| <?xml version="1.0" encoding="UTF-8"?>
|
|
|
| <vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="Alpha_Version_7.7.0_build_15">
|
| <BioModel Name="TinySpacialProject_Application0">
|
| <Model Name="unnamed">
|
| <ModelParameters>
|
| <Parameter Name="Kf_r0" Role="user defined" Unit="s-1">1.0</Parameter>
|
| <Parameter Name="Kr_r0" Role="user defined" Unit="s-1">0.5</Parameter>
|
| </ModelParameters>
|
| <Compound Name="s0">
|
| <Annotation>s0</Annotation>
|
| </Compound>
|
| <Compound Name="s1">
|
| <Annotation>s1</Annotation>
|
| </Compound>
|
| <Feature Name="c0" />
|
| <LocalizedCompound Name="s0" SbmlName="s0" CompoundRef="s0" Structure="c0" OverrideName="true" />
|
| <LocalizedCompound Name="s1" SbmlName="s1" CompoundRef="s1" Structure="c0" OverrideName="true" />
|
| <SimpleReaction Structure="c0" Name="r0" Reversible="true" FluxOption="MolecularOnly" SbmlName="r0">
|
| <Reactant LocalizedCompoundRef="s0" Stoichiometry="1" />
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| <Product LocalizedCompoundRef="s1" Stoichiometry="1" />
|
| <Kinetics KineticsType="GeneralKinetics">
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| <Parameter Name="J" Role="reaction rate" Unit="umol.l-1.s-1">((Kf_r0 * s0) - (Kr_r0 * s1))</Parameter>
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| </Kinetics>
|
| </SimpleReaction>
|
| <Diagram Name="c0" Structure="c0">
|
| <LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s1" LocationX="470" LocationY="220" />
|
| <SimpleReactionShape NodeReferenceModeAttrTag="full" SimpleReactionRef="r0" LocationX="244" LocationY="129" />
|
| <LocalizedCompoundShape NodeReferenceModeAttrTag="full" LocalizedCompoundRef="s0" LocationX="14" LocationY="34" />
|
| </Diagram>
|
| <ModelUnitSystem VolumeSubstanceUnit="umol" MembraneSubstanceUnit="umol" LumpedReactionSubstanceUnit="umol" VolumeUnit="l" AreaUnit="dm2" LengthUnit="dm" TimeUnit="s" />
|
| </Model>
|
| <SimulationSpec Name="unnamed_spatialGeom" Stochastic="false" UseConcentration="true" SpringSaLaD="false" RuleBased="false" MassConservationModelReduction="false" InsufficientIterations="false" InsufficientMaxMolecules="false" CharacteristicSize="0.021090187684898395">
|
| <NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800" RbmReactionsLimit="2500" />
|
| <Annotation />
|
| <Geometry Name="spatialGeom" Dimension="1">
|
| <Extent X="10.0" Y="1.0" Z="1.0" />
|
| <Origin X="0.0" Y="0.0" Z="0.0" />
|
| <SubVolume Name="subdomain0" Handle="0" Type="Analytical">
|
| <AnalyticExpression>1.0</AnalyticExpression>
|
| </SubVolume>
|
| <SurfaceDescription NumSamplesX="50" NumSamplesY="1" NumSamplesZ="1" CutoffFrequency="0.3">
|
| <VolumeRegion Name="subdomain00" RegionID="0" SubVolume="subdomain0" Size="10.0" Unit="um" />
|
| </SurfaceDescription>
|
| </Geometry>
|
| <GeometryContext>
|
| <FeatureMapping Feature="c0" GeometryClass="subdomain0" SubVolume="subdomain0" Size="50000.0" VolumePerUnitVolume="1.0">
|
| <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>(100000.0 * x)</InitialConcentration>
|
| <Diffusion>1.0E-9</Diffusion>
|
| <Boundaries Xm="0.0" Xp="0.0" />
|
| </LocalizedCompoundSpec>
|
| <LocalizedCompoundSpec LocalizedCompoundRef="s1" ForceConstant="false" WellMixed="false" ForceContinuous="false">
|
| <InitialConcentration>(10.0 - (1.0 * 100000.0 * x))</InitialConcentration>
|
| <Diffusion>1.0E-9</Diffusion>
