Team:UFMG Brazil/Modeling

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=Modeling=
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Given the complexity regarding both detection systems, we made computational models to describe them, and to try and predict their behaviour, so as to aid on the lab experiments. Check out our models for <a href='https://2013.igem.org/Team:UFMG_Brazil/TMAO'>TMAO</a> and <a href='https://2013.igem.org/Team:UFMG_Brazil/IMA'>IMA</a>.
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This is the sketch of our modeling.<br>
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We are going to use TMAO as a biomarker.
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<div id="variables_description">
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<p> $M$ is TMAO. </p>
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<p> $T$ is TorT. </p>
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<p> $TM$ is the complex of T and M. </p>
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<p> $S$ is TorS. </p>
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<p> $STM$ is the complex of S and TM. </p>
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<p> $R$ is TorR. </p>
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<p> $R^{ *}$ is TorR Phosophorilated. </p>
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<p><h1> Reactions:</h1></p>
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\[
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\begin{aligned}
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\\
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M+T{{k_{1} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-1}}}TM
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\\
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2TM+S{{k_{2} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-2}}}STM
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\\
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STM+R{{k_{3} \atop\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow \atop k_{-3}}} X {{k_{cat}\atop\longrightarrow} \atop {\quad  \atop \quad }}R^{ *} + STM
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\\
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R^{ *} + P {{\displaystyle\longrightarrow} \atop {\displaystyle\longleftarrow}} PR^{ *}
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\\
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\begin{eqnarray}
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\begin{cases}
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{d M(t)\over d t}&=& -k_1 \cdot  M\cdot T + k_{-1}\cdot TM\\\\
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\\\\
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{d T(t)\over d t}&=& -k_1 \cdot  M\cdot T + k_{-1}\cdot TM\\\\
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\\\\
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{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\\\\
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\\\\
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{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\\\\
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\\\\
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{d STM(t)\over d t}&=& k_2 \cdot  TM^{2} \cdot S - k_{-2}\cdot STM \\\\
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\\\\
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{d R^{ *}(t)\over d t}&=& k_{cat}\cdot STM \over{k_m + STM}\\\\
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\\\\
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{d mRNA(t)\over d t}&=& {\alpha \cdot  R^{ *^{\gamma}} \over{\beta + R^{ *^{\gamma}}}} - \mu \cdot mRNA\\\\
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\\
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\end{cases}
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\end{eqnarray}
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\\
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\end{aligned}
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Latest revision as of 17:49, 28 October 2013

Modeling

Given the complexity regarding both detection systems, we made computational models to describe them, and to try and predict their behaviour, so as to aid on the lab experiments. Check out our models for TMAO and IMA.

Our Sponsors

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