Circle Dance
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Demonstration of dynamically regulated cell-cell adhesion as a function of changing cell properties
Model
CircleDance.xml
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<MorpheusModel version="4">
<Description>
<Title>Example-CircleDance</Title>
<Details>Demonstration of dynamically regulated cell-cell adhesion as a function of changing cell properties.
Date: May 8, 2020
Author: joern.starruss@tu-dresden.de
Software: Morpheus (open-source), download from https://morpheus.gitlab.io
</Details>
</Description>
<Global>
<Constant symbol="adhesive_d" value="0.0"/>
</Global>
<Space>
<SpaceSymbol symbol="l"/>
<Lattice class="square">
<Size symbol="size" value="200, 200, 0"/>
<BoundaryConditions>
<Condition type="periodic" boundary="x"/>
<Condition type="periodic" boundary="y"/>
</BoundaryConditions>
<Neighborhood>
<Order>2</Order>
</Neighborhood>
</Lattice>
</Space>
<Time>
<StartTime value="0"/>
<StopTime value="12000"/>
<RandomSeed value="0"/>
<TimeSymbol symbol="time"/>
</Time>
<CellTypes>
<CellType class="biological" name="ct1">
<VolumeConstraint target="200" strength="1"/>
<Property symbol="contact_length" value="0.0"/>
<NeighborhoodReporter>
<Input value="cell.type == celltype.ct1.id" scaling="length"/>
<Output symbol-ref="contact_length" mapping="sum"/>
</NeighborhoodReporter>
<Property symbol="contact_fraction" value="0"/>
<Equation symbol-ref="contact_fraction">
<Expression>contact_length / cell.surface</Expression>
</Equation>
<Property symbol="adhesive" value="0.0"/>
<System solver="adaptive45">
<DiffEqn symbol-ref="adhesive">
<Expression>0.05*(1-contact_fraction) - 0.01 * adhesive</Expression>
</DiffEqn>
</System>
<Equation symbol-ref="adhesive_d">
<Expression>adhesive</Expression>
</Equation>
<DelayProperty delay="500" name="adhesive concentration in Membrane, delayed due to transport." symbol="adhesive_d" value="0.0"/>
</CellType>
<CellType class="medium" name="medium"/>
</CellTypes>
<CPM>
<Interaction default="0.0">
<Contact type1="ct1" value="6" type2="medium"/>
<Contact type1="ct1" value="16" type2="ct1">
<HomophilicAdhesion strength="-3.0" adhesive="adhesive_d"/>
</Contact>
</Interaction>
<MonteCarloSampler stepper="edgelist">
<MCSDuration value="1"/>
<Neighborhood>
<Order>2</Order>
</Neighborhood>
<MetropolisKinetics temperature="2"/>
</MonteCarloSampler>
<ShapeSurface scaling="norm">
<Neighborhood>
<Order>6</Order>
</Neighborhood>
</ShapeSurface>
</CPM>
<CellPopulations>
<Population type="ct1" size="0">
<InitCircle number-of-cells="50" mode="random">
<Dimensions center="size.x/2, size.y/2, 0" radius="size.x/3"/>
</InitCircle>
</Population>
</CellPopulations>
<Analysis>
<Gnuplotter decorate="true" time-step="100">
<Terminal name="png"/>
<Plot>
<Cells value="adhesive_d" flooding="true">
<ColorMap>
<Color value="3" color="red"/>
<Color value="1.5" color="yellow"/>
<Color value="0" color="white"/>
</ColorMap>
</Cells>
</Plot>
<!-- <Disabled>
<Plot>
<Cells value="contact_fraction" flooding="true"/>
</Plot>
</Disabled>
-->
</Gnuplotter>
<DependencyGraph reduced="false" format="svg"/>
</Analysis>
</MorpheusModel>
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