Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011)

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Accession:139655
This is a multi-compartmental, stochastic version of the Kim et al. 2010 paper. There are a few additional reactions, and some of the rate constants have been updated. It addresses the role of molecule anchoring in PKA dependent hippocampal LTP.
Reference:
1 . Kim M, Park AJ, Havekes R, Chay A, Guercio LA, Oliveira RF, Abel T, Blackwell KT (2011) Colocalization of protein kinase A with adenylyl cyclase enhances protein kinase A activity during induction of long-lasting long-term-potentiation. PLoS Comput Biol 7:e1002084 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s): Dopaminergic Receptor;
Gene(s):
Transmitter(s): Dopamine;
Simulation Environment: NeuroRD;
Model Concept(s): Long-term Synaptic Plasticity; Signaling pathways;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Dopaminergic Receptor; Dopamine;
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    <!-- these apply to everything unless overridden -->
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   <!-- CaB reaction does not need for Ca dynamics -->
    
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	<NanoMolarity specieID="GluR1_S845_S831" value="0"/>
	<NanoMolarity specieID="GluR1_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_CKpCam" value="0"/>
        <NanoMolarity specieID="GluR1_CKp" value="2"/>
	<NanoMolarity specieID="GluR1_S845_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKpCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKp" value="0"/>

	<NanoMolarity specieID="GluR1_S831_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_S845_PP1" value="678"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP1" value="0"/>
        <NanoMolarity specieID="GluR1_S831_PP1" value="75"/>
	<NanoMolarity specieID="GluR1_S845_PP2B" value="0"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP2B" value="0"/>

        <NanoMolarity specieID="PKAcAMP4_GluR1" value="0" />
        <NanoMolarity specieID="PKAcAMP4_GluR1_S831" value="0" />

       <NanoMolarity specieID="pmca" value="0"/>
       <NanoMolarity specieID="pmcaCa" value="0"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
 </ConcentrationSet> 



<ConcentrationSet region="neck" >
        
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="14980"/>
       <NanoMolarity specieID="ncxCa" value="784"/>
 </ConcentrationSet>


 <SurfaceDensitySet region="dendrite1">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
 </SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite2">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
 </SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite3">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
 </SurfaceDensitySet>

  

<ConcentrationSet region="head" >
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>

       <NanoMolarity specieID="R" value="1012"/>
	<NanoMolarity specieID="G" value="38427"/>
	<NanoMolarity specieID="LR" value="0"/>
	<NanoMolarity specieID="LRG" value="0"/>
	<NanoMolarity specieID="GR" value="6523"/>
	<NanoMolarity specieID="GaGTP" value="15"/>
	<NanoMolarity specieID="GaGDP" value="0"/>
	<NanoMolarity specieID="Gbg" value="483"/>
        <NanoMolarity specieID="LRGbg" value="0"/>

	<NanoMolarity specieID="AC1" value="34078"/>
	<NanoMolarity specieID="AC1GaGTP" value="151"/>
	<NanoMolarity specieID="AC1GaGTPCaMCa4" value="0.0"/>
        <NanoMolarity specieID="AC1GaGTPCaMCa4ATP" value="60"/>
        <NanoMolarity specieID="AC1CaMCa4" value="377"/>
	<NanoMolarity specieID="AC1CaMCa4ATP" value="3397"/>
	<NanoMolarity specieID="AC8" value="37098"/>
	<NanoMolarity specieID="AC8CaMCa4" value="60"/>
	<NanoMolarity specieID="AC8CaMCa4ATP" value="649"/>

       
       
        
 </ConcentrationSet>

</InitialConditions>
IC_D_FocalDend_0.5um.xml0000644000076400007650000001567111564511527015215 0ustar  avramastochdiff<InitialConditions>

    <!-- these apply to everything unless overridden -->
   <!-- CaOut need to be half of previous value: due to no CaB -->
   <!-- CaB reaction does not need for Ca dynamics -->
    
<ConcentrationSet>

<NanoMolarity specieID="Ca" value="51"/>
<NanoMolarity specieID="CaOut" value="2015100"/>
<NanoMolarity specieID="Calbin" value="149590"/>
<NanoMolarity specieID="CalbinC" value="11348"/>
<NanoMolarity specieID="CaBCa" value="0"/>
<NanoMolarity specieID="CaB" value="0"/>

<NanoMolarity specieID="L" value="10.379"/>
<NanoMolarity specieID="LOut" value="1019100"/>

        


      	<NanoMolarity specieID="ATP" value="1997200"/>
       	<NanoMolarity specieID="cAMP" value="60"/>

	<NanoMolarity specieID="PDE1" value="3371"/>
	<NanoMolarity specieID="PDE1CaMCa4" value="574"/>
	<NanoMolarity specieID="PDE1CaMCa4cAMP" value="3"/>
	<NanoMolarity specieID="AMP" value="839"/>
	

	<NanoMolarity specieID="CaM" value="9126"/>
	<NanoMolarity specieID="CaMCa2" value="315"/>
	<NanoMolarity specieID="CaMCa4" value="2"/>
	<NanoMolarity specieID="PP2B" value="0"/>
	<NanoMolarity specieID="PP2BCaM" value="2960"/>
	<NanoMolarity specieID="PP2BCaMCa2" value="1020"/>
	<NanoMolarity specieID="PP2BCaMCa4" value="6"/>

	<NanoMolarity specieID="CK" value="19266"/>
	<NanoMolarity specieID="CKCaMCa4" value="112"/>
	<NanoMolarity specieID="CKpCaMCa4" value="598"/>
        <NanoMolarity specieID="CKp" value="26"/>
	<NanoMolarity specieID="Complex" value="0"/>
	<NanoMolarity specieID="pComplex" value="0"/>
	<NanoMolarity specieID="CKpPP1" value="0"/>
        <NanoMolarity specieID="CKpCaMCa4PP1" value="0" />

       	

	<NanoMolarity specieID="I1" value="530"/>
	<NanoMolarity specieID="I1PKAc" value="2"/>
	<NanoMolarity specieID="Ip35" value="6"/>
	<NanoMolarity specieID="PP1" value="587"/>
	<NanoMolarity specieID="Ip35PP1" value="884"/>
	<NanoMolarity specieID="Ip35PP2BCaMCa4" value="0"/>
	<NanoMolarity specieID="Ip35PP1PP2BCaMCa4" value="0"/>
        <NanoMolarity specieID="PP1PP2BCaMCa4" value="0"/>



    <NanoMolarity specieID="PDE4B" value="902"/>
    <NanoMolarity specieID="PDE4BcAMP" value="24"/>
    <NanoMolarity specieID="PKAcPDE4B" value="9"/>
    <NanoMolarity specieID="pPDE4B" value="48"/>
    <NanoMolarity specieID="pPDE4BcAMP" value="0"/>

    <NanoMolarity specieID="PDE4D" value="915" />
    <NanoMolarity specieID="PDE4DcAMP" value="13" />
    <NanoMolarity specieID="PKAcPDE4D" value="9" />
    <NanoMolarity specieID="pPDE4D" value="45" />
    <NanoMolarity specieID="pPDE4DcAMP" value="0" />

    <NanoMolarity specieID="PKAc_PDE4B_cAMP" value="0" />
    <NanoMolarity specieID="PKAc_PDE4D_cAMP" value="0" />
   

 </ConcentrationSet>


<ConcentrationSet region="PSD" >

        <NanoMolarity specieID="PKA" value="18666"/>
	<NanoMolarity specieID="PKAcAMP2" value="7225"/>
	<NanoMolarity specieID="PKAcAMP4" value="319"/>
	<NanoMolarity specieID="PKAr" value="387"/>
	<NanoMolarity specieID="PKAc" value="365"/>
        <NanoMolarity specieID="R2C_cAMP4" value="205"/>
       
       <NanoMolarity specieID="PKAcAMP4_I1" value="0"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4B" value="160"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4D" value="137"/>

        <NanoMolarity specieID="GluR1" value="9756"/>
	<NanoMolarity specieID="GluR1_S845" value="1580"/>
	<NanoMolarity specieID="GluR1_S831" value="279"/>
	<NanoMolarity specieID="GluR1_S845_S831" value="0"/>
	<NanoMolarity specieID="GluR1_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_CKpCam" value="0"/>
        <NanoMolarity specieID="GluR1_CKp" value="2"/>
	<NanoMolarity specieID="GluR1_S845_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKpCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKp" value="0"/>

	<NanoMolarity specieID="GluR1_S831_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_S845_PP1" value="836"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP1" value="0"/>
        <NanoMolarity specieID="GluR1_S831_PP1" value="93"/>
	<NanoMolarity specieID="GluR1_S845_PP2B" value="0"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP2B" value="0"/>

        <NanoMolarity specieID="PKAcAMP4_GluR1" value="0" />
        <NanoMolarity specieID="PKAcAMP4_GluR1_S831" value="0" />

       <NanoMolarity specieID="pmca" value="0"/>
       <NanoMolarity specieID="pmcaCa" value="0"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
</ConcentrationSet> 



<ConcentrationSet region="neck" >
        
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="14980"/>
       <NanoMolarity specieID="ncxCa" value="784"/>
 </ConcentrationSet>


 <SurfaceDensitySet region="dendrite2">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>

            <PicoSD specieID="R" value="110"/>
	    <PicoSD specieID="G" value="4192"/>
	    <PicoSD specieID="LR" value="0"/>
	    <PicoSD specieID="LRG" value="0"/>
	    <PicoSD specieID="GR" value="712"/>
	    <PicoSD specieID="GaGTP" value="2"/>
	    <PicoSD specieID="GaGDP" value="0"/>
	    <PicoSD specieID="Gbg" value="53"/>
	    <PicoSD specieID="LRGbg" value="0"/>
	    
	    <PicoSD specieID="AC1" value="3717"/>
	    <PicoSD specieID="AC1GaGTP" value="16"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4" value="0"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4ATP" value="3"/>
	    <PicoSD specieID="AC1CaMCa4" value="41"/>
	    <PicoSD specieID="AC1CaMCa4ATP" value="371"/>
	    <PicoSD specieID="AC8" value="4047"/>
	    <PicoSD specieID="AC8CaMCa4" value="7"/>
   	    <PicoSD specieID="AC8CaMCa4ATP" value="71"/>

 </SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite1">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite3">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>
  

<ConcentrationSet region="head" >
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>

       <NanoMolarity specieID="PKA" value="18666"/>
       <NanoMolarity specieID="PKAcAMP2" value="7225"/>
       <NanoMolarity specieID="PKAcAMP4" value="319"/>
       <NanoMolarity specieID="PKAr" value="387"/>
       <NanoMolarity specieID="PKAc" value="365"/>
       <NanoMolarity specieID="R2C_cAMP4" value="205"/>
        
       <NanoMolarity specieID="PKAcAMP4_I1" value="0"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4B" value="160"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4D" value="205"/>
</ConcentrationSet>

</InitialConditions>
IC_E_bothinDend2_0.5um.xml0000644000076400007650000001465211564511527015535 0ustar  avramastochdiff<InitialConditions>

   <!-- these apply to everything unless overridden -->
   <!-- CaOut need to be half of previous value: due to no CaB -->
   <!-- CaB reaction does not need for Ca dynamics -->
    
<ConcentrationSet>

<NanoMolarity specieID="Ca" value="51"/>
<NanoMolarity specieID="CaOut" value="2015100"/>
<NanoMolarity specieID="Calbin" value="149590"/>
<NanoMolarity specieID="CalbinC" value="11348"/>
<NanoMolarity specieID="CaBCa" value="0"/>
<NanoMolarity specieID="CaB" value="0"/>

<NanoMolarity specieID="L" value="10.379"/>
<NanoMolarity specieID="LOut" value="1019100"/>

        


      	<NanoMolarity specieID="ATP" value="1997200"/>
       	<NanoMolarity specieID="cAMP" value="60"/>

	<NanoMolarity specieID="PDE1" value="3371"/>
	<NanoMolarity specieID="PDE1CaMCa4" value="574"/>
	<NanoMolarity specieID="PDE1CaMCa4cAMP" value="3"/>
	<NanoMolarity specieID="AMP" value="839"/>
	

	<NanoMolarity specieID="CaM" value="9126"/>
	<NanoMolarity specieID="CaMCa2" value="315"/>
	<NanoMolarity specieID="CaMCa4" value="2"/>
	<NanoMolarity specieID="PP2B" value="0"/>
	<NanoMolarity specieID="PP2BCaM" value="2960"/>
	<NanoMolarity specieID="PP2BCaMCa2" value="1020"/>
	<NanoMolarity specieID="PP2BCaMCa4" value="6"/>

