Difference between revisions of "Team:Pasteur Paris/TrainingThomas2"

 
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<h1>MODELING</h1>
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<h1> Let's meet our team! </h1>
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<p><a href="#Introduction" class="link">Introduction</a></p>
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<p><a href="#Production" class="link">NGF Production</a></p>
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<p><a href="#Diffusion" class="link">NGF Diffusion</a></p>
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<p><a href="#Growth" class="link">Neurons Growth</a></p>
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<p>The aim of our mathematical model is to simulate the growth of neurons towards our biofilm in response of the presence of Nerve Growth Factor (NGF). Nerve growth factor is one of a group of small proteins called neurotrophins that are re-sponsible for the development of new neurons, and for the health and maintenance of mature ones. We created a determin-istic model to help the wetlab establish the optimal concen-tration gradients of NGF needed for the regrowth of the nerves. NGF concentration and concentration gradient are key parameters affecting the growth rate and direction of neu-rites. Neurites growth have shown to be NGF dose-dependent: if NGF concentration si too low or too high, the growth rate is attenuated. In order to visualize the results of the model on a microfluidic chip we used MATLAB, App Designer, Python, Gmsh and FreeFem. This is an important part of our project since it creates the link between the wetlab and drylab. </p>
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<p>We divided our model in three parts:
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<li>Production of NGF by the <i>E. coli</i> genetically modified</li>
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<li>Simulation of the diffusion of NGF in a given environment</li>
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<li>Neurons growth in the presence of NGF</li>
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<h1>Context of our model</h1>
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<p>Our project aims at creating a biofilm composed of genetically modified <i>E. coli</i> able to release a neurotrophic factor: NGF. It helps to accelerate the connection between the neurons and the implant of the prothesis; hence aiming at connecting directly the prothesis amputee’s neurons. This will enable the patient to have a more instinctive control of his prothesis device. The nerves will be guided towards a conductive membrane surrounding our genetically modified biofilm. This membrane will then pass the neural signal of the regenerated nerves towards the electronic chip of the implant through wires.  It will allow the patient to have a more instinctive and natural control than any other current prosthesis, and a reduced reeducation time.</p>
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<p>The aim of the wetllab is to test the biofilm on a microfluidic chip as a proof of concept. The chip is composed of two compartments: one made of the E. coli genetically modified to produce NGF and the other one of neurons. Micro canals link the two compartments in the middle of the chip, allowing the diffusion of NGF and the growth of the neurites. Our model will hence be established on a micro-fluidic chip shape in order to share our results with the wetlab and indicate them the optimal concentration of NGF needed according to their model.</p>
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<p><i>We introduce different parameters in order to create our model :</i></p>
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<td>g</td>
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<td>Length of the neurite outgrowth</td>
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<div class="frac"><span>dg</span><span class="symbol">/</span><span class="bottom">dt</span></div>
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<td>Neurite outgrowth rate</td>
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<td>u(x,t)</td>
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<td>Concentration of NGF at the position x and time t</td>
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<td>NGF concentration gradient at the position x and time t</td>
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<td>C<SUB>diff</SUB></td>
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<td>Diffusion coefficient of NGF</td>
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<td>K</td>
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<td>Gradient factor (growth rate of the neurite under the stimulation of the NGF concentration gradient)</td>
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<td>G<SUB><FONT face="Raleway">&theta;</FONT></SUB></td>
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<td>Baseline growth rate (neurite growth rate in absence of NGF concentration gradient)</td>
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<td>L</td>
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<td>Length of the conduit </td>
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  <h1 class="team-h1">Students</h1>
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<h4>NGF Production by genetically modified <i>E. coli</i></h4>
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<h1 style="padding-top: 50px;">NGF Production by genetically modified <i>E. coli</i></h1>
 
