Team:Paris Saclay/modeling/fnr0.xml

From 2013.igem.org

(Difference between revisions)
Line 3: Line 3:
<sim>
<sim>
-
<yscale>300</yscale>
+
<yscale>1300</yscale>
<volume>0.7</volume> <!-- 0.7 micrometres cube -->
<volume>0.7</volume> <!-- 0.7 micrometres cube -->
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<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" -->
<!-- Molecule declaration curve_show="true" curve_color="#AAAA00" -->
-
<molecule name="FNR" quantity="5000"  adjustable="true"/>
+
<molecule name="FNR" quantity="10000"  adjustable="true"/>
<molecule name="O2" const="true" adjustable="true" quantity="5000"/>
<molecule name="O2" const="true" adjustable="true" quantity="5000"/>
<molecule name="FNR_ox"  adjustable="true"/>
<molecule name="FNR_ox"  adjustable="true"/>

Revision as of 16:55, 8 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="10000" 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="0.2">

<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="1.2">

<in>FNR</in>
<in>Pfnr_activator</in>
<out>Pfnr_activator_bond</out>

</reaction> <reaction probability="0.005">

<in>Pfnr_activator_bond</in>
<out>Pfnr_activator</out>
<out>FNR</out>

</reaction> <reaction probability="0.025">

<in>Pfnr_activator_bond</in>
<out>Pfnr_activator_bond</out>
<out>GP</out>

</reaction>


<reaction probability="0.9">

<in>FNR</in>
<in>Pfnr_repressor</in>
<out>Pfnr_repressor_bond</out>

</reaction> <reaction probability="0.001">

<in>Pfnr_repressor_bond</in>
<out>Pfnr_repressor</out>
<out>FNR</out>

</reaction> <reaction probability="0.018">

<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>