	<NanoMolarity specieID="CK" value="19266"/>
	<NanoMolarity specieID="CKCaMCa4" value="112"/>
	<NanoMolarity specieID="CKpCaMCa4" value="598"/>
        <NanoMolarity specieID="CKp" value="26"/>
	<NanoMolarity specieID="Complex" value="0"/>
	<NanoMolarity specieID="pComplex" value="0"/>
	<NanoMolarity specieID="CKpPP1" value="0"/>
        <NanoMolarity specieID="CKpCaMCa4PP1" value="0" />

       	

	<NanoMolarity specieID="I1" value="530"/>
	<NanoMolarity specieID="I1PKAc" value="2"/>
	<NanoMolarity specieID="Ip35" value="6"/>
	<NanoMolarity specieID="PP1" value="587"/>
	<NanoMolarity specieID="Ip35PP1" value="884"/>
	<NanoMolarity specieID="Ip35PP2BCaMCa4" value="0"/>
	<NanoMolarity specieID="Ip35PP1PP2BCaMCa4" value="0"/>
        <NanoMolarity specieID="PP1PP2BCaMCa4" value="0"/>



    <NanoMolarity specieID="PDE4B" value="902"/>
    <NanoMolarity specieID="PDE4BcAMP" value="24"/>
    <NanoMolarity specieID="PKAcPDE4B" value="9"/>
    <NanoMolarity specieID="pPDE4B" value="48"/>
    <NanoMolarity specieID="pPDE4BcAMP" value="0"/>

    <NanoMolarity specieID="PDE4D" value="915" />
    <NanoMolarity specieID="PDE4DcAMP" value="13" />
    <NanoMolarity specieID="PKAcPDE4D" value="9" />
    <NanoMolarity specieID="pPDE4D" value="45" />
    <NanoMolarity specieID="pPDE4DcAMP" value="0" />

    <NanoMolarity specieID="PKAc_PDE4B_cAMP" value="0" />
    <NanoMolarity specieID="PKAc_PDE4D_cAMP" value="0" />
   

 </ConcentrationSet>


<ConcentrationSet region="PSD" >

        <NanoMolarity specieID="GluR1" value="9756"/>
	<NanoMolarity specieID="GluR1_S845" value="1580"/>
	<NanoMolarity specieID="GluR1_S831" value="279"/>
	<NanoMolarity specieID="GluR1_S845_S831" value="0"/>
	<NanoMolarity specieID="GluR1_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_CKpCam" value="0"/>
        <NanoMolarity specieID="GluR1_CKp" value="2"/>
	<NanoMolarity specieID="GluR1_S845_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKpCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKp" value="0"/>

	<NanoMolarity specieID="GluR1_S831_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_S845_PP1" value="836"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP1" value="0"/>
        <NanoMolarity specieID="GluR1_S831_PP1" value="93"/>
	<NanoMolarity specieID="GluR1_S845_PP2B" value="0"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP2B" value="0"/>

        <NanoMolarity specieID="PKAcAMP4_GluR1" value="0" />
        <NanoMolarity specieID="PKAcAMP4_GluR1_S831" value="0" />
       <NanoMolarity specieID="pmca" value="0"/>
       <NanoMolarity specieID="pmcaCa" value="0"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
 </ConcentrationSet> 



<ConcentrationSet region="neck" >
        
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="14980"/>
       <NanoMolarity specieID="ncxCa" value="784"/>
 </ConcentrationSet>


 <SurfaceDensitySet region="dendrite2">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
     
            <PicoSD specieID="R" value="110"/>
	    <PicoSD specieID="G" value="4192"/>
	    <PicoSD specieID="LR" value="0"/>
	    <PicoSD specieID="LRG" value="0"/>
	    <PicoSD specieID="GR" value="712"/>
	    <PicoSD specieID="GaGTP" value="2"/>
	    <PicoSD specieID="GaGDP" value="0"/>
	    <PicoSD specieID="Gbg" value="53"/>
	    <PicoSD specieID="LRGbg" value="0"/>
	    
	    <PicoSD specieID="AC1" value="3717"/>
	    <PicoSD specieID="AC1GaGTP" value="16"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4" value="0"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4ATP" value="3"/>
	    <PicoSD specieID="AC1CaMCa4" value="41"/>
	    <PicoSD specieID="AC1CaMCa4ATP" value="371"/>
	    <PicoSD specieID="AC8" value="4047"/>
	    <PicoSD specieID="AC8CaMCa4" value="7"/>
   	    <PicoSD specieID="AC8CaMCa4ATP" value="71"/>

            <PicoSD specieID="PKA" value="2698"/>
	    <PicoSD specieID="PKAcAMP2" value="1044"/>
	    <PicoSD specieID="PKAcAMP4" value="46"/>
	    <PicoSD specieID="PKAr" value="56"/>
	    <PicoSD specieID="PKAc" value="53"/>
            <PicoSD specieID="R2C_cAMP4" value="30"/>
    
            <PicoSD specieID="PKAcAMP4_I1" value="0" />
            <PicoSD specieID="PKAcAMP4_PDE4B" value="23" />
            <PicoSD specieID="PKAcAMP4_PDE4D" value="20" />

 </SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite1">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite3">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>
  

<ConcentrationSet region="head" >
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
</ConcentrationSet>

</InitialConditions>
IC_F_ACinDend2PKAew.xml0000644000076400007650000001467611564511527015037 0ustar  avramastochdiff<InitialConditions>

    <!-- these apply to everything unless overridden -->
   <!-- CaOut need to be half of previous value: due to no CaB -->
   <!-- CaB reaction does not need for Ca dynamics -->
    
<ConcentrationSet>

<NanoMolarity specieID="Ca" value="51"/>
<NanoMolarity specieID="CaOut" value="2015100"/>
<NanoMolarity specieID="Calbin" value="149590"/>
<NanoMolarity specieID="CalbinC" value="11348"/>
<NanoMolarity specieID="CaBCa" value="0"/>
<NanoMolarity specieID="CaB" value="0"/>

<NanoMolarity specieID="L" value="10.379"/>
<NanoMolarity specieID="LOut" value="1019100"/>

        


      	<NanoMolarity specieID="ATP" value="1997200"/>
       	<NanoMolarity specieID="cAMP" value="60"/>

	<NanoMolarity specieID="PDE1" value="3371"/>
	<NanoMolarity specieID="PDE1CaMCa4" value="574"/>
	<NanoMolarity specieID="PDE1CaMCa4cAMP" value="3"/>
	<NanoMolarity specieID="AMP" value="839"/>
	

	<NanoMolarity specieID="CaM" value="9126"/>
	<NanoMolarity specieID="CaMCa2" value="315"/>
	<NanoMolarity specieID="CaMCa4" value="2"/>
	<NanoMolarity specieID="PP2B" value="0"/>
	<NanoMolarity specieID="PP2BCaM" value="2960"/>
	<NanoMolarity specieID="PP2BCaMCa2" value="1020"/>
	<NanoMolarity specieID="PP2BCaMCa4" value="6"/>

	<NanoMolarity specieID="CK" value="19266"/>
	<NanoMolarity specieID="CKCaMCa4" value="112"/>
	<NanoMolarity specieID="CKpCaMCa4" value="598"/>
        <NanoMolarity specieID="CKp" value="26"/>
	<NanoMolarity specieID="Complex" value="0"/>
	<NanoMolarity specieID="pComplex" value="0"/>
	<NanoMolarity specieID="CKpPP1" value="0"/>
        <NanoMolarity specieID="CKpCaMCa4PP1" value="0" />

       	

	<NanoMolarity specieID="I1" value="530"/>
	<NanoMolarity specieID="I1PKAc" value="2"/>
	<NanoMolarity specieID="Ip35" value="6"/>
	<NanoMolarity specieID="PP1" value="587"/>
	<NanoMolarity specieID="Ip35PP1" value="884"/>
	<NanoMolarity specieID="Ip35PP2BCaMCa4" value="0"/>
	<NanoMolarity specieID="Ip35PP1PP2BCaMCa4" value="0"/>
        <NanoMolarity specieID="PP1PP2BCaMCa4" value="0"/>



    <NanoMolarity specieID="PDE4B" value="902"/>
    <NanoMolarity specieID="PDE4BcAMP" value="24"/>
    <NanoMolarity specieID="PKAcPDE4B" value="9"/>
    <NanoMolarity specieID="pPDE4B" value="48"/>
    <NanoMolarity specieID="pPDE4BcAMP" value="0"/>

    <NanoMolarity specieID="PDE4D" value="915" />
    <NanoMolarity specieID="PDE4DcAMP" value="13" />
    <NanoMolarity specieID="PKAcPDE4D" value="9" />
    <NanoMolarity specieID="pPDE4D" value="45" />
    <NanoMolarity specieID="pPDE4DcAMP" value="0" />

    <NanoMolarity specieID="PKAc_PDE4B_cAMP" value="0" />
    <NanoMolarity specieID="PKAc_PDE4D_cAMP" value="0" />

       <NanoMolarity specieID="PKA" value="819"/>
	<NanoMolarity specieID="PKAcAMP2" value="317"/>
	<NanoMolarity specieID="PKAcAMP4" value="14"/>
	<NanoMolarity specieID="PKAr" value="17"/>
	<NanoMolarity specieID="PKAc" value="16"/>
        <NanoMolarity specieID="R2C_cAMP4" value="9"/>
        
       <NanoMolarity specieID="PKAcAMP4_I1" value="0"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4B" value="7"/>
       <NanoMolarity specieID="PKAcAMP4_PDE4D" value="6"/>
   

 </ConcentrationSet>


<ConcentrationSet region="PSD" >

       

        <NanoMolarity specieID="GluR1" value="7905"/>
	<NanoMolarity specieID="GluR1_S845" value="1280"/>
	<NanoMolarity specieID="GluR1_S831" value="226"/>
	<NanoMolarity specieID="GluR1_S845_S831" value="0"/>
	<NanoMolarity specieID="GluR1_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_CKpCam" value="0"/>
        <NanoMolarity specieID="GluR1_CKp" value="2"/>
	<NanoMolarity specieID="GluR1_S845_CKCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKpCam" value="0"/>
	<NanoMolarity specieID="GluR1_S845_CKp" value="0"/>

	<NanoMolarity specieID="GluR1_S831_PKAc" value="0"/>
	<NanoMolarity specieID="GluR1_S845_PP1" value="678"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP1" value="0"/>
        <NanoMolarity specieID="GluR1_S831_PP1" value="75"/>
	<NanoMolarity specieID="GluR1_S845_PP2B" value="0"/>
	<NanoMolarity specieID="GluR1_S845_S831_PP2B" value="0"/>

        <NanoMolarity specieID="PKAcAMP4_GluR1" value="0" />
        <NanoMolarity specieID="PKAcAMP4_GluR1_S831" value="0" />

       <NanoMolarity specieID="pmca" value="0"/>
       <NanoMolarity specieID="pmcaCa" value="0"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
 </ConcentrationSet> 



<ConcentrationSet region="neck" >
        
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="14980"/>
       <NanoMolarity specieID="ncxCa" value="784"/>
 </ConcentrationSet>


 <SurfaceDensitySet region="dendrite2">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
      
            <PicoSD specieID="R" value="110"/>
	    <PicoSD specieID="G" value="4192"/>
	    <PicoSD specieID="LR" value="0"/>
	    <PicoSD specieID="LRG" value="0"/>
	    <PicoSD specieID="GR" value="712"/>
	    <PicoSD specieID="GaGTP" value="2"/>
	    <PicoSD specieID="GaGDP" value="0"/>
	    <PicoSD specieID="Gbg" value="53"/>
	    <PicoSD specieID="LRGbg" value="0"/>
	    
	    <PicoSD specieID="AC1" value="3717"/>
	    <PicoSD specieID="AC1GaGTP" value="16"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4" value="0"/>
	    <PicoSD specieID="AC1GaGTPCaMCa4ATP" value="3"/>
	    <PicoSD specieID="AC1CaMCa4" value="41"/>
	    <PicoSD specieID="AC1CaMCa4ATP" value="371"/>
	    <PicoSD specieID="AC8" value="4047"/>
	    <PicoSD specieID="AC8CaMCa4" value="7"/>
   	    <PicoSD specieID="AC8CaMCa4ATP" value="71"/>
</SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite1">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>

 <SurfaceDensitySet region="dendrite3">
	    <PicoSD specieID="pmca" value="65.86"/>
	    <PicoSD specieID="pmcaCa" value="17.79"/>
	    <PicoSD specieID="ncx" value="2996"/>
	    <PicoSD specieID="ncxCa" value="157"/>
</SurfaceDensitySet>
  

<ConcentrationSet region="head" >
       <NanoMolarity specieID="pmca" value="329.28"/>
       <NanoMolarity specieID="pmcaCa" value="88.94"/>
       <NanoMolarity specieID="ncx" value="0"/>
       <NanoMolarity specieID="ncxCa" value="0"/>
</ConcentrationSet>

