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danv61danv61
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WIP slurm script for batch execution
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‎vcell-server/src/test/resources/slurm_fixtures/langevin/SimID_999999999_0_.langevinInput‎

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<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
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<MathDescription Name="Application1_generated">
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<LangevinParticleMolecularType Name="MT0">
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<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="RED">
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<AllowableState Name="state0" />
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</Component>
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</LangevinParticleMolecularType>
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<LangevinParticleMolecularType Name="MT1">
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<Component Name="Site0" Radius="1.0" DiffusionRate="1.0" Location="Intracellular" SiteCoordX="0.0" SiteCoordY="0.0" SiteCoordZ="0.0" NamedColor="RED">
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<AllowableState Name="state0" />
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</Component>
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</LangevinParticleMolecularType>
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<Constant Name="_F_">96485.3321</Constant>
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<Constant Name="_F_nmol_">9.64853321E-5</Constant>
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<Constant Name="_N_pmol_">6.02214179E11</Constant>
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<Constant Name="_PI_">3.141592653589793</Constant>
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<Constant Name="_R_">8314.46261815</Constant>
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<Constant Name="_T_">300.0</Constant>
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<Constant Name="Kf">1.0</Constant>
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<Constant Name="KMOLE">0.001660538783162726</Constant>
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<Constant Name="Kr">0.0</Constant>
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<Constant Name="s0_Count_init_uM">0.0</Constant>
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<Constant Name="s1_Count_init_uM">0.0</Constant>
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<Constant Name="Size_Extracellular">1.0499999999999999E-4</Constant>
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<Constant Name="Size_Intracellular">8.949999999999999E-4</Constant>
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<Constant Name="Size_Membrane">0.009999999999999827</Constant>
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<Constant Name="UnitFactor_molecules_uM_neg_1_um_neg_3">(1.0 * pow(KMOLE, - 1.0))</Constant>
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<Constant Name="UnitFactor_uM_um3_molecules_neg_1">(1.0 * pow(KMOLE,1.0))</Constant>
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<Constant Name="Voltage_Membrane">0.0</Constant>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern0" Domain="Intracellular">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="?" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern1" Domain="Intracellular">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="?" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern2" Domain="Intracellular">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern3" Domain="Intracellular">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern4" Domain="Intracellular">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="1" />
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</MolecularType>
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="*" Bond="1" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern5" Domain="Intracellular">
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<MolecularType Name="MT0" MatchLabel="*">
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<Component Name="Site0" State="state0" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleSpeciesPattern Location="Intracellular" Name="speciesPattern6" Domain="Intracellular">
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<MolecularType Name="MT1" MatchLabel="*">
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<Component Name="Site0" State="state0" Bond="-" />
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</MolecularType>
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</VolumeParticleSpeciesPattern>
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<VolumeParticleObservable Name="O0_MT0_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern0" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="O0_MT1_tot_Count" Domain="Intracellular" MolecularType="Molecules" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern1" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="s0_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern5" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<VolumeParticleObservable Name="s1_Count" Domain="Intracellular" MolecularType="Species" SequenceType="Multimolecular">
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<VolumeParticleSpeciesPatterns>
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<VolumeParticleSpeciesPattern Name="speciesPattern6" />
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</VolumeParticleSpeciesPatterns>
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</VolumeParticleObservable>
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<Function Name="O0_MT0_tot" Domain="Intracellular">((O0_MT0_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="O0_MT1_tot" Domain="Intracellular">((O0_MT1_tot_Count * UnitFactor_uM_um3_molecules_neg_1) / Size_Intracellular)</Function>
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<Function Name="P_r0_probabilityRate" Domain="Intracellular">Kf</Function>
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<Function Name="P_r0_reverse_probabilityRate" Domain="Intracellular">Kr</Function>
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<Function Name="s0" Domain="Intracellular">((UnitFactor_uM_um3_molecules_neg_1 * s0_Count) / Size_Intracellular)</Function>
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<Function Name="s0_Count_initCount" Domain="Intracellular">(Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3 * s0_Count_init_uM)</Function>
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<Function Name="s1" Domain="Intracellular">((UnitFactor_uM_um3_molecules_neg_1 * s1_Count) / Size_Intracellular)</Function>
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<Function Name="s1_Count_initCount" Domain="Intracellular">(Size_Intracellular * UnitFactor_molecules_uM_neg_1_um_neg_3 * s1_Count_init_uM)</Function>
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<CompartmentSubDomain Name="Intracellular">
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<BoundaryType Boundary="Xm" Type="Flux" />
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<BoundaryType Boundary="Xp" Type="Flux" />
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<BoundaryType Boundary="Ym" Type="Flux" />
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<BoundaryType Boundary="Yp" Type="Flux" />
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<BoundaryType Boundary="Zm" Type="Flux" />
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<BoundaryType Boundary="Zp" Type="Flux" />
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<LangevinParticleJumpProcess Name="r0" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
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<SelectedParticle Name="speciesPattern2" />
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<SelectedParticle Name="speciesPattern3" />
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<MacroscopicRateConstant>P_r0_probabilityRate</MacroscopicRateConstant>
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<Effect VarName="speciesPattern2" Operation="destroy" />
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<Effect VarName="speciesPattern3" Operation="destroy" />
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<Effect VarName="speciesPattern4" Operation="create" />
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</LangevinParticleJumpProcess>
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<LangevinParticleJumpProcess Name="r0_reverse" Subtype="Binding" BondLength="1.0" ProcessSymmetryFactor="1.0">
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<SelectedParticle Name="speciesPattern4" />
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<MacroscopicRateConstant>P_r0_reverse_probabilityRate</MacroscopicRateConstant>
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<Effect VarName="speciesPattern2" Operation="create" />
