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<?xml version="1.0" encoding="UTF-8"?>
<!--This biomodel was generated in VCML Version Rel_Version_7.4.0_build_34-1p-->
<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="Rel_Version_7.4.0_build_34-1p">
<BioModel Name="BioModel2">
<Model Name="model">
<Compound Name="s0" />
<Compound Name="s1" />
<Feature Name="c0" />
<LocalizedCompound Name="s0" CompoundRef="s0" Structure="c0" OverrideName="true" />
<LocalizedCompound Name="s1" CompoundRef="s1" Structure="c0" OverrideName="true" />
<SimpleReaction Structure="c0" Name="r0" Reversible="true" FluxOption="MolecularOnly">
<Reactant LocalizedCompoundRef="s0" Stoichiometry="1" />
<Product LocalizedCompoundRef="s1" Stoichiometry="1" />
<Kinetics KineticsType="MassAction">
<Parameter Name="J" Role="reaction rate" Unit="uM.s-1">((Kf * s0) - (Kr * s1))</Parameter>
<Parameter Name="Kf" Role="forward rate constant" Unit="s-1">1.0</Parameter>
<Parameter Name="Kr" Role="reverse rate constant" Unit="s-1">2.0</Parameter>
</Kinetics>
</SimpleReaction>
<Diagram Name="c0" Structure="c0">
<SimpleReactionShape NodeReferenceModeAttrTag="full" SimpleReactionRef="r0" LocationX="244" LocationY="128" />
<LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s0" LocationX="470" LocationY="220" />
<LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s1" LocationX="14" LocationY="34" />
<SimpleReactionShape NodeReferenceModeAttrTag="molecule" SimpleReactionRef="r0" LocationX="252" LocationY="102" />
<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s0" LocationX="144" LocationY="86" />
<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s1" LocationX="361" LocationY="118" />
</Diagram>
<ModelUnitSystem VolumeSubstanceUnit="uM.um3" MembraneSubstanceUnit="molecules" LumpedReactionSubstanceUnit="molecules" VolumeUnit="um3" AreaUnit="um2" LengthUnit="um" TimeUnit="s" />
</Model>
<SimulationSpec Name="Application0" Stochastic="false" UseConcentration="true" RuleBased="false" MassConservationModelReduction="false" InsufficientIterations="false" InsufficientMaxMolecules="false">
<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500" />
<Annotation></Annotation>
<Geometry Name="non-spatial" Dimension="0">
<Extent X="10.0" Y="10.0" Z="10.0" />
<Origin X="0.0" Y="0.0" Z="0.0" />
<SubVolume Name="Compartment" Handle="0" Type="Compartmental" />
</Geometry>
<GeometryContext>
<FeatureMapping Feature="c0" GeometryClass="Compartment" SubVolume="Compartment" Size="50000.0">
<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
</FeatureMapping>
</GeometryContext>
<ReactionContext>
<LocalizedCompoundSpec LocalizedCompoundRef="s0" ForceConstant="false" WellMixed="false" ForceContinuous="false">
<InitialConcentration>5.0</InitialConcentration>
<Diffusion>0.0</Diffusion>
</LocalizedCompoundSpec>
<LocalizedCompoundSpec LocalizedCompoundRef="s1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
<InitialConcentration>4.0</InitialConcentration>
<Diffusion>0.0</Diffusion>
</LocalizedCompoundSpec>
<ReactionSpec ReactionStepRef="r0" ReactionMapping="included" />
</ReactionContext>
<MathDescription Name="Application0_generated">
<Constant Name="_F_">96485.3321</Constant>
<Constant Name="_F_nmol_">9.64853321E-5</Constant>
<Constant Name="_K_GHK_">1.0E-9</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="K_millivolts_per_volt">1000.0</Constant>
<Constant Name="Kf">1.0</Constant>
<Constant Name="KMOLE">0.001660538783162726</Constant>
<Constant Name="Kr">2.0</Constant>
<Constant Name="s0_init_uM">5.0</Constant>
<Constant Name="s1_init_uM">4.0</Constant>
<Constant Name="Size_c0">50000.0</Constant>
<VolumeVariable Name="s0" Domain="Compartment" />
<VolumeVariable Name="s1" Domain="Compartment" />
<Function Name="J_r0" Domain="Compartment">((Kf * s0) - (Kr * s1))</Function>
<CompartmentSubDomain Name="Compartment">
<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" />
