Difference between revisions of "Team:Aalto-Helsinki/Modeling propane"
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<ul id="sidenav" class="nav nav-stacked bottom"><!-- nav-pills if we want rounded corners --> | <ul id="sidenav" class="nav nav-stacked bottom"><!-- nav-pills if we want rounded corners --> | ||
− | <li><a href="#introduction"><h3>Introduction</h3></a></li> | + | <li><a href="#" data-scroll="introduction"><h3>Introduction</h3></a></li> |
− | <li><a href="#mm"><h3>Materials and methods</h3></a></li> | + | <li><a href="#" data-scroll="mm"><h3>Materials and methods</h3></a></li> |
− | <li><a href="#results"><h3>Results and implications</h3></a></li> | + | <li><a href="#" data-scroll="results"><h3>Results and implications</h3></a></li> |
− | <li><a href="#discussion"><h3 style="border-bottom:solid;">Discussion</h3></a></li> | + | <li><a href="#" data-scroll="discussion"><h3 style="border-bottom:solid;">Discussion</h3></a></li> |
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<!-- Introduction --> | <!-- Introduction --> | ||
− | < | + | <section id="introduction" data-anchor="introduction"> |
+ | <h2> Introduction </h2> | ||
<p>Propane is a commonly used, convenient and clean-burning fuel, currently produced from non-renewable sources. Our project is about producing propane in bacteria, paving way for its sustainable production from renewable biomass. Ultimately, the pathway could be transferred to cyanobacteria, producing propane from CO2 and solar energy. </p> | <p>Propane is a commonly used, convenient and clean-burning fuel, currently produced from non-renewable sources. Our project is about producing propane in bacteria, paving way for its sustainable production from renewable biomass. Ultimately, the pathway could be transferred to cyanobacteria, producing propane from CO2 and solar energy. </p> | ||
<p> In our mathematical model our goal is to grasp the important concepts underlying the experiments made in the lab, and to see how those concepts could help us produce more propane. By having a better understanding of the ideas that govern our project, we could see the influence of each compound in the reaction pathway and have a basis to make decisions that would have a long term impact in our results.</p> | <p> In our mathematical model our goal is to grasp the important concepts underlying the experiments made in the lab, and to see how those concepts could help us produce more propane. By having a better understanding of the ideas that govern our project, we could see the influence of each compound in the reaction pathway and have a basis to make decisions that would have a long term impact in our results.</p> | ||
+ | </section> | ||
− | + | <section id="mm" data-anchor="mm"> | |
− | < | + | <h2>Materials and methods: Building the model / our pathway</h2> |
<p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a basic way to model enzyme reactions that assumes that the change that enzyme causes is faster than the binding of the enzyme and releasing of the substrate.</p> | <p>We built a model of our propane pathway based on Michaelis-Menten enzyme kinetics. It is a basic way to model enzyme reactions that assumes that the change that enzyme causes is faster than the binding of the enzyme and releasing of the substrate.</p> | ||
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<p>For modeling this propane pathway we used <a href="http://www.copasi.org/tiki-view_articles.php">Copasi</a> and <a href="http://se.mathworks.com/">Matlab</a>.</p> | <p>For modeling this propane pathway we used <a href="http://www.copasi.org/tiki-view_articles.php">Copasi</a> and <a href="http://se.mathworks.com/">Matlab</a>.</p> | ||
+ | </section> | ||
− | < | + | <section id="results" data-anchor="results"> |
+ | <h2>Results and implications</h2> | ||
<p>Here text about our results in all subcategories:</p> | <p>Here text about our results in all subcategories:</p> | ||
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<div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/b/ba/Aalto-Helsinki_Michaelis_plots_varying_enzymes.png" style="max-width:100%;" /></div> | <div style="width:80%;margin-left:auto;margin-right:auto;"><img src="https://static.igem.org/mediawiki/2015/b/ba/Aalto-Helsinki_Michaelis_plots_varying_enzymes.png" style="max-width:100%;" /></div> | ||
+ | </section> | ||
− | + | <section id="sensitivity" data-anchor="sensitivity"> | |
<h3 id="sensitivity">Sensitivity analysis</h3> | <h3 id="sensitivity">Sensitivity analysis</h3> | ||
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<p>The predicted amount of propane produced isn't very high. To produce propane more efficiently in the future, we would need to greatly improve the performance of our pathway. This could be done by taking a look into bottlenecks of our pathway and other limiting factors such as NADPH.</p> | <p>The predicted amount of propane produced isn't very high. To produce propane more efficiently in the future, we would need to greatly improve the performance of our pathway. This could be done by taking a look into bottlenecks of our pathway and other limiting factors such as NADPH.</p> | ||
+ | </section> | ||
− | + | <section id="discussion" data-anchor="discussion"> | |
− | < | + | <h2>Discussion</h2> |
<p>Our model isn't perfect. We have made a lot of simplifying assumptions when building the model, maybe the most important of them being irreversibility of reversible reactions. Even though the reactions were quite strongly forward-favored the accuracy might suffer.</p> | <p>Our model isn't perfect. We have made a lot of simplifying assumptions when building the model, maybe the most important of them being irreversibility of reversible reactions. Even though the reactions were quite strongly forward-favored the accuracy might suffer.</p> | ||
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<p>One disadvantage in our model of propane pathway is that it isn't taking into account anything that is happening outside the cell. Right now we have for example NADPH concentration as a constant in the model, but what if its creation is so slow that it becomes a problem? This and similar questions remain unanswered.</p> | <p>One disadvantage in our model of propane pathway is that it isn't taking into account anything that is happening outside the cell. Right now we have for example NADPH concentration as a constant in the model, but what if its creation is so slow that it becomes a problem? This and similar questions remain unanswered.</p> | ||
+ | </section> | ||
</div> | </div> | ||
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Revision as of 06:15, 19 August 2015