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<?xml version="1.0" encoding="UTF-8"?>
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<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="DanDev_Version_7.0_build_99">
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<BioModel Name="___SpringSalad_SolverSuite">
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<Annotation>cloned from '___SpringSalad_SolverSuite' owned by user schaff</Annotation>
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<Model Name="model">
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<Annotation>cloned from 'model' owned by user schaff</Annotation>
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<Compound Name="s0" />
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<Compound Name="s1" />
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<Feature Name="Extracellular" KeyValue="264839547" />
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<Feature Name="Intracellular" KeyValue="264839549" />
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<Membrane MembraneVoltage="Voltage_Membrane" Name="Membrane" KeyValue="264839551" />
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<LocalizedCompound Name="MT0" CompoundRef="s0" Structure="Intracellular" OverrideName="true" KeyValue="264839553">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT0" />
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<ComponentPattern MolecularComponent="Site0" ComponentStatePattern="state0" BondType="-" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</LocalizedCompound>
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<LocalizedCompound Name="MT1" CompoundRef="s1" Structure="Intracellular" OverrideName="true" KeyValue="264839554">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT1" />
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<ComponentPattern MolecularComponent="Site0" ComponentStatePattern="state0" BondType="-" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</LocalizedCompound>
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<RbmModelContainer>
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<MolecularTypeList>
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<MolecularType Name="MT0" AnchorAll="true">
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<MolecularComponent Name="Site0" Index="1">
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<AllowableState Name="state0" />
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</MolecularComponent>
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</MolecularType>
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<MolecularType Name="MT1" AnchorAll="true">
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<MolecularComponent Name="Site0" Index="1">
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<AllowableState Name="state0" />
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</MolecularComponent>
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</MolecularType>
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</MolecularTypeList>
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<RbmObservableList>
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<Observable Name="O0_MT0_tot" ObservableType="Molecules" Sequence="Multimolecular" LengthEqual="2" LengthGreater="1" Structure="Intracellular">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT0" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="?" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</Observable>
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<Observable Name="O0_MT1_tot" ObservableType="Molecules" Sequence="Multimolecular" LengthEqual="2" LengthGreater="1" Structure="Intracellular">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT1" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="?" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</Observable>
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</RbmObservableList>
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<ReactionRuleList>
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<ReactionRule Name="r0" Structure="Intracellular" ReactionRuleLabel="r0" ReactionRuleReversible="true">
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<ReactantPatternsList>
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<ReactantPattern Structure="Intracellular">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT0" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="-" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</ReactantPattern>
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<ReactantPattern Structure="Intracellular">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT1" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="-" />
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</MolecularTypePattern>
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</SpeciesPattern>
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</ReactantPattern>
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</ReactantPatternsList>
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<ProductPatternsList>
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<ProductPattern Structure="Intracellular">
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<SpeciesPattern>
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<MolecularTypePattern Index="1">
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<MolecularType Name="MT0" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="1">
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<Bond MolecularTypePattern="MT1" ComponentPattern="Site0" />
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</ComponentPattern>
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</MolecularTypePattern>
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<MolecularTypePattern Index="2">
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<MolecularType Name="MT1" />
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<ComponentPattern MolecularComponent="Site0" Any="true" BondType="1">
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<Bond MolecularTypePattern="MT0" ComponentPattern="Site0" />
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</ComponentPattern>
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</MolecularTypePattern>
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</SpeciesPattern>
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</ProductPattern>
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</ProductPatternsList>
