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Team:Paris Saclay/modeling/fnr0.xml
From 2013.igem.org
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<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" --> | <!-- Molecule declaration curve_show="true" curve_color="#AAAA00" --> | ||
| - | <molecule name="FNR" quantity=" | + | <molecule name="FNR" quantity="1200" adjustable="true"/> |
| - | <molecule name="O2" const="true" adjustable="true" quantity=" | + | <molecule name="O2" const="true" adjustable="true" quantity="5000"/> |
<molecule name="FNR_ox" adjustable="true"/> | <molecule name="FNR_ox" adjustable="true"/> | ||
<molecule name="Pfnr_activator" quantity="1" adjustable="true"/> | <molecule name="Pfnr_activator" quantity="1" adjustable="true"/> | ||
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<!-- Activating promoter bonding --> | <!-- Activating promoter bonding --> | ||
| - | <reaction probability=" | + | <reaction probability="0.8"> |
<in>FNR</in> | <in>FNR</in> | ||
<in>Pfnr_activator</in> | <in>Pfnr_activator</in> | ||
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</reaction> | </reaction> | ||
<!-- Activating promoter unbonding --> | <!-- Activating promoter unbonding --> | ||
| - | <reaction probability="0. | + | <reaction probability="0.0001"> |
<in>Pfnr_activator_bond</in> | <in>Pfnr_activator_bond</in> | ||
<out>Pfnr_activator</out> | <out>Pfnr_activator</out> | ||
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</reaction> | </reaction> | ||
<!-- Green reporter protein production --> | <!-- Green reporter protein production --> | ||
| - | <reaction probability="0. | + | <reaction probability="0.0001"> |
<in>Pfnr_activator_bond</in> | <in>Pfnr_activator_bond</in> | ||
<out>Pfnr_activator_bond</out> | <out>Pfnr_activator_bond</out> | ||
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<!-- Repressor bonding --> | <!-- Repressor bonding --> | ||
| - | <reaction probability=" | + | <reaction probability="0.8"> |
<in>FNR</in> | <in>FNR</in> | ||
<in>Pfnr_repressor</in> | <in>Pfnr_repressor</in> | ||
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</reaction> | </reaction> | ||
<!-- Repressor unbonding --> | <!-- Repressor unbonding --> | ||
| - | <reaction probability="0. | + | <reaction probability="0.0001"> |
<in>Pfnr_repressor_bond</in> | <in>Pfnr_repressor_bond</in> | ||
<out>Pfnr_repressor</out> | <out>Pfnr_repressor</out> | ||
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</reaction> | </reaction> | ||
<!-- Blue reporter protein production --> | <!-- Blue reporter protein production --> | ||
| - | <reaction probability="0. | + | <reaction probability="0.0001"> |
<in>Pfnr_repressor</in> | <in>Pfnr_repressor</in> | ||
<out>Pfnr_repressor</out> | <out>Pfnr_repressor</out> | ||
Revision as of 22:54, 9 September 2013
<?xml version="1.0" encoding="ISO-8859-1"?>
<sim>
<yscale>1300</yscale>
<volume>0.7</volume> <timestep>0.0001</timestep> <alpha>7.4e-7</alpha>
<molecule name="FNR" quantity="1200" adjustable="true"/>
<molecule name="O2" const="true" adjustable="true" quantity="5000"/>
<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"/>
<reaction probability="0.8">
<in>FNR</in> <in>O2</in> <out>FNR_ox</out>
</reaction> <reaction probability="0.002">
<in>FNR_ox</in> <out>O2</out> <out>FNR</out>
</reaction>
<reaction probability="0.8">
<in>FNR</in> <in>Pfnr_activator</in> <out>Pfnr_activator_bond</out>
</reaction> <reaction probability="0.0001">
<in>Pfnr_activator_bond</in> <out>Pfnr_activator</out> <out>FNR</out>
</reaction> <reaction probability="0.0001">
<in>Pfnr_activator_bond</in> <out>Pfnr_activator_bond</out> <out>GP</out>
</reaction>
<reaction probability="0.8">
<in>FNR</in> <in>Pfnr_repressor</in> <out>Pfnr_repressor_bond</out>
</reaction> <reaction probability="0.0001">
<in>Pfnr_repressor_bond</in> <out>Pfnr_repressor</out> <out>FNR</out>
</reaction> <reaction probability="0.0001">
<in>Pfnr_repressor</in> <out>Pfnr_repressor</out> <out>BP</out>
</reaction>
<reaction probability="0.0001">
<in>GP</in>
</reaction> <reaction probability="0.0001">
<in>BP</in>
</reaction>
</sim>
