Response of AMPA receptor kinetic model to glutamate release distance (Allam et al., 2015)

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Accession:184410
These files model the response of an AMPA receptor kinetic model to the release (and diffusion) of glutamate as a function of distance between receptor and release site.
Reference:
1 . Allam SL, Bouteiller JM, Hu EY, Ambert N, Greget R, Bischoff S, Baudry M, Berger TW (2015) Synaptic Efficacy as a Function of Ionotropic Receptor Distribution: A Computational Study. PLoS One 10:e0140333 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Channel/Receptor;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s): AMPA; Glutamate;
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: SBML; LibRoadRunner;
Model Concept(s):
Implementer(s): Allam, Sushmita [sushmita.allam at gmail.com]; Bouteiller, Jean-Marie C [jbouteil at usc.edu]; Hu, Eric [ehu at usc.edu]; Ambert, Nicolas [nicolas.ambert at rhenovia.com]; Greget, Renaud [renaud.greget at rhenovia.com]; Bischoff, Serge [serge.bischoff at rhenovia.com; Baudry, Michel [michel.baudry at rhenovia.com]; Berger, Theodore W. [berger at usc.edu];
Search NeuronDB for information about:  AMPA; Glutamate; Glutamate;
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      <parameter metaid="tempVar1_2" id="tempVar1_2" name="tempVar1 of 2" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="tempVar2_2" id="tempVar2AMPA_2" name="tempVar2AMPA of 2" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="k0_2" id="k0_2" name="k0 of 2" value="0.002188" units="dimensionless" constant="true"/>
      <parameter metaid="distance_2" id="distanceAMPA_2" name="distanceAMPA of 2" value="0.03" units="microm" constant="true"/>
      <parameter metaid="cleftWidth_2" id="cleftWidth_2" name="cleftWidth of 2" value="0.02" units="microm" constant="true"/>
      <parameter metaid="NTdiffCoeff_2" id="NTdiffCoef_2" name="NTdiffCoef of 2" value="0.4" units="micromsquare_per_ms" constant="true"/>
      <parameter metaid="PiValue_2" id="PiValue_2" name="pi  of 2" value="3.14159" units="dimensionless" constant="true"/>
      <parameter metaid="uptime_2" id="temp_time_2" name="temp variable for time of 2" value="0" units="ms" constant="false"/>
      <parameter metaid="upnt_2" id="temp_nt_2" name="temp variable for nt of 2" value="0" units="substance" constant="false"/>
      <parameter metaid="tmp_fake_2" id="tmp_fake_2" name="feke deriv of 2" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="memorySize_2" id="memorySize_2" name="memorySize of 2" value="40" units="ms" constant="true"/>
      <parameter metaid="position_2" id="position_unused_2" name="position_unused of 2" value="0.205" units="microm" constant="true"/>
      <parameter metaid="t0_2" id="t0_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t1_2" id="t1_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t2_2" id="t2_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t3_2" id="t3_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t4_2" id="t4_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t5_2" id="t5_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t6_2" id="t6_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="t7_2" id="t7_2" value="-1" units="ms" constant="false"/>
      <parameter metaid="nt0_2" id="nt0_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt1_2" id="nt1_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt2_2" id="nt2_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt3_2" id="nt3_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt4_2" id="nt4_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt5_2" id="nt5_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt6_2" id="nt6_2" value="0" units="mM" constant="false"/>
      <parameter metaid="nt7_2" id="nt7_2" value="0" units="mM" constant="false"/>
      <parameter metaid="NTconcNMDA_2" id="NTconcNMDA_2" name="NTconcNMDA of 2" value="0" units="mM" constant="false"/>
      <parameter metaid="NTconcmGluR_2" id="NTconcmGluR_2" name="NTconcmGluR of 2" value="0" units="mM" constant="false"/>
      <parameter metaid="positionNMDA_2" id="distanceNMDA_2" name="distanceNMDA of 2" value="0.1" units="microm" constant="true"/>
      <parameter metaid="positionmGluR_2" id="distancemGluR_2" name="distancemGluR of 2" value="1" units="microm" constant="true"/>
      <parameter metaid="tempVar2NMDA_2" id="tempVar2NMDA_2" name="tempVar2NMDA of 2" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="tempVar2mGluR_2" id="tempVar2mGluR_2" name="tempVar2mGluR of 2" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="kass_re1_3" id="kass_re1_3" value="10" units="per_mM_per_msec" constant="true"/>
      <parameter metaid="kdiss_re1_3" id="kdiss_re1_3" value="7" units="per_msec" constant="true"/>
      <parameter metaid="kass_re5_3" id="kass_re5_3" value="10" units="per_mM_per_msec" constant="true"/>
      <parameter metaid="kdiss_re5_3" id="kdiss_re5_3" value="0.00041" units="per_msec" constant="true"/>
      <parameter metaid="kass_re11_3" id="kass_re11_3" value="0" units="per_msec" constant="false"/>
      <parameter metaid="kdiss_re11_3" id="kdiss_re11_3" value="0.001" units="per_msec" constant="true"/>
      <parameter metaid="kass_re12_3" id="kass_re12_3" value="0" units="per_msec" constant="false"/>
      <parameter metaid="kdiss_re12_3" id="kdiss_re12_3" value="0.017" units="per_msec" constant="true"/>
      <parameter metaid="kass_re16_3" id="kass_re16_3" value="0.55" units="per_msec" constant="true"/>
      <parameter metaid="kdiss_re16_3" id="kdiss_re16_3" value="0" units="per_msec" constant="false"/>
      <parameter metaid="kass_re19_3" id="kass_re19_3" value="0.2" units="per_msec" constant="true"/>
      <parameter metaid="kdiss_re19_3" id="kdiss_re19_3" value="0.035" units="per_msec" constant="true"/>
      <parameter metaid="conduc_O2_3" id="conduc_O2_3" name="conductance for state O2 of 3" value="9" units="pS" constant="true"/>
      <parameter metaid="conduc_O3_3" id="conduc_O3_3" name="conductance for state O3 of 3" value="15" units="pS" constant="true"/>
      <parameter metaid="conduc_O4_3" id="conduc_O4_3" name="conductance for state 04 of 3" value="21" units="pS" constant="true"/>
      <parameter metaid="Erev_AMPA_3" id="Erev_AMPA_3" name="AMPA reversal potential  of 3" value="0" units="mV" constant="true"/>
      <parameter metaid="current_AMPA_3" id="current_AMPA_3" name="AMPA current of 3" value="0" units="pA" constant="false"/>
      <parameter metaid="sumOpen_3" id="sumOpen_3" name="sumOpen = O2+O3+O4 of 3" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="PNa_3" id="PNa_3" name="Permeability for Sodium (Na) of 3" value="50" units="percent" constant="true"/>
      <parameter metaid="PK_3" id="PK_3" name="Permeability for Potassium (K) of 3" value="49.5" units="percent" constant="true"/>
