<?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="diff_ellipse">
      <Model Name="unnamed">
         <Compound Name="c" />
         <Feature Name="ECM" KeyValue="31616300" />
         <Feature Name="cell" KeyValue="31616303" />
         <Membrane InsideFeature="cell" OutsideFeature="ECM" MembraneVoltage="Voltage_pm" Name="pm" KeyValue="31616302" />
         <LocalizedCompound Name="c_cell" CompoundRef="c" Structure="cell" OverrideName="false" KeyValue="31616306" />
         <Diagram Name="Unnamed compartment" Structure="ECM" />
         <Diagram Name="cell" Structure="cell" />
         <Diagram Name="pm" Structure="pm" />
         <Version Name="unnamed" KeyValue="31616296" BranchId="31616297" Archived="0" Date="01-Feb-2009 20:27:13" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </Model>
      <SimulationSpec Name="pde_ellipse" 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="1" />
            </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="Value" Xp="Value" Ym="Value" Yp="Value" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
            <MembraneMapping Membrane="pm" 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)</InitialConcentration>
               <Diffusion>1.0</Diffusion>
               <Boundaries Xm="0.0" Xp="0.0" Ym="0.0" Yp="0.0" />
            </LocalizedCompoundSpec>
         </ReactionContext>
         <MathDescription Name="pde_ellipse_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="Voltage_pm">0.0</Constant>
            <VolumeVariable Name="c" />
            <Function Name="c_cell_init">((((2.6 + x) ^ 2.0) + ((0.1 + y) ^ 2.0)) &lt; 1.0)</Function>
            <CompartmentSubDomain Name="subVolume0" Priority="200">
               <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" />
               <PdeEquation Name="c" SolutionType="Unknown">
                  <Boundaries Xm="0.0" Xp="0.0" Ym="0.0" Yp="0.0" />
                  <Rate>0.0</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="pde_ellipse_generated" KeyValue="31616332" BranchId="31616294" Archived="0" Date="01-Feb-2009 20:28:51" 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="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="Simulation0" KeyValue="31616340" BranchId="31616323" Archived="0" Date="01-Feb-2009 20:28:51" 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="60.0" />
               <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="31652320" BranchId="31652321" Archived="0" Date="03-Feb-2009 16:00:03" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Simulation>
         <Version Name="pde_ellipse" KeyValue="31616334" BranchId="31616311" Archived="0" Date="01-Feb-2009 20:28:51" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </SimulationSpec>
      <Version Name="diff_ellipse" KeyValue="31652323" BranchId="31616318" Archived="0" Date="03-Feb-2009 16:00:03" FromVersionable="false">
         <Owner Name="satarupa" Identifier="29129705" />
         <GroupAccess Type="1" />
      </Version>
   </BioModel>
</vcml>