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<Kinetics KineticsType="MassAction">
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<Parameter Name="ruleRate" Role="RuleRate" Unit="uM.s-1" />
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<Parameter Name="Kf" Role="MassActionKf" Unit="s-1.uM-1">200.0</Parameter>
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<Parameter Name="Kr" Role="MassActionKr" Unit="s-1">0.0</Parameter>
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</Kinetics>
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</ReactionRule>
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</ReactionRuleList>
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</RbmModelContainer>
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<Diagram Name="c1" Structure="Extracellular">
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT1" LocationX="170" LocationY="34" />
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<ReactionRuleShapeTag NodeReferenceModeAttrTag="molecule" ReactionRuleRef2AttrTag="r0" LocationX="93" LocationY="162" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT0" LocationX="14" LocationY="220" />
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</Diagram>
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<Diagram Name="m0" Structure="Membrane">
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT1" LocationX="170" LocationY="34" />
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<ReactionRuleShapeTag NodeReferenceModeAttrTag="molecule" ReactionRuleRef2AttrTag="r0" LocationX="93" LocationY="162" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT0" LocationX="14" LocationY="220" />
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</Diagram>
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<Diagram Name="c0" Structure="Intracellular">
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<RuleParticipantShortShapeTag NodeReferenceModeAttrTag="molecule" RuleParticipantRefAttrTag="MT0(Site0!1).MT1(Site0!1)" LocationX="55" LocationY="132" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT1" LocationX="170" LocationY="34" />
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<ReactionRuleShapeTag NodeReferenceModeAttrTag="molecule" ReactionRuleRef2AttrTag="r0" LocationX="93" LocationY="162" />
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<RuleParticipantShortShapeTag NodeReferenceModeAttrTag="molecule" RuleParticipantRefAttrTag="MT0(Site0)" LocationX="107" LocationY="196" />
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<RuleParticipantShortShapeTag NodeReferenceModeAttrTag="molecule" RuleParticipantRefAttrTag="MT1(Site0)" LocationX="120" LocationY="132" />
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<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="MT0" LocationX="14" LocationY="220" />
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</Diagram>
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<Version Name="model" KeyValue="264839543" BranchId="264837076" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
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<Owner Name="danv" Identifier="26766043" />
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<GroupAccess Type="1" />
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<Annotation>cloned from 'model' owned by user schaff</Annotation>
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</Version>
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<ModelUnitSystem VolumeSubstanceUnit="uM.um3" MembraneSubstanceUnit="molecules" LumpedReactionSubstanceUnit="molecules" VolumeUnit="um3" AreaUnit="um2" LengthUnit="um" TimeUnit="s" />
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</Model>
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<SimulationSpec Name="Application0" Stochastic="false" UseConcentration="true" SpringSaLaD="false" RuleBased="true" RandomizeInitCondition="false" MassConservationModelReduction="false" InsufficientIterations="false" InsufficientMaxMolecules="false">
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<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500">
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<MaxStoichiometry MolecularType="MT0" Integer="100" />
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<MaxStoichiometry MolecularType="MT1" Integer="100" />
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</NetworkConstraints>
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<Annotation>cloned from 'Application0' owned by user schaff</Annotation>
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<Geometry Name="non-spatial365807313" Dimension="0">
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<Annotation>cloned from 'non-spatial365807313' owned by user schaff</Annotation>
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<Extent X="10.0" Y="10.0" Z="10.0" />
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<Origin X="0.0" Y="0.0" Z="0.0" />
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<SubVolume Name="Compartment" Handle="0" Type="Compartmental" KeyValue="264837041" />
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<Version Name="non-spatial365807313" KeyValue="264837037" BranchId="264837038" Archived="0" Date="19-Dec-2023 14:35:25" FromVersionable="false">
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<Owner Name="danv" Identifier="26766043" />
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<GroupAccess Type="1" />
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<Annotation>cloned from 'non-spatial365807313' owned by user schaff</Annotation>
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</Version>
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</Geometry>
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<GeometryContext>
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<FeatureMapping Feature="Extracellular" GeometryClass="Compartment" SubVolume="Compartment" Size="5.0">
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<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
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</FeatureMapping>
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<FeatureMapping Feature="Intracellular" GeometryClass="Compartment" SubVolume="Compartment" Size="50.0">
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<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
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</FeatureMapping>