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<div class="block title"> <h2>Etienne Axelos</h2> </div>
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<h4>NGF diffusion simultation in a given environment</h4>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/0/0e/T--Pasteur_Paris--Team_Members_Etienne.jpg">
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    </br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div>
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 +
      <content>Etienne is one of our designers. He studies at the ENSCI-les Ateliers in Paris. He is always wearing black and fluorescent colors, which is very convenient because you can’t miss him. He is also a big music fan, and has special skills in rock’n’roll dance (very impressive!). As you can imagine, he is one of our funniest team members, you are never bored with him. But he is as funny as he is a hard worker, and we can always count on his help. </br> <i>By Emma</i></content>
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<div class="block title"> <h2>Alice Dejoux</h2> </div>
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      <content> Calm, determined, attentive and engaged: that’s how we see Alice. This young Parisian born in Marseille is currently studying at the prestigious school Chimie Paristech. Talented and always smiling she was one of the leaders of the Parisian meet up organisation and she also attended the Mediterranean meet up in Marseille. Her scientific experience made her show great involvement and perseverance in the lab while doing the modeling of the project. She is part of the 23 strong links of the team iGEM Paris Pasteur 2018. </br><i> By Florian</i></content>
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      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/8/89/T--Pasteur_Paris--Team_Members_Alice.jpg">
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      </br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/alice-dejoux-bb2503150/"><content >LinkedIn</content></a></div>
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<div class="block title"> <h2>Claire Dumont</h2> </div> 
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      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/3/34/T--Pasteur_Paris--Team_Members_Claire.jpg"> </br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/claire-dumont-55a41910b"><content >LinkedIn</content></a></div>
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      <content> Claire is one of our three marvelous designers from ENSCi les Ateliers. But that’s not it! She is also the key to keeping calm and focused the other two designers, who are more extroverted. Yet, she still loves to make movie references and silly jokes. In the team, she works very hard to create amazing graphics and she co-developed our final 3D-printed interface. It wouldn’t be an easy task to count the hours she spent on Rhino software to achieve her great results. </br> <i>By Jonathan</i></content>
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      <content> He is one of our dearest physicists studying at ESPCI Paris. He may seem like a shy person, but believe us: he is a man capable of wonders and knows a thing or two about inspirationnal speechs. In fact, you could consider him as our never ending source of encouragement. Each word that comes out of him fills you with determination. " You have to push back your limits each and everyday!" </br> <i>By Aymen</i></content>
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      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/2/20/T--Pasteur_Paris--Team_Members_Antoine.jpg"> </br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/antoine-ehret-303219161
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<div class="block title"> <h2>Andreas Fyrillas</h2> </div>
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      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/7/7c/T--Pasteur_Paris--Team_Members_Andreas.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/andreas-fyrillas-460732163/"><content >LinkedIn</content></a></div>
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    <div class="block half">
 +
      <content> Behind his calm and hard-working look, Andreas Fyrillas will not hesitate to throw a punchline at you. His studies at the engineering school ESPCI Paris give him the skills to be an expert on microfluidic chips. Not only does he work the oscilloscope like no other, but he also has a secret talent in the kitchen that he uses to delight us from time to time. Apart from coding the wiki, he enjoys sharing his self-made dubstep music with us. </br><i> By Alice</i></content>
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<div class="block title"> <h2>Aymen Ghaneme</h2> </div>
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      <content> Aymen, currently a second-year student at CentraleSupelec, is a smiling Morrocan who is always in for a break and above all a great fruit sugar-free ice cream (in fact, after a while, we realized the break is only a pretext for the icecream). However, when he gets sufficient sleep, this hyper-active guy can use all his mathematical abilities on making models and will work for hours to solve any software bug. </br> <i>By Thomas</i></content>
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      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/f/fa/T--Pasteur_Paris--Team_Members_Aymen.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div>