|
| <Boundaries Xm="0.0" Xp="0.0" />
|
| </LocalizedCompoundSpec>
|
| <ReactionSpec ReactionStepRef="r0" ReactionMapping="included" />
|
| </ReactionContext>
|
| <MathDescription Name="unnamed_spatialGeom_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_r0">1.0</Constant>
|
| <Constant Name="KMOLE">0.001660538783162726</Constant>
|
| <Constant Name="Kr_r0">0.5</Constant>
|
| <Constant Name="s0_boundaryXm">0.0</Constant>
|
| <Constant Name="s0_boundaryXp">0.0</Constant>
|
| <Constant Name="s0_diffusionRate">1.0E-9</Constant>
|
| <Constant Name="s1_boundaryXm">0.0</Constant>
|
| <Constant Name="s1_boundaryXp">0.0</Constant>
|
| <Constant Name="s1_diffusionRate">1.0E-9</Constant>
|
| <Constant Name="VolumePerUnitVolume_c0">1.0</Constant>
|
| <VolumeVariable Name="s0" Domain="subdomain0" />
|
| <VolumeVariable Name="s1" Domain="subdomain0" />
|
| <Function Name="J_r0" Domain="subdomain0">((Kf_r0 * s0) - (Kr_r0 * s1))</Function>
|
| <Function Name="s0_init_umol_l_1" Domain="subdomain0">(100000.0 * x)</Function>
|
| <Function Name="s1_init_umol_l_1" Domain="subdomain0">(10.0 - (1.0 * 100000.0 * x))</Function>
|
| <Function Name="Size_c0" Domain="subdomain0">(VolumePerUnitVolume_c0 * vcRegionVolume('subdomain0'))</Function>
|
| <Function Name="vobj_subdomain00_size" Domain="subdomain0">vcRegionVolume('subdomain0')</Function>
|
| <CompartmentSubDomain Name="subdomain0">
|
| <BoundaryType Boundary="Xm" Type="Flux" />
|
| <BoundaryType Boundary="Xp" Type="Flux" />
|
| <BoundaryType Boundary="Ym" Type="Value" />
|
| <BoundaryType Boundary="Yp" Type="Value" />
|
| <BoundaryType Boundary="Zm" Type="Value" />
|
| <BoundaryType Boundary="Zp" Type="Value" />
|
| <PdeEquation Name="s0" SolutionType="Unknown">
|
| <Boundaries Xm="s0_boundaryXm" Xp="s0_boundaryXp" />
|
| <Rate>- J_r0</Rate>
|
| <Diffusion>s0_diffusionRate</Diffusion>
|
| <Initial>s0_init_umol_l_1</Initial>
|
| </PdeEquation>
|
| <PdeEquation Name="s1" SolutionType="Unknown">
|
| <Boundaries Xm="s1_boundaryXm" Xp="s1_boundaryXp" />
|
| <Rate>J_r0</Rate>
|
| <Diffusion>s1_diffusionRate</Diffusion>
|
| <Initial>s1_init_umol_l_1</Initial>
|
| </PdeEquation>
|
| </CompartmentSubDomain>
|
| </MathDescription>
|
| <Simulation Name="Simulation0">
|
| <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Sundials Stiff PDE Solver (Variable Time Step)">
|
| <TimeBound StartTime="0.0" EndTime="1.0" />
|
| <TimeStep DefaultTime="0.05" MinTime="0.0" MaxTime="0.1" />
|
| <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-7" />
|
| <OutputOptions OutputTimeStep="0.05" />
|
| <SundialsSolverOptions>
|
| <maxOrderAdvection>2</maxOrderAdvection>
|
| </SundialsSolverOptions>
|
| <NumberProcessors>1</NumberProcessors>
|
| </SolverTaskDescription>
|
| <MathOverrides />
|
| <MeshSpecification>
|
| <Size X="200" Y="1" Z="1" />
|
| </MeshSpecification>
|
| </Simulation>
|
| <SpatialObjects>
|
| <SpatialObject Name="vobj_subdomain00" Type="Volume" subVolume="subdomain0" regionId="0">
|
| <QuantityCategoryList>
|
| <QuantityCategory Name="VolumeCentroid" Enabled="false" />
|
| <QuantityCategory Name="InteriorVelocity" Enabled="false" />
|
| <QuantityCategory Name="VolumeRegionSize" Enabled="true" />
|
| </QuantityCategoryList>
|
| </SpatialObject>
|
| </SpatialObjects>
|
| <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>
|
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|