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<MembraneMapping Membrane="Membrane" Size="6.0" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" GeometryClass="Compartment">
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<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
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</MembraneMapping>
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</GeometryContext>
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<ReactionContext>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT0" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>1.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>2.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<ReactionRuleSpecs>
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<ReactionRuleSpec ReactionRuleRef="r0" ReactionRuleMapping="included" />
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</ReactionRuleSpecs>
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</ReactionContext>
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<MathDescription Name="Application0_generated">
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<Annotation>cloned from 'Application0_generated' owned by user schaff</Annotation>
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<ParticleMolecularType Name="MT0">
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<Component Name="Site0">
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<AllowableState Name="state0" />
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</Component>
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</ParticleMolecularType>
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<ParticleMolecularType Name="MT1">
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<Component Name="Site0">
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<AllowableState Name="state0" />
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</Component>
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</ParticleMolecularType>
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="Kf">200.0</Constant>
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr">0.0</Constant>
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<Constant Name="MT0_Count_init_uM">1.0</Constant>
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<Constant Name="MT1_Count_init_uM">2.0</Constant>
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<Constant Name="Size_Extracellular">5.0</Constant>
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<Constant Name="Size_Intracellular">50.0</Constant>
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<Constant Name="Size_Membrane">6.0</Constant>
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<Constant Name="UnitFactor_molecules_uM_neg_1_um_neg_3">(1.0 * pow(KMOLE, - 1.0))</Constant>
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<Constant Name="UnitFactor_uM_um3_molecules_neg_1">(1.0 * pow(KMOLE,1.0))</Constant>
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<Constant Name="Voltage_Membrane">0.0</Constant>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern0" Domain="Compartment">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="?" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern1" Domain="Compartment">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="?" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern2" Domain="Compartment">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern3" Domain="Compartment">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern4" Domain="Compartment">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="1" />
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</MolecularType>
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="1" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern5" Domain="Compartment">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="state0" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern6" Domain="Compartment">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="state0" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleObservable Name="MT0_Count" Domain="Compartment" MolecularType="Species" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern5" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="MT1_Count" Domain="Compartment" MolecularType="Species" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern6" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="O0_MT0_tot_Count" Domain="Compartment" MolecularType="Molecules" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern0" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="O0_MT1_tot_Count" Domain="Compartment" MolecularType="Molecules" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern1" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<Function Name="MT0" Domain="Compartment">((MT0_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="MT0_Count_initCount" Domain="Compartment">(Size_Intracellular * MT0_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
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<Function Name="MT1" Domain="Compartment">((MT1_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="MT1_Count_initCount" Domain="Compartment">(Size_Intracellular * MT1_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
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<Function Name="O0_MT0_tot" Domain="Compartment">((O0_MT0_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="O0_MT1_tot" Domain="Compartment">((O0_MT1_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="P_r0_probabilityRate" Domain="Compartment">((UnitFactor_uM_um3_molecules_neg_1 * Kf) / Size_Intracellular)</Function>
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<Function Name="P_r0_reverse_probabilityRate" Domain="Compartment">Kr</Function>
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<CompartmentSubDomain Name="Compartment">
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<BoundaryType Boundary="Xm" Type="Value" />
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<BoundaryType Boundary="Xp" Type="Value" />
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<BoundaryType Boundary="Ym" Type="Value" />
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<BoundaryType Boundary="Yp" Type="Value" />
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<BoundaryType Boundary="Zm" Type="Value" />
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<BoundaryType Boundary="Zp" Type="Value" />
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<ParticleJumpProcess Name="r0" ProcessSymmetryFactor="1.0">
