<?xml version="1.0" encoding="UTF-8"?>
<!--This biomodel was generated in VCML Version 0.4-->
<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="0.4">
   <BioModel Name="ellipse_2source_Diff_reac">
      <Model Name="unnamed">
         <Compound Name="c" />
         <Feature Name="ecm" KeyValue="31812325" />
         <Feature Name="cell" KeyValue="31812328" />
         <Membrane InsideFeature="cell" OutsideFeature="ecm" MembraneVoltage="Voltage_m" Name="m" KeyValue="31812327" />
         <LocalizedCompound Name="c_cell" CompoundRef="c" Structure="cell" OverrideName="false" KeyValue="31812331" />
         <SimpleReaction Structure="cell" Name="reaction0" FluxCarrierValence="0" FluxOption="MolecularOnly" KeyValue="31812332">
            <Reactant LocalizedCompoundRef="c_cell" Stoichiometry="1" KeyValue="31812333" />
            <Kinetics KineticsType="GeneralKinetics">
               <Parameter Name="J" Role="reaction rate" Unit="uM.s-1">(r * c_cell)</Parameter>
               <Parameter Name="r" Role="user defined" Unit="s-1">1.0</Parameter>
            </Kinetics>
            <Annotation />
         </SimpleReaction>
         <Diagram Name="Unnamed compartment" Structure="ecm" />
         <Diagram Name="egg" Structure="cell">
            <LocalizedCompoundShape LocalizedCompoundRef="c_cell" LocationX="85" LocationY="100" />
            <SimpleReactionShape SimpleReactionRef="reaction0" LocationX="207" LocationY="104" />
         </Diagram>
         <Diagram Name="m" Structure="m" />
         <Version Name="unnamed" KeyValue="31812322" BranchId="31783447" Archived="0" Date="09-Feb-2009 17:22:13" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </Model>
      <SimulationSpec Name="sptial" Stochastic="false" UseConcentration="true" CharacteristicSize="0.02">
         <Geometry Name="ellipse_diff" Dimension="2">
            <Extent X="10.0" Y="10.0" Z="10.0" />
            <Origin X="-5.0" Y="-5.0" Z="0.0" />
            <SubVolume Name="subVolume0" Handle="1" Type="Analytical" KeyValue="31616175">
               <AnalyticExpression>(((0.2 * (x ^ 2.0)) + (0.5 * (y ^ 2.0))) &lt; 4.0)</AnalyticExpression>
            </SubVolume>
            <SubVolume Name="subVolume1" Handle="0" Type="Analytical" KeyValue="31616176">
               <AnalyticExpression>1.0</AnalyticExpression>
            </SubVolume>
            <SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="1" CutoffFrequency="0.3">
               <VolumeRegion Name="subVolume10" RegionID="0" SubVolume="subVolume1" Size="60.27" Unit="um2" />
               <VolumeRegion Name="subVolume01" RegionID="1" SubVolume="subVolume0" Size="39.730000000000004" Unit="um2" />
               <MembraneRegion Name="membrane_subVolume10_subVolume01" VolumeRegion1="subVolume01" VolumeRegion2="subVolume10" Size="23.28232051620389" Unit="um" />
            </SurfaceDescription>
            <Version Name="ellipse_diff" KeyValue="31616171" BranchId="31616172" Archived="0" Date="01-Feb-2009 19:32:38" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="0" />
            </Version>
         </Geometry>
         <GeometryContext>
            <FeatureMapping Feature="ecm" SubVolume="subVolume1" Resolved="true">
               <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
            <FeatureMapping Feature="cell" SubVolume="subVolume0" Resolved="true">
               <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
            <MembraneMapping Membrane="m" SurfaceToVolumeRatio="1.0" VolumeFraction="0.2" CalculateVoltage="false" SpecificCapacitance="1.0" InitialVoltage="0.0" />
         </GeometryContext>
         <ReactionContext>
            <LocalizedCompoundSpec LocalizedCompoundRef="c_cell" ForceConstant="false" EnableDiffusion="true">
               <InitialConcentration>(((((2.6 + x) ^ 2.0) + ((0.1 + y) ^ 2.0)) &lt; 1.0) || ((((-2.8 + x) ^ 2.0) + ((0.1 + y) ^ 2.0)) &lt; 1.0))</InitialConcentration>
               <Diffusion>1.0</Diffusion>
               <Boundaries Xm="0.0" Xp="0.0" Ym="0.0" Yp="0.0" />
            </LocalizedCompoundSpec>
            <ReactionSpec ReactionStepRef="reaction0" ReactionMapping="included" />
         </ReactionContext>
         <MathDescription Name="sptial_generated">
            <Constant Name="_F_">96480.0</Constant>
            <Constant Name="_F_nmol_">9.648E-5</Constant>
            <Constant Name="_K_GHK_">1.0E-9</Constant>
            <Constant Name="_N_pmol_">6.02E11</Constant>
