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Team:Paris Bettencourt/Modeling/Designs
From 2011.igem.org
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<h1>Modeling our constructs</h1> | <h1>Modeling our constructs</h1> | ||
| - | <p>We modeled | + | <p>We modeled our constructs when it was relevant. We chose not to model the <a href="https://2011.igem.org/Team:Paris_Bettencourt/GFPLac_diffusion">YFP-TetR design</a> since it does not involve any feedback or amplification but rather a simple change in phenotype (apparition of fluorescence dots). For the <a href="https://2011.igem.org/Team:Paris_Bettencourt/Lambda_switch">Lambda switch</a> and the <a href="https://2011.igem.org/Team:Paris_Bettencourt/SinOp">Sin Operon</a>, extensive models already existed for those switches we hi-jacked. We therefore prefered to focus on the new devices and the ComS/ComK system.</p> |
| + | <p>The models for <em>T7 RNA polymerase diffusion</em>, <em>tRNA amber diffusion</em> and <em>ComS diffusion</em> can be found here:</p> | ||
<table> | <table> | ||
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<td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/T7_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/e/e4/T7_button.png"></a> | <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/T7_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/e/e4/T7_button.png"></a> | ||
</td> | </td> | ||
| - | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/T7_diffusion">T7 polymerase diffusion</a> | + | <td><em><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/T7_diffusion">T7 polymerase diffusion</a></em> The model suggest that this system should be very sensitive, requiring only a few T7 RNA polymerases passing through the tubes to be activated. You can find more about it <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/T7_diffusion">here</a>. |
</td> | </td> | ||
</tr> | </tr> | ||
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<td style="width:200px; text-align:center;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/tRNA_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/5/53/TRNAamber-button.png"></a> | <td style="width:200px; text-align:center;"><a href="https://2011.igem.org/Team:Paris_Bettencourt/tRNA_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/5/53/TRNAamber-button.png"></a> | ||
</td> | </td> | ||
| - | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion">tRNA amber diffusion</a> | + | <td><em><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion">tRNA amber diffusion</a></em> For this design, we had to investigate further the <a href="https://2011.igem.org/Team:Paris_Bettencourt/tRNA_diffusion/Random_walker">diffusion assumptions</a>. The model suggest that this construct will work perfectly in a reasonable time. You can find more about it <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/tRNA_diffusion">here</a> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/2/21/ComS-button.png"></a> | <td style="width:200px; text-align:center"><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion"><img style="width:150px; margin-top:20px;" src="https://static.igem.org/mediawiki/2011/2/21/ComS-button.png"></a> | ||
</td> | </td> | ||
| - | <td><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion"> | + | <td><em><a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion">ComK/ComS system</a></em> This model is less strong than the other ones. The ComK/ComS system exists only outside of exponential phase. The parameters we have are therefore only assumptions. The model also suggest that stochastic leakage might lead to very noisy signal. You can find more about it <a href="https://2011.igem.org/Team:Paris_Bettencourt/Modeling/ComS_diffusion">here</a>. |
</td> | </td> | ||
</tr> | </tr> | ||
Latest revision as of 13:11, 10 October 2011
Modeling our constructs
We modeled our constructs when it was relevant. We chose not to model the YFP-TetR design since it does not involve any feedback or amplification but rather a simple change in phenotype (apparition of fluorescence dots). For the Lambda switch and the Sin Operon, extensive models already existed for those switches we hi-jacked. We therefore prefered to focus on the new devices and the ComS/ComK system.
The models for T7 RNA polymerase diffusion, tRNA amber diffusion and ComS diffusion can be found here:
|
T7 polymerase diffusion The model suggest that this system should be very sensitive, requiring only a few T7 RNA polymerases passing through the tubes to be activated. You can find more about it here. |
|
tRNA amber diffusion For this design, we had to investigate further the diffusion assumptions. The model suggest that this construct will work perfectly in a reasonable time. You can find more about it here |
|
ComK/ComS system This model is less strong than the other ones. The ComK/ComS system exists only outside of exponential phase. The parameters we have are therefore only assumptions. The model also suggest that stochastic leakage might lead to very noisy signal. You can find more about it here. |
