<MathModel Name="NocodazoleTubulin_3D" Annotation="full 2D T-N dynamics, length unit 7.5 um">
  <Geometry Name="NocodazoleTubulin_3D" Dimension="3" Annotation="">
    <Extent X="158.0" Y="34.0" Z="4.0" />
    <Origin X="-79.0" Y="0.0" Z="0.0" />
    <SubVolume Name="nucleus" Handle="2" Type="Analytical">
      <AnalyticExpression>(((x * x) + (y * y)) &amp;lt; 100.0)</AnalyticExpression>
    </SubVolume>
    <SubVolume Name="cytosol" Handle="1" Type="Analytical">
      <AnalyticExpression>((x &amp;gt;  - 75.0) * (x &amp;lt; 75.0) * (y &amp;lt; 30.0) * (z &amp;lt; 2.0))</AnalyticExpression>
    </SubVolume>
    <SubVolume Name="extracellular" Handle="0" Type="Analytical">
      <AnalyticExpression>1.0</AnalyticExpression>
    </SubVolume>
    <Version Name="NocodazoleTubulin_3D" FromVersionable="true"></Version>
  </Geometry>
  <MathDescription Name="NoName" Annotation="">
    <Constant Name="P">75.0</Constant>
    <Constant Name="Dn">120.0</Constant>
    <Constant Name="Dt">6.0</Constant>
    <Constant Name="Dtn">6.0</Constant>
    <Constant Name="Nm">33.0</Constant>
    <Constant Name="N_init">0.0</Constant>
    <Constant Name="TN_init">0.0</Constant>
    <Constant Name="T_init">10.0</Constant>
    <Constant Name="kon">1.0</Constant>
    <Constant Name="Kd">10.0</Constant>
    <Constant Name="SIGMA">15.3</Constant>
    <Constant Name="ALPHA">0.02</Constant>
    <Constant Name="TM">30.0</Constant>
    <Constant Name="v">0.0375</Constant>
    <Constant Name="X_STEP">1.0</Constant>
    <VolumeVariable Name="T" />
    <VolumeVariable Name="N" />
    <VolumeVariable Name="TN" />
    <Function Name="J_flux0">(P * (N_OUTSIDE - N_INSIDE))</Function>
    <Function Name="ST">(T + TN)</Function>
    <Function Name="SN">(N + TN)</Function>
    <Function Name="J_reaction0">(kon * ((T * N) - (Kd * TN)))</Function>
    <Function Name="J_reaction1">(TM * v * ((x + 75.0) &amp;gt; (v * t)) * ((x + 75.0) &amp;lt; ((v * t) + X_STEP)) / X_STEP * (x &amp;lt; 0.0))</Function>
    <Function Name="Nboundary">(Nm * SIGMA * exp(( - ALPHA * ALPHA * (((x + 75.0) * (x + 75.0)) + (y * y) + (z * z)))) / (sqrt((((x + 75.0) * (x + 75.0)) + (y * y) + (z * z))) + SIGMA))</Function>
    <CompartmentSubDomain Name="nucleus" Priority="3">
      <BoundaryType Boundary="Xm" Type="Value" />
      <BoundaryType Boundary="Xp" Type="Value" />
      <BoundaryType Boundary="Ym" Type="Flux" />
      <BoundaryType Boundary="Yp" Type="Value" />
      <BoundaryType Boundary="Zm" Type="Flux" />
      <BoundaryType Boundary="Zp" Type="Value" />
      <PdeEquation Name="N">
        <Rate>0.0</Rate>
        <Diffusion>Dn</Diffusion>
        <Initial>0.0</Initial>
      </PdeEquation>
      <PdeEquation Name="T">
        <Rate>0.0</Rate>
        <Diffusion>Dt</Diffusion>
        <Initial>0.0</Initial>
      </PdeEquation>
      <PdeEquation Name="TN">
        <Rate>0.0</Rate>
        <Diffusion>Dtn</Diffusion>
        <Initial>0.0</Initial>
      </PdeEquation>
    </CompartmentSubDomain>
    <CompartmentSubDomain Name="cytosol" Priority="2">
      <BoundaryType Boundary="Xm" Type="Value" />
      <BoundaryType Boundary="Xp" Type="Value" />
      <BoundaryType Boundary="Ym" Type="Flux" />
      <BoundaryType Boundary="Yp" Type="Value" />
      <BoundaryType Boundary="Zm" Type="Flux" />
      <BoundaryType Boundary="Zp" Type="Value" />
      <PdeEquation Name="N">
        <Boundaries Ym="0.0" Zm="0.0" />
        <Rate>0.0</Rate>
        <Diffusion>Dn</Diffusion>
        <Initial>N_init</Initial>
      </PdeEquation>
      <PdeEquation Name="T">
        <Boundaries Ym="0.0" />
        <Rate>J_reaction1</Rate>
        <Diffusion>Dt</Diffusion>
        <Initial>T_init</Initial>
      </PdeEquation>
      <PdeEquation Name="TN">
        <Boundaries Ym="0.0" />
        <Rate>0.0</Rate>
        <Diffusion>Dtn</Diffusion>
        <Initial>TN_init</Initial>
      </PdeEquation>
      <FastSystem>
        <FastInvariant>(N + TN)</FastInvariant>
        <FastInvariant>(T + TN)</FastInvariant>
        <FastRate>J_reaction0</FastRate>
      </FastSystem>
    </CompartmentSubDomain>
    <CompartmentSubDomain Name="extracellular" Priority="1">
      <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="T">