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  <div class="block title"> <h2>Léa Guerassimoff</h2> </div>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/b/b3/T--Pasteur_Paris--Team_Members_Lea.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/léa-guerassimoff-252816162/?originalSubdomain=fr"><content >LinkedIn</content></a></div>
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<div class="block half">
 +
      <content>Léa is our little chemist from Chimie ParisTech who specializes in making everything she does, cute. Her kindness and good mood always delight everyone. She is a real ray of sunshine even when she blows a fuse on the Wiki. She is very organized and serious in what she undertakes, but don’t bother her if she is watching a video of a toy goat: toy goats make her crazy, like really crazy. Regardless, she is one of the best people I have met, thanks to iGEM. We are now bosom buddies, that’s why people nickname us Tic & Tac. </br><i> By Ellyn</i></content>
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      <content>Samuel is a 20 year-old engineering student from Chimie ParisTech. Despite being the youngest member of our team, Samuel was the first person to imagine and believe in this ambitious project and convinced us to create NeuronArch. His skills in biological engineering and programming help us to model scientific concepts of our project. </br> <i>By Etienne</i></content>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/f/f1/T--Pasteur_Paris--Team_Members_Samuel.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/samuel-jaoui-3009bb14b/"><content >LinkedIn</content></a></div>
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<div class="block title"> <h2>Manon Madelenat</h2> </div>
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<div class="block half">
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/0/06/T--Pasteur_Paris--Team_Members_Manon.png"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/manon-madelenat/"><content >LinkedIn</content></a></div>
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<div class="block half">
 +
      <content>Behind her strong character, Manon hides a very big heart! She is studying biotechnologies at Sup’Biotech Paris. She is in her last year of study and she actually works in health and production fields. Her next step is to work in neuroscience and understand neurodegenerative diseases! She is an essential member of the team and is the queen of mini and midi prep! Manon is truly as beautiful on the inside as she is on the outside, trust me! </br><i> By Léa</i></content>
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<content>Jon is really motivated and commited to the lab work! Studying biotechnologies at Sup’Biotech Paris for the past five years, he is very passionate about synthetic biology and would like to continue in this field of study by getting his Master of research next year. In the team, he spends a lot of time in the lab but also on illustrator to make amazing explanatory schemes!
 +
      </br> <i> By Manon </i></content>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/0/07/T--Pasteur_Paris--Team_Members_Jonathan.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/jonaccache/"><content >LinkedIn</content></a></div>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/8/86/T--Pasteur_Paris--Team_Members_Elea.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/el%C3%A9a-paillares-b3305911a/"><content >LinkedIn</content></a></div>
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<div class="block half">
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      <content>Motivated and always smiling, Éléa always sets a happy mood in the room and never misses an occasion to crack you up. Although she spends her days locked in the laboratory working hard, making use of the skills she learned at Sup’Biotech, she has the spirit of a true traveler. Sometimes, she likes to go on spontaneous trips, not even bothering to book a hotel beforehand. She looks forward to the Giant Jamboree: she has never been to the United States!
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    </br> <i>By Andreas </i></content>
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<div class="block title"> <h2>Emma Picaud-Lucet</h2> </div>
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      <content> What is more important to Emma than her cat’s happiness? IGEM of course! As a law student from the Faculté Jean Monnet, she is one of the members in charge of all of the legal aspects of the project. Never afraid of giving her opinions on various matters, she often deals with subjects beyond law, such as the human practices collaboration with other iGEM teams. Her secret talent: she’s a very talented cartoonist! </br><i> By Samuel </i></content>
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<div class="block title"> <h2>Sarah Porte</h2> </div>
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    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/6/64/T--Pasteur_Paris--Team_Members_Sarah.jpg"></br></br></br><a class="linkedIn" href="https://fr.linkedin.com/in/sporte"><content >LinkedIn</content></a></div>
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<div class="block half">
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      <content>Sarah is a biology major getting her Master’s at the sorbonne-Université Pierre et Marie Curie. She is highly organized and is very good at multi-tasking, which is very useful. Sarah appreciates her independence as she works best this way, but will lend a helping hand if she is needed. She will also gladly borrow other people’s sweaters if it helps her stay warm! </br>
 +
      <i> By Deshmukh </i></content>
 +
    </div> </div>
 +
 
