Difference between revisions of "Team:Aalto-Helsinki/Modeling"
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<h2>Models of propane pathway</h2> | <h2>Models of propane pathway</h2> | ||
− | <p>The main goal of our project was the production of propane with <span style="font-style:italic;">E. coli</span>, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with <a href="http:// | + | <p>The main goal of our project was the production of propane with <span style="font-style:italic;">E. coli</span>, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with <a href="http://copasi.org/" target="_blank">Copasi</a> and <a href="http://se.mathworks.com/" target="_blank">Matlab</a>. With these tools we found the bottlenecks and most sensitive parts of our reaction. We also got some ideas on how much propane will be produced in our system. For more information, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_propane">modeling propane pathway</a>.</p> |
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− | <p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the | + | <p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the of the last enzymes in our pathway, CAR and ADO, who have toxic butyraldehyde as a substrate between them. Since there are many butyraldehyde-consuming enzymes in a cell, the speed up we could get would be even better. We did a <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_synergy">stochastic model of synergy with python</a> to confirm if this approach would really work as we hope.</p> |
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<h2>Cellulose pathway</h2> | <h2>Cellulose pathway</h2> | ||
− | <p style="padding-bottom:8%;">Our project involves creating renewable propane from cellulose, which is why we wanted to model the pathway responsible for hydrolysing cellulose. The pathway consists of three different genes that cut the cellulose to glucose which the cell can then use as an energy source for propane production. While building a beneficial model of this wasn't possible for us, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">modeling cellulose pathway</a> to see what thoughts our modeling team had on this.</p> | + | <p style="padding-bottom:8%;margin-bottom:0;">Our project involves creating renewable propane from cellulose, which is why we wanted to model the pathway responsible for hydrolysing cellulose. The pathway consists of three different genes that cut the cellulose to glucose which the cell can then use as an energy source for propane production. While building a beneficial model of this wasn't possible for us, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">modeling cellulose pathway</a> to see what thoughts our modeling team had on this.</p> |
<!--<p>In our project we produce propane from cellulose, so our modeling team also <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">took a look into cellulose pathway</a>.</p>--> | <!--<p>In our project we produce propane from cellulose, so our modeling team also <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">took a look into cellulose pathway</a>.</p>--> | ||
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Latest revision as of 21:27, 18 September 2015