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<SelectedParticle Name="speciesPattern2" />
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<SelectedParticle Name="speciesPattern3" />
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<MacroscopicRateConstant>P_r0_probabilityRate</MacroscopicRateConstant>
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<Effect VarName="speciesPattern2" Operation="destroy" />
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<Effect VarName="speciesPattern3" Operation="destroy" />
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<Effect VarName="speciesPattern4" Operation="create" />
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</ParticleJumpProcess>
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<ParticleJumpProcess Name="r0_reverse" ProcessSymmetryFactor="1.0">
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<SelectedParticle Name="speciesPattern4" />
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<MacroscopicRateConstant>P_r0_reverse_probabilityRate</MacroscopicRateConstant>
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<Effect VarName="speciesPattern2" Operation="create" />
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<Effect VarName="speciesPattern3" Operation="create" />
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<Effect VarName="speciesPattern4" Operation="destroy" />
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</ParticleJumpProcess>
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<ParticleProperties Name="speciesPattern5">
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<ParticleInitialCount>
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<ParticleCount>MT0_Count_initCount</ParticleCount>
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<ParticleLocationX>0.0</ParticleLocationX>
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<ParticleLocationY>u</ParticleLocationY>
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<ParticleLocationZ>u</ParticleLocationZ>
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</ParticleInitialCount>
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<ParticleDiffusion>0.0</ParticleDiffusion>
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<ParticleDriftX>0.0</ParticleDriftX>
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<ParticleDriftY>0.0</ParticleDriftY>
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<ParticleDriftZ>0.0</ParticleDriftZ>
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</ParticleProperties>
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<ParticleProperties Name="speciesPattern6">
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<ParticleInitialCount>
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<ParticleCount>MT1_Count_initCount</ParticleCount>
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<ParticleLocationX>0.0</ParticleLocationX>
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<ParticleLocationY>u</ParticleLocationY>
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<ParticleLocationZ>u</ParticleLocationZ>
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</ParticleInitialCount>
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<ParticleDiffusion>0.0</ParticleDiffusion>
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<ParticleDriftX>0.0</ParticleDriftX>
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<ParticleDriftY>0.0</ParticleDriftY>
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|
|
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<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500">
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<MaxStoichiometry MolecularType="MT0" Integer="100" />
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<ReactionContext>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT0" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>1.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>2.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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<ReactionRuleSpec ReactionRuleRef="r0" ReactionRuleMapping="included" />
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</ReactionRuleSpecs>
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<MathDescription Name="Copy of Application0_generated">
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<Annotation>cloned from 'Copy of Application0_generated' owned by user schaff</Annotation>
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_K_GHK_">1.0E-9</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="K_millivolts_per_volt">1000.0</Constant>
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<Constant Name="Kf">200.0</Constant>
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr">0.0</Constant>
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<Constant Name="MT0_init_uM">1.0</Constant>
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<Constant Name="MT1_init_uM">2.0</Constant>
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<Constant Name="s2_init_uM">0.0</Constant>
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<Constant Name="Size_Extracellular">5.0</Constant>
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<Constant Name="Size_Intracellular">50.0</Constant>
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<Constant Name="Size_Membrane">6.0</Constant>
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<Constant Name="Voltage_Membrane">0.0</Constant>
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<VolumeVariable Name="MT0" Domain="Compartment" />
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<VolumeVariable Name="MT1" Domain="Compartment" />
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<VolumeVariable Name="s2" Domain="Compartment" />
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<Function Name="J_r0_DirectHalf" Domain="Compartment">(((Kf * MT0) * MT1) - (Kr * s2))</Function>
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<Function Name="O0_MT0_tot">(MT0 + s2)</Function>
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<Function Name="O0_MT1_tot">(MT1 + s2)</Function>
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<CompartmentSubDomain Name="Compartment">
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<BoundaryType Boundary="Xm" Type="Value" />
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<BoundaryType Boundary="Xp" Type="Value" />
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<BoundaryType Boundary="Yp" Type="Value" />
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<BoundaryType Boundary="Zm" Type="Value" />