      <parameter metaid="PCa_3" id="PCa_3" name="Permeability for Calcium (Ca) of 3" value="0.5" units="percent" constant="true"/>
      <parameter metaid="ICa_AMPA_3" id="ICa_AMPA_3" name="AMPA mediated current by Ca of 3" value="0" units="pA" constant="false"/>
      <parameter metaid="INa_AMPA_3" id="INa_AMPA_3" name="AMPA mediated current by Na of 3" value="0" units="pA" constant="false"/>
      <parameter metaid="IK_AMPA_3" id="IK_AMPA_3" name="AMPA mediated current by K of 3" value="0" units="pA" constant="false"/>
      <parameter metaid="nbAMPAR_3" id="nbAMPAR_3" name="nbAMPAR of 3" value="1" units="dimensionless" constant="true"/>
      <parameter metaid="NewNbAMPAR_3" id="NewNbAMPAR_3" value="0" units="dimensionless" constant="false"/>
      <parameter metaid="Deact_factor_3" id="Deact_factor_3" name="1.4601 for 1 Mm and 1.9725 for 5 mM of 3" value="1" units="dimensionless" constant="true"/>
      <parameter metaid="Desens_factor_3" id="Desens_factor_3" name="1.8560 for 1mM and 13.4046 for 5 mM of 3" value="1" units="dimensionless" constant="true"/>
      <parameter metaid="kdiss_re16_Init_3" id="kdiss_re16_Init_3" value="0.3" units="per_msec" constant="true"/>
      <parameter metaid="kass_re11_Init_3" id="kass_re11_Init_3" value="3.3e-006" units="per_msec" constant="true"/>
      <parameter metaid="kass_re12_Init_3" id="kass_re12_Init_3" value="0.42" units="per_msec" constant="true"/>
    </listOfParameters>
    <listOfRules>
      <assignmentRule metaid="V_1" variable="V_1">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <piecewise>
            <piece>
              <ci> Vmax_1 </ci>
              <apply>
                <and/>
                <apply>
                  <gt/>
                  <ci> ON_1 </ci>
                  <cn type="integer"> 0 </cn>
                </apply>
                <apply>
                  <lt/>
                  <ci> OFF_1 </ci>
                  <cn type="integer"> 1 </cn>
                </apply>
              </apply>
            </piece>
            <otherwise>
              <ci> Vmin_1 </ci>
            </otherwise>
          </piecewise>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00012_2" variable="tempVar1_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <times/>
            <cn type="integer"> 4 </cn>
            <ci> PiValue_2 </ci>
            <ci> cleftWidth_2 </ci>
            <ci> NTdiffCoef_2 </ci>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00013_2" variable="tempVar2AMPA_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <minus/>
              <apply>
                <times/>
                <ci> distanceAMPA_2 </ci>
                <ci> distanceAMPA_2 </ci>
              </apply>
            </apply>
            <apply>
              <times/>
              <cn type="integer"> 4 </cn>
              <ci> NTdiffCoef_2 </ci>
            </apply>
          </apply>
        </math>
      </assignmentRule>
      <rateRule metaid="CDMT00010_2" variable="tmp_fake_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <cn type="integer"> 0 </cn>
        </math>
      </rateRule>
      <assignmentRule metaid="CDMT00001_2" variable="NTconcAMPA_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <times/>
              <ci> k0_2 </ci>
              <apply>
                <plus/>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt0_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t0_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t0_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt1_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t1_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t1_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt2_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t2_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t2_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt3_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t3_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t3_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt4_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t4_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t4_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt5_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t5_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t5_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt6_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t6_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t6_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt7_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t7_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2AMPA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t7_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
              </apply>
            </apply>
            <cn type="integer"> 1000 </cn>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00038_2" variable="tempVar2NMDA_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <minus/>
              <apply>
                <times/>
                <ci> distanceNMDA_2 </ci>
                <ci> distanceNMDA_2 </ci>
              </apply>
            </apply>
            <apply>
              <times/>
              <cn type="integer"> 4 </cn>
              <ci> NTdiffCoef_2 </ci>
            </apply>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00039_2" variable="tempVar2mGluR_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <minus/>
              <apply>
                <times/>
                <ci> distancemGluR_2 </ci>
                <ci> distancemGluR_2 </ci>
              </apply>
            </apply>
            <apply>
              <times/>
              <cn type="integer"> 4 </cn>
              <ci> NTdiffCoef_2 </ci>
            </apply>
          </apply>
        </math>
      </assignmentRule>
      <assignmentRule metaid="CDMT00040_2" variable="NTconcNMDA_2">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <times/>
              <ci> k0_2 </ci>
              <apply>
                <plus/>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt0_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t0_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t0_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt1_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t1_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t1_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt2_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t2_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t2_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt3_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t3_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t3_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt4_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t4_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t4_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt5_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t5_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t5_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt6_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t6_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
