<MathModel Annotation='full 2D T-N dynamics, length unit 7.5 um' Name='NocodazoleTubulin_3D'>
  <Geometry Dimension='3' Annotation='' Name='NocodazoleTubulin_3D'>
    <Extent X='158.0' Y='34.0' Z='4.0' />
    <Origin X='-79.0' Y='0.0' Z='0.0' />
    <SubVolume Handle='2' Type='Analytical' Name='nucleus'>
      <AnalyticExpression>(((x * x) + (y * y)) &amp;lt; 100.0)</AnalyticExpression>
    </SubVolume>
    <SubVolume Handle='1' Type='Analytical' Name='cytosol'>
      <AnalyticExpression>((x &amp;gt;  - 75.0) * (x &amp;lt; 75.0) * (y &amp;lt; 

30.0) * (z &amp;lt; 2.0))</AnalyticExpression>
    </SubVolume>
    <SubVolume Handle='0' Type='Analytical' Name='extracellular'>
      <AnalyticExpression>1.0</AnalyticExpression>
    </SubVolume>
    <Version FromVersionable='true' Name='NocodazoleTubulin_3D'></Version>
  </Geometry>
  <MathDescription Annotation='' Name='NoName'>
    <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 Type='Value' Boundary='Xm' />
      <BoundaryType Type='Value' Boundary='Xp' />
      <BoundaryType Type='Flux' Boundary='Ym' />
      <BoundaryType Type='Value' Boundary='Yp' />
      <BoundaryType Type='Flux' Boundary='Zm' />
      <BoundaryType Type='Value' Boundary='Zp' />
      <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 Type='Value' Boundary='Xm' />
      <BoundaryType Type='Value' Boundary='Xp' />
      <BoundaryType Type='Flux' Boundary='Ym' />
      <BoundaryType Type='Value' Boundary='Yp' />
      <BoundaryType Type='Flux' Boundary='Zm' />
      <BoundaryType Type='Value' Boundary='Zp' />
      <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 Type='Value' Boundary='Xm' />
      <BoundaryType Type='Value' Boundary='Xp' />
      <BoundaryType Type='Value' Boundary='Ym' />
      <BoundaryType Type='Value' Boundary='Yp' />
      <BoundaryType Type='Value' Boundary='Zm' />
      <BoundaryType Type='Value' Boundary='Zp' />
      <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 Yp='Nboundary' Zp='Nboundary' Xm='Nboundary' Ym='Nboundary' Xp='Nboundary' 

Zm='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 FromVersionable='true' Name='NoName'></Version>
  </MathDescription>
  <Simulation Annotation='' Name='Simulation 1'>
    <SolverTaskDescription TaskType='Unsteady' KeepAtMost='1000' Solver='Finite Volume, Regular 

Grid' KeepEvery='600'>
      <TimeBound StartTime='0.0' EndTime='60.0' />
      <TimeStep MaxTime='1.0' MinTime='1.0E-8' DefaultTime='0.01' />
      <ErrorTolerance Relative='1.0E-9' Absolut='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 FromVersionable='true' Name='Simulation 1'></Version>
  </Simulation>
  <Simulation Annotation='' Name='copy of Simulation 1'>
    <SolverTaskDescription TaskType='Unsteady' KeepAtMost='1000' Solver='Finite Volume, Regular 

Grid' KeepEvery='1200'>
      <TimeBound StartTime='0.0' EndTime='1200.0' />
      <TimeStep MaxTime='1.0' MinTime='1.0E-8' DefaultTime='0.01' />
      <ErrorTolerance Relative='1.0E-9' Absolut='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 FromVersionable='true' Name='copy of Simulation 1'></Version>
  </Simulation>
  <Version FromVersionable='true' Name='NocodazoleTubulin_3D'>full 2D T-N dynamics, length unit 

7.5 um</Version>
</MathModel>