<?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_box">
      <Annotation>Value_flux_Mixed_bc</Annotation>
      <Model Name="unnamed">
         <Compound Name="c" />
         <Feature Name="R" KeyValue="31616092" />
         <LocalizedCompound Name="c_R" CompoundRef="c" Structure="R" OverrideName="false" KeyValue="31616094" />
         <Diagram Name="Unnamed compartment" Structure="R" />
         <Version Name="unnamed" KeyValue="31616088" BranchId="31616089" Archived="0" Date="01-Feb-2009 19:03:15" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </Model>
      <SimulationSpec Name="pde" Stochastic="false" UseConcentration="true" CharacteristicSize="0.02">
         <Geometry Name="box_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="box" Handle="0" Type="Analytical" KeyValue="31544654">
               <AnalyticExpression>1.0</AnalyticExpression>
            </SubVolume>
            <SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="1" CutoffFrequency="0.3">
               <VolumeRegion Name="box0" RegionID="0" SubVolume="box" Size="100.0" Unit="um2" />
            </SurfaceDescription>
            <Version Name="box_diff" KeyValue="31544650" BranchId="31544651" Archived="0" Date="27-Jan-2009 15:24:25" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Geometry>
         <GeometryContext>
            <FeatureMapping Feature="R" SubVolume="box" Resolved="true">
               <BoundariesTypes Xm="Value" Xp="Value" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
         </GeometryContext>
         <ReactionContext>
            <LocalizedCompoundSpec LocalizedCompoundRef="c_R" ForceConstant="false" EnableDiffusion="true">
               <InitialConcentration>(((x ^ 2.0) + (y ^ 2.0)) &lt; 4.0)</InitialConcentration>
               <Diffusion>1.0</Diffusion>
               <Boundaries Xm="1.0" 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_R_diffusionRate">1.0</Constant>
            <Constant Name="K_millivolts_per_volt">1000.0</Constant>
            <Constant Name="KMOLE">0.0016611295681063123</Constant>
            <VolumeVariable Name="c" />
            <Function Name="c_R_init">(((x ^ 2.0) + (y ^ 2.0)) &lt; 4.0)</Function>
            <CompartmentSubDomain Name="box" Priority="100">
               <BoundaryType Boundary="Xm" Type="Value" />
               <BoundaryType Boundary="Xp" Type="Value" />
               <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="1.0" Xp="0.0" Ym="0.0" Yp="0.0" />
                  <Rate>0.0</Rate>
                  <Diffusion>c_R_diffusionRate</Diffusion>
                  <Initial>c_R_init</Initial>
               </PdeEquation>
            </CompartmentSubDomain>
            <Version Name="pde_generated" KeyValue="31616156" BranchId="31616086" Archived="0" Date="01-Feb-2009 19:22:25" 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="31616162" BranchId="31616117" Archived="0" Date="01-Feb-2009 19:22:25" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Simulation>
         <Version Name="pde" KeyValue="31616158" BranchId="31616097" Archived="0" Date="01-Feb-2009 19:22:25" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </SimulationSpec>
      <Version Name="diff_box" KeyValue="31616249" BranchId="31616102" Archived="0" Date="01-Feb-2009 20:13:07" FromVersionable="false">
         <Owner Name="satarupa" Identifier="29129705" />
         <GroupAccess Type="1" />
         <Annotation>Value_flux_Mixed_bc</Annotation>
      </Version>
   </BioModel>
</vcml>