                    <apply>
                      <divide/>
                      <ci> tempVar2NMDA_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t6_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                </apply>
                <apply>
                  <times/>
                  <apply>
                    <divide/>
                    <ci> nt7_2 </ci>
                    <apply>
                      <times/>
                      <ci> tempVar1_2 </ci>
                      <apply>
                        <minus/>
                        <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                        <ci> t7_2 </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <exp/>
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                  <apply>
                    <divide/>
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                        <minus/>
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                    <exp/>
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                    </apply>
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                </apply>
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            <apply>
              <plus/>
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              <minus/>
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        </math>
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            <times/>
            <apply>
              <divide/>
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        </math>
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        </math>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
</body>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
</body>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
</body>
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          </math>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
</body>
          </html>
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        <annotation>
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              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 1 </cn>
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                <ci> kdiss_re12_3 </ci>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
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        <kineticLaw metaid="CDMT00050">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
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              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 2 </cn>
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              <apply>
                <times/>
                <ci> kdiss_re12_3 </ci>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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              <celldesigner:extension>
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        <kineticLaw metaid="CDMT00053">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
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              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 3 </cn>
                <ci> kass_re12_Init_3 </ci>
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              <apply>
                <times/>
                <ci> kdiss_re12_3 </ci>
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        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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          <speciesReference metaid="CDMT00054_3" species="R4_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa5</celldesigner:alias>
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        <listOfProducts>
          <speciesReference metaid="CDMT00055_3" species="D4_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa14</celldesigner:alias>
              </celldesigner:extension>
            </annotation>
          </speciesReference>
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        <kineticLaw metaid="CDMT00056">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 4 </cn>
                <ci> kass_re12_Init_3 </ci>
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              <apply>
                <times/>
                <ci> kdiss_re12_3 </ci>
                <ci> D4_3 </ci>
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          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re16_3" id="re16_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
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            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="O2" alias="sa18">
                <celldesigner:linkAnchor position="S"/>
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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          <speciesReference metaid="CDMT00057_3" species="R2_3" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa3</celldesigner:alias>
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        <listOfProducts>
          <speciesReference metaid="CDMT00058_3" species="O2_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa18</celldesigner:alias>
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        <kineticLaw metaid="CDMT00059">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 2 </cn>
                <ci> kass_re16_3 </ci>
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              <apply>
                <times/>
                <ci> kdiss_re16_3 </ci>
                <ci> O2_3 </ci>
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          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re17_3" id="re17_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
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            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="O3" alias="sa19">
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            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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          <speciesReference metaid="CDMT00060_3" species="R3_3" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa4</celldesigner:alias>
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        <listOfProducts>