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<BoundaryType Boundary="Zp" Type="Value" />
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<OdeEquation Name="MT0" SolutionType="Unknown">
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<Rate>- J_r0_DirectHalf</Rate>
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<Initial>MT0_init_uM</Initial>
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</OdeEquation>
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<OdeEquation Name="MT1" SolutionType="Unknown">
|
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<Rate>- J_r0_DirectHalf</Rate>
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<Initial>MT1_init_uM</Initial>
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</OdeEquation>
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<OdeEquation Name="s2" SolutionType="Unknown">
|
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<Rate>J_r0_DirectHalf</Rate>
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<Initial>s2_init_uM</Initial>
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</OdeEquation>
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</CompartmentSubDomain>
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<TimeBound StartTime="0.0" EndTime="0.01" />
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<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
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<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
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<OutputOptions KeepEvery="1" KeepAtMost="1000" />
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<NumberProcessors>1</NumberProcessors>
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<Version Name="Simulation5" KeyValue="264837129" BranchId="264837130" Archived="0" Date="19-Dec-2023 14:35:27" FromVersionable="false">
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(copied from Application0)</Annotation>
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</Version>
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<MicroscopeMeasurement Name="fluor">
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<ConvolutionKernel Type="ProjectionZKernel" />
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<SimulationSpec Name="Copy of Application0 1" Stochastic="true" UseConcentration="true" RandomizeInitCondition="false" SpringSaLaD="false" RuleBased="false" MassConservationModelReduction="false" InsufficientIterations="true" InsufficientMaxMolecules="false">
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<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500">
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<MaxStoichiometry MolecularType="MT0" Integer="100" />
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</FeatureMapping>
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<MembraneMapping Membrane="Membrane" Size="6.0" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" GeometryClass="Compartment">
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</MembraneMapping>
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</GeometryContext>
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<ReactionContext>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT0" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>1.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<LocalizedCompoundSpec LocalizedCompoundRef="MT1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
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<InitialConcentration>2.0</InitialConcentration>
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<Diffusion>0.0</Diffusion>
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</LocalizedCompoundSpec>
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<ReactionRuleSpecs>
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<ReactionRuleSpec ReactionRuleRef="r0" ReactionRuleMapping="included" />
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</ReactionRuleSpecs>
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</ReactionContext>
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<MathDescription Name="Copy of Application0 1_generated">
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<Annotation>cloned from 'Copy of Application0 1_generated' owned by user schaff</Annotation>
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
|
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="Kf">200.0</Constant>
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|
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr">0.0</Constant>
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<Constant Name="MT0_Count_init_uM">1.0</Constant>
|
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<Constant Name="MT1_Count_init_uM">2.0</Constant>
|
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<Constant Name="s2_Count_init_uM">0.0</Constant>
|
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<Constant Name="Size_Extracellular">5.0</Constant>
|
|
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<Constant Name="Size_Intracellular">50.0</Constant>
|
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<Constant Name="Size_Membrane">6.0</Constant>
|
|
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<Constant Name="UnitFactor_molecules_uM_neg_1_um_neg_3">(1.0 * pow(KMOLE, - 1.0))</Constant>
|
|
|
<Constant Name="UnitFactor_uM_um3_molecules_neg_1">(1.0 * pow(KMOLE,1.0))</Constant>
|
|
|
<Constant Name="Voltage_Membrane">0.0</Constant>
|
|
|
<StochasticVolumeVariable Name="MT0_Count" />
|
|
|
<StochasticVolumeVariable Name="MT1_Count" />
|
|
|
<StochasticVolumeVariable Name="s2_Count" />
|
|
|
<Function Name="J_r0_DirectHalf" Domain="Compartment">(((Kf * MT0) * MT1) - (Kr * s2))</Function>
|
|
|
<Function Name="MT0" Domain="Compartment">((MT0_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="MT0_Count_initCount" Domain="Compartment">(Size_Intracellular * MT0_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="MT1" Domain="Compartment">((MT1_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="MT1_Count_initCount" Domain="Compartment">(Size_Intracellular * MT1_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="O0_MT0_tot" Domain="Compartment">(MT0 + s2)</Function>
|
|
|
<Function Name="O0_MT0_tot_Count" Domain="Compartment">(O0_MT0_tot * Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="O0_MT1_tot" Domain="Compartment">(MT1 + s2)</Function>
|
|
|