            <Constant Name="_R_">8314.0</Constant>
            <Constant Name="_T_">300.0</Constant>
            <Constant Name="c_cell_diffusionRate">1.0</Constant>
            <Constant Name="K_millivolts_per_volt">1000.0</Constant>
            <Constant Name="KMOLE">0.0016611295681063123</Constant>
            <Constant Name="r">1.0</Constant>
            <Constant Name="Voltage_m">0.0</Constant>
            <VolumeVariable Name="c" />
            <Function Name="c_cell_init">(((((2.6 + x) ^ 2.0) + ((0.1 + y) ^ 2.0)) &lt; 1.0) || ((((-2.8 + x) ^ 2.0) + ((0.1 + y) ^ 2.0)) &lt; 1.0))</Function>
            <Function Name="J_reaction0">(r * c)</Function>
            <CompartmentSubDomain Name="subVolume0" Priority="200">
               <BoundaryType Boundary="Xm" Type="Flux" />
               <BoundaryType Boundary="Xp" Type="Flux" />
               <BoundaryType Boundary="Ym" Type="Flux" />
               <BoundaryType Boundary="Yp" Type="Flux" />
               <BoundaryType Boundary="Zm" Type="Value" />
               <BoundaryType Boundary="Zp" Type="Value" />
               <PdeEquation Name="c" SolutionType="Unknown">
                  <Boundaries Xm="0.0" Xp="0.0" Ym="0.0" Yp="0.0" />
                  <Rate> - J_reaction0</Rate>
                  <Diffusion>c_cell_diffusionRate</Diffusion>
                  <Initial>c_cell_init</Initial>
               </PdeEquation>
            </CompartmentSubDomain>
            <CompartmentSubDomain Name="subVolume1" Priority="101">
               <BoundaryType Boundary="Xm" Type="Flux" />
               <BoundaryType Boundary="Xp" Type="Flux" />
               <BoundaryType Boundary="Ym" Type="Flux" />
               <BoundaryType Boundary="Yp" Type="Flux" />
               <BoundaryType Boundary="Zm" Type="Value" />
               <BoundaryType Boundary="Zp" Type="Value" />
               <PdeEquation Name="c" SolutionType="Unknown">
                  <Rate>0.0</Rate>
                  <Diffusion>c_cell_diffusionRate</Diffusion>
                  <Initial>0.0</Initial>
               </PdeEquation>
            </CompartmentSubDomain>
            <MembraneSubDomain InsideCompartment="subVolume0" OutsideCompartment="subVolume1">
               <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" />
               <JumpCondition Name="c">
                  <InFlux>0.0</InFlux>
                  <OutFlux>0.0</OutFlux>
               </JumpCondition>
            </MembraneSubDomain>
            <Version Name="sptial_generated" KeyValue="31812320" BranchId="31783444" Archived="0" Date="09-Feb-2009 17:22:13" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </MathDescription>
         <Simulation Name="Simulation0">
            <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Finite Volume, Regular Grid">
               <TimeBound StartTime="0.0" EndTime="1.0" />
               <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" />
            </SolverTaskDescription>
            <MathOverrides />
            <MeshSpecification>
               <Size X="101" Y="101" Z="1" />
            </MeshSpecification>
            <Version Name="Simulation0" KeyValue="31812344" BranchId="31785037" Archived="0" Date="09-Feb-2009 17:22:13" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Simulation>
         <Simulation Name="Simulation1">
            <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Finite Volume, Regular Grid">
               <TimeBound StartTime="0.0" EndTime="10.0" />
               <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" />
            </SolverTaskDescription>
            <MathOverrides />
            <MeshSpecification>
               <Size X="101" Y="101" Z="1" />
            </MeshSpecification>
            <Version Name="Simulation1" KeyValue="31818147" BranchId="31818148" Archived="0" Date="10-Feb-2009 02:59:06" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Simulation>
         <Version Name="sptial" KeyValue="31812337" BranchId="31783461" Archived="0" Date="09-Feb-2009 17:22:13" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </SimulationSpec>
      <Version Name="ellipse_2source_Diff_reac" KeyValue="31818150" BranchId="31783468" Archived="0" Date="10-Feb-2009 02:59:06" FromVersionable="false">
         <Owner Name="satarupa" Identifier="29129705" />
         <GroupAccess Type="1" />
      </Version>
   </BioModel>
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