 +
<div class="block full">
 +
 
 +
</div>
 +
 
 +
    <!-- member-->
 +
<div class="block title"> <h2>Ellyn Redheuil</h2> </div>
 +
<div class="team-member">
 +
<div class="block half">
 +
      <content>Nicknamed Tic because of her inseparable bond with Léa (aka Tac), Ellyn lit up our summer with her continuous smiles, laughter, and amazing ideas and animations for our wiki page! She is an engineer student at ESPCI Paris, and you would be impressed by the range of her abilities: from coding the wiki to transforming bacteria. Whether in the lab or behind her computer, she seems to know how to do anything and everything. Her best specialty is her delicious cookies which are better than anyone else’s! </br><i> By Charlotte </i></content>
 +
    </div>
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/b/b1/T--Pasteur_Paris--Team_Members_Ellyn.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/ellyn-redheuil-64a521b0/"><content >LinkedIn</content></a></div></div>
 +
 
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<div class="block full">
 +
 
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 +
 
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    <!-- member-->
 +
<div class="block title"> <h2>Charlotte Richard</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/8/82/T--Pasteur_Paris--Team_Members_Charlotte.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div>
 +
<div class="block half">
 +
      <content>Engineer, biologist, adventurer and athlete, Charlotte has it all ! She is in her second year at Ecole Polytechnique, a military engineer school, and wants to specialize in Biology. In the lab, she is the best at Mini-preps, but she is also involved in the modeling part. In her spare time, she likes scouting and teaching the youth how to survive in the wild. That’s why she has the best BBQ skills!
 +
      </br> <i> By Gabriela </i> </content>
 +
    </div> </div>
 +
 
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<div class="block full">
 +
 
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</div>
 +
 
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    <!-- member-->
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  <div class="block title"> <h2>Gabriela Sachet</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
      <content>Studying biology at Sup’Biotech, Gabriela has played a key part in the laboratory. She has also contributed a lot to the bibliography, which helped keep the project on track. She has had the privilege of living in many different countries, which has made her a modern adventurer, always seeking new experiences. She recently participated in the 4L Rally (France to Morocco in a French retro car) before focusing on the iGEM competition !
 +
      </br> <i> By Claire </i> </content>
 +
    </div>
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/d/d8/T--Pasteur_Paris--Team_Members_Gabriela.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/gabriela-sachet-570891b5/"><content >LinkedIn</content></a></div></div>
 +
 
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<div class="block full">
 +
 
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</div>
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 +
<!-- member-->
 +
<div class="block title"> <h2>Thomas Starck</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/e/e5/T--Pasteur_Paris--Team_Members_Thomas.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/thomas-starck-8b3828148/"><content >LinkedIn</content></a></div>
 +
<div class="block half">
 +
      <content>Spirit-son of Tony Stark, great defender of planet Earth and member of the Avengers, Thomas Starck chose a different path. Full of imagination and a practical spirit, Thomas is in his second year in Ecole Polytechnique, a military engineer school. In addition to his lab work, he also dedicated his time to the making of this wiki page. In his free time, he loves to help his “dad” save the world, but also go out and enjoy life.
 +
      </br><i> By Sarah </i></content>
 +
    </div> </div>
 +
 
 +
<div class="block full">
 +
 
 +
</div>
 +
 
 +
  <!-- member-->
 +
<div class="block title"> <h2>Florian Thomas</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
      <content>Florian has many skills in his designer toolbox, he studied cabinet-making and he is now finishing his studies at ENSCi les Ateliers. He enjoys the beauty of raw material and well made products, which is reflected in his work. While being a calm and thoughtful person, Florian still knows how to make his point, especially when it comes to the topic of the use of animals in research. Do not let his backwards cap and youthful smile fool you, Florian is actually our oldest team member! </br> <i> By Éléa </i> </content>
 +
  </br>
 +
    </div>
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/2/23/T--Pasteur_Paris--Team_Members_Florian.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/florian-thomas-80b401aa/"><content >LinkedIn</content></a></div></div>
 +
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<div class="block full">
 +
 
