Circle Dance

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Demonstration of dynamically regulated cell-cell adhesion as a function of changing cell properties

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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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