          <speciesReference metaid="CDMT00061_3" species="O3_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa19</celldesigner:alias>
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        <kineticLaw metaid="CDMT00062">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 3 </cn>
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              <apply>
                <times/>
                <ci> kdiss_re16_3 </ci>
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        </kineticLaw>
      </reaction>
      <reaction metaid="re18_3" id="re18_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="O4" alias="sa20">
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            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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          <speciesReference metaid="CDMT00063_3" species="R4_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa5</celldesigner:alias>
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        <listOfProducts>
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              <celldesigner:extension>
                <celldesigner:alias>sa20</celldesigner:alias>
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          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00065">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 4 </cn>
                <ci> kass_re16_3 </ci>
                <ci> R4_3 </ci>
              </apply>
              <apply>
                <times/>
                <ci> kdiss_re16_3 </ci>
                <ci> O4_3 </ci>
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            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction metaid="re19_3" id="re19_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
            <celldesigner:baseReactants>
              <celldesigner:baseReactant species="D2" alias="sa12">
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              </celldesigner:baseReactant>
            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="E2" alias="sa15">
                <celldesigner:linkAnchor position="N"/>
              </celldesigner:baseProduct>
            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
              <celldesigner:listOfLineDirection>
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            <celldesigner:line width="1.0" color="ff000000"/>
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          <speciesReference metaid="CDMT00066_3" species="D2_3" stoichiometry="1" constant="true">
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              <celldesigner:extension>
                <celldesigner:alias>sa12</celldesigner:alias>
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          </speciesReference>
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        <listOfProducts>
          <speciesReference metaid="CDMT00067_3" species="E2_3" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa15</celldesigner:alias>
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            </annotation>
          </speciesReference>
        </listOfProducts>
        <kineticLaw metaid="CDMT00068">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 1 </cn>
                <ci> kass_re19_3 </ci>
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              <apply>
                <times/>
                <ci> kdiss_re19_3 </ci>
                <ci> E2_3 </ci>
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          </math>
        </kineticLaw>
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      <reaction metaid="re20_3" id="re20_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="E3" alias="sa16">
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            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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              <celldesigner:extension>
                <celldesigner:alias>sa16</celldesigner:alias>
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          </speciesReference>
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        <kineticLaw metaid="CDMT00071">
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              <minus/>
              <apply>
                <times/>
                <cn type="integer"> 2 </cn>
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              <apply>
                <times/>
                <ci> kdiss_re19_3 </ci>
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      <reaction metaid="re21_3" id="re21_3" reversible="true" fast="false">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <head>
              <title/>
            </head>
            <body>mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
</body>
          </html>
        </notes>
        <annotation>
          <celldesigner:extension>
            <celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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            </celldesigner:baseReactants>
            <celldesigner:baseProducts>
              <celldesigner:baseProduct species="E4" alias="sa17">
                <celldesigner:linkAnchor position="N"/>
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            </celldesigner:baseProducts>
            <celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
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                <celldesigner:alias>sa14</celldesigner:alias>
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          <speciesReference metaid="CDMT00073_3" species="E4_3" stoichiometry="1" constant="true">
            <annotation>
              <celldesigner:extension>
                <celldesigner:alias>sa17</celldesigner:alias>
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          </speciesReference>
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        <kineticLaw metaid="CDMT00074">
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              <minus/>
              <apply>
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                <cn type="integer"> 3 </cn>
                <ci> kass_re19_3 </ci>
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              <apply>
                <times/>
                <ci> kdiss_re19_3 </ci>
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        </kineticLaw>
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                  <plus/>
                  <apply>
                    <times/>
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                    </apply>
                  </apply>
                  <ci> Delay_1 </ci>
                </apply>
              </apply>
              <apply>
                <lt/>
                <ci> pulseNb_1 </ci>
                <ci> Npulses_1 </ci>
              </apply>