 +
</div>
 +
 
 +
    <!-- member-->
 +
<div class="block title"> <h2>Kelly Trang</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/f/f7/T--Pasteur_Paris--Team_Members_Kelly.jpg"></br></br></br><a class="linkedIn" href="https://www.linkedin.com/in/kelly-trang-134558123/"><content >LinkedIn</content></a></div>
 +
<div class="block half">
 +
      <content><p>Don’t let her fool you, behind her cute smile and freckles Kelly is actually a big fan of hardcore heavy metal. A first year Master’s student studying intellectual property law at the Faculté Jean Monnet, she is also a true scientist at heart and loves to follow the scientists around in the lab. When she is not baking something delicious or stealing food from her team members, she is very responsible and in charge of the legal work.</p> </br> <i> By Antoine </i></content>
 +
</content></a>
 +
    </div></div>
 +
 
 +
 
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</section>
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 +
<section class="cf team-container">
 +
  <h1 class="team-h1">Supervisors</h1>
 +
 
 +
 
 +
  <!-- member-->
 +
<div class="block title" id="Deshmukh"> <h2>Deshmukh Gopaul</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/c/c0/T--Pasteur_Paris--Team_Members_Deshmukh.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div>
 +
<div class="block half">
 +
      <content>Deshmukh Gopaul, researcher and Head of Design in Biology at the Institut Pasteur, has been coaching the iGEM Pasteur Paris teams for 4 years now. Although he specializes in Biology, he is well versed in a variety of topics, allowing him to always have an interesting anecdote to share. He is very meticulous and although working with him may take a lot of time, patience, and tears, we know that it’s worth it in the end! </br><i> By Kelly </i></content>
 +
    </div></div>
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<div class="block full">
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</div>
 +
 
 +
    <!-- member--> 
 +
<div class="block title" id="Guillian"> <h2>Guillian Graves</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
      <content> Guillian is an industrial designer specialized in biomimicry, working in Paris at his design studio BIG BANG Project. He also teaches at ENSCI-Les Ateliers (National School for Advanced Studies in Design). His professionalism and his high expectations go hand in hand with his sympathy. He helps our team think about the design of our device and uses his expertise to support our designers in creating a global project. </br> <i> By Claire </i></content>
 +
    </div>
 +
<div class="block half">
 +
      <img class="team-photo" src="https://static.igem.org/mediawiki/2018/b/be/T--Pasteur_Paris--Team_Members_Guillian.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div></div>
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<div class="block full">
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    <!-- member-->
 +
<div class="block title" id="Serena"> <h2>Serena Petracchini</h2> </div>
 +
    <div class="team-member">
 +
  <div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/b/b3/T--Pasteur_Paris--Team_Members_Serena.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div>
 +
<div class="block half">
 +
      <content>Serena has been the key to answering many of our question, thanks to her extensive experience in microbiology. Her major contribution to the project as a coach has been in the Interlab, along with the many great ideas she has! When she doesn’t agree with something you will hear her Italian come out as she says “ma no!” followed, of course, by some hand motion. If still you disagree with her, try her delicious tiramisu. I am sure she (it) will convince you! </br> <i> By Anna </i> </content>
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    <div class="block title" id="Anna"> <h2>Anna Segú Cristina</h2> </div>
 +
    <div class="team-member">
 +
<div class="block half">
 +
      <content>With a true catalan heart and a great french accent, Anna is putting the best of her energies in her tutoring role for iGem Pasteur. A soon-to-be second year PhD student, she finds time between a neuron an a miniprep to do sports and other extracurriculars, always leaving her friends astonished. Full of board game evenings and genetic engineering, she’s able to enjoy the best of Parisian life!  </br> <i>  By Serena </i> </content>
 +
    </div>
 +
<div class="block half">
 +
    <img class="team-photo" src="https://static.igem.org/mediawiki/2018/d/dd/T--Pasteur_Paris--Team_Members_Anna.jpg"></br></br></br><a class="linkedIn" href=""><content >LinkedIn</content></a></div></div>
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/* ENDS Team Member CSS
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 +
MIT Licensed- Copyright (c) 2018 by Jose Morales-Mendizabal (https://codepen.io/moralejf/pen/YPxMpN)
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Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 +
-->
  
