Application of a common kinetic formalism for synaptic models (Destexhe et al 1994)

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Accession:18198
Application to AMPA, NMDA, GABAA, and GABAB receptors is given in a book chapter. The reference paper synthesizes a comprehensive general description of synaptic transmission with Markov kinetic models. This framework is applicable to modeling ion channels, synaptic release, and all receptors. Please see the references for more details. A simple introduction to this method is given in a seperate paper Destexhe et al Neural Comput 6:14-18 , 1994). More information and papers at http://cns.iaf.cnrs-gif.fr/Main.html and through email: Destexhe@iaf.cnrs-gif.fr
References:
1 . Destexhe A, Mainen ZF, Sejnowski TJ (1994) Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. J Comput Neurosci 1:195-230 [PubMed]
2 . Destexhe A, Mainen Z, Sejnowski TJ (1994) An efficient method for computing synaptic conductances based on a kinetic model of receptor binding Neural Comput 6:14-18
3 . Destexhe A, Mainen Z, Sejnowski T (1995) Fast Kinetic Models for Simulating AMPA, NMDA, GABAA and GABAB Receptors The Neurobiology of Computation, Bower J, ed. pp.9
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Electrogenic pump;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s): Nicotinic; M1; M3; M4; M5; M2; mGluR1; mGluR2; mGluR3; mGluR4; mGluR5; mGluR6; mGluR7; mGluR8; Alpha; Alpha1; Alpha2; Beta; D1; D2; 5-HT1; 5-HT2; 5-HT4; H2; GabaA; GabaB; Muscarinic; AMPA; NMDA; mGluR; 5-HT3; Kainate; Monoamine Receptors; Glutamate; Gaba; Adrenergic; Serotonin; Histamine; Cholinergic Receptors; Amino Acid Receptors; Sensory Receptors; Olfactory Receptors; Opsins; Dopaminergic Receptor; Glycine; Gaseous Receptors; NO; Peptide Receptors; Dynorphin; H1; Ion Receptors; Zn2+; CO;
Gene(s):
Transmitter(s): Acetylcholine; Glycine; Dopamine; Zn2+; NO; CO; Dynorphin; Ephinephrine; Norephinephrine; Amino Acids; Gaba; Glutamate; Monoamines; Peptides; Ions; Gases; Histamine; Serotonin;
Simulation Environment: NEURON;
Model Concept(s): Ion Channel Kinetics; Markov-type model;
Implementer(s): Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr]; Mainen, Zach [Mainen at cshl.edu];
Search NeuronDB for information about:  Nicotinic; M1; M3; M4; M5; M2; mGluR1; mGluR2; mGluR3; mGluR4; mGluR5; mGluR6; mGluR7; mGluR8; Alpha; Alpha1; Alpha2; Beta; D1; D2; 5-HT1; 5-HT2; 5-HT4; H2; GabaA; GabaB; Muscarinic; AMPA; NMDA; mGluR; 5-HT3; Kainate; Monoamine Receptors; Glutamate; Gaba; Adrenergic; Serotonin; Histamine; Cholinergic Receptors; Amino Acid Receptors; Sensory Receptors; Olfactory Receptors; Opsins; Dopaminergic Receptor; Glycine; Gaseous Receptors; NO; Peptide Receptors; Dynorphin; H1; Ion Receptors; Zn2+; CO; Acetylcholine; Glycine; Dopamine; Zn2+; NO; CO; Dynorphin; Ephinephrine; Norephinephrine; Amino Acids; Gaba; Glutamate; Monoamines; Peptides; Ions; Gases; Histamine; Serotonin;
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SYN_NEW
README
ampa.mod *
ampa5.mod *
caL3d.mod *
gabaa.mod *
gabaa5.mod *
gabab.mod *
gabab3.mod
HH2.mod *
nmda.mod *
nmda5.mod *
release.mod
ampa.hoc
ampa5.hoc
gabaa.hoc
gabaa5.hoc
gabab.hoc
gabab3.hoc
mosinit.hoc *
nmda.hoc
nmda5.hoc
release.hoc
rundemo.hoc
                            
/*----------------------------------------------------------------------------

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

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

    Kinetic model from Destexhe, A. and Sejnowski, T.J.  Proc. Natl.
    Acad. Sci. USA 92: 9515-9519, 1995.


  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 = 800
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 = 5
stim.dur = 28       // to get a burst of 10 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 now incorporated in rel

// 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 GABAb3()            // create synapse
POST c.loc(0.5)             // assign postsynaptic compartment
setpointer c.C, PRE.T_rel(0.5)      // assign presynaptic compartment

K1_GABAb3   = 0.66  //  (/ms mM) forward binding rate to receptor
K2_GABAb3   = 0.020 //  (/ms)   backward (unbinding) rate of receptor
K3_GABAb3   = 0.083 //  (/ms)   rate of G-protein production
K4_GABAb3   = 0.0079 // (/ms)   rate of G-protein decay
d1_GABAb3   = 0.017 //  (/ms)   rate of receptor desensitization
d2_GABAb3   = 0.0053 // (/ms)   rate of receptor resensitization
KD_GABAb3   = 100   //      dissociation constant of K+ channel
n_GABAb3    = 4 //      nb of binding sites of G-protein on K+
Erev_GABAb3 = -95   //  (mV)    reversal potential (E_K)
c.gmax = 0.0001     //  (umho)      : maximum conductance



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


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

addgraph("c.i",-0.0001,0.001)
addgraph("POST.v(0.5)",v_init-4,v_init+1)

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