<?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_sq_rectangle">
      <Model Name="unnamed">
         <Compound Name="c" />
         <Feature Name="ECM" KeyValue="31616261" />
         <Feature Name="cell" KeyValue="31616264" />
         <Membrane InsideFeature="cell" OutsideFeature="ECM" MembraneVoltage="Voltage_PM" Name="PM" KeyValue="31616263" />
         <LocalizedCompound Name="c_cell" CompoundRef="c" Structure="cell" OverrideName="false" KeyValue="31616267" />
         <Diagram Name="Unnamed compartment" Structure="ECM" />
         <Diagram Name="cell" Structure="cell" />
         <Diagram Name="PM" Structure="PM" />
         <Version Name="unnamed" KeyValue="31616257" BranchId="31616258" Archived="0" Date="01-Feb-2009 20:20:39" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </Model>
      <SimulationSpec Name="pde" Stochastic="false" UseConcentration="true" CharacteristicSize="0.040545730590820304">
         <Geometry Name="diff_sq_rectang" Dimension="2">
            <Extent X="20.0" Y="10.0" Z="10.0" />
            <Origin X="-5.0" Y="-5.0" Z="0.0" />
            <SubVolume Name="subVolume1" Handle="0" Type="Analytical" KeyValue="31616026">
               <AnalyticExpression>(((x &gt; -5.0) * (y &gt; -2.0) * (x &lt; -1.0) * (y &lt; 2.0)) || ((x &gt;= -2.0) * (y &gt; -0.5) * (x &lt;= 10.0) * (y &lt; 0.5)))</AnalyticExpression>
            </SubVolume>
            <SubVolume Name="subVolume0" Handle="1" Type="Analytical" KeyValue="31616027">
               <AnalyticExpression>1.0</AnalyticExpression>
            </SubVolume>
            <SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="1" CutoffFrequency="0.3">
               <VolumeRegion Name="subVolume00" RegionID="0" SubVolume="subVolume0" Size="175.1" Unit="um2" />
               <VolumeRegion Name="subVolume11" RegionID="1" SubVolume="subVolume1" Size="24.900000000000002" Unit="um2" />
               <MembraneRegion Name="membrane_subVolume00_subVolume11" VolumeRegion1="subVolume11" VolumeRegion2="subVolume00" Size="36.78294472711216" Unit="um" />
            </SurfaceDescription>
            <Version Name="diff_sq_rectang" KeyValue="31616022" BranchId="31616023" Archived="0" Date="01-Feb-2009 17:57:58" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Geometry>
         <GeometryContext>
            <FeatureMapping Feature="ECM" SubVolume="subVolume0" Resolved="true">
               <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
            <FeatureMapping Feature="cell" SubVolume="subVolume1" Resolved="true">
               <BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" 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>((x &gt; -5.0) * (y &gt; -2.0) * (x &lt; -1.0) * (y &lt; 2.0))</InitialConcentration>
               <Diffusion>1.0</Diffusion>
               <Boundaries Xm="0.0" Xp="0.0" Ym="0.0" Yp="0.0" />
            </LocalizedCompoundSpec>
         </ReactionContext>
         <MathDescription Name="pde_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">((x &gt; -5.0) * (y &gt; -2.0) * (x &lt; -1.0) * (y &lt; 2.0))</Function>
            <CompartmentSubDomain Name="subVolume1" 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>0.0</Rate>
                  <Diffusion>c_cell_diffusionRate</Diffusion>
                  <Initial>c_cell_init</Initial>
               </PdeEquation>
            </CompartmentSubDomain>
            <CompartmentSubDomain Name="subVolume0" 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="subVolume1" OutsideCompartment="subVolume0">
               <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_generated" KeyValue="31616254" BranchId="31616255" Archived="0" Date="01-Feb-2009 20:20:39" 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="143" Y="71" Z="1" />
            </MeshSpecification>
            <Version Name="Simulation0" KeyValue="31616283" BranchId="31616284" Archived="0" Date="01-Feb-2009 20:21:01" 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="200.0" />
               <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="143" Y="71" Z="1" />
            </MeshSpecification>
            <Version Name="Simulation1" KeyValue="31649696" BranchId="31648929" Archived="0" Date="03-Feb-2009 15:05:31" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Simulation>
         <Version Name="pde" KeyValue="31616271" BranchId="31616272" Archived="0" Date="01-Feb-2009 20:20:39" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </SimulationSpec>
      <Version Name="diff_sq_rectangle" KeyValue="31649698" BranchId="31616279" Archived="0" Date="03-Feb-2009 15:05:31" FromVersionable="false">
         <Owner Name="satarupa" Identifier="29129705" />
         <GroupAccess Type="1" />
      </Version>
   </BioModel>
</vcml>