</InitialConditions>
IO.xml0000644000076400007650000001273311564511527012137 0ustar  avramastochdiff<OutputScheme>
<!--
     Each file will have a set of concentrations in compartments
     sampled according to a specific dt
-->

<!--
    Every Output block must have in its definition one (and only)
    instance of:
     * filename
    And might have one (and only) instance of:
     * region or
     * dt
    If "region" is ommited then the concs for the whole system will be
    saved.
    If "dt" is ommited than the concs will be written at each time step.
    So th "io file" will be dependent on information stated in the
    "morph" (regions) and "model" (dt).
-->
<!--#of column to check ** Ca:2,G:7,GR:10,AC1:15,cAMP:20,PDE1:26,
    CaM:30,PP2BCaMCa4:36,PKA:44,PKAc:48, Ip35:51,PP1:52,GRluR1:63 -->

    <OutputSet filename ="4tr" dt="100">

        <OutputSpecie       name="Ca"           />

        <OutputSpecie       name="CaOut"       />

        <OutputSpecie       name="L"           />
        <OutputSpecie       name="LOut"       />
        <OutputSpecie       name="R"           />
        <OutputSpecie       name="G"           />
        <OutputSpecie       name="LR"          />
        <OutputSpecie       name="LRG"         />
        <OutputSpecie       name="GR"          />
        <OutputSpecie       name="GaGTP"       />
        <OutputSpecie       name="GaGDP"       />
        <OutputSpecie       name="Gbg"         /> 
        <OutputSpecie       name="LRGbg"         />

        <OutputSpecie       name="AC1"         />
        <OutputSpecie       name="AC1GaGTP"    />
        <OutputSpecie       name="AC1GaGTPCaMCa4"        />
        <OutputSpecie       name="ATP"         />
        <OutputSpecie       name="AC1GaGTPCaMCa4ATP"     />

        <OutputSpecie       name="cAMP"        />
 
        <OutputSpecie       name="AC1CaMCa4"      />
        <OutputSpecie       name="AC1CaMCa4ATP"   />
        <OutputSpecie       name="AC8"         />
        <OutputSpecie       name="AC8CaMCa4"      />
        <OutputSpecie       name="AC8CaMCa4ATP"   /> 

        <OutputSpecie       name="PDE1"        />
        <OutputSpecie       name="PDE1CaMCa4"     />
        <OutputSpecie       name="PDE1CaMCa4cAMP"    />
        <OutputSpecie       name="AMP"         />
       
        <OutputSpecie       name="CaM"         />
        <OutputSpecie       name="CaMCa2"      />
        <OutputSpecie       name="CaMCa4"      />

        <OutputSpecie       name="PP2B"         />
        <OutputSpecie       name="PP2BCaM"      />
        <OutputSpecie       name="PP2BCaMCa2"   /> 
        <OutputSpecie       name="PP2BCaMCa4"   />

        <OutputSpecie       name="CK"          />
        <OutputSpecie       name="CKCaMCa4"       />
        <OutputSpecie       name="CKpCaMCa4"      />
        <OutputSpecie       name="CKp"      />
        <OutputSpecie       name="CKpPP1" />
        <OutputSpecie       name="Complex" />
        <OutputSpecie       name="pComplex" />

        <OutputSpecie      name="CKpCaMCa4PP1"  /> 

        <OutputSpecie       name="PKA"         />
        <OutputSpecie       name="PKAcAMP2"    />
        <OutputSpecie       name="PKAcAMP4"    />
        <OutputSpecie       name="PKAr"        />
        <OutputSpecie       name="PKAc"        />

        <OutputSpecie       name="I1"          />
        <OutputSpecie       name="I1PKAc"      />
        <OutputSpecie       name="Ip35"        />
        <OutputSpecie       name="PP1"        />
        <OutputSpecie       name="Ip35PP1"     />
        <OutputSpecie       name="Ip35PP2BCaMCa4"     />
        <OutputSpecie       name="Ip35PP1PP2BCaMCa4"    />
        <OutputSpecie       name="PP1PP2BCaMCa4"    />
	
        <OutputSpecie       name="Calbin"       />
        <OutputSpecie       name="CalbinC"       />
        <OutputSpecie       name="ncx"       />
        <OutputSpecie       name="ncxCa"       />
        <OutputSpecie       name="pmca"       />
        <OutputSpecie       name="pmcaCa"       />
      
     	<OutputSpecie      name="GluR1"  />
	<OutputSpecie      name="GluR1_S845" />
	<OutputSpecie      name="GluR1_S831" />
	<OutputSpecie      name="GluR1_S845_S831" />
	<OutputSpecie      name="GluR1_PKAc" />
	<OutputSpecie      name="GluR1_CKCam" />
	<OutputSpecie      name="GluR1_CKpCam" />
        <OutputSpecie      name="GluR1_CKp" />
	<OutputSpecie      name="GluR1_S845_CKCam" />
	<OutputSpecie      name="GluR1_S845_CKpCam" />
	<OutputSpecie      name="GluR1_S845_CKp" />
	
	<OutputSpecie      name="GluR1_S831_PKAc" />
	<OutputSpecie      name="GluR1_S845_PP1" />
	<OutputSpecie      name="GluR1_S845_S831_PP1" />
        <OutputSpecie      name="GluR1_S831_PP1" />
	<OutputSpecie      name="GluR1_S845_PP2B" />
	<OutputSpecie      name="GluR1_S845_S831_PP2B" />

    <OutputSpecie      name="PDE4B"  />
    <OutputSpecie      name="PDE4BcAMP"  />
    <OutputSpecie      name="PKAcPDE4B"  />
    <OutputSpecie      name="pPDE4B"  />
    <OutputSpecie      name="pPDE4BcAMP" />

    <OutputSpecie      name="PDE4D"  />
    <OutputSpecie      name="PDE4DcAMP"  />
    <OutputSpecie      name="PKAcPDE4D"  />
    <OutputSpecie      name="pPDE4D"  />
    <OutputSpecie      name="pPDE4DcAMP"  />

    <OutputSpecie      name="PKAcAMP4_GluR1"  />
    <OutputSpecie      name="PKAcAMP4_GluR1_S831"  />
    <OutputSpecie      name="PKAcAMP4_I1"  />
    <OutputSpecie      name="PKAcAMP4_PDE4B"  />
    <OutputSpecie      name="PKAcAMP4_PDE4D" />
    <OutputSpecie      name="R2C_cAMP4"  />

    <OutputSpecie      name="PKAc_PDE4B_cAMP"  />
    <OutputSpecie      name="PKAc_PDE4D_cAMP"  />
    
   
        

    </OutputSet>

</OutputScheme>
ModelA_sp_0.5um.xml0000644000076400007650000000462211564511527014415 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_A_half_RGAC_0.5um</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
ModelB_sp_0.5um.xml0000644000076400007650000000462311564511527014417 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_B_PKAinDend2_0.5um</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
ModelC_sp_0.5um.xml0000644000076400007650000000461711564511527014423 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_C_halfAC_PKAew</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
ModelD_sp_0.5um.xml0000644000076400007650000000462211564511527014420 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_D_FocalDend_0.5um</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
ModelE_sp_0.5um.xml0000644000076400007650000000462411564511527014423 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_E_bothinDend2_0.5um</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
ModelF_sp_0.5um.xml0000644000076400007650000000462111564511527014421 0ustar  avramastochdiff
<SDRun>
    <!-- this file defines a single run of the calculation, using morphology and 
	 reaction data brought in from other files --> 

    <reactionSchemeFile>Reac_gradedkdiff_10kdiffCaB_kf2.8e-5</reactionSchemeFile>
    <morphologyFile> morph_3dends_0.5um</morphologyFile>
    <stimulationFile>Stim4tr_CaB_2inj_sp</stimulationFile>
    <initialConditionsFile>IC_F_ACinDend2PKAew</initialConditionsFile>
    <outputSchemeFile>IO</outputSchemeFile>

    <!--2D means the morphology is interpreted like a flatworm, 3D for
roundworms. The 2D case is good for testing as it is easy to visualize the
results (also, 3D may not work yet...)  -->
    
    <geometry>          2D           </geometry>
    <depth2D>           0.4          </depth2D>
    <distribution>      BINOMIAL     </distribution>
    <algorithm>         INDEPENDENT  </algorithm>
    <simulationSeed>    245          </simulationSeed>


    <!-- run time for the calculation, milliseconds -->
    <runtime>600000</runtime>

    <!-- set the seed to get the same spines each time testing -->
    <spineSeed>123</spineSeed>

    <discretization>
	<!-- default largest size for elements in bulk volumes (dendrites), microns -->	
	<defaultMaxElementSide>0.2</defaultMaxElementSide>
       <MaxElementSide region="dendrite1">0.12</MaxElementSide>
       <MaxElementSide region="dendrite2">0.12</MaxElementSide>
       <MaxElementSide region="dendrite3">0.12</MaxElementSide>
        
	<!-- discretization for spines, microns -->
	<spineDeltaX>0.1</spineDeltaX>

	<!-- override the default for a particular region. -->
	<!-- Matches against id or regionClass in the morphology file -->

<!--
	<MaxElementSide region="head">0.2</MaxElementSide>
        <MaxElementSide region="neck">0.2</MaxElementSide>
-->
<!--
        <MaxElementSide region="PSD">0.1</MaxElementSide>
-->
    </discretization>

    <!-- timestep used in fixed step calculations, in milliseconds: to match ca:0.01 ms
         :slow rxns case OK specially PKA part but Ca basal at dt=0.2 ms is best -->
    <fixedStepDt>0.005</fixedStepDt>


    <!-- the tolerace is not used yet -->
    <tolerance>0.001</tolerance>

    <outputInterval>1000</outputInterval>



    <!-- calculation types include GRID_STEPPED_STOCHASTIC and GRID_STEPPED_CONTINUOUS for 
	 reaction-diffusion systems. Single mixed pool calculations should be listed here too (TODO) -->
    <calculation>GRID_STEPPED_STOCHASTIC</calculation>

</SDRun>
morph_3dends_0.5um.xml0000644000076400007650000000244211564511527015135 0ustar  avramastochdiff<Morphology>


    <!-- spine morphologies: width for sections along the spine -->

    <SpineType id="spineA">
	<Section width="0.2" at="0.0" regionClass="neck"/>
	<Section width="0.2" at="0.2" regionClass="neck"/>
	<Section width="0.2" at="0.3" regionClass="head"/>
	<Section width="0.6" at="0.4" regionClass="head"/>  
	<Section width="0.6" at="0.5" regionClass="PSD"/>
	<Section width="0.2" at="0.6" label="pointA"/>
    </SpineType>

    <!-- regionClass labels can apply to sections or segments and label regions for applying initial conditaions etc -->


    <!-- lengthDensity means you set the number per micron along the segment -->
    <SpineAllocation id="sa1" spineType="spineA" region="dendrite3" lengthDensity="0.2"/>

<!--    
    <Segment id="seg1" region="region1">
	<start x="1.0" y="1.0" z="0.0" r="0.3"/>
	<end x="5.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>
-->

    <Segment id="seg1" region="dendrite1">
	<start x="1.0" y="1.0" z="0.0" r="0.3"/>
	<end x="3.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    <Segment id="seg2" region="dendrite2">
	<start on="seg1" at="end"/>
	<end x="3.5" y="1.0" z="0.0" r="0.3" label="pointB"/>
    </Segment>

    <Segment id="seg3" region="dendrite3">
	<start on="seg2" at="end"/>
	<end x="6.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>


</Morphology>

morph_long0.5umDend2.xml0000644000076400007650000000240711564500704015426 0ustar  avramastochdiff<Morphology>


    <!-- spine morphologies: width for sections along the spine -->

    <SpineType id="spineA">
	<Section width="0.2" at="0.0" regionClass="neck"/>
	<Section width="0.2" at="0.8" regionClass="neck"/>
	<Section width="0.2" at="0.9" regionClass="head"/>
	<Section width="0.6" at="1.0" regionClass="head"/>  
	<Section width="0.6" at="1.1" regionClass="PSD"/>
	<Section width="0.2" at="1.2" label="pointA"/>
    </SpineType>

    <!-- regionClass labels can apply to sections or segments and label regions for applying initial conditaions etc -->


    <!-- lengthDensity means you set the number per micron along the segment -->
    <SpineAllocation id="sa1" spineType="spineA" region="dend3" lengthDensity="0.2"/>

<!--    
    <Segment id="seg1" region="region1">
	<start x="1.0" y="1.0" z="0.0" r="0.3"/>
	<end x="5.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>
-->

  <Segment id="seg1" region="dend1">
	<start x="1.0" y="1.0" z="0.0" r="0.3"/>
	<end x="3.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    <Segment id="seg2" region="dend2">
	<start on="seg1" at="end"/>
	<end x="3.5" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    <Segment id="seg3" region="dend3">
	<start on="seg2" at="end"/>
	<end x="6.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    


