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Team:UFMG Brazil/Modeling
From 2013.igem.org
(Difference between revisions)
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<div id="variables_description"> | <div id="variables_description"> | ||
| - | $M$ is TMAO. | + | <p> $M$ is TMAO. </p> |
| - | + | <p> $T$ is TorT. </p> | |
| - | $T$ is TorT. | + | <p> $TM$ is the complex of T and M. </p> |
| - | + | <p> $S$ is TorS. </p> | |
| - | $TM$ is the complex of T and M. | + | <p> $STM$ is the complex of S and TM. </p> |
| - | + | <p> $R$ is TorR. </p> | |
| - | $S$ is TorS. | + | <p> $R^{ *}$ is TorR Phosophorilated. </p> |
| - | + | ||
| - | $STM$ is the complex of S and TM. | + | |
| - | + | ||
| - | $R$ is TorR. | + | |
| - | + | ||
| - | $R^{ *}$ is TorR Phosophorilated. | + | |
</div> | </div> | ||
| - | + | <p> Reactions: </p> | |
| - | Reactions: | + | |
\[ | \[ | ||
Revision as of 19:13, 23 June 2013
This is the sketch of our modeling. We are going to use TMAO as a biomarker.
$M$ is TMAO.
$T$ is TorT.
$TM$ is the complex of T and M.
$S$ is TorS.
$STM$ is the complex of S and TM.
$R$ is TorR.
$R^{ *}$ is TorR Phosophorilated.
Reactions:
\[ \begin{aligned} \\ $M+T{{k_{1} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-1}}}TM$ \\ $2TM+S{{k_{2} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-2}}}STM$ \\ $STM+R{{k_{3} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-3}}} X {{k_{cat}\atop\longrightarrow} \atop {\quad \atop \quad }}R^{ *} + STM$ \\ $R^{ *} + P {{\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow}} PR^{ *}$ \\ \begin{eqnarray} \begin{cases} {d M(t)\over d t}&=& -k_1 \cdot M\cdot T + k_{-1}\cdot TM\\\\ \\\\ {d T(t)\over d t}&=& -k_1 \cdot M\cdot T + k_{-1}\cdot TM\\\\ \\\\ {d TM(t)\over d t}&=& k_1 \cdot M\cdot T - k_{-1}\cdot TM - k_2\cdot TM^{2} \cdot S + k_{-2} \cdot STM\\\\ \\\\ {d S(t)\over d t}&=& -k_2 \cdot S\cdot TM^{2} - k_{-1}\cdot TM - k_2\cdot TM^{2} \cdot S + k_{-2} \cdot STM\\\\ \\\\ {d STM(t)\over d t}&=& k_2 \cdot TM^{2} \cdot S - k_{-2}\cdot STM \\\\ \\\\ {d R^{ *}(t)\over d t}&=& k_{cat}\cdot STM \over{k_m + STM}\\\\ \\\\ {d mRNA(t)\over d t}&=& {\alpha \cdot R^{ *^{\gamma}} \over{\beta + R^{ *^{\gamma}}}} - \mu \cdot mRNA\\\\ \\ \end{cases} \end{eqnarray} \\ \end{aligned} \]
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