Topology-streamlines.cece

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<!-- Simulation definition -->
<simulation world-size="1280um 800um" dt="13ms" background="#C0C0C0" length-coefficient="1e-1">

    <plugin name="cell" />
    <plugin name="obstacle" />
    <plugin name="streamlines" />
    <plugin name="diffusion-streamlines" />
    <plugin name="stochastic-reactions" />
    <plugin name="object-generator" />
    <plugin name="obstacles-svg" filename="Topology-streamlines.svg" color="white" />

    <!-- Define visualization layers -->
    <visualization enabled="true">
        <layer name="velocity" key="V" />
        <layer name="density" key="B" />
        <layer name="physics" key="D" />
        <layer name="fluid" key="N" />
    </visualization>

    <!-- Define diffusion module -->
    <module name="diffusion" grid="641 401" inner-iterations="2">
        <signal name="GFP" diffusion-rate="50um2/s" degradation-rate="0.01/s" color="green"  saturation="0.010uM" />
        <signal name="RFP" diffusion-rate="50um2/s" degradation-rate="0.01/s" color="red"    saturation="0.010uM" />
        <signal name="YFP" diffusion-rate="50um2/s" degradation-rate="0.01/s" color="yellow" saturation="0.010uM" />
    </module>

    <!-- Define streamlines -->
    <module name="streamlines"
            inlet-velocity="200um/s"
            layout="none outlet none inlet"
            init-iterations="20000"
            init-file="%temp%/Topology-streamlines.cece.streamlines"
            char-length="40um"
            number-nodes="20"
            tau="1.5"
            dynamic="false"
            height="40um"
            layer-magnitude="velocity"
            layer-density="density"
            layer-dynamics="fluid"
    />

    <program name="p1" language="stochastic-reactions">
<![CDATA[
        null > 90/s > env GFP;
        if env RFP > 1nM: null > 30/s > GFP;
]]>
    </program>

    <program name="p2" language="stochastic-reactions">
<![CDATA[
        null > 90/s > env RFP;
        if env GFP > 1nM: null > 30/s > RFP;
]]>
    </program>

    <!-- Generate yeast cells -->
    <module name="object-generator">
        <object class="cell.Yeast" rate="10/s" programs="p1" velocity="50um/s 0" position-min="-600um -300um" position-max="-600um -200um" />
        <object class="cell.Yeast" rate="10/s" programs="p2" velocity="50um/s 0" position-min="-600um -300um" position-max="-600um -200um" />
    </module>

</simulation>