AutocrineChemotaxis.xml 3.78 KB
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<MorpheusModel version="3">
    <Description>
        <Title>Example-AutocrineChemotaxis</Title>
        <Details></Details>
    </Description>
    <Global>
        <Field symbol="U" value="0" name="chemoattractant">
            <Diffusion rate="0.1"/>
        </Field>
        <System solver="euler" time-step="10.0">
            <DiffEqn symbol-ref="U">
                <Expression>p - d*U</Expression>
            </DiffEqn>
            <Constant symbol="d" value="0.01" name="degradation U"/>
        </System>
        <Constant symbol="cell_density" value="0.003"/>
    </Global>
    <Space>
        <Lattice class="square">
            <Size symbol="size" value="200 200 0"/>
            <BoundaryConditions>
                <Condition boundary="x" type="periodic"/>
                <Condition boundary="y" type="periodic"/>
            </BoundaryConditions>
            <NodeLength value="1.0"/>
            <Neighborhood>
                <Distance>2.5</Distance>
            </Neighborhood>
        </Lattice>
        <SpaceSymbol symbol="space"/>
    </Space>
    <Time>
        <StartTime value="0"/>
        <StopTime value="2.5e4"/>
        <SaveInterval value="0"/>
        <RandomSeed value="0"/>
        <TimeSymbol symbol="time"/>
    </Time>
    <CellTypes>
        <CellType class="biological" name="cells">
            <!--    <Disabled>
        <Property symbol="cell" value="1.0"/>
    </Disabled>
-->
            <Property symbol="c" value="100.0" name="chemotactic strength"/>
            <Property symbol="p" value="0.01" name="production chemoattractant"/>
            <Property symbol="neighbors" value="0" name="number of neighboring cells"/>
            <VolumeConstraint target="60" strength="1"/>
            <SurfaceConstraint target="0.85" mode="aspherity" strength="1"/>
            <Chemotaxis field="U" contact-inhibition="false" strength="c" retraction="true"/>
            <NeighborhoodReporter>
                <Input scaling="cell" value="cell.type == celltype.cells.id"/>
                <Output symbol-ref="neighbors" mapping="sum"/>
            </NeighborhoodReporter>
        </CellType>
        <CellType class="medium" name="medium">
            <Constant symbol="neighbors" value="0.0"/>
            <Constant symbol="p" value="0.0" name="production"/>
        </CellType>
    </CellTypes>
    <CPM>
        <Interaction default="0.0">
            <Contact type1="cells" type2="medium" value="-10"/>
            <Contact type1="cells" type2="cells" value="-20"/>
        </Interaction>
        <MonteCarloSampler stepper="edgelist">
            <MCSDuration value="1.0"/>
            <Neighborhood>
                <Order>2</Order>
            </Neighborhood>
            <MetropolisKinetics temperature="10.0"/>
        </MonteCarloSampler>
        <ShapeSurface scaling="norm">
            <Neighborhood>
                <Distance>2.5</Distance>
            </Neighborhood>
        </ShapeSurface>
    </CPM>
    <CellPopulations>
        <Population size="0" type="cells">
            <InitRectangle mode="regular" number-of-cells="cell_density * size.x * size.y">
                <Dimensions size="size.x, size.y, 0" origin="0.0, 0.0, 0.0"/>
            </InitRectangle>
        </Population>
    </CellPopulations>
    <Analysis>
        <Gnuplotter time-step="500" decorate="false">
            <Terminal opacity="0.55" persist="true" name="png"/>
            <Plot>
                <Field symbol-ref="U" isolines="5" min="0.0" surface="true"/>
                <Cells>
                    <ColorMap>
                        <Color value="2.0" color="gray"/>
                        <Color value="0" color="gray"/>
                    </ColorMap>
                </Cells>
            </Plot>
        </Gnuplotter>
        <DependencyGraph format="svg" exclude-plugins="Gnuplotter"/>
    </Analysis>
</MorpheusModel>