<?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_0value_BC">
      <Annotation>value of the concentration is zero at all boundaries</Annotation>
      <Model Name="unnamed">
         <Compound Name="c" />
         <Feature Name="r" KeyValue="31628522" />
         <LocalizedCompound Name="c_r" CompoundRef="c" Structure="r" OverrideName="false" KeyValue="31628524" />
         <Diagram Name="Unnamed compartment" Structure="r" />
         <Version Name="unnamed" KeyValue="31628518" BranchId="31628519" Archived="0" Date="03-Feb-2009 02:23:59" 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_1" Dimension="2">
            <Extent X="10.0" Y="10.0" Z="10.0" />
            <Origin X="0.0" Y="0.0" Z="0.0" />
            <SubVolume Name="subVolume1" Handle="0" Type="Analytical" KeyValue="31620883">
               <AnalyticExpression>1.0</AnalyticExpression>
            </SubVolume>
            <SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="1" CutoffFrequency="0.3">
               <VolumeRegion Name="subVolume10" RegionID="0" SubVolume="subVolume1" Size="100.0" Unit="um2" />
            </SurfaceDescription>
            <Version Name="box_1" KeyValue="31620879" BranchId="31620880" Archived="0" Date="02-Feb-2009 14:54:49" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </Geometry>
         <GeometryContext>
            <FeatureMapping Feature="r" SubVolume="subVolume1" Resolved="true">
               <BoundariesTypes Xm="Value" Xp="Value" Ym="Value" Yp="Value" Zm="Flux" Zp="Flux" />
            </FeatureMapping>
         </GeometryContext>
         <ReactionContext>
            <LocalizedCompoundSpec LocalizedCompoundRef="c_r" ForceConstant="false" EnableDiffusion="true">
               <InitialConcentration>((((-5.0 + x) ^ 2.0) + ((-5.0 + y) ^ 2.0)) &lt; 0.4)</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_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">((((-5.0 + x) ^ 2.0) + ((-5.0 + y) ^ 2.0)) &lt; 0.4)</Function>
            <CompartmentSubDomain Name="subVolume1" Priority="100">
               <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_r_diffusionRate</Diffusion>
                  <Initial>c_r_init</Initial>
               </PdeEquation>
            </CompartmentSubDomain>
            <Version Name="pde_generated" KeyValue="31628515" BranchId="31628516" Archived="0" Date="03-Feb-2009 02:23:59" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
            </Version>
         </MathDescription>
         <Simulation Name="Simulation0">
            <Annotation>c=0 value at all boundaries</Annotation>
            <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Finite Volume, Regular Grid">
               <TimeBound StartTime="0.0" EndTime="40.0" />
               <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="33089321" BranchId="31628547" Archived="0" Date="05-May-2009 16:20:28" FromVersionable="false">
               <Owner Name="satarupa" Identifier="29129705" />
               <GroupAccess Type="1" />
               <Annotation>c=0 value at all boundaries</Annotation>
               <ParentSimRef KeyValue="31628590" />
            </Version>
         </Simulation>
         <Version Name="pde" KeyValue="31628526" BranchId="31628527" Archived="0" Date="03-Feb-2009 02:23:59" FromVersionable="false">
            <Owner Name="satarupa" Identifier="29129705" />
            <GroupAccess Type="1" />
         </Version>
      </SimulationSpec>
      <Version Name="diff_0value_BC" KeyValue="33538631" BranchId="31628532" Archived="0" Date="26-May-2009 16:09:37" FromVersionable="false">
         <Owner Name="satarupa" Identifier="29129705" />
         <GroupAccess Type="33205538" Hash="860399096">
            <User Name="KNguyen" KeyValue="33148196" IsHidden="false" />
            <User Name="tkulangara" KeyValue="32749881" IsHidden="false" />
            <User Name="Education" KeyValue="30625624" IsHidden="false" />
            <User Name="raquell" KeyValue="447" IsHidden="false" />
            <User Name="Satarupa_Alex" KeyValue="33090547" IsHidden="false" />
         </GroupAccess>
         <Annotation>value of the concentration is zero at all boundaries</Annotation>
      </Version>
   </BioModel>
</vcml>

