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Team:UFMG Brazil/Modeling
From 2013.igem.org
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<div id="variables_description"> | <div id="variables_description"> | ||
| - | + | $M$ is TMAO. | |
T is TorT. | T is TorT. | ||
Revision as of 19:11, 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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