Difference between revisions of "Team:UMaryland/Model"

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<div class="titleText">Modeling</div>
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<div class="subtitleText">Why Degrade to PCA?</div>
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Our PET degradation system is entirely cell free, created from lysed cells that have had the pathway enzymes inserted into their genomes as plasmids. PET degradation starts with the cleavage of the monomers of PET into their constituents, MHET and TPA, by the enzyme PETase.<br><br>
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We created cells that can act as a sensor for PET degradation. When the cells import PCA (a molecule produced from degraded TPA, which is produced from degraded PET),  PCAU binds to PCA, creating activated PCAU. Using activated PCAU as the promoter for GFP translation, the cells will fluoresce green in the presence of PCA, showing that PET degradation has occurred.<br><br>
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All of the parameters of our model have been taken from experimentally verified results, and we have verified the validity of our model by successfully detecting PCA using our modified  cells.<br><br>
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We attempted to go further down the degradation pathway with the same cells metabolising PCA into 3-carboxy-cis,cis-muconate, but were unsuccessful. We leave this part of the pathway to future IGEM teams and researchers.<br>
  
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Explaination of our Parameters
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<h1> Modeling</h1>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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It's really long. Just download this <a href="https://static.igem.org/mediawiki/2018/e/e7/T--UMaryland--simbioparameters.xlsx"><u>Excel file</u></a> instead.
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Results of Simulation
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<h3> Gold Medal Criterion #3</h3>
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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<img src="https://static.igem.org/mediawiki/2018/a/a9/T--UMaryland--modelresults.png" style="max-width: 100%" alt="Waluigi Time!">
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<div class="imageBoxDescription">Figure 1 - Results of the model</div>
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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Medals Page</a> for more information.  
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Comparison to Experimental Results
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<h3>Best Model Special Prize</h3>
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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<h3> Inspiration </h3>
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Here are a few examples from previous teams:
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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Revision as of 23:20, 15 October 2018

Template Title Template Title

Modeling
Why Degrade to PCA?
Our PET degradation system is entirely cell free, created from lysed cells that have had the pathway enzymes inserted into their genomes as plasmids. PET degradation starts with the cleavage of the monomers of PET into their constituents, MHET and TPA, by the enzyme PETase.

We created cells that can act as a sensor for PET degradation. When the cells import PCA (a molecule produced from degraded TPA, which is produced from degraded PET), PCAU binds to PCA, creating activated PCAU. Using activated PCAU as the promoter for GFP translation, the cells will fluoresce green in the presence of PCA, showing that PET degradation has occurred.

All of the parameters of our model have been taken from experimentally verified results, and we have verified the validity of our model by successfully detecting PCA using our modified cells.

We attempted to go further down the degradation pathway with the same cells metabolising PCA into 3-carboxy-cis,cis-muconate, but were unsuccessful. We leave this part of the pathway to future IGEM teams and researchers.
Explaination of our Parameters
It's really long. Just download this Excel file instead.
Results of Simulation
Waluigi Time!
Figure 1 - Results of the model
Comparison to Experimental Results

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