<Function Name="O0_MT1_tot_Count" Domain="Compartment">(O0_MT1_tot * Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="P_r0_DirectHalf_probabilityRate" Domain="Compartment">(Kf * MT0_Count * MT1_Count * UnitFactor_molecules_uM_neg_1_um_neg_3 * UnitFactor_uM_um3_molecules_neg_1 * UnitFactor_uM_um3_molecules_neg_1 / Size_Intracellular)</Function>
|
|
|
<Function Name="P_r0_DirectHalf_reverse_probabilityRate" Domain="Compartment">(Kr * s2_Count * UnitFactor_molecules_uM_neg_1_um_neg_3 * UnitFactor_uM_um3_molecules_neg_1)</Function>
|
|
|
<Function Name="s2" Domain="Compartment">((UnitFactor_uM_um3_molecules_neg_1 * s2_Count) / Size_Intracellular)</Function>
|
|
|
<Function Name="s2_Count_initCount" Domain="Compartment">(Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3 * s2_Count_init_uM)</Function>
|
|
|
<CompartmentSubDomain Name="Compartment">
|
|
|
<BoundaryType Boundary="Xm" Type="Value" />
|
|
|
<BoundaryType Boundary="Xp" Type="Value" />
|
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|
<BoundaryType Boundary="Ym" Type="Value" />
|
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|
<BoundaryType Boundary="Yp" Type="Value" />
|
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|
<BoundaryType Boundary="Zm" Type="Value" />
|
|
|
<BoundaryType Boundary="Zp" Type="Value" />
|
|
|
<VariableInitialCount Name="MT0_Count">MT0_Count_initCount</VariableInitialCount>
|
|
|
<VariableInitialCount Name="MT1_Count">MT1_Count_initCount</VariableInitialCount>
|
|
|
<VariableInitialCount Name="s2_Count">s2_Count_initCount</VariableInitialCount>
|
|
|
<JumpProcess Name="r0_DirectHalf">
|
|
|
<ProbabilityRate>P_r0_DirectHalf_probabilityRate</ProbabilityRate>
|
|
|
<Effect VarName="MT0_Count" Operation="inc">-1.0</Effect>
|
|
|
<Effect VarName="MT1_Count" Operation="inc">-1.0</Effect>
|
|
|
<Effect VarName="s2_Count" Operation="inc">1.0</Effect>
|
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</JumpProcess>
|
|
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<JumpProcess Name="r0_DirectHalf_reverse">
|
|
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<ProbabilityRate>P_r0_DirectHalf_reverse_probabilityRate</ProbabilityRate>
|
|
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<Effect VarName="MT0_Count" Operation="inc">1.0</Effect>
|
|
|
<Effect VarName="MT1_Count" Operation="inc">1.0</Effect>
|
|
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<Effect VarName="s2_Count" Operation="inc">-1.0</Effect>
|
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</JumpProcess>
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</CompartmentSubDomain>
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<Version Name="Copy of Application0 1_generated" KeyValue="264837069" BranchId="264837070" Archived="0" Date="19-Dec-2023 14:35:26" FromVersionable="false">
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<Annotation>cloned from 'Copy of Application0 1_generated' owned by user schaff</Annotation>
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</Version>
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</MathDescription>
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<Simulation Name="Simulation6">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Gibson (Next Reaction Stochastic Method)">
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<TimeBound StartTime="0.0" EndTime="0.01" />
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<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
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<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-8" />
|
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<StochSimOptions UseCustomSeed="false" NumberOfTrial="1" Histogram="false" />
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<OutputOptions OutputTimeStep="5.0E-4" />
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<NumberProcessors>1</NumberProcessors>
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</SolverTaskDescription>
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<MathOverrides />
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<Version Name="Simulation6" KeyValue="264837132" BranchId="264837133" Archived="0" Date="19-Dec-2023 14:35:27" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
</Version>
|
|
|
</Simulation>
|
|
|
<Version Name="Copy of Application0 1" KeyValue="264839572" BranchId="264837108" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
<Annotation>cloned from 'Copy of Application0 1' owned by user schaff
|
|
|
(copied from Application0)</Annotation>
|
|
|
</Version>
|
|
|
<MicroscopeMeasurement Name="fluor">
|
|
|
<ConvolutionKernel Type="ProjectionZKernel" />
|
|
|
</MicroscopeMeasurement>
|
|
|
</SimulationSpec>
|
|
|
<SimulationSpec Name="Application2" Stochastic="false" UseConcentration="true" SpringSaLaD="true" RuleBased="false" MassConservationModelReduction="false" InsufficientIterations="false" InsufficientMaxMolecules="false" CharacteristicSize="5.201580382836481E-4">
|
|
|
<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500">
|
|
|
<MaxStoichiometry MolecularType="MT0" Integer="100" />
|
|
|
<MaxStoichiometry MolecularType="MT1" Integer="100" />
|
|
|
</NetworkConstraints>
|
|
|
<Annotation />
|
|
|
<Geometry Name="spatial1186592510" Dimension="3">
|
|
|
<Extent X="0.1" Y="0.1" Z="0.1" />
|
|
|
<Origin X="0.0" Y="0.0" Z="0.0" />
|
|
|
<SubVolume Name="Intracellular" Handle="0" Type="Analytical" KeyValue="264837056">
|
|
|
<AnalyticExpression>(z < 0.09)</AnalyticExpression>
|
|
|
</SubVolume>
|
|
|
<SubVolume Name="Extracellular" Handle="1" Type="Analytical" KeyValue="264837057">
|
|
|
<AnalyticExpression>0.1</AnalyticExpression>
|
|
|
</SubVolume>
|
|
|
<SurfaceClass Name="Extracellular_Intracellular_membrane" SubVolume1Ref="Extracellular" SubVolume2Ref="Intracellular" KeyValue="264837058" />
|
|
|
<SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="101" CutoffFrequency="0.3">
|
|
|
<VolumeRegion Name="Intracellular0" RegionID="0" SubVolume="Intracellular" Size="8.949999999999999E-4" Unit="um3" />
|
|
|
<VolumeRegion Name="Extracellular1" RegionID="1" SubVolume="Extracellular" Size="1.0499999999999999E-4" Unit="um3" />
|
|
|
<MembraneRegion Name="membrane_Intracellular0_Extracellular1" VolumeRegion1="Extracellular1" VolumeRegion2="Intracellular0" Size="0.009999999999999827" Unit="um2" />
|
|
|
</SurfaceDescription>
|
|
|
<Version Name="spatial1186592510" KeyValue="264837052" BranchId="264837053" Archived="0" Date="19-Dec-2023 14:35:26" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
</Version>
|
|
|
</Geometry>
|
|
|
<GeometryContext>
|
|
|
<FeatureMapping Feature="Extracellular" GeometryClass="Extracellular" SubVolume="Extracellular" Size="50000.0" VolumePerUnitVolume="1.0">