        <Rate>0.0</Rate>
        <Diffusion>Dt</Diffusion>
        <Initial>0.0</Initial>
      </PdeEquation>
      <PdeEquation Name="TN">
        <Rate>0.0</Rate>
        <Diffusion>Dtn</Diffusion>
        <Initial>0.0</Initial>
      </PdeEquation>
      <PdeEquation Name="N">
        <Boundaries Xm="Nboundary" Xp="Nboundary" Ym="Nboundary" Yp="Nboundary" Zm="Nboundary" Zp="Nboundary" />
        <Rate>0.0</Rate>
        <Diffusion>Dn</Diffusion>
        <Initial>Nboundary</Initial>
      </PdeEquation>
    </CompartmentSubDomain>
    <MembraneSubDomain InsideCompartment="nucleus" OutsideCompartment="cytosol">
      <JumpCondition Name="N">
        <InFlux>0.0</InFlux>
        <OutFlux>0.0</OutFlux>
      </JumpCondition>
      <JumpCondition Name="T">
        <InFlux>0.0</InFlux>
        <OutFlux>0.0</OutFlux>
      </JumpCondition>
      <JumpCondition Name="TN">
        <InFlux>0.0</InFlux>
        <OutFlux>0.0</OutFlux>
      </JumpCondition>
    </MembraneSubDomain>
    <MembraneSubDomain InsideCompartment="cytosol" OutsideCompartment="extracellular">
      <JumpCondition Name="N">
        <InFlux>J_flux0</InFlux>
        <OutFlux> - J_flux0</OutFlux>
      </JumpCondition>
      <JumpCondition Name="T">
        <InFlux>0.0</InFlux>
        <OutFlux>0.0</OutFlux>
      </JumpCondition>
      <JumpCondition Name="TN">
        <InFlux>0.0</InFlux>
        <OutFlux>0.0</OutFlux>
      </JumpCondition>
    </MembraneSubDomain>
    <Version Name="NoName" FromVersionable="true"></Version>
  </MathDescription>
  <Simulation Name="Simulation 1" Annotation="">
    <SolverTaskDescription TaskType="Unsteady" KeepEvery="600" KeepAtMost="1000" Solver="Finite Volume, Regular Grid">
      <TimeBound StartTime="0.0" EndTime="60.0" />
      <TimeStep DefaultTime="0.01" MinTime="1.0E-8" MaxTime="1.0" />
      <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
    </SolverTaskDescription>
    <MathOverrides>
      <Constant Name="Dt">6.0</Constant>
      <Constant Name="SIGMA">15.3</Constant>
      <Constant Name="P">75.0</Constant>
      <Constant Name="TN_init">0.0</Constant>
      <Constant Name="Nm">33.0</Constant>
      <Constant Name="TM">30.0</Constant>
      <Constant Name="T_init">10.0</Constant>
      <Constant Name="X_STEP">1.0</Constant>
      <Constant Name="Dn">120.0</Constant>
      <Constant Name="Dtn">6.0</Constant>
      <Constant Name="v">0.0375</Constant>
      <Constant Name="kon">1.0</Constant>
      <Constant Name="N_init">0.0</Constant>
      <Constant Name="Kd">10.0</Constant>
      <Constant Name="ALPHA">0.02</Constant>
    </MathOverrides>
    <MeshSpecification>
      <Size X="159" Y="35" Z="5" />
    </MeshSpecification>
    <Version Name="Simulation 1" FromVersionable="true"></Version>
  </Simulation>
  <Simulation Name="copy of Simulation 1" Annotation="">
    <SolverTaskDescription TaskType="Unsteady" KeepEvery="1200" KeepAtMost="1000" Solver="Finite Volume, Regular Grid">
      <TimeBound StartTime="0.0" EndTime="1200.0" />
      <TimeStep DefaultTime="0.01" MinTime="1.0E-8" MaxTime="1.0" />
      <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
    </SolverTaskDescription>
    <MathOverrides>
      <Constant Name="Dt">6.0</Constant>
      <Constant Name="SIGMA">15.3</Constant>
      <Constant Name="P">75.0</Constant>
      <Constant Name="TN_init">0.0</Constant>
      <Constant Name="Nm">33.0</Constant>
      <Constant Name="TM">30.0</Constant>
      <Constant Name="T_init">10.0</Constant>
      <Constant Name="X_STEP">1.0</Constant>
      <Constant Name="Dn">120.0</Constant>
      <Constant Name="Dtn">6.0</Constant>
      <Constant Name="v">0.0375</Constant>
      <Constant Name="kon">1.0</Constant>
      <Constant Name="N_init">0.0</Constant>
      <Constant Name="Kd">10.0</Constant>
      <Constant Name="ALPHA">0.02</Constant>
    </MathOverrides>
    <MeshSpecification>
      <Size X="159" Y="35" Z="5" />
    </MeshSpecification>
    <Version Name="copy of Simulation 1" FromVersionable="true"></Version>
  </Simulation>
  <Version Name="NocodazoleTubulin_3D" FromVersionable="true">full 2D T-N dynamics, length unit 7.5 um</Version>
</MathModel>