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<Effect VarName="speciesPattern3" Operation="create" />
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<Effect VarName="speciesPattern4" Operation="destroy" />
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</LangevinParticleJumpProcess>
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<ParticleProperties Name="speciesPattern5">
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<ParticleInitialCount>
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<ParticleCount>s0_Count_initCount</ParticleCount>
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<ParticleLocationX>0.0</ParticleLocationX>
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<ParticleLocationY>0.0</ParticleLocationY>
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<ParticleLocationZ>0.0</ParticleLocationZ>
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</ParticleInitialCount>
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<ParticleDiffusion>0.0</ParticleDiffusion>
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<ParticleDriftX>0.0</ParticleDriftX>
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<ParticleDriftY>0.0</ParticleDriftY>
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<ParticleDriftZ>0.0</ParticleDriftZ>
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</ParticleProperties>
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<ParticleProperties Name="speciesPattern6">
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<ParticleInitialCount>
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<ParticleCount>s1_Count_initCount</ParticleCount>
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<ParticleLocationX>0.0</ParticleLocationX>
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<ParticleLocationY>0.0</ParticleLocationY>
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<ParticleLocationZ>0.0</ParticleLocationZ>
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</ParticleInitialCount>
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<ParticleDiffusion>0.0</ParticleDiffusion>
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<ParticleDriftX>0.0</ParticleDriftX>
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<ParticleDriftY>0.0</ParticleDriftY>
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<ParticleDriftZ>0.0</ParticleDriftZ>
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</ParticleProperties>
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</CompartmentSubDomain>
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<CompartmentSubDomain Name="Extracellular">
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<BoundaryType Boundary="Xm" Type="Flux" />
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<BoundaryType Boundary="Xp" Type="Flux" />
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<BoundaryType Boundary="Ym" Type="Flux" />
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<BoundaryType Boundary="Yp" Type="Flux" />
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<BoundaryType Boundary="Zm" Type="Flux" />
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<BoundaryType Boundary="Zp" Type="Flux" />
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</CompartmentSubDomain>
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<MembraneSubDomain Name="Extracellular_Intracellular_membrane" InsideCompartment="Extracellular" OutsideCompartment="Intracellular">
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<BoundaryType Boundary="Xm" Type="Value" />
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<BoundaryType Boundary="Xp" Type="Value" />
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<BoundaryType Boundary="Ym" Type="Value" />
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<BoundaryType Boundary="Yp" Type="Value" />
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<BoundaryType Boundary="Zm" Type="Value" />
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<BoundaryType Boundary="Zp" Type="Value" />
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</MembraneSubDomain>
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<Version Name="Application1_generated" KeyValue="274672103" BranchId="264499072" Archived="0" Date="22-Aug-2024 13:46:20" FromVersionable="false">
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<Owner Name="schaff" Identifier="17" />
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<GroupAccess Type="1" />
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</Version>
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</MathDescription>
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<Simulation Name="Copy of Simulation3">
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<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Langevin">
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<TimeBound StartTime="0.0" EndTime="1.0" />
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<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
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<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
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<OutputOptions OutputTimeStep="0.05" />
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<LangevinSimulationOptions>
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<NumOfTrials>1</NumOfTrials>
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<IntervalSpring>1.0E-9</IntervalSpring>
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<IntervalImage>1.0E-4</IntervalImage>
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</LangevinSimulationOptions>
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<NumberProcessors>1</NumberProcessors>
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</SolverTaskDescription>
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<MathOverrides />
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<MeshSpecification>
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<Size X="51" Y="51" Z="51" />
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</MeshSpecification>
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<Version Name="Copy of Simulation3" KeyValue="274672135" BranchId="274672136" Archived="0" Date="22-Aug-2024 13:46:20" FromVersionable="false">
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<Owner Name="schaff" Identifier="17" />
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<GroupAccess Type="1" />
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</Version>
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</Simulation>
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<Geometry Name="Geometry1240938551" Dimension="3">
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<Extent X="0.1" Y="0.1" Z="0.1" />
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<Origin X="0.0" Y="0.0" Z="0.0" />
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<SubVolume Name="Intracellular" Handle="1" Type="Analytical" KeyValue="267873106">
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<AnalyticExpression>(z &lt; 0.09)</AnalyticExpression>
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</SubVolume>
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<SubVolume Name="Extracellular" Handle="0" Type="Analytical" KeyValue="267873107">
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<AnalyticExpression>1.0</AnalyticExpression>
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</SubVolume>
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<SurfaceClass Name="Extracellular_Intracellular_membrane" SubVolume1Ref="Extracellular" SubVolume2Ref="Intracellular" KeyValue="267873108" />
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<SurfaceDescription NumSamplesX="101" NumSamplesY="101" NumSamplesZ="101" CutoffFrequency="0.3">
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<VolumeRegion Name="Intracellular0" RegionID="0" SubVolume="Intracellular" Size="8.949999999999999E-4" Unit="um3" />
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<VolumeRegion Name="Extracellular1" RegionID="1" SubVolume="Extracellular" Size="1.0499999999999999E-4" Unit="um3" />
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<MembraneRegion Name="membrane_Intracellular0_Extracellular1" VolumeRegion1="Extracellular1" VolumeRegion2="Intracellular0" Size="0.009999999999999827" Unit="um2" />
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</SurfaceDescription>
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<Version Name="Geometry1240938551" KeyValue="267873103" BranchId="264499055" Archived="0" Date="07-Feb-2024 14:47:29" FromVersionable="false">
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<Owner Name="schaff" Identifier="17" />
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<GroupAccess Type="1" />
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</Version>
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</Geometry>
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</SimulationTask>

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