−
<div class="block hiddenContent">
 
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<span class="closeCross"><img src="https://static.igem.org/mediawiki/2018/6/67/T--Pasteur_Paris--CloseCross.svg"></span>
 
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<div class="block title">
 
−
<h1 style="padding-top: 50px;">NGF diffusion diffusion in a given environment</h1><br>
 
−
<p><i>We are looking to understand the way the NGF spreads inside the conduit once it is produced. This will help us to determine the NGF concentration u(x,t) (ng.mL<SUP>-1</SUP>) as a function of the distance x (cm) from the production site of NGF.</i></p>
 
−
</div>
 
−
<!-- Fick's diffusion law -->
 
−
<div class="block full">
 
−
<h3>Fick’s diffusion law </h3>
 
−
<p>To simulate NGF diffusion in the microfluidic chip we consider a unidimensional conduit of axe x and a constant concentration of NGF introduced at one end of the canals. In this part, diffusion is assumed to be the only mechanism producing the gradient decay in the micro canals. We can model the diffusion characteristics of NGF with Fick’s second law of diffusion:<br>
 
−
<span style="position: relative; display: inline-block; width: 100%; text-align: center;">
 
−
<span class="frac">
 
−
<span>du</span>
 
−
<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
−
</span>
 
−
= C<SUB>diff</SUB>
 
−
<span class="frac">
 
−
<span>d<SUP>2</SUP>u</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dx<SUP>2</SUP></span>
 
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</span>
 
−
&emsp;&emsp;&emsp;(1)
 
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</span>
 
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</p>
 
−
<p>Cdiff is assumed to be constant inside the conduit and depends on the material used.<br>
 
−
There are also two boundary conditions:<br>
 
−
at x=0: &emsp;&emsp;
 
−
<span class="frac">
 
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<span>du</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dx</span>
 
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</span>
 
−
|<SUB>(0,t)</SUB>&emsp;&emsp;&emsp;(2)<br>
 
−
at x=L: &emsp;&emsp;
 
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<span style="text-align: left;">
 
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<span class="frac">
 
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<span>du</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dx</span>
 
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</span>
 
−
|<SUB>(L,t)</SUB>&emsp;&emsp;&emsp;(3)<br>
 
−
</span>
 
−
</p>
 
−
<p>Indeed, in the same material, the rate transfer of the diffusing NGF through the cross section of the micro canal is proportional to the concentration gradient normal to the cross section. It is assumed that the leakage of NGF at both ends of the micro canal is negligible because there should be little NGF at the ends the micro canals compared to the total amount of NGF and second because of a low NGF diffusion rate.
 
−
The equation (1) can be solved with Euler’s method and we find the NGF concentration gradient at the position x and time t. The MatLab code is the following:</p>
 
−
</div>
 
−
<div class="block half">
 
−
 
−
</div>
 
−
<div class="block half">
 
−
<p>We displayed our results showing a decrease of the concentration of NGF (u(x,t)) depending on the distance of the conduit x.</p>
 
−
<p>We used the following parameters for the model: </p>
 
−
<table class="tableData">
 
−
<tr>
 
−
<td>Length of the conduit: L</td>
 
−
<td>0.1 cm </td>
 
−
</tr>
 
−
<tr>
 
−
<td>Diffusion coefficient of NGF : Cdiff</td>
 
−
<td>7,8*10<SUP>-7</SUP> cm<SUP>2</SUP>.s<SUP>-1</SUP></td>
 
−
</tr>
 
−
<tr>
 
−
<td>Time length of the experiment: t_final</td>
 
−
<td>3 600 s </td>
 
−
</tr>
 
−
</table>
 
−
</div>
 
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<div class="block full">
 
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<p style="text-align: center;">We obtain the following graphs: </p>
 