</Morphology>

morph_short0.5umDend2.xml0000644000076400007650000000310511564500710015617 0ustar  avramastochdiff<Morphology>


    <!-- spine morphologies: width for sections along the spine -->
    <!-- The regionClass defined below only creates boundary lines. They will possess any voxels (the width/heighth of which is defined by spineDeltaX) closer to it than any other defined regionClass. This includes any voxels above and below (except in the case of a section beginning at 0.0, in which case there are voxels above only). In the case that a voxel(s) is equidistant from two regionClass boundary lines, the lesser (or lower) regionClass has precedence. For example, when there are three voxels in between two boundary lines, the lower two will be taken by the lower regionClass and the upper one will be taken by the upper regionClass. -->
    <SpineType id="spineA">
	<Section width="0.2" at="0.0" regionClass="head"/>
	<Section width="0.6" at="0.1" regionClass="head"/>  
	<Section width="0.6" at="0.2" regionClass="PSD"/>
	<Section width="0.2" at="0.3" label="pointA"/>
    </SpineType>

    <!-- regionClass labels can apply to sections or segments and label regions for applying initial conditaions etc -->

    <SpineAllocation id="sa1" spineType="spineA" region="dend3" lengthDensity="0.2"/>



    <Segment id="seg1" region="dend1">
	<start x="1.0" y="1.0" z="0.0" r="0.3"/>
	<end x="3.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    <Segment id="seg2" region="dend2">
	<start on="seg1" at="end"/>
	<end x="3.5" y="1.0" z="0.0" r="0.3"/>
    </Segment>

    <Segment id="seg3" region="dend3">
	<start on="seg2" at="end"/>
	<end x="6.0" y="1.0" z="0.0" r="0.3"/>
    </Segment>


</Morphology>

   

Reac_gradedkdiff_10kdiffCaB_kf2.8e-5.xml0000644000076400007650000014243111564511527020104 0ustar  avramastochdiff<ReactionScheme>
    <!-- you can specify the units of the diffusion constant. If they are not
	 specified they are assumed to be micron^2/second, (microns written "mu" here)
	 it should understand microns, mm, and m for distances and seconds and ms for times -->

    <!-- This code is implemented CaMKII_bimols Rxns -0.44, 0.28, 0.088
         Fix 3 products 2rxns break down to 2nd order rxn : LRG/Ip35P1P2 -->
    <!-- last rxn of Ip35p1p2 was wrong reactant:fixed on Aug,8th,2008
         Chosen katp=1 sec(not 10 sec) is enough   -->
  <!-- Suggested by avrama Ca kdiff=600 for helping fast decay on Feb.24th 2009-->

    <Specie name="Ca" id="Ca" kdiff="174.3" kdiffunit="mu2/s"/>
    <Specie name="CaOut" id="CaOut" kdiff="174.3" kdiffunit="mu2/s"/>
    <Specie name="Calbin" id="Calbin" kdiff="9.3" kdiffunit="mu2/s"/>
    <Specie name="CalbinC" id="CalbinC" kdiff="9.3" kdiffunit="mu2/s"/>
    <Specie name="CaBCa" id="CaBCa" kdiff="10" kdiffunit="mu2/s"/>
    <Specie name="CaB" id="CaB" kdiff="10" kdiffunit="mu2/s"/>
<Specie name="pmca" id="pmca" kdiff="0" kdiffunit="mu2/s"/>
<Specie name="ncx" id="ncx" kdiff="0" kdiffunit="mu2/s"/>
<Specie name="pmcaCa" id="pmcaCa" kdiff="0" kdiffunit="mu2/s"/>
<Specie name="ncxCa" id="ncxCa" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="L" id="L" kdiff="111.3" kdiffunit="mu2/s"/>
    <Specie name="LOut" id="LOut" kdiff="111.3" kdiffunit="mu2/s"/>

    <Specie name="R" id="R" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="G" id="G" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="LR" id="LR" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="LRG" id="LRG" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GR" id="GR" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GaGTP" id="GaGTP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GaGDP" id="GaGDP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="Gbg" id="Gbg" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="LRGbg" id="LRGbg" kdiff="0" kdiffunit="mu2/s"/>

  <Specie name="AC1" id="AC1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC1GaGTP" id="AC1GaGTP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC1GaGTPCaMCa4" id="AC1GaGTPCaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="ATP" id="ATP" kdiff="74.7" kdiffunit="mu2/s"/>
    <Specie name="AC1GaGTPCaMCa4ATP" id="AC1GaGTPCaMCa4ATP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="cAMP" id="cAMP" kdiff="86.4" kdiffunit="mu2/s"/>
    <Specie name="AC1CaMCa4" id="AC1CaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC1CaMCa4ATP" id="AC1CaMCa4ATP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC8" id="AC8" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC8CaMCa4" id="AC8CaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AC8CaMCa4ATP" id="AC8CaMCa4ATP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PDE1" id="PDE1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PDE1CaMCa4" id="PDE1CaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PDE1CaMCa4cAMP" id="PDE1CaMCa4cAMP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="AMP" id="AMP" kdiff="85.5" kdiffunit="mu2/s"/>
   

  <Specie name="CaM" id="CaM" kdiff="11" kdiffunit="mu2/s"/>
    <Specie name="CaMCa2" id="CaMCa2" kdiff="11" kdiffunit="mu2/s"/>
    <Specie name="CaMCa4" id="CaMCa4" kdiff="11" kdiffunit="mu2/s"/>
    <Specie name="PP2B" id="PP2B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PP2BCaM" id="PP2BCaM" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PP2CaMCa2" id="PP2BCaMCa2" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PP2BCaMCa4" id="PP2BCaMCa4" kdiff="0" kdiffunit="mu2/s"/>

  <Specie name="CK" id="CK" kdiff="3.6" kdiffunit="mu2/s"/>
    <Specie name="CKCaMCa4" id="CKCaMCa4" kdiff="3.6" kdiffunit="mu2/s"/>
    <Specie name="CKpCaMCa4" id="CKpCaMCa4" kdiff="3.6" kdiffunit="mu2/s"/>
    <Specie name="CKp" id="CKp" kdiff="3.6" kdiffunit="mu2/s"/>
    <Specie name="Complex" id="Complex" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="pComplex" id="pComplex" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="CKpPP1" id="CKpPP1" kdiff="0" kdiffunit="mu2/s"/>

  <Specie name="PKA" id="PKA" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP2" id="PKAcAMP2" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP4" id="PKAcAMP4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAr" id="PKAr" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAc" id="PKAc" kdiff="8.1" kdiffunit="mu2/s"/>

  <Specie name="I1" id="I1" kdiff="10.6" kdiffunit="mu2/s"/>
    <Specie name="I1PKAc" id="I1PKAc" kdiff="10.6" kdiffunit="mu2/s"/>
    <Specie name="Ip35" id="Ip35" kdiff="10.6" kdiffunit="mu2/s"/>
    <Specie name="PP1" id="PP1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="Ip35PP1" id="Ip35PP1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="Ip35PP2BCaMCa4" id="Ip35PP2BCaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="Ip35PP1PP2BCaMCa4" id="Ip35PP1PP2BCaMCa4" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PP1PP2BCaMCa4" id="PP1PP2BCaMCa4" kdiff="0" kdiffunit="mu2/s"/>

<!-- AddRxns -->

    <Specie name="GluR1" id="GluR1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845" id="GluR1_S845" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S831" id="GluR1_S831" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845_S831" id="GluR1_S845_S831" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="GluR1_PKAc" id="GluR1_PKAc" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_CKCam" id="GluR1_CKCam" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_CKpCam" id="GluR1_CKpCam" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_CKp" id="GluR1_CKp" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="GluR1_S845_CKCam" id="GluR1_S845_CKCam" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845_CKpCam" id="GluR1_S845_CKpCam" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845_CKp" id="GluR1_S845_CKp" kdiff="0" kdiffunit="mu2/s"/>

  
    <Specie name="GluR1_S831_PKAc" id="GluR1_S831_PKAc" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="GluR1_S845_PP1" id="GluR1_S845_PP1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845_S831_PP1" id="GluR1_S845_S831_PP1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S831_PP1" id="GluR1_S831_PP1" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="GluR1_S845_PP2B" id="GluR1_S845_PP2B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="GluR1_S845_S831_PP2B" id="GluR1_S845_S831_PP2B" kdiff="0" kdiffunit="mu2/s"/>


<!-- PDE -->

    <Specie name="PDE4B" id="PDE4B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PDE4BcAMP" id="PDE4BcAMP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcPDE4B" id="PKAcPDE4B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="pPDE4B" id="pPDE4B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="pPDE4BcAMP" id="pPDE4BcAMP" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="PDE4D" id="PDE4D" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PDE4DcAMP" id="PDE4DcAMP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcPDE4D" id="PKAcPDE4D" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="pPDE4D" id="pPDE4D" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="pPDE4DcAMP" id="pPDE4DcAMP" kdiff="0" kdiffunit="mu2/s"/>

    <Specie name="PKAc_PDE4B_cAMP" id="PKAc_PDE4B_cAMP" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAc_PDE4D_cAMP" id="PKAc_PDE4D_cAMP" kdiff="0" kdiffunit="mu2/s"/>
   


<!-- Other forms of active PKA -->

    <Specie name="PKAcAMP4_GluR1" id="PKAcAMP4_GluR1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP4_GluR1_S831" id="PKAcAMP4_GluR1_S831" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP4_I1" id="PKAcAMP4_I1" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP4_PDE4B" id="PKAcAMP4_PDE4B" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="PKAcAMP4_PDE4D" id="PKAcAMP4_PDE4D" kdiff="0" kdiffunit="mu2/s"/>
    <Specie name="R2C_cAMP4" id="R2C_cAMP4" kdiff="0" kdiffunit="mu2/s"/>


     <Specie name="CKpCaMCa4PP1" id="CKpCaMCa4PP1" kdiff="0" kdiffunit="mu2/s"/>



<!-- Ca pump high affinity -    Ca + pmca <-> pmcaCa -->
    <Reaction name = "Ca_pump1a" id="Ca_pump1a">
	<Reactant specieID="Ca"/>
	<Reactant specieID="pmca"/>
	<Product specieID="pmcaCa"/>

	<forwardRate>0.5e-4</forwardRate>
	<reverseRate>0.007</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Ca pump high affinity -    pmcaCa <-> pmca + CaOut -->
    <Reaction name = "Ca_pump1b" id="Ca_pump1b">
	<Reactant specieID="pmcaCa"/>
	<Product specieID="pmca"/>
	<Product specieID="CaOut"/>

	<forwardRate>0.0035</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Ca pump low affinity -    Ca + ncx <-> ncxCa -->
    <Reaction name = "Ca_pump2a" id="Ca_pump2a">
	<Reactant specieID="Ca"/>
	<Reactant specieID="ncx"/>
	<Product specieID="ncxCa"/>

	<forwardRate>1.68e-5</forwardRate>
	<reverseRate>0.0112</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Ca pump low affinity -    ncxCa <-> ncx + CaOut -->
    <Reaction name = "Ca_pump2b" id="Ca_pump2b">
	<Reactant specieID="ncxCa"/>
	<Product specieID="ncx"/>
	<Product specieID="CaOut"/>

	<forwardRate>0.0056</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Ca leak -    Caout <-> Ca -->
    <Reaction name = "Ca_leak" id="Ca_leak">
	<Reactant specieID="CaOut"/>
	<Product specieID="Ca"/>

    <forwardRate>1.5e-6</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Ca Buffer    Ca + Calbindin <-> calbinCa -->
    <Reaction name = "Ca_buffer" id="Ca_Buffer">
        <Reactant specieID="Ca"/>
        <Reactant specieID="Calbin"/>
        <Product specieID="CalbinC"/>

        <forwardRate>2.8e-5</forwardRate>
        <reverseRate>0.0196</reverseRate>
        <Q10>0.2</Q10>
    </Reaction>

<!-- Irreversible IC Ca Buffer    Ca + CaB <-> CaBCa -->
    <Reaction name = "CaIn_buffer" id="CaIn_buffer">
         <Reactant specieID="Ca"/>
         <Reactant specieID="CaB"/>
         <Product specieID="CaBCa"/>

         <forwardRate>2.8e-5</forwardRate>
         <reverseRate>0</reverseRate>
         <Q10>0.2</Q10>
    </Reaction>



<!-- L Buffer-    L <-> LOut -->

    <Reaction name = "L_buffer" id="L_Buffer">
	<Reactant specieID="L"/>
	<Product specieID="LOut"/>

	<forwardRate>2e-3</forwardRate>
	<reverseRate>2e-8</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- G_protein part -->


<!-- 1) L + R <-> LR    -->
    <Reaction name = "LR_bind" id="LR_bind">
	<Reactant specieID="L"/>
	<Reactant specieID="R"/>
	<Product specieID="LR"/>

