Team:Paris Saclay/modeling/fnr0.xml

<?xml version="1.0" encoding="ISO-8859-1"?>

<sim>

<yscale>1300</yscale>

<volume>0.7</volume> <!-- 0.7 micrometres cube -->
<timestep>0.0001</timestep> <!-- seconde -->
<alpha>7.4e-7</alpha> <!-- alpha -->

<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" -->

<molecule name="FNR" quantity="5000"  adjustable="true"/>
<molecule name="O2" const="true" adjustable="true" quantity="10000"/>
<molecule name="FNR_ox"  adjustable="true"/>
<molecule name="Pfnr_activator" quantity="1" adjustable="true"/>
<molecule name="Pfnr_activator_bond" adjustable="true"/>
<molecule name="GP" curve_show="true" curve_color="#00AA00" adjustable="true"/>
<molecule name="Pfnr_repressor" quantity="1" adjustable="true"/>
<molecule name="Pfnr_repressor_bond" adjustable="true"/>
<molecule name="BP" curve_show="true" curve_color="#0000FF" adjustable="true"/>

<!-- FNR oxydation -->
<reaction probability="0.9">
 <in>FNR</in>
 <in>O2</in>
 <out>FNR_ox</out>
</reaction>
<!-- FNR reduction -->
<reaction probability="0.0001">
 <in>FNR_ox</in>
 <out>O2</out>
 <out>FNR</out>
</reaction>

<!-- Activating promoter bonding -->
<reaction probability="0.8">
 <in>FNR</in>
 <in>Pfnr_activator</in>
 <out>Pfnr_activator_bond</out>
</reaction>
<!-- Activating promoter unbonding -->
<reaction probability="0.001">
 <in>Pfnr_activator_bond</in>
 <out>Pfnr_activator</out>
 <out>FNR</out>
</reaction>
<!-- Green reporter protein production -->
<reaction probability="0.005">
 <in>Pfnr_activator_bond</in>
 <out>Pfnr_activator_bond</out>
 <out>GP</out>
</reaction>


<!-- Repressor bonding -->
<reaction probability="0.8">
 <in>FNR</in>
 <in>Pfnr_repressor</in>
 <out>Pfnr_repressor_bond</out>
</reaction>
<!-- Repressor unbonding -->
<reaction probability="0.001">
 <in>Pfnr_repressor_bond</in>
 <out>Pfnr_repressor</out>
 <out>FNR</out>
</reaction>
<!-- Blue reporter protein production -->
<reaction probability="0.01">
 <in>Pfnr_repressor</in>
 <out>Pfnr_repressor</out>
 <out>BP</out>
</reaction>

<!-- Reporter degradation -->
<reaction probability="0.0001">
 <in>GP</in>
</reaction>
<reaction probability="0.0001">
 <in>BP</in>
</reaction>

</sim>