Difference between revisions of "Team:Paris Bettencourt/Model"

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<h2> Modeling</h2>
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    width : 80%;
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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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<h5> Inspiration </h5>
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<div id=topheader> </div>
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<h1 class="red">Modelling Group: Computationally model stain removal using enzymes </h1>
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<!----------------------- BEGIN SUMMARY BOXES-------------------------> 
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<div class="projtile1">
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    <h2 class="red" style="text-align:center;">Goals</h2>
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    <ul>
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        <li>To make a computational model to analyze stain-enzyme dynamics</li>
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        <li>To find optimum parameters</li>
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    </ul>
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</div>
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<div style="clear: both;"></div>
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<div class="projtile2">
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    <h2 class="red" style="text-align:center;">BioBricks</h2>
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            <ul>
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                  <li>BioBrick 1
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                  <li>BioBrick 2
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                  <li>BioBrick 3
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            </ul>
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</div>
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<div style="clear: both;"></div>
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<div class="projtile3">
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      <h2 class="red" style="text-align:center;">Results</h2>
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      <ul>
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            <li> Developed a differential equation model to analyze stain dynamics
 +
            <li> A computational approach using Gillespie algorithm
 +
            <li> A computational approach using explicit finite difference method for three dimensional modelling
 +
 
 +
      </ul>
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</div>
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<div style="clear: both;"></div>
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<div class="projtile4">
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    <h2 class="red" style="text-align:center;">Methods</h2>
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    <ul>
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        <li>Matlab
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        <li>ODE solvers
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        <li>Gillespie Algorithm
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        <li>Explicit Finite Difference method (FDM)
 +
    </ul>
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</div>
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<div style="clear: both;"></div>
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<!----------------------- END SUMMARY BOXES------------------------->   
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<div id=subheader>
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<div id="input">
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<h2 class="red">Abstract</h2>
 
<p>
 
<p>
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Here are a few examples from previous teams:
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<b>
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<br>
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</b>
 
</p>
 
</p>
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<h2 class="red"> Motivation and Background</h2>
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<h3>Challenge: Modelling stain removal in a compact washing machine</h3>
 +
 +
<p>
 +
A typical garment is composed of several square meters of fabric and a typical washing machine has a volme of 100 liters.
 +
 +
<br>
 +
 +
</p>
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 +
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<div id="figurebox">
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<img src="https://static.igem.org/mediawiki/2016/9/9c/Paris_Bettencourt-Project_Model_Model_Equations.jpg" alt="Quercetin strains degradation" style="width:500px;">
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<p>
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<b> Example figure box</b>
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</p>
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</div>
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 +
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<h2 class="red">Results</h2>
 +
 +
<h3>Model1: Ode-based</h3>
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 +
<h3>Model2: Gillespie Algorithm-based</h3>
 +
 +
<h3>Model3: 3D modelling using FDM</h3>
 +
 +
 +
 +
 +
<br>
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</p>
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<h2 class="red">Methods</h2>
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 +
                           
 +
<p>
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blabla ###.
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</p>
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 +
 +
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<h2 class="red">Attributions</h3>
 +
<p>
 +
This project was done mostly by Jake Wintermute, Mislav Acman and Mani Sai Suryateja Jammalamadaka. 
 +
</p>
 +
 +
<h2 class="red">References</h2>
 
<ul>
 
<ul>
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
+
        <li>
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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        <li>
 +
        <li>
 
</ul>
 
</ul>
  
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</div> <! End subheader Div> 
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    Assay
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    <center><img src="https://static.igem.org/mediawiki/2016/f/f8/Paris_Bettencourt-Logo_Microbiology.png" style="height:60px;"/></center>
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    Microbiology
 +
  </div>
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</div>
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      </a>
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      <a href="https://2016.igem.org/Team:Paris_Bettencourt/Project/Enzyme" title="Enzyme">
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    <center><img src="https://static.igem.org/mediawiki/2016/9/9d/Paris_Bettencourt-Logo_Enzyme.png" style="height:60px;"/></center>
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  Enzyme
 +
  </div>
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</div>
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    Binding
 +
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</div>
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 +
    <center><img src="https://static.igem.org/mediawiki/2016/f/f0/Paris_Bettencourt-Logo_Indigo.png" style="height:60px;"/></center>
 +
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 +
    Indigo
 +
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 +
</div>
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      </a>
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{{Paris_Bettencourt/Footer2}}

Revision as of 15:55, 18 October 2016


Modelling Group: Computationally model stain removal using enzymes

Goals

  • To make a computational model to analyze stain-enzyme dynamics
  • To find optimum parameters

BioBricks

  • BioBrick 1
  • BioBrick 2
  • BioBrick 3

Results

  • Developed a differential equation model to analyze stain dynamics
  • A computational approach using Gillespie algorithm
  • A computational approach using explicit finite difference method for three dimensional modelling

Methods

  • Matlab
  • ODE solvers
  • Gillespie Algorithm
  • Explicit Finite Difference method (FDM)

Abstract

Motivation and Background

Challenge: Modelling stain removal in a compact washing machine

A typical garment is composed of several square meters of fabric and a typical washing machine has a volme of 100 liters.

Quercetin strains degradation

Example figure box

Results

Model1: Ode-based

Model2: Gillespie Algorithm-based

Model3: 3D modelling using FDM


Methods

blabla ###.

Attributions

This project was done mostly by Jake Wintermute, Mislav Acman and Mani Sai Suryateja Jammalamadaka.

References

Centre for Research and Interdisciplinarity (CRI)
Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
Paris Descartes University
24, rue du Faubourg Saint Jacques
75014 Paris, France
+33 1 44 41 25 22/25
igem2016parisbettencourt@gmail.com
2016.igem.org