	<forwardRate>0.0011111e-3</forwardRate>
	<reverseRate>10e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 2) LR + G <-> LRG    -->
    <Reaction name = "LRG_bind" id="LRG_bind">
	<Reactant specieID="LR"/>
	<Reactant specieID="G"/>
	<Product specieID="LRG"/>

	<forwardRate>0.0006e-3</forwardRate>
	<reverseRate>0.001e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 3) G + R <-> GR    -->
    <Reaction name = "GR_bind" id="GR_bind">
	<Reactant specieID="G"/>
	<Reactant specieID="R"/>
	<Product specieID="GR"/>

	<forwardRate>0.00006e-3</forwardRate>
	<reverseRate>0.0003e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 4) GR + L <-> LRG    -->
    <Reaction name = "GRL_bind" id="GRL_bind">
	<Reactant specieID="GR"/>
	<Reactant specieID="L"/>
	<Product specieID="LRG"/>

	<forwardRate>0.00333333e-3</forwardRate>
	<reverseRate>10e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 5a) LRG -> LRGbg + GaGTP -->
    <Reaction name = "GaGTP_bind" id="GaGTP_bind">
	<Reactant specieID="LRG"/>
	<Product specieID="LRGbg"/>
	<Product specieID="GaGTP"/>


	<forwardRate>20e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>
<!--Above reactions are fine - thermodynamically balanced.-->

<!-- 5b) LRGbg ->LR + Gbg (tried 3X faster than 5a -->
    <Reaction name = "LRGbg_disso" id="LRGbg_disso">
	<Reactant specieID="LRGbg"/>
	<Product specieID="LR"/>
	<Product specieID="Gbg"/>

	<forwardRate>80e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 6) GaGTP -> GaGDP    -->
    <Reaction name = "GaGTP_disso" id="GaGTP_disso">
	<Reactant specieID="GaGTP"/>
	<Product specieID="GaGDP"/>

        <forwardRate>10e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 7) GaGDP + Gbg -> G    -->
    <Reaction name = "G_form" id="G_form">
	<Reactant specieID="GaGDP"/>
        <Reactant specieID="Gbg"/>
	<Product specieID="G"/>

        <forwardRate>100e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>
<!--Fine, but I in future would like to compare above to Linderman who studies G proteins.  Above is old from Destexhe-->

<!-- AC part:AC1 & AC8 activation through CaMCa4  -->
<!-- Add 1 more reaction(11) for AC1 bound CaMCa4 form binds Gsa-->
<!-- reaction 4, kcat adjusted by 4X faster than previous due to facilitate-->


<!-- 1) GaGTP + AC1 <-> E(AC1GaGTP)   -->
    <Reaction name = "GaGTP_AC1_reac" id="GaGTP_AC1_reac">
	<Reactant specieID="GaGTP"/>
	<Reactant specieID="AC1"/>
	<Product specieID="AC1GaGTP"/>

	<forwardRate>0.0385e-3</forwardRate>
	<reverseRate>10e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 2) E + CaMCa4 <-> ECam(AC1GaGTPCaMCa4)    -->
    <Reaction name = "AC1GaGTP_CaMCa4_Reac" id="AC1GaGTP_CaMCa4_Reac">
	<Reactant specieID="AC1GaGTP"/>
	<Reactant specieID="CaMCa4"/>
	<Product specieID="AC1GaGTPCaMCa4"/>

	<forwardRate>0.012e-3</forwardRate>
	<reverseRate>0.9e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 3) ECam + ATP <-> ECamATP    -->
    <Reaction name = "AC1GaGTPCaMCa4_ATP_Reac" id="AC1GaGTPCaMCa4_ATP_Reac">
	<Reactant specieID="AC1GaGTPCaMCa4"/>
	<Reactant specieID="ATP"/>
	<Product specieID="AC1GaGTPCaMCa4ATP"/>

	<forwardRate>0.01e-3</forwardRate>
	<reverseRate>2273e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 4) ECamATP -> ECam + cAMP    -->
    <Reaction name = "AC1GaGTPCaMCa4ATP_diss" id="AC1GaGTPCaMCa4ATP_diss">
	<Reactant specieID="AC1GaGTPCaMCa4ATP"/>
	<Product specieID="cAMP"/>
	<Product specieID="AC1GaGTPCaMCa4"/>

	<forwardRate>28.42e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 5) AC1 + CaMCa4 <-> AC1Cam    -->
    <Reaction name = "AC1CaMCa4_Reac" id="AC1CaMCa4_Reac">
	<Reactant specieID="AC1"/>
	<Reactant specieID="CaMCa4"/>
	<Product specieID="AC1CaMCa4"/>

	<forwardRate>0.006e-3</forwardRate>
	<reverseRate>0.9e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 11) AC1CaMCa4 + GaGTP <-> AC1GaGTPCaMCa4 -->
<!--
    <Reaction name = "AC1CaMCa4_GaGTP_bind" id="AC1CaMCa4_GaGTP_bind">
	<Reactant specieID="AC1CaMCa4"/>
	<Product specieID="GaGTP"/>
	<Product specieID="AC1GaGTPCaMCa4"/>

	<forwardRate>0.077e-3</forwardRate>
	<reverseRate>10.0e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>
-->
<!-- 6) AC1Cam + ATP <-> AC1CamATP    -->
    <Reaction name = "AC1CaMCa4ATP_bind" id="AC1CaMCa4ATP_bind">
	<Reactant specieID="AC1CaMCa4"/>
	<Reactant specieID="ATP"/>
	<Product specieID="AC1CaMCa4ATP"/>

	<forwardRate>0.01e-3</forwardRate>
	<reverseRate>2273e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 7) AC1CamATP -> AC1Cam +cAMP    -->
    <Reaction name = "AC1CaMCa4ATP_disso" id="AC1CaMCa4ATP_disso">
	<Reactant specieID="AC1CaMCa4ATP"/>
	<Product specieID="cAMP"/>
	<Product specieID="AC1CaMCa4"/>

	<forwardRate>2.842e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--AC1 is fine - thermodynamically balanced.  But what is source for affinity to ATP?  2273 is very large backward rate;large Kb prevents large E-S intermidiate complex, Kd(cAMP)=2.3(+-)0.8 mM, low affinity -->


<!-- 8) AC8 + CaMCa4 <-> AC8Cam   -->
    <Reaction name = "AC8_CaMCa4_bind" id="AC8_CaMCa4_bind">
	<Reactant specieID="AC8"/>
	<Reactant specieID="CaMCa4"/>
	<Product specieID="AC8CaMCa4"/>

	<forwardRate>0.00125e-3</forwardRate>
	<reverseRate>1e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 9) AC8Cam + ATP <-> AC8CamATP   -->
    <Reaction name = "AC8CaMCa4_ATP_bind" id="AC8CaMCa4_ATP_bind">
	<Reactant specieID="AC8CaMCa4"/>
	<Reactant specieID="ATP"/>
	<Product specieID="AC8CaMCa4ATP"/>

	<forwardRate>0.01e-3</forwardRate>
	<reverseRate>2273e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 10) AC8CamATP -> AC8Cam + cAMP   -->
    <Reaction name = "AC8CaMCa4ATP_disso" id="AC8CaMCa4ATP_disso">
	<Reactant specieID="AC8CaMCa4ATP"/>
	<Product specieID="cAMP"/>
	<Product specieID="AC8CaMCa4"/>

	<forwardRate>2.842e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>




<!-- CaM, CaMCa4 and PP2B Binding -->

<!--1) CaM  + 2Ca <-> CaMCa2 -->
    <Reaction name = "CaM_bind" id="CaM_bind">
	<Reactant specieID="CaM"/>
	<Reactant specieID="Ca" n="2"/>
	<Product specieID="CaMCa2"/>

	<forwardRate>6e-6</forwardRate>
	<reverseRate>9.1e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--2) CaMCa2  + 2Ca <-> CaMCa4 -->
    <Reaction name = "CaMCa2_bind" id="CaMCa2_bind">
	<Reactant specieID="CaMCa2"/>
	<Reactant specieID="Ca" n="2"/>
	<Product specieID="CaMCa4"/>

	<forwardRate>0.1e-3</forwardRate>
	<reverseRate>1000e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--3) CaM  + PP2B <-> PP2CaM -->
    <Reaction name = "PP2_bind" id="PP2_bind">
	<Reactant specieID="CaM"/>
	<Reactant specieID="PP2B"/>
	<Product specieID="PP2BCaM"/>

	<forwardRate>0.046e-4</forwardRate>
	<reverseRate>0.0012e-3</reverseRate>
<!--Above new rate conts from Rodrigo for obeying thermodynamic law;
	<forwardRate>1e-3</forwardRate>
	<reverseRate>3e-3</reverseRate>
-->

	<Q10>0.2</Q10>
    </Reaction>

<!--4) CaMCa2  + PP2B <-> PP2BCaMCa2 -->
    <Reaction name = "PP2CaMC2_bind" id="PP2CaMC2_bind">
	<Reactant specieID="CaMCa2"/>
	<Reactant specieID="PP2B"/>
	<Product specieID="PP2BCaMCa2"/>

    <forwardRate>0.046e-3</forwardRate>
    <reverseRate>0.0012e-3</reverseRate>
<!--

<forwardRate>1e-3</forwardRate>
<reverseRate>0.3e-3</reverseRate>
-->
	<Q10>0.2</Q10>
    </Reaction>

<!--5) CaMCa4  + PP2 <-> PP2B -->
    <Reaction name = "PP2CaMCa4_bind" id="PP2CaMCa4_bind">
	<Reactant specieID="CaMCa4"/>
	<Reactant specieID="PP2B"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>0.046e-3</forwardRate>
	<reverseRate>0.0012e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--6) PP2BCaM  + 2Ca <-> PP2BCaMCa2 -->
    <Reaction name = "PP2CaMCa_bind" id="PP2CaMCa_bind">
	<Reactant specieID="PP2BCaM"/>
	<Reactant specieID="Ca" n="2"/>
	<Product specieID="PP2BCaMCa2"/>

	<forwardRate>6e-6</forwardRate>
	<reverseRate>0.91e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--7) PP2CaMC2  + 2Ca <-> PP2B -->
    <Reaction name = "PP2CaMCa2Ca_bind" id="PP2CaMCa2Ca_bind">
	<Reactant specieID="PP2BCaMCa2"/>
	<Reactant specieID="Ca" n="2"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>0.1e-3</forwardRate>
	<reverseRate>1000e-3</reverseRate>


<!--
	<forwardRate>0.1e-3</forwardRate>
	<reverseRate>10e-3</reverseRate>
-->
	<Q10>0.2</Q10>
    </Reaction>
<!--These are fine.-->

<!-- New CaMKII part -->

<!-- After adding AMPA as read out, too much AMPA_S831 at basal-->
<!-- which mean too high CaMKII act vs PP1 act, so decide adding 2 sides of PP1 reactions on June_16th_2009 after meeting-->


  

  <!--1) CaMCa4 + CK <-> CKCam  -->
    <Reaction name = "CK_bind" id="CK_bind">
	<Reactant specieID="CaMCa4"/>
	<Reactant specieID="CK"/>
	<Product specieID="CKCaMCa4"/>

	<forwardRate>0.01e-3</forwardRate>
	<reverseRate>3e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--2a) CKCam + CKCam <-> Complex -->
    <Reaction name = "CKCam_bind" id="CKCam_bind">
	<Reactant specieID="CKCaMCa4"/>
        <Reactant specieID="CKCaMCa4"/>
	<Product specieID="Complex"/>

	<forwardRate>0.0001e-3</forwardRate>
        <reverseRate>10e-3</reverseRate>
	<Q10>2</Q10>
    </Reaction>

<!--2b) CKpCam + CKCam <-> pComplex -->
    <Reaction name = "pComplex_bind" id="pComplex_bind">
	<Reactant specieID="CKpCaMCa4"/>
        <Reactant specieID="CKCaMCa4"/>
	<Product specieID="pComplex"/>

	<forwardRate>0.0001e-3</forwardRate>
        <reverseRate>10e-3</reverseRate>
	<Q10>2</Q10>
    </Reaction>

<!--3a) CKpCam + Complex <-> CKpCam + pComplex -->
    <Reaction name = "CKpCamCompl_bind" id="CKpCamCompl_bind">
	<Reactant specieID="CKpCaMCa4"/>
        <Reactant specieID="Complex"/>
        <Product specieID="CKpCaMCa4"/>
	<Product specieID="pComplex"/>

	<forwardRate>0.0001e-3</forwardRate>
        <reverseRate>0</reverseRate>
	<Q10>2</Q10>
    </Reaction>

<!--3b) CKCam + Complex <-> CKCam + pComplex -->
    <Reaction name = "CKCamCompl_bind" id="CKCamCompl_bind">
	<Reactant specieID="CKCaMCa4"/>
        <Reactant specieID="Complex"/>
        <Product specieID="CKCaMCa4"/>
	<Product specieID="pComplex"/>

