Difference between revisions of "Team:Edinburgh/Modeling"

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<h2> Modeling</h2>
 
  
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Team">Team</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Attributions">Attributions</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Collaborations">Collaboration</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Sponsors">Sponsors</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Description">Overview</a></li>
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                    <!-- <li><a href="https://2015.igem.org/Team:Edinburgh/Experiments">Experiments</a> </li> -->
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/HeroinBiosensor">Heroin Biosensor</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/DNPBiosensor">DNP Biosensor</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/PMABiosensor">PMA Biosensor</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/CBD">Making it Stick</a></li>           
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Results">Limits of Detection</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Parts">Team Parts</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Part_Collection">Part Collection</a> </li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Improved_Part">Improved Parts</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Characterisation_Part">Improved Characterisation</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Modeling">Modeling</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Design">Design</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Software">Software</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Safety">Safety</a> </li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Outreach">Outreach</a> </li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Project/Protocols">Protocols</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Notebook/HeroinPurity">Heroin Purity</a></li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Notebook/PMADetection">PMA Detection</a> </li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Notebook/DNPDetection">DNP Detection</a> </li>
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                      <li><a href="https://2015.igem.org/Team:Edinburgh/Notebook/FluidDynamics">Fluid Dynamics</a> </li>
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                    </ul>
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                  </li>
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                  <li><a href="https://2015.igem.org/Team:Edinburgh/MedalCriteria">Accomplishments</a></li> 
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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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      <header class="intro">
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        <div class="intro-body">
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          <div class="container">
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            <div class="row">
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              <div class="col-md-12">
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                <h1 class="brand-heading">Modeling</h1>
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                <p class="intro-text">
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                </p>
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                <div align="center">
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                    <a href="#cd-team">
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                        <span class="arrowtext">Scroll down to read more</span>
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                        <img src="https://static.igem.org/mediawiki/2014/3/3e/Aalto_Helsinki_Nuoli.png" class="arrow">
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                    </a>
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                </div>
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              </div>
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            </div>
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          </div>
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        </div>
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      </header>
  
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<p>
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<section id="first">
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Here are a few examples from previous teams:
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<h2>Overview</h2>
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</p>
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          <p>
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<ul>
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This year we focused our modeling efforts on the development of our device design.
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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We worked on reaction-diffusion systems which helped us to find the weak points in our designs and to come up with new prototypes.
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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            </p>
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</ul>
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<p>    
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The model consists of two main parts; diffusion and reaction. The diffusion part predicts how the solution, once applied, will move through the paper and the reaction part models how the different enzymes and chemicals present on the paper will react with each other.
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          </p>
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</section>
  
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<!-- END OVERVIEW -->
  
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</div>
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<svg id="bigHalfCircle" xmlns="http://www.w3.org/2000/svg" version="1.1" width="100%" height="100" viewBox="0 0 100 100" preserveAspectRatio="none">
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<path d="M0 100 C40 0 60 0 100 100 Z"/>
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</svg>
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<section class="col-2 color" id="second">
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                        <div class="column">
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                            <img class="img-responsive" src="https://static.igem.org/mediawiki/2015/7/7f/Finalsensorbase.png" width="300">
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                        </div>
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                        <div class="column text">
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<h2>The Base Conditions</h2>
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          <p>
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The starting conditions of the model are made by using a png image import which defines the different parts of the biosensor i.e.: where the solution is applied, hydrophobic areas, frontiers and where the enzymes are freeze dried.
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          </p>
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                        </div>
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</section>
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<svg id="bigTriangleShadow" xmlns="http://www.w3.org/2000/svg" version="1.1" width="100%" height="100" viewBox="0 0 100 100" preserveAspectRatio="none">
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<path id="trianglePath1" d="M0 0 L50 100 L100 0 Z" />
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<path id="trianglePath2" d="M50 100 L100 40 L100 0 Z" />
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</svg>
  
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<!-- END BASE -->
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<section class = "col-2">
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                            <div class="column text pull-left">
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<h2>Diffusion-reaction </h2>
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        <p>
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A diffusion kernel, along with a diffusion matrix, control the movement of the solution on paper and form the backbone of the diffusion model. Our “world” is updated at every time step which, in turn, updates the concentration on every point of the paper.
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At every time step we also use a list of the reaction rates to update the model with changing concentrations. We use vector calculus throughout the code to make efficient use of resources.
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      <p>
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<a href="https://github.com/aseemnarang17/Classafied-modelling"> Go to code</a>
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      </p>
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                            </div>
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                            <div class="column">
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                              <img class="img-responsive" src="https://static.igem.org/mediawiki/2015/e/e5/Finalmodelanimation.gif" width = "300" hspace="80">
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                            </div>
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</section>
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<!-- END PROTOTYPE 2 -->
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</div>
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</body>
 
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Latest revision as of 19:11, 20 November 2015

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Modeling

Overview

This year we focused our modeling efforts on the development of our device design. We worked on reaction-diffusion systems which helped us to find the weak points in our designs and to come up with new prototypes.

The model consists of two main parts; diffusion and reaction. The diffusion part predicts how the solution, once applied, will move through the paper and the reaction part models how the different enzymes and chemicals present on the paper will react with each other.

The Base Conditions

The starting conditions of the model are made by using a png image import which defines the different parts of the biosensor i.e.: where the solution is applied, hydrophobic areas, frontiers and where the enzymes are freeze dried.

Diffusion-reaction

A diffusion kernel, along with a diffusion matrix, control the movement of the solution on paper and form the backbone of the diffusion model. Our “world” is updated at every time step which, in turn, updates the concentration on every point of the paper. At every time step we also use a list of the reaction rates to update the model with changing concentrations. We use vector calculus throughout the code to make efficient use of resources.

Go to code