|
|
|
<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
|
|
|
</FeatureMapping>
|
|
|
<FeatureMapping Feature="Intracellular" GeometryClass="Intracellular" SubVolume="Intracellular" Size="50000.0" VolumePerUnitVolume="1.0">
|
|
|
<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
|
|
|
</FeatureMapping>
|
|
|
<MembraneMapping Membrane="Membrane" Size="6563.0" AreaPerUnitArea="1.0" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" GeometryClass="Extracellular_Intracellular_membrane">
|
|
|
<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
|
|
|
</MembraneMapping>
|
|
|
</GeometryContext>
|
|
|
<ReactionContext>
|
|
|
<LocalizedCompoundSpec LocalizedCompoundRef="MT0" ForceConstant="false" WellMixed="false" ForceContinuous="false">
|
|
|
<InitialConcentration>1.2E-6</InitialConcentration>
|
|
|
<SiteAttributesSpec SiteRef="Site0" MoleculeRef="MT0" SiteLocationRef="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" SiteRadius="1.0" SiteDiffusion="1.0" SiteColor="RED" />
|
|
|
</LocalizedCompoundSpec>
|
|
|
<LocalizedCompoundSpec LocalizedCompoundRef="MT1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
|
|
|
<InitialConcentration>1.0E-6</InitialConcentration>
|
|
|
<SiteAttributesSpec SiteRef="Site0" MoleculeRef="MT1" SiteLocationRef="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" SiteRadius="1.0" SiteDiffusion="1.0" SiteColor="RED" />
|
|
|
</LocalizedCompoundSpec>
|
|
|
<ReactionRuleSpecs>
|
|
|
<ReactionRuleSpec ReactionRuleRef="r0" ReactionRuleMapping="included" SubType="Binding" BondLength="1.0" />
|
|
|
</ReactionRuleSpecs>
|
|
|
</ReactionContext>
|
|
|
<MathDescription Name="Application2_generated">
|
|
|
<LangevinParticleMolecularType Name="MT0">
|
|
|
<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="RED">
|
|
|
<AllowableState Name="state0" />
|
|
|
</Component>
|
|
|
</LangevinParticleMolecularType>
|
|
|
<LangevinParticleMolecularType Name="MT1">
|
|
|
<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="BLUE">
|
|
|
<AllowableState Name="state0" />
|
|
|
</Component>
|
|
|
</LangevinParticleMolecularType>
|
|
|
<Constant Name="_F_">96485.3321</Constant>
|
|
|
<Constant Name="_F_nmol_">9.64853321E-5</Constant>
|
|
|
<Constant Name="_N_pmol_">6.02214179E11</Constant>
|
|
|
<Constant Name="_PI_">3.141592653589793</Constant>
|
|
|
<Constant Name="_R_">8314.46261815</Constant>
|
|
|
<Constant Name="_T_">300.0</Constant>
|
|
|
<Constant Name="Kf">200.0</Constant>
|
|
|
<Constant Name="KMOLE">0.001660538783162726</Constant>
|
|
|
<Constant Name="Kr">0.0</Constant>
|
|
|
<Constant Name="MT0_Count_init_uM">1.2E-6</Constant>
|
|
|
<Constant Name="MT1_Count_init_uM">1.0E-6</Constant>
|
|
|
<Constant Name="Size_Extracellular">50000.0</Constant>
|
|
|
<Constant Name="Size_Intracellular">50000.0</Constant>
|
|
|
<Constant Name="Size_Membrane">6563.0</Constant>
|
|
|
<Constant Name="UnitFactor_molecules_uM_neg_1_um_neg_3">(1.0 * pow(KMOLE, - 1.0))</Constant>
|
|
|
<Constant Name="UnitFactor_uM_um3_molecules_neg_1">(1.0 * pow(KMOLE,1.0))</Constant>
|
|
|
<Constant Name="Voltage_Membrane">0.0</Constant>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern0" Domain="Intracellular">
|
|
|
<MolecularType Name="MT0" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="?" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern1" Domain="Intracellular">
|
|
|
<MolecularType Name="MT1" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="?" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern2" Domain="Intracellular">
|
|
|
<MolecularType Name="MT0" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="-" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern3" Domain="Intracellular">
|
|
|
<MolecularType Name="MT1" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="-" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern4" Domain="Intracellular">
|
|
|
<MolecularType Name="MT0" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="1" />
|
|
|
</MolecularType>
|
|
|
<MolecularType Name="MT1" MatchLabel="*">
|
|
|
<Component Name="Site0" State="*" Bond="1" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern5" Domain="Intracellular">
|
|
|
<MolecularType Name="MT0" MatchLabel="*">
|
|
|
<Component Name="Site0" State="state0" Bond="-" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern6" Domain="Intracellular">
|
|
|
<MolecularType Name="MT1" MatchLabel="*">
|
|
|
<Component Name="Site0" State="state0" Bond="-" />
|
|
|
</MolecularType>
|
|
|
</VolumeParticleSpeciesPattern>
|
|
|
<VolumeParticleObservable Name="MT0_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
|
|
|
<VolumeParticleSpeciesPatterns>
|
|
|
<VolumeParticleSpeciesPattern Name="speciesPattern5" />
|
|
|
</VolumeParticleSpeciesPatterns>
|
|
|
</VolumeParticleObservable>
|
|
|
<VolumeParticleObservable Name="MT1_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
|
|
|
<VolumeParticleSpeciesPatterns>
|
|
|
<VolumeParticleSpeciesPattern Name="speciesPattern6" />
|
|
|
</VolumeParticleSpeciesPatterns>
|
|
|
</VolumeParticleObservable>
|
|
|
<VolumeParticleObservable Name="O0_MT0_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
|
|
|
<VolumeParticleSpeciesPatterns>
|
|
|
<VolumeParticleSpeciesPattern Name="speciesPattern0" />
|
|
|
</VolumeParticleSpeciesPatterns>
|
|
|
</VolumeParticleObservable>
|
|
|
<VolumeParticleObservable Name="O0_MT1_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
|
|
|
<VolumeParticleSpeciesPatterns>
|
|
|
<VolumeParticleSpeciesPattern Name="speciesPattern1" />
|
|
|
</VolumeParticleSpeciesPatterns>
|
|
|
</VolumeParticleObservable>
|
|
|
<Function Name="MT0" Domain="Intracellular">((MT0_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="MT0_Count_initCount" Domain="Intracellular">(Size_Intracellular * MT0_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="MT1" Domain="Intracellular">((MT1_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="MT1_Count_initCount" Domain="Intracellular">(Size_Intracellular * MT1_Count_init_uM * UnitFactor_molecules_uM_neg_1_um_neg_3)</Function>
|
|
|
<Function Name="O0_MT0_tot" Domain="Intracellular">((O0_MT0_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="O0_MT1_tot" Domain="Intracellular">((O0_MT1_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
|
|
|
<Function Name="P_r0_probabilityRate" Domain="Intracellular">Kf</Function>
|
|
|
<Function Name="P_r0_reverse_probabilityRate" Domain="Intracellular">Kr</Function>
|
|
|
<CompartmentSubDomain Name="Intracellular">
|
|
|
<BoundaryType Boundary="Xm" Type="Flux" />
|
|
|