	<forwardRate>0.0001e-3</forwardRate>
        <reverseRate>0</reverseRate>
	<Q10>2</Q10>
    </Reaction>

 <!--4a) Complex + Complex <-> Complex + Pcomplex -->
    <Reaction name = "2Complex_bind" id="2Complex_bind">
	<Reactant specieID="Complex"/>
        <Reactant specieID="Complex"/>
	<Product specieID="Complex"/>
        <Product specieID="pComplex"/>

	<forwardRate>0.01e-3</forwardRate>
        <reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--Don't know why I didn't consider this before, but I wonder if we can produce Dekoninck and Schulman better if both products are pComplex for above, and if CKpCaMCa4 is product in previous reaction.  I might try this at some point using the xpp Dupont simulations, or single comp Dupont stochastic sims.-->

 <!--4b) Complex + pComplex <-> Pcomplex + pComplex-->
    <Reaction name = "ComplpCompl_bind" id="ComplpCompl_bind">
	<Reactant specieID="Complex"/>
	<Reactant specieID="pComplex"/>
	<Product specieID="pComplex"/>
        <Product specieID="pComplex"/>

	<forwardRate>0.03e-3</forwardRate>
        <reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- CKpCam + CaMCa4 <-> CKp -->
    <Reaction name = "CKp_auto" id="CKp_auto">
	<Reactant specieID="CKpCaMCa4"/>
        <Product specieID="CaMCa4"/>
	<Product specieID="CKp"/>

	<forwardRate>0.0008e-3</forwardRate>
	<reverseRate>0.01e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--Allow two sides(CKpCam and CKp)dephosphorate due to high AMPA_basal-->
<!-- binding with PP1 rate and quantity needs to be adjusted from Fret data-->
<!-- kf from 0.000039 to 6e-7, kb and kcat are same;reduced affinity-->

    <!-- CKp + PP1 <-> CKpPP1 -->
    <Reaction name = "CKp_bind" id="CKp_bind">
	<Reactant specieID="CKp"/>
        <Reactant specieID="PP1"/>
	<Product specieID="CKpPP1"/>

	<forwardRate>6e-10</forwardRate>
        <reverseRate>0.34e-3</reverseRate>
	<Q10>2</Q10>
    </Reaction>

    <!-- CKpPP1 -> PP1 + CK -->
    <Reaction name = "CKpPP1_reac" id="CKpPP1_reac">
	<Reactant specieID="CKpPP1"/>
	<Product specieID="PP1"/>
        <Product specieID="CK"/>

	<forwardRate>0.086e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- CKpCaMCa4 + PP1 <-> CKpCaMCa4PP1 -->
    <Reaction name = "CKpCamPP1_bind" id="CKpCamPP1_bind">
	<Reactant specieID="CKpCaMCa4"/>
        <Reactant specieID="PP1"/>
	<Product specieID="CKpCaMCa4PP1"/>

	<forwardRate>6e-10</forwardRate>
        <reverseRate>0.34e-3</reverseRate>
	<Q10>2</Q10>
    </Reaction>

    <!-- CKpCaMCa4PP1 -> PP1 + CKCaMCa4 -->
    <Reaction name = "CKpCamPP1_reac" id="CKpCamPP1_reac">
	<Reactant specieID="CKpCaMCa4PP1"/>
	<Product specieID="PP1"/>
        <Product specieID="CKCaMCa4"/>

	<forwardRate>0.086e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>



<!-- PKA part -->
<!-- Implements of PKAcAMP4 molecule binds to substrates & consider to effect-->
<!-- of autophosphorylation (Kd reduced by factor of 10), inspired by Ddavid Johnson's email on June_10th_2009-->


    <!--1) PKA + 2cAMP <-> PKAcAMP2 -->
    <Reaction name = "PKA_bind" id="PKA_bind">
	<Reactant specieID="PKA"/>
        <Reactant specieID="cAMP" n="2"/>
	<Product specieID="PKAcAMP2"/>


        <forwardRate>8.6956e-8</forwardRate>
	<reverseRate>0.02e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--2) PKAcAMP2 + 2cAMP <-> PKAcAMP4 -->
    <Reaction name = "PKAcAMP2_bind" id="PKAcAMP2_bind">
	<Reactant specieID="PKAcAMP2"/>
        <Reactant specieID="cAMP" n="2"/>
	<Product specieID="PKAcAMP4"/>

    <forwardRate>11.5406e-8</forwardRate>
	<reverseRate>0.2e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>






<!-- Inhibitor 1 Phospho and Dephosphorylation -->



    <!--1) I1 + PKAc <-> I1PKAc -->
    <Reaction name = "I1_bind" id="I1_bind">
	<Reactant specieID="I1"/>
        <Reactant specieID="PKAc"/>
	<Product specieID="I1PKAc"/>

	<forwardRate>0.0014e-3</forwardRate>
	<reverseRate>5.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--2) I1PKAc -> Ip35 + PKAc: default kb=0 -->
    <Reaction name = "I1PKAc_reac" id="I1PKAc_reac">
	<Reactant specieID="I1PKAc"/>
        <Product specieID="Ip35"/>
	<Product specieID="PKAc"/>

	<forwardRate>1.4e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--3) Ip35 + PP1 <-> Ip35pp1 -->
    <Reaction name = "Ip35_bind" id="Ip35_bind">
	<Reactant specieID="Ip35"/>
        <Reactant specieID="PP1"/>
	<Product specieID="Ip35PP1"/>

	<forwardRate>0.001e-3</forwardRate>
	<reverseRate>0.0011e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--4) Ip35 + PP2B <-> Ip35pp2b -->
    <Reaction name = "Ip35pp2b_bind" id="Ip35pp2b_bind">
	<Reactant specieID="Ip35"/>
        <Reactant specieID="PP2BCaMCa4"/>
	<Product specieID="Ip35PP2BCaMCa4"/>

	<forwardRate>0.00233e-3</forwardRate>
	<reverseRate>11.2e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--5) Ip35pp2b -> I1 + PP2B -->
    <Reaction name = "Ip35pp2b_reac" id="Ip35pp2b_reac">
	<Reactant specieID="Ip35PP2BCaMCa4"/>
        <Product specieID="I1"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>2.8e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--6) Ip35pp1 + PP2B <-> Ip35p1p2 -->
    <Reaction name = "Ip35pp1_bind" id="Ip35pp1_bind">
	<Reactant specieID="Ip35PP1"/>
        <Reactant specieID="PP2BCaMCa4"/>
	<Product specieID="Ip35PP1PP2BCaMCa4"/>

	<forwardRate>0.00233e-3</forwardRate>
	<reverseRate>11.2e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

    <!--7a) Ip35p1p2 -> I1 + PP1PP2B -->
    <Reaction name = "Ip35p1p2_reac" id="Ip35p1p2_reac">
	<Reactant specieID="Ip35PP1PP2BCaMCa4"/>
        <Product specieID="I1"/>
        <Product specieID="PP1PP2BCaMCa4"/>

	<forwardRate>2.8e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

 <!--7b) PP1PP2B -> PP1 + PP2B-->
    <Reaction name = "PP1PP2CaMCa4_diss" id="PP1PP2CaMCa4_diss">
	<Reactant specieID="PP1PP2BCaMCa4"/>
        <Product specieID="PP1"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>1.5e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- AMPA receptor is phosporylation by PKAc,PhospCaMKII -->
<!-- And also dephosphorylation by PP1 and PP2B --->
<!--For now, rate constants are adopted from Upi Bhalla-->

<!--1)affinity of phospho_GluR1 by PKAc is 7.5 uM; k1=0.074072 #^-1s^-1, k2=24s^-1, k3=6s^-1;kf=0.00402 nM^-1s^-1 -->

<!--1) GluR1 + PKAc <-> GluR1_PKAc -->
    <Reaction name = "GluR1_PKAc_bind" id="GluR1_PKAc_bind">
	<Reactant specieID="GluR1"/>
	<Reactant specieID="PKAc"/>
	<Product specieID="GluR1_PKAc"/>

	<forwardRate>0.00402e-3</forwardRate>
	<reverseRate>24e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_PKAc -> GluR1_S845 + PKAc -->
    <Reaction name = "GluR1_PKAc_diss" id="GluR1_PKAc_diss">
	<Reactant specieID="GluR1_PKAc"/>
	<Product specieID="GluR1_S845"/>
	<Product specieID="PKAc"/>

	<forwardRate>6e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>
<!--3)affinity of phospho_GluR1 by phosp_CaMKII is 90 uM; k1=0.0046296 #^-1s^-1,k2=2s^-1, k3=0.5s^-1;kf=2.778e-5 nM^-1s^-1 but other CKCam and CKp adjusted by factor og qt=0.8, qa=0.8 -->

<!--2) GluR1 + CKCam <-> GluR1_CKCam -->
    <Reaction name = "GluR1_CKCam_bind" id="GluR1_CKCam_bind">
	<Reactant specieID="GluR1"/>
	<Reactant specieID="CKCaMCa4"/>
	<Product specieID="GluR1_CKCam"/>

	<forwardRate>2.224e-8</forwardRate>
	<reverseRate>1.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_CKCam -> GluR1_S831 + CKCam -->
    <Reaction name = "GluR1_CKCam_diss" id="GluR1_CKCam_diss">
	<Reactant specieID="GluR1_CKCam"/>
	<Product specieID="GluR1_S831"/>
	<Product specieID="CKCaMCa4"/>

	<forwardRate>0.4e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--Double check!!! This Km is 8.99e-1.  It is so high that of course all of GluR1 is phosphorylated.  Even if these values agree with Upi's website, we will have to change this to have lower affinity (and perhaps higher affinity of PKAc).  Same goes for the two other forms of activated Camkinase.-->


<!-- forward rate typo(was dropped off e-5 factor added up; rechecked Upi's data and confirmed calculation which matched either k1 as #^-1s-1 by converting each volume's concentration or from Km, k1=0.0046296 #^-1s^-1, kb=2s^-1,kcat=0.5s^-1, Km=90 uM: therefore k1=2.78e^-8 nM^-1 msec^-1-->

<!--3) GluR1 + CKpCam <-> GluR1_CKpCam -->
    <Reaction name = "GluR1_CKpCam_bind" id="GluR1_CKpCam_bind">
	<Reactant specieID="GluR1"/>
	<Reactant specieID="CKpCaMCa4"/>
	<Product specieID="GluR1_CKpCam"/>

	<forwardRate>2.78e-8</forwardRate>
	<reverseRate>2e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_CKpCam -> GluR1_S831 + CKpCam -->
    <Reaction name = "GluR1_CKpCam_diss" id="GluR1_CKpCam_diss">
	<Reactant specieID="GluR1_CKpCam"/>
	<Product specieID="GluR1_S831"/>
	<Product specieID="CKpCaMCa4"/>

	<forwardRate>0.5e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 4)GluR1 + CKp <-> GluR1_CKp -->
    <Reaction name = "GluR1_CKp_bind" id="GluR1_CKp_bind">
	<Reactant specieID="GluR1"/>
	<Reactant specieID="CKp"/>
	<Product specieID="GluR1_CKp"/>

	<forwardRate>2.224e-8</forwardRate>
	<reverseRate>1.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_CKp -> GluR1_S831 + CKp -->
    <Reaction name = "GluR1_CKp_diss" id="GluR1_CKp_diss">
	<Reactant specieID="GluR1_CKp"/>
	<Product specieID="GluR1_S831"/>
	<Product specieID="CKp"/>

	<forwardRate>0.4e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- 5) GluR1_S845 + CKCam <-> GluR1_S845_CKCam -->
    <Reaction name = "GluR1_S845_CKCam_bind" id="GluR1_S845_CKCam_bind">
	<Reactant specieID="GluR1_S845"/>
	<Reactant specieID="CKCaMCa4"/>
	<Product specieID="GluR1_S845_CKCam"/>

	<forwardRate>2.224e-8</forwardRate>
	<reverseRate>1.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S845_CKCam -> GluR1_S845_S831 + CKCam -->
    <Reaction name = "GluR1_S845_CKCam_diss" id="GluR1_S845_CKCam_diss">
	<Reactant specieID="GluR1_S845_CKCam"/>
	<Product specieID="GluR1_S845_S831"/>
	<Product specieID="CKCaMCa4"/>

	<forwardRate>0.4e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--6) GluR1_S845 + CKpCam <-> GluR1_S845_CKpCam -->
    <Reaction name = "GluR1_CKpCam_bind" id="GluR1_CKpCam_bind">
	<Reactant specieID="GluR1_S845"/>
	<Reactant specieID="CKpCaMCa4"/>
	<Product specieID="GluR1_S845_CKpCam"/>