            </apply>
          </math>
        </trigger>
        <delay metaid="CDMT00027_1">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <cn type="integer"> 0 </cn>
          </math>
        </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="CDMT00021_1" variable="pulseNb_1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <apply>
                <plus/>
                <ci> pulseNb_1 </ci>
                <cn type="integer"> 1 </cn>
              </apply>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00018_1" variable="ON_1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 1 </cn>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00028_1" variable="OFF_1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 0 </cn>
            </math>
          </eventAssignment>
        </listOfEventAssignments>
      </event>
      <event metaid="newPulseEnd_1" id="newPulseEnd_1" name="newPulseEnd of 1" useValuesFromTriggerTime="true">
        <trigger metaid="CDMT00029_1" initialValue="true" persistent="true">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <and/>
              <apply>
                <gt/>
                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                <apply>
                  <plus/>
                  <apply>
                    <times/>
                    <apply>
                      <minus/>
                      <ci> pulseNb_1 </ci>
                      <cn type="integer"> 1 </cn>
                    </apply>
                    <apply>
                      <plus/>
                      <ci> tup_1 </ci>
                      <ci> tdown_1 </ci>
                    </apply>
                  </apply>
                  <ci> Delay_1 </ci>
                  <ci> tup_1 </ci>
                </apply>
              </apply>
              <apply>
                <leq/>
                <ci> pulseNb_1 </ci>
                <ci> Npulses_1 </ci>
              </apply>
            </apply>
          </math>
        </trigger>
        <delay metaid="CDMT00030_1">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <cn type="integer"> 0 </cn>
          </math>
        </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="CDMT00022_1" variable="ON_1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 0 </cn>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00023_1" variable="OFF_1">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 1 </cn>
            </math>
          </eventAssignment>
        </listOfEventAssignments>
      </event>
      <event metaid="dd_2" id="diffusion_ON_2" name="diffusion_ON of 2" useValuesFromTriggerTime="true">
        <trigger metaid="CDMT00034_2" initialValue="true" persistent="true">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <gt/>
              <ci> NT_2 </ci>
              <cn type="integer"> 0 </cn>
            </apply>
          </math>
        </trigger>
        <delay metaid="CDMT00035_2">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <cn type="integer"> 0 </cn>
          </math>
        </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="CDMT00026_2" variable="temp_nt_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> NT_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00043_2" variable="temp_time_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00016_2" variable="t0_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <apply>
                <minus/>
                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                <cn type="e-notation"> 1 <sep/> -10 </cn>
              </apply>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00018_2" variable="nt0_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> NT_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00015_2" variable="t1_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t0_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00017_2" variable="t2_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t1_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00019_2" variable="t3_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t2_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00020_2" variable="t4_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t3_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00021_2" variable="t5_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t4_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00022_2" variable="t6_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t5_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00023_2" variable="t7_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> t6_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00024_2" variable="nt1_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt0_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00025_2" variable="nt2_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt1_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00027_2" variable="nt3_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt2_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00028_2" variable="nt4_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt3_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00029_2" variable="nt5_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt4_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00030_2" variable="nt6_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt5_2 </ci>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00031_2" variable="nt7_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <ci> nt6_2 </ci>
            </math>
          </eventAssignment>
        </listOfEventAssignments>
      </event>
      <event metaid="diffusion_OFF_2" id="diffusion_OFF_2" name="diffusion_OFF of 2" useValuesFromTriggerTime="true">
        <trigger metaid="CDMT00036_2" initialValue="true" persistent="true">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <eq/>
              <ci> NT_2 </ci>
              <cn type="integer"> 0 </cn>
            </apply>
          </math>
        </trigger>
        <delay metaid="CDMT00037_2">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <cn type="integer"> 0 </cn>
          </math>
        </delay>
        <listOfEventAssignments>
          <eventAssignment metaid="CDMT00046_2" variable="temp_nt_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 0 </cn>
            </math>
          </eventAssignment>
          <eventAssignment metaid="CDMT00047_2" variable="temp_time_2">
            <math xmlns="http://www.w3.org/1998/Math/MathML">
              <cn type="integer"> 0 </cn>
            </math>
          </eventAssignment>
        </listOfEventAssignments>
      </event>
    </listOfEvents>
  </model>
</sbml>

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