao0_na_ion           
	hco3i = hco3i0_hco3_ion  
	hco3o = hco3o0_hco3_ion     
}