<OdeEquation Name="s0" SolutionType="Unknown">
<Rate> - J_r0</Rate>
<Initial>s0_init_uM</Initial>
</OdeEquation>
<OdeEquation Name="s1" SolutionType="Unknown">
<Rate>J_r0</Rate>
<Initial>s1_init_uM</Initial>
</OdeEquation>
</CompartmentSubDomain>
</MathDescription>
<Simulation Name="SimulationNominal">
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
<TimeBound StartTime="0.0" EndTime="2.0" />
<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
<OutputOptions KeepEvery="1" KeepAtMost="1000" />
<NumberProcessors>1</NumberProcessors>
</SolverTaskDescription>
<MathOverrides />
<Version Name="temp simulation" KeyValue="487586140" BranchId="1" Archived="1" Date="30-Nov-2022 12:21:03" FromVersionable="false">
<Owner Name="temp" Identifier="123" />
<GroupAccess Type="1" />
</Version>
</Simulation>
<Simulation Name="SimulationDataGen">
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
<TimeBound StartTime="0.0" EndTime="2.0" />
<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
<OutputOptions KeepEvery="1" KeepAtMost="1000" />
<NumberProcessors>1</NumberProcessors>
</SolverTaskDescription>
<MathOverrides>
<Constant Name="Kr">1.0</Constant>
<Constant Name="Kf">0.5</Constant>
<Constant Name="s0_init_uM">2.5</Constant>
</MathOverrides>
</Simulation>
<AnalysisTaskList>
<ParameterEstimationTask Name="DefaultTask">
<parameterMappingSpecList>
<parameterMappingSpec parameterReferenceAttribute="model.r0.Kf" lowLimit="0.1" highLimit="10.0" currentValue="0.2" selected="true" />
<parameterMappingSpec parameterReferenceAttribute="model.r0.Kr" lowLimit="0.2" highLimit="20.0" currentValue="0.3" selected="true" />
<parameterMappingSpec parameterReferenceAttribute="Application0.s0_scs.initConc" lowLimit="0.0" highLimit="20.0" currentValue="2.0" selected="true" />
<parameterMappingSpec parameterReferenceAttribute="Application0.s1_scs.initConc" lowLimit="0.0" highLimit="0.0" currentValue="0.0" selected="false" />
<parameterMappingSpec parameterReferenceAttribute="Application0.c0_mapping.Size" lowLimit="5000.0" highLimit="500000.0" currentValue="50000.0" selected="false" />
</parameterMappingSpecList>
<referenceData numRows="25" numColumns="2">
<dataColumnList>
<dataColumn Name="t" weight="1.0" />
<dataColumn Name="s1" weight="1.0" />
</dataColumnList>
<dataRowList>
<dataRow>0.0 4.0</dataRow>
<dataRow>1.6535399245133132E-4 3.9995453382905546</dataRow>
<dataRow>6.276635144329321E-4 3.998274743619277</dataRow>
<dataRow>0.0034306276215528586 3.990590010029197</dataRow>
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<dataRow>0.8462661539452475 2.681834033949502</dataRow>
<dataRow>0.9794988011683902 2.588513744615282</dataRow>
<dataRow>1.1127314483915325 2.5120980127515082</dataRow>
<dataRow>1.2459640956146747 2.449524652625187</dataRow>
<dataRow>1.379196742837817 2.398286179857271</dataRow>
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<dataRow>1.7788946845072435 2.293839762543596</dataRow>
<dataRow>1.9121273317303857 2.270802918851185</dataRow>
<dataRow>2.0 2.257942965982347</dataRow>
</dataRowList>
</referenceData>
<referenceDataMappingSpecList>
<referenceDataMappingSpec referenceDataColumnName="t" referenceDataModelSymbol="t" />
<referenceDataMappingSpec referenceDataColumnName="s1" referenceDataModelSymbol="s1" />
</referenceDataMappingSpecList>
<optimizationSolverSpec optimizationSolverType="Evolutionary Programming" NumOfRuns="1">
<ListOfParameters>
<Parameter Name="Number of Generations" Value="200.0" />
<Parameter Name="Population Size" Value="20.0" />
<Parameter Name="Random Number Generator" Value="1.0" />
<Parameter Name="Seed" Value="3.0" />
</ListOfParameters>
</optimizationSolverSpec>
</ParameterEstimationTask>
</AnalysisTaskList>
<MicroscopeMeasurement Name="fluor">
<ConvolutionKernel Type="ProjectionZKernel" />
</MicroscopeMeasurement>
</SimulationSpec>
<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>