	<forwardRate>2.78e-8</forwardRate>
	<reverseRate>2e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S845_CKpCam -> GluR1_S845_S831 + CKpCam -->
    <Reaction name = "GluR1_CKpCam_diss" id="GluR1_CKpCam_diss">
	<Reactant specieID="GluR1_S845_CKpCam"/>
	<Product specieID="GluR1_S845_S831"/>
	<Product specieID="CKpCaMCa4"/>

	<forwardRate>0.5e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--7) GluR1_S845 + CKp <-> GluR1_S845_CKp -->
    <Reaction name = "GluR1_S845_CKp_bind" id="GluR1_S845_CKp_bind">
	<Reactant specieID="GluR1_S845"/>
	<Reactant specieID="CKp"/>
	<Product specieID="GluR1_S845_CKp"/>

	<forwardRate>2.224e-8</forwardRate>
	<reverseRate>1.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_CKp -> GluR1_S845_S831 + CKp -->
    <Reaction name = "GluR1_S845_CKp_diss" id="GluR1_S845_CKp_diss">
	<Reactant specieID="GluR1_S845_CKp"/>
	<Product specieID="GluR1_S845_S831"/>
	<Product specieID="CKp"/>

	<forwardRate>0.4e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>



<!-- 8)GluR1_S831 + PKAc <-> GluR1_S831_PKAc -->
    <Reaction name = "GluR1_S831_PKAc_bind" id="GluR1_S831_PKAc_bind">
	<Reactant specieID="GluR1_S831"/>
	<Reactant specieID="PKAc"/>
	<Product specieID="GluR1_S831_PKAc"/>

	<forwardRate>0.004e-3</forwardRate>
	<reverseRate>24e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S831_PKAc -> GluR1_S845_S831 + PKAc -->
    <Reaction name = "GluR1_S831_PKAc_diss" id="GluR1_S831_PKAc_diss">
	<Reactant specieID="GluR1_S831_PKAc"/>
	<Product specieID="GluR1_S845_S831"/>
	<Product specieID="PKAc"/>

	<forwardRate>6e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Upi's rate constants : k1=0.14583#^-1s^-1, kb=0.68s^-1, kcat=0.17s^-1, Km=0.97145 uM; kf=0.00087 nM^-1s^-1-->
<!--9) GluR1_S845 + PP1 <-> GluR1_S845_PP1 -->
    <Reaction name = "GluR1_S845_PP1_bind" id="GluR1_S845_PP1_bind">
	<Reactant specieID="GluR1_S845"/>
	<Reactant specieID="PP1"/>
	<Product specieID="GluR1_S845_PP1"/>

	<forwardRate>0.00087e-3</forwardRate>
	<reverseRate>0.68e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S845_PP1 -> GluR1 + PP1 -->
    <Reaction name = "GluR1_S845_PP1_diss" id="GluR1_S845_PP1_diss">
	<Reactant specieID="GluR1_S845_PP1"/>
	<Product specieID="GluR1"/>
	<Product specieID="PP1"/>

	<forwardRate>0.17e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--10) GluR1_S845_S831 + PP1 <-> GluR1_S845_S831_PP1 -->
    <Reaction name = "GluR1_S845_S831_PP1_bind" id="GluR1_S845_S831_PP1_bind">
	<Reactant specieID="GluR1_S845_S831"/>
	<Reactant specieID="PP1"/>
	<Product specieID="GluR1_S845_S831_PP1"/>

	<forwardRate>0.875e-6</forwardRate>
	<reverseRate>1.4e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--10a) GluR1_S845_S831_PP1 -> GluR1_S845 + PP1 -->
    <Reaction name = "GluR1_S845_S831_PP1_diss" id="GluR1_S845_S831_PP1_diss">
	<Reactant specieID="GluR1_S845_S831_PP1"/>
	<Product specieID="GluR1_S845"/>
	<Product specieID="PP1"/>

	<forwardRate>0.35e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--10b) GluR1_S845_S831_PP1 -> GluR1_S831 + PP1 -->
    <Reaction name = "GluR1_S845_S831_PP1_diss2" id="GluR1_S845_S831_PP1_diss2">
	<Reactant specieID="GluR1_S845_S831_PP1"/>
	<Product specieID="GluR1_S831"/>
	<Product specieID="PP1"/>

	<forwardRate>0.35e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--11) GluR1_S831 + PP1 <-> GluR1_S831_PP1 -->
    <Reaction name = "GluR1_S831_PP1_bind" id="GluR1_S831_PP1_bind">
	<Reactant specieID="GluR1_S831"/>
	<Reactant specieID="PP1"/>
	<Product specieID="GluR1_S831_PP1"/>

	<forwardRate>0.875e-6</forwardRate>
	<reverseRate>1.4e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S831_PP1 -> GluR1 + PP1 -->
    <Reaction name = "GluR1_S831_PP1_diss" id="GluR1_S831_PP1_diss">
	<Reactant specieID="GluR1_S831_PP1"/>
	<Product specieID="GluR1"/>
	<Product specieID="PP1"/>

	<forwardRate>0.35e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>


<!--12) GluR1_S845 + PP2B <-> GluR1_S845_PP2B -->
    <Reaction name = "GluR1_S845_PP2B_bind" id="GluR1_S845_PP2B_bind">
	<Reactant specieID="GluR1_S845"/>
	<Reactant specieID="PP2BCaMCa4"/>
	<Product specieID="GluR1_S845_PP2B"/>

	<forwardRate>0.00201e-3</forwardRate>
	<reverseRate>8e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S845_PP2B -> GluR1 + PP2B -->
    <Reaction name = "GluR1_S845_PP2B_diss" id="GluR1_S845_PP2B_diss">
	<Reactant specieID="GluR1_S845_PP2B"/>
	<Product specieID="GluR1"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>2e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--13) GluR1_S845_S831 + PP2B <-> GluR1_S845_S831_PP2B -->
    <Reaction name = "GluR1_S845_S831_PP2B_bind" id="GluR1_S845_S831_PP2B_bind">
	<Reactant specieID="GluR1_S845_S831"/>
	<Reactant specieID="PP2BCaMCa4"/>
	<Product specieID="GluR1_S845_S831_PP2B"/>

	<forwardRate>0.00201e-3</forwardRate>
	<reverseRate>8e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- GluR1_S845_S831_PP2B -> GluR1_S831 + PP2BCaMCa4 -->
    <Reaction name = "GluR1_S845_S831_PP2B_diss" id="GluR1_S845_S831_PP2B_diss">
	<Reactant specieID="GluR1_S845_S831_PP2B"/>
	<Product specieID="GluR1_S831"/>
	<Product specieID="PP2BCaMCa4"/>

	<forwardRate>2e-3</forwardRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- PDE Part -->

<!--1) PDE1 + CaMCa4 <-> PDE1Cam -->
       <Reaction name = "PDE1CaMCa4_bind" id="PDE1CaMCa4_bind">
	<Reactant specieID="PDE1"/>
	<Reactant specieID="CaMCa4"/>
	<Product specieID="PDE1CaMCa4"/>

	<forwardRate>0.1e-3</forwardRate>
	<reverseRate>1e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--2) PDE1Cam + cAMP <-> PDE1Cam_cAMP(=PDE1cAMP) -->
       <Reaction name = "PDE1CaMCa4cAMP_bind" id="PDE1CaMCa4cAMP_bind">
	<Reactant specieID="PDE1CaMCa4"/>
	<Reactant specieID="cAMP"/>
	<Product specieID="PDE1CaMCa4cAMP"/>

	<forwardRate>0.0046e-3</forwardRate>
	<reverseRate>44e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--3) PDE1cAMP -> PDE1Cam + AMP -->
       <Reaction name = "PDE1cAMP_disso" id="PDE1cAMP_disso">
	<Reactant specieID="PDE1CaMCa4cAMP"/>
	<Product specieID="PDE1CaMCa4"/>
	<Product specieID="AMP"/>

	<forwardRate>11e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>



<!--6) AMP -> ATP  -->
       <Reaction name = "ATP_regen" id="ATP_regen">
	<Reactant specieID="AMP"/>
	<Product specieID="ATP"/>

	<forwardRate>1e-3</forwardRate>
	<reverseRate>0</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- Below PDE4B/D reactions from Rodrigo:PKAc compete with I1 and PDE4B/D -->
<!-- Current affinity with PKAc to PDE4B/D too high so nothing left binding for I1-->

<!-- 7)  cAMP + PDE4B  <-> PDE4BcAMP -->
    <Reaction name = "PDE4B enzyme1" id="PDE4Bbind">
        <Reactant specieID="PDE4B"           />
        <Reactant specieID="cAMP"            />
        <Product  specieID="PDE4BcAMP"       />

        <forwardRate> 0.03038e-03   </forwardRate>
        <reverseRate> 77.78e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 8)  PDE4BcAMP -> AMP + PDE4B -->
    <Reaction name = "PDE4B actvcomp" id="PDE4Bcat">
        <Reactant specieID="PDE4BcAMP"       />
        <Product  specieID="PDE4B"           />
        <Product  specieID="AMP"             />

        <forwardRate> 19.44e-03  </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 9)  PKAc + PDE4B -> PKAcPDE4B -->
    <Reaction name = "PDE4B phosp1" id="phospPDE4B1">
        <Reactant specieID="PKAc"            />
        <Reactant specieID="PDE4B"           />
        <Product  specieID="PKAcPDE4B"       />
         <forwardRate> 0.00428e-03 </forwardRate>
        <reverseRate> 5.6e-03   </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 10)  PKAcPDE4B -> PKAc + pPDE4B -->
    <!-- <forwardRate> 5.56e-06   </forwardRate> -->
    <Reaction name = "PDE4B phosp2" id="phospPDE4B2">
        <Reactant specieID="PKAcPDE4B"       />
        <Product  specieID="pPDE4B"          />
        <Product  specieID="PKAc"            />

        <forwardRate> 1.25e-03   </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 11)  pPDE4B -> PDE4B -->
    <!-- <forwardRate> 1.36e-07   </forwardRate> -->
    <Reaction name = "PDE4B d_phosp" id="dphospPDE4B">
        <Reactant specieID="pPDE4B"          />
        <Product  specieID="PDE4B"           />

        <forwardRate> 0.25e-03   </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 12)  cAMP + pPDE4B  <-> pPDE4BcAMP -->
    <Reaction name = "pPDE4B enzyme1" id="pPDE4Bbind">
        <Reactant specieID="pPDE4B"           />
        <Reactant specieID="cAMP"             />
        <Product  specieID="pPDE4BcAMP"       />

        <forwardRate> 0.03038e-03   </forwardRate>
        <reverseRate> 77.78e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 13)  pPDE4BcAMP -> AMP + pPDE4B -->
    <Reaction name = "pPDE4B actvcomp" id="pPDE4Bcat">
        <Reactant specieID="pPDE4BcAMP"       />
        <Product  specieID="pPDE4B"           />
        <Product  specieID="AMP"              />

        <forwardRate> 38.88e-03 </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>


    <!-- 21)  PDE4BcAMP + PKAc  <-> PKAc_PDE4B_cAMP -->
   
    <Reaction name = "PKAc_PDE4B_cAMP-bind" id="PKAc_PDE4B_cAMP-bind">
        <Reactant specieID="PDE4BcAMP"           />
        <Reactant specieID="PKAc"             />
        <Product  specieID="PKAc_PDE4B_cAMP"       />

        <forwardRate> 0.00428e-03  </forwardRate>
        <reverseRate> 5.6e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>

    <!-- 22)  PKAc_PDE4B_cAMP -> pPDE4BcAMP + PKAc -->
    
    <Reaction name = "PKAc_PDE4B_cAMP-diss" id="PKAc_PDE4B_cAMP-diss">
        <Reactant specieID="PKAc_PDE4B_cAMP"       />
        <Product  specieID="pPDE4BcAMP"           />
        <Product  specieID="PKAc"              />

        <forwardRate> 1.25e-03  </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>


    <!-- 14)  cAMP + PDE4D  <-> PDE4DcAMP -->
    <Reaction name = "PDE4D enzyme1" id="PDE4Dbind">
        <Reactant specieID="PDE4D"           />
        <Reactant specieID="cAMP"            />
        <Product  specieID="PDE4DcAMP"       />

        <forwardRate> 0.01296e-03  </forwardRate>
        <reverseRate> 60.1399e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 15)  PDE4DcAMP -> AMP + PDE4D -->
    <!-- <forwardRate> 14.70e-03  </forwardRate> -->
    <Reaction name = "PDE4D actvcomp" id="PDE4Dcat">
        <Reactant specieID="PDE4DcAMP"       />
        <Product  specieID="PDE4D"           />
        <Product  specieID="AMP"             />