<BoundaryType Boundary="Xp" Type="Flux" />
|
|
|
<BoundaryType Boundary="Ym" Type="Flux" />
|
|
|
<BoundaryType Boundary="Yp" Type="Flux" />
|
|
|
<BoundaryType Boundary="Zm" Type="Flux" />
|
|
|
<BoundaryType Boundary="Zp" Type="Flux" />
|
|
|
<LangevinParticleJumpProcess Name="r0" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
|
|
|
<SelectedParticle Name="speciesPattern2" />
|
|
|
<SelectedParticle Name="speciesPattern3" />
|
|
|
<MacroscopicRateConstant>P_r0_probabilityRate</MacroscopicRateConstant>
|
|
|
<Effect VarName="speciesPattern2" Operation="destroy" />
|
|
|
<Effect VarName="speciesPattern3" Operation="destroy" />
|
|
|
<Effect VarName="speciesPattern4" Operation="create" />
|
|
|
</LangevinParticleJumpProcess>
|
|
|
<LangevinParticleJumpProcess Name="r0_reverse" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
|
|
|
<SelectedParticle Name="speciesPattern4" />
|
|
|
<MacroscopicRateConstant>P_r0_reverse_probabilityRate</MacroscopicRateConstant>
|
|
|
<Effect VarName="speciesPattern2" Operation="create" />
|
|
|
<Effect VarName="speciesPattern3" Operation="create" />
|
|
|
<Effect VarName="speciesPattern4" Operation="destroy" />
|
|
|
</LangevinParticleJumpProcess>
|
|
|
<ParticleProperties Name="speciesPattern5">
|
|
|
<ParticleInitialCount>
|
|
|
<ParticleCount>MT0_Count_initCount</ParticleCount>
|
|
|
<ParticleLocationX>0.0</ParticleLocationX>
|
|
|
<ParticleLocationY>0.0</ParticleLocationY>
|
|
|
<ParticleLocationZ>0.0</ParticleLocationZ>
|
|
|
</ParticleInitialCount>
|
|
|
<ParticleDiffusion>0.0</ParticleDiffusion>
|
|
|
<ParticleDriftX>0.0</ParticleDriftX>
|
|
|
<ParticleDriftY>0.0</ParticleDriftY>
|
|
|
<ParticleDriftZ>0.0</ParticleDriftZ>
|
|
|
</ParticleProperties>
|
|
|
<ParticleProperties Name="speciesPattern6">
|
|
|
<ParticleInitialCount>
|
|
|
<ParticleCount>MT1_Count_initCount</ParticleCount>
|
|
|
<ParticleLocationX>0.0</ParticleLocationX>
|
|
|
<ParticleLocationY>0.0</ParticleLocationY>
|
|
|
<ParticleLocationZ>0.0</ParticleLocationZ>
|
|
|
</ParticleInitialCount>
|
|
|
<ParticleDiffusion>0.0</ParticleDiffusion>
|
|
|
<ParticleDriftX>0.0</ParticleDriftX>
|
|
|
<ParticleDriftY>0.0</ParticleDriftY>
|
|
|
<ParticleDriftZ>0.0</ParticleDriftZ>
|
|
|
</ParticleProperties>
|
|
|
</CompartmentSubDomain>
|
|
|
<CompartmentSubDomain Name="Extracellular">
|
|
|
<BoundaryType Boundary="Xm" Type="Flux" />
|
|
|
<BoundaryType Boundary="Xp" Type="Flux" />
|
|
|
<BoundaryType Boundary="Ym" Type="Flux" />
|
|
|
<BoundaryType Boundary="Yp" Type="Flux" />
|
|
|
<BoundaryType Boundary="Zm" Type="Flux" />
|
|
|
<BoundaryType Boundary="Zp" Type="Flux" />
|
|
|
</CompartmentSubDomain>
|
|
|
<MembraneSubDomain Name="Extracellular_Intracellular_membrane" InsideCompartment="Extracellular" OutsideCompartment="Intracellular">
|
|
|
<BoundaryType Boundary="Xm" Type="Value" />
|
|
|
<BoundaryType Boundary="Xp" Type="Value" />
|
|
|
<BoundaryType Boundary="Ym" Type="Value" />
|
|
|
<BoundaryType Boundary="Yp" Type="Value" />
|
|
|
<BoundaryType Boundary="Zm" Type="Value" />
|
|
|
<BoundaryType Boundary="Zp" Type="Value" />
|
|
|
</MembraneSubDomain>
|
|
|
<Version Name="Application2_generated" KeyValue="264839541" BranchId="264837073" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
</Version>
|
|
|
</MathDescription>
|
|
|
<Simulation Name="Simulation4">
|
|
|
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Langevin">
|
|
|
<TimeBound StartTime="0.0" EndTime="0.01" />
|
|
|
<TimeStep DefaultTime="1.0E-8" MinTime="1.0E-8" MaxTime="1.0" />
|
|
|
<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
|
|
|
<OutputOptions OutputTimeStep="1.0E-4" />
|
|
|
<LangevinSimulationOptions>
|
|
|
<NumOfTrials>1</NumOfTrials>
|
|
|
<IntervalSpring>1.0E-9</IntervalSpring>
|
|
|
<IntervalImage>1.0E-4</IntervalImage>
|
|
|
</LangevinSimulationOptions>
|
|
|
<NumberProcessors>1</NumberProcessors>
|
|
|
</SolverTaskDescription>
|
|
|
<MathOverrides />
|
|
|
<MeshSpecification>
|
|
|
<Size X="51" Y="51" Z="51" />
|
|
|
</MeshSpecification>
|
|
|
<Version Name="Simulation4" KeyValue="264839588" BranchId="264837136" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
</Version>
|
|
|
</Simulation>
|
|
|
<SpatialObjects>
|
|
|
<SpatialObject Name="vobj_Intracellular0" Type="Volume" subVolume="Intracellular" regionId="0">
|
|
|
<QuantityCategoryList>
|
|
|
<QuantityCategory Name="VolumeCentroid" Enabled="false" />
|
|
|
<QuantityCategory Name="InteriorVelocity" Enabled="false" />
|
|
|
<QuantityCategory Name="VolumeRegionSize" Enabled="true" />
|
|
|
</QuantityCategoryList>
|
|
|
</SpatialObject>
|
|
|
<SpatialObject Name="vobj_Extracellular1" Type="Volume" subVolume="Extracellular" regionId="1">
|
|
|
<QuantityCategoryList>
|
|
|
<QuantityCategory Name="VolumeCentroid" Enabled="false" />
|
|
|
<QuantityCategory Name="InteriorVelocity" Enabled="false" />
|
|
|
<QuantityCategory Name="VolumeRegionSize" Enabled="true" />
|
|
|
</QuantityCategoryList>
|
|
|
</SpatialObject>
|
|
|
<SpatialObject Name="sobj_Extracellular1_Intracellular0" Type="Surface" subVolumeInside="Extracellular" regionIdInside="1" subVolumeOutside="Intracellular" regionIdOutside="0">
|
|
|
<QuantityCategoryList>
|
|
|
<QuantityCategory Name="SurfaceNormal" Enabled="false" />
|
|
|
<QuantityCategory Name="SurfaceVelocity" Enabled="false" />
|
|
|
<QuantityCategory Name="DistanceToSurface" Enabled="false" />
|
|
|
<QuantityCategory Name="DirectionToSurface" Enabled="false" />
|
|
|
<QuantityCategory Name="SurfaceSize" Enabled="true" />
|
|
|
</QuantityCategoryList>
|
|
|
</SpatialObject>
|
|
|
</SpatialObjects>
|
|
|
<Version Name="Application2" KeyValue="264839579" BranchId="264837116" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
</Version>
|
|
|
<MicroscopeMeasurement Name="fluor">
|
|
|
<ConvolutionKernel Type="ProjectionZKernel" />
|
|
|
</MicroscopeMeasurement>
|
|
|
</SimulationSpec>
|
|
|
<Version Name="___SpringSalad_SolverSuite" KeyValue="264839590" BranchId="264837139" Archived="0" Date="19-Dec-2023 15:30:10" FromVersionable="false">
|
|
|
<Owner Name="danv" Identifier="26766043" />
|
|
|
<GroupAccess Type="1" />
|
|
|
<Annotation>cloned from '___SpringSalad_SolverSuite' owned by user schaff</Annotation>
|
|
|
</Version>
|
|
|
<pathwayModel>
|
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" version="3.0" />
|
|
|
</pathwayModel>
|
|
|
<relationshipModel>
|
|
|
<RMNS version="3.0" />
|
|
|
</relationshipModel>
|
|
|
<vcmetadata>
|
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" />
|
|
|
<nonrdfAnnotationList />
|
|
|
<uriBindingList />
|
|
|
</vcmetadata>
|
|
|
</BioModel>
|
|
|
</vcml>
|
|
|
|
|
|
|
