/*----------------------------------------------------------------------------

    Detailed kinetic synapse mechanism
    ----------------------------------

    Demo file to show the behavior of a synaptic currents mediated by
    glutamate AMPA receptors, using a detailed kinetic model of these
    receptors and a kinetic model for the release of transmitter.

    Kinetic model from Patneau et al, J Neurosci 13: 3496, 1993.


  See details in:

  Destexhe, A., Mainen, Z.F. and Sejnowski, T.J.  Kinetic models of 
  synaptic transmission.  In: Methods in Neuronal Modeling (2nd edition; 
  edited by Koch, C. and Segev, I.), MIT press, Cambridge, 1998, pp. 1-25.

  (electronic copy available at http://cns.iaf.cnrs-gif.fr)


  Written by Alain Destexhe, Laval University, 1995

----------------------------------------------------------------------------*/



//----------------------------------------------------------------------------
//  load and define general graphical procedures
//----------------------------------------------------------------------------

// xopen("$(NEURONHOME)/lib/hoc/stdrun.hoc")

objectvar g[20]         // max 20 graphs
ngraph = 0

proc addgraph() { local ii  // define subroutine to add a new graph
                // addgraph("variable", minvalue, maxvalue)
    ngraph = ngraph+1
    ii = ngraph-1
    g[ii] = new Graph()
    g[ii].size(0,tstop,$2,$3)
    g[ii].xaxis()
    g[ii].yaxis()
    g[ii].addvar($s1,1,0)
    g[ii].save_name("graphList[0].")
    graphList[0].append(g[ii])
}

if(ismenu==0) {
  nrnmainmenu()         // create main menu
  nrncontrolmenu()      // crate control menu
  ismenu=1
}



//----------------------------------------------------------------------------
//  general parameters
//----------------------------------------------------------------------------

dt=0.025
tstop = 40
runStopAt = tstop
steps_per_ms = 1/dt
celsius = 36
v_init = -70



//----------------------------------------------------------------------------
//  create compartments and insert passive properties
//----------------------------------------------------------------------------

create PRE,POST
forall {
  diam=10
  L=10
  insert pas
  g_pas=1/5000
  e_pas=v_init
}



//----------------------------------------------------------------------------
//  insert presynaptic mechanisms
//----------------------------------------------------------------------------

access PRE      // insert Hodgk-Hux. Na+ and K+ currents for spikes

insert hh2
ek = -90
gnabar_hh2 = 0.1
gkbar_hh2 = 0.03


objectvar stim      // insert current injection
PRE stim = new IClamp(.5)
// note: for older versions of neuron, use PulseStim instead of IClamp
stim.del = 2
stim.dur = 2        // increase stim.dur to get a burst of presynaptic spikes
stim.amp = 0.1


insert caL      // HV Ca++ channel for transmitter release
p_caL=0.0002
q_caL=10
Ra_caL=1.6
Rb_caL=1.6


insert rel      // transmitter release
Ves_rel = 0.01      // conc of vesicles (mM)
Fmax_rel = 0.001    // tot conc of proteins (F and V) (mM)
b_rel   = 1e16      // rate cst for Ca++ binding to fusion factor
u_rel   = 0.1       // rate cst for Ca++ unbinding
k1_rel  = 1000      // rate cst for activation of vesicle
k2_rel  = 0.1       // rate cst for deactivation of vesicle
k3_rel  = 4     // rate cst for exocytosis
nt_rel  = 10000     // number of transmitter molecule per vesicle
kh_rel  = 10        // transmitter hydolysis constant

// cad is now in rel mechanism 
// insert cad      // Ca++ ATPase pump
kd_rel = 1e-5
kt_rel = 1e-3       // fast Ca++ removal
depth_rel = 1
taur_rel = 1e10



//----------------------------------------------------------------------------
//  insert postsynaptic mechansisms
//----------------------------------------------------------------------------

objectvar c
c = new AMPA5()             // create synapse
POST c.loc(0.5)             // assign postsynaptic compartment
setpointer c.C, PRE.T_rel(0.5)      // assign presynaptic compartment

Erev_AMPA5  = 0 //  (mV)    reversal potential (E_K)
Rb_AMPA5    = 13   //   (/mM /ms) binding, diffusion limited (DO NOT ADJUST)
Ru1_AMPA5   = 0.0059  //    (/ms) unbinding (1st site)
Ru2_AMPA5   = 86  //    (/ms) unbinding (2nd site)      
Rd_AMPA5    = 0.9    // (/ms) desensitization
Rr_AMPA5    = 0.064 //  (/ms) resensitization 
Ro_AMPA5    = 2.7    // (/ms) opening
Rc_AMPA5    = 0.2    // (/ms) closing
c.gmax      = 300   //  (pS)    maximum conductance




//----------------------------------------------------------------------------
//  add graphs
//----------------------------------------------------------------------------


addgraph("PRE.v(0.5)",-90,40)
addgraph("PRE.T_rel(0.5)",0,1.5)

addgraph("c.i",-0.003,0.0001)
addgraph("POST.v(0.5)",v_init-2,v_init+8)