        <forwardRate> 15.03e-03  </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 16)  PKAc + PDE4D -> PKAcPDE4D -->
    <Reaction name = "PDE4D phosp1" id="phospPDE4D1">
        <Reactant specieID="PKAc"            />
        <Reactant specieID="PDE4D"           />
        <Product  specieID="PKAcPDE4D"       />
         <forwardRate> 0.00428e-03 </forwardRate>
        <reverseRate> 5.6e-03   </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 17)  PKAcPDE4D -> PKAc + pPDE4D -->
    <!-- <forwardRate> 5.56e-06   </forwardRate> -->
    <Reaction name = "PDE4D phosp2" id="phospPDE4D2">
        <Reactant specieID="PKAcPDE4D"       />
        <Product  specieID="pPDE4D"          />
        <Product  specieID="PKAc"            />

        <forwardRate> 1.25e-03   </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 18)  pPDE4D -> PDE4D -->
    <!-- <forwardRate> 1.36e-06  5.46e-06 </forwardRate> -->
    <Reaction name = "PDE4D d_phosp" id="dphospPDE4D">
        <Reactant specieID="pPDE4D"          />
        <Product  specieID="PDE4D"           />

        <forwardRate> 0.25e-03   </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 19)  cAMP + pPDE4D  <-> pPDE4DcAMP -->
    <!-- <forwardRate> 0.96e-03   </forwardRate> -->
    <Reaction name = "pPDE4D enzyme1" id="pPDE4Dbind">
        <Reactant specieID="pPDE4D"           />
        <Reactant specieID="cAMP"             />
        <Product  specieID="pPDE4DcAMP"       />

        <forwardRate> 0.01296e-03  </forwardRate>
        <reverseRate> 60.1399e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>
    <!-- 20)  pPDE4DcAMP -> AMP + pPDE4D -->
    <!-- <forwardRate> 92.58e-03  </forwardRate> -->
    <Reaction name = "pPDE4D actvcomp" id="pPDE4Dcat">
        <Reactant specieID="pPDE4DcAMP"       />
        <Product  specieID="pPDE4D"           />
        <Product  specieID="AMP"              />

        <forwardRate> 30.06e-03  </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>


    <!-- 23)  PDE4DcAMP + PKAc  <-> PKAc_PDE4D_cAMP -->
   
    <Reaction name = "PKAc_PDE4D_cAMP-bind" id="PKAc_PDE4D_cAMP-bind">
        <Reactant specieID="PDE4DcAMP"           />
        <Reactant specieID="PKAc"             />
        <Product  specieID="PKAc_PDE4D_cAMP"       />

        <forwardRate> 0.00428e-03  </forwardRate>
        <reverseRate> 5.6e-03  </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>

    <!-- 24*)  PKAc_PDE4D_cAMP -> pPDE4DcAMP + PKAc -->
    
    <Reaction name = "PKAc_PDE4D_cAMP-diss" id="PKAc_PDE4D_cAMP-diss">
        <Reactant specieID="PKAc_PDE4D_cAMP"       />
        <Product  specieID="pPDE4DcAMP"           />
        <Product  specieID="PKAc"              />

        <forwardRate> 1.25e-03  </forwardRate>
        <reverseRate> 0          </reverseRate>
        <Q10>         0.2        </Q10>
    </Reaction>


<!-- New reactions added from PKAcAMP4 bound to substrates-->
<!-- active PKAcAMP4 molecules react substrates and autophosphorylation-->
<!-- of RII enhance activation of PKAc-->
<!-- Denote that PKAcAMP4 is R2cAMP4C2 in here-->


<!-- Binding of PKAcAMP4 to substrate -->

<!-- R2cAMP4C2 + S <->R2cAMP4C2_S->(S* + R2cAMP4C2)-->
<!-- this reaction(Kcat) is no longer believe to true by Johnson's email on June_10th_2009 -->
<!-- The rate constants of thease reactions are adjusted by factor of 10X lower forward rate-->
<!-- by considering steric hinderance, compare to PKAc bind to S-->
 
<!--1) PKAcAMP4 + GluR1 <-> PKAcAMP4_GluR1 -->
    <Reaction name = "PKAcAMP4_GluR1_bind" id="PKAcAMP4_GluR1_bind">
	<Reactant specieID="PKAcAMP4"/>
	<Reactant specieID="GluR1"/>
	<Product specieID="PKAcAMP4_GluR1"/>

	<forwardRate>0.000402e-3</forwardRate>
	<reverseRate>24e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>



<!--2) PKAcAMP4 + GluR1_S831 <-> PKAcAMP4_GluR1_S831 -->
    <Reaction name = "PKAcAMP4_GluR1_S831_bind" id="PKAcAMP4_GluR1_S831_bind">
	<Reactant specieID="PKAcAMP4"/>
	<Reactant specieID="GluR1_S831"/>
	<Product specieID="PKAcAMP4_GluR1_S831"/>

	<forwardRate>0.000402e-3</forwardRate>
	<reverseRate>24e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>




<!--3) PKAcAMP4 + I1 <-> PKAcAMP4_I1 -->
    <Reaction name = "PKAcAMP4_I1_bind" id="PKAcAMP4_I1_bind">
	<Reactant specieID="PKAcAMP4"/>
	<Reactant specieID="I1"/>
	<Product specieID="PKAcAMP4_I1"/>

	<forwardRate>0.00014e-3</forwardRate>
	<reverseRate>5.6e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>




<!--4) PKAcAMP4 + PDE4B <-> PKAcAMP4_PDE4B -->
    <Reaction name = "PKAcAMP4_PDE4B_bind" id="PKAcAMP4_PDE4B_bind">
	<Reactant specieID="PKAcAMP4"/>
	<Reactant specieID="PDE4B"/>
	<Product specieID="PKAcAMP4_PDE4B"/>

	<forwardRate>0.0625e-6</forwardRate>
	<reverseRate>5.44e-6</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!--5) PKAcAMP4 + PDE4D <-> PKAcAMP4_PDE4D -->
    <Reaction name = "PKAcAMP4_PDE4D_bind" id="PKAcAMP4_PDE4D_bind">
	<Reactant specieID="PKAcAMP4"/>
	<Reactant specieID="PDE4D"/>
	<Product specieID="PKAcAMP4_PDE4D"/>

	<forwardRate>0.0625e-6</forwardRate>
	<reverseRate>5.44e-6</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- dissociation of C-substrate from PKAcMP4S-->
<!-- R2cAMP4C2S <->R2C_cAMP4 + SC -->
<!--dissociate  10X faster(facilitate factor) for forward rate than PKAcAMP4-->

<!--1) PKAcAMP4_GluR1 <-> R2C_cAMP4 + GluR1_PKAc -->
    <Reaction name = "PKAcAMP4_GluR1_diss2" id="PKAcAMP4_GluR1_diss2">
	<Reactant specieID="PKAcAMP4_GluR1"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="GluR1_PKAc"/>

	<forwardRate>0.38e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- 7 -->
<!-- PKAcAMP4_GluR1_S831 <-> R2C_cAMP4 + GluR1_S831_PKAc -->
    <Reaction name = "PKAcAMP4_GluR1_S831_diss2" id="PKAcAMP4_GluR1_S831_diss2">
	<Reactant specieID="PKAcAMP4_GluR1_S831"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="GluR1_S831_PKAc"/>

	<forwardRate>0.38e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- 8 -->
<!-- PKAcAMP4_I1 <-> R2C_cAMP4 + I1PKAc -->
    <Reaction name = "PKAcAMP4_I1_diss2" id="PKAcAMP4_I1_diss2">
	<Reactant specieID="PKAcAMP4_I1"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="I1PKAc"/>

	<forwardRate>0.38e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- 9 -->
<!-- PKAcAMP4_PDE4B <-> R2C_cAMP4 + PKAcPDE4B -->
    <Reaction name = "PKAcAMP4_PDE4B_diss2" id="PKAcAMP4_PDE4B_diss2">
	<Reactant specieID="PKAcAMP4_PDE4B"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="PKAcPDE4B"/>

	<forwardRate>0.38e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>


<!-- 10 -->
<!-- PKAcAMP4_PDE4D <-> R2C_cAMP4 + PKAcPDE4D -->
    <Reaction name = "PKAcAMP4_PDE4D_diss2" id="PKAcAMP4_PDE4D_diss2">
	<Reactant specieID="PKAcAMP4_PDE4D"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="PKAcPDE4D"/>

	<forwardRate>0.38e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!-- 11)-->

<!-- C subunits dissociate one at a time (required for above reactions -->
<!-- Autophosphorylation makes affinity lower, and most PKA is autophosphorylated basal state -->
<!-- Make the following rates ALL 3 x faster to match speed of prior PKA model-->
<!-- OR by Zakhay_JAHA2000, Phos causes 10X lower affinity>
<!-- dissociation of substrate bound PKAcAMP4 (6-10) needs to be 10 x faster than this forward rate -->

<!--11a,b) Upi's rate constants are different as ours; 11a; kf=60^s-1, kb=18 uM^-1s^-1 -->

<!--11a) PKAcAMP4 <-> R2C_cAMP4 + PKAc -->
    <Reaction name = "PKAcAMP4_diss2" id="PKAcAMP4_diss2">
	<Reactant specieID="PKAcAMP4"/>
	<Product specieID="R2C_cAMP4"/>
	<Product specieID="PKAc"/>

	<forwardRate>0.038e-3</forwardRate>
	<reverseRate>0.016e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>

<!--11b) R2C_cAMP4 <-> PKAr + PKAc -->
    <Reaction name = "R2C_cAMP_diss" id="R2C_cAMP4_diss">
	<Reactant specieID="R2C_cAMP4"/>
	<Product specieID="PKAr"/>
	<Product specieID="PKAc"/>

	<forwardRate>0.152e-3</forwardRate>
	<reverseRate>0.004e-3</reverseRate>
	<Q10>0.2</Q10>
    </Reaction>





</ReactionScheme>

Stim4tr_CaB_2inj_sp.xml0000644000076400007650000001032011564511527015315 0ustar  avramastochdiff<StimulationSet>

    <!-- the injectionSite must match a regionLabel deefined in the morphology -->
   

<!-- Train I -->

<InjectionStim specieID="Ca" injectionSite="sa1[0].pointA">
        <onset>10000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>11000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="sa1[0].pointA">
        <onset>11150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>12150</end>

  </InjectionStim>

<InjectionStim specieID="Ca" injectionSite="pointB">
        <onset>10000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>11000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="pointB">
        <onset>11150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>12150</end>

  </InjectionStim>

<InjectionStim specieID="L" injectionSite="sa1[0].pointA">
	  <onset>10000</onset>
	  <duration>1000</duration>
	  <rate>0.8</rate>
	  <end>11000</end> 
	  
  </InjectionStim>





<!-- Train II -->


<InjectionStim specieID="Ca" injectionSite="sa1[0].pointA">
        <onset>90000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>91000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="sa1[0].pointA">
        <onset>91150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>92150</end>

  </InjectionStim>

<InjectionStim specieID="Ca" injectionSite="pointB">
        <onset>90000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>91000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="pointB">
        <onset>91150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>92150</end>

  </InjectionStim>

<InjectionStim specieID="L" injectionSite="sa1[0].pointA">
	  <onset>90000</onset>
	  <duration>1000</duration>
	  <rate>0.8</rate>
	  <end>91000</end> 
	  
  </InjectionStim>




<!-- Train III -->


<InjectionStim specieID="Ca" injectionSite="sa1[0].pointA">
        <onset>170000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>171000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="sa1[0].pointA">
        <onset>171150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>172150</end>

  </InjectionStim>

<InjectionStim specieID="Ca" injectionSite="pointB">
        <onset>170000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>171000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="pointB">
        <onset>171150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>172150</end>

  </InjectionStim>

<InjectionStim specieID="L" injectionSite="sa1[0].pointA">
	  <onset>170000</onset>
	  <duration>1000</duration>
	  <rate>0.8</rate>
	  <end>171000</end> 
	  
  </InjectionStim>



<!-- Train IV -->


<InjectionStim specieID="Ca" injectionSite="sa1[0].pointA">
        <onset>250000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>251000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="sa1[0].pointA">
        <onset>251150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>252150</end>

  </InjectionStim>

<InjectionStim specieID="Ca" injectionSite="pointB">
        <onset>250000</onset>
	<duration>3</duration>
	<rate>62.5</rate>
        <period>10</period>
        <end>251000</end> 
       
  </InjectionStim>

<InjectionStim specieID="CaB" injectionSite="pointB">
        <onset>251150</onset>
        <duration>1000</duration>
        <rate>11.25</rate>
        <end>252150</end>

  </InjectionStim>

<InjectionStim specieID="L" injectionSite="sa1[0].pointA">
	  <onset>250000</onset>
	  <duration>1000</duration>
	  <rate>0.8</rate>
	  <end>251000</end> 
	  
  </InjectionStim>



    <!-- onset and duration are times measured in milliseconds. The rate is in numbers of particles 
	 per millisecond -->


 



</StimulationSet>