−
</div>
 
  
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−
<img src="https://static.igem.org/mediawiki/2018/b/b4/T--Pasteur_Paris--gif.gif" style="max-width: 500px; box-shadow: 0px 0px 8px -2px;">
 
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</div>
 
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<div class="block half">
 
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<!-- Optimisation of the gradient -->
 
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<div class="block full">
 
−
<h3>Optimisation of the NGF gradient</h3>
 
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</div>
 
−
<div class="block half">
 
−
<p>To optimize the accuracy of the NGF gradient we interpolate the curve u(x)=f(x). Consequently, we obtain the f polynomial function easier to derive and a polynomial function of the gradient with a better accuracy than with the first method. The program is the following:</p>
 
−
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<div class="block two-third">
 
−
<p>With the same parameters as with the previous model we obtain the following graphs: </p>
 
−
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<div class="block two-third">
 
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</div>
 
−
<!-- Analysis of the model -->
 
−
<div class="block full">
 
−
<h3>Analysis of the model </h3>
 
−
<p><i>To validate the model, we vary the three parameters (L, t_final, C<SUB>diff</SUB>) to verify if the program corresponds to a diffusion phenomenon described in Fick’s second law of diffusion. </i></p>
 
−
</div>
 
−
<div class="block two-third">
 
−
<img src="https://static.igem.org/mediawiki/2018/4/41/T--Pasteur_Paris--gif-fct-L.gif" style="max-width: 500px; box-shadow: 0px 0px 8px -2px;">
 
−
</div>
 
−
<div class="block full">
 
−
<p>Observations:<br>
 
−
<ol style="text-align: left; list-style-type: disc;">
 
−
<li>When the length of the conduit increases but the duration of the experiment is fixed the NGF doesn’t have the time to diffuse in the entire conduit.</li>
 
−
<li>For instance, with a t_final= 3 600s the NGF molecules can’t diffuse further than x=0.2cm.</li>
 
−
</ol>
 
−
</p>
 
−
</div>
 
−
<div class="block two-third">
 
−
<img src="https://static.igem.org/mediawiki/2018/0/07/T--Pasteur_Paris--fct-Cdiff.gif" style="max-width: 500px; box-shadow: 0px 0px 8px -2px;">
 
−
</div>
 
−
<div class="block full">
 
−
<p>The higher the diffusion coefficient, the faster the molecules will diffuse in the conduit. Indeed, we observe in the model that with a fixed t_final:<br>
 
−
<ol style="text-align: left; list-style-type: disc;">
 
−
<li>NGF concentration at x=0.1 cm is 675 000 ng.ml<SUP>-1</SUP> for a diffusion coefficient C<SUB>diff</SUB> = 15*10<SUP>-7</SUP> cm<SUP>2</SUP>.s<SUP>-1</SUP></li>
 
−
<li>For a diffusion coefficient two times lower, the NGF concentration is 380 ng.ml<SUP>1</SUP></li>
 
−
</ol>
 
−
</p>
 
−
<p>The results confirm the prediction of the Fick’s law model. </p>
 
−
</div>
 
−
<div class="block full">
 
−
<p>When the time length of the experiment lasts from 1 hour to 2 hours, the concentration of NGF is almost homogeneous in the entire conduit. At the end of the conduit, for x= 0.1 cm, the concentration of NGF equals to 910 ng.ml-1 when t_final= 7 200s whereas the concentration is 3 900 ng.ml<SUP>-1</SUP> when t_final=3 600s. </p>
 
−
<p>It is interesting to observe that when the duration of the experiment increases, the stationary regime is established: the NGF concentration in the conduit becomes independent of the position and time. Indeed, the concentation gradient of NGF in the conduit moves toward 0 for any position. </p>
 
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<h4>Neurons growth in the presence of NGF</h4>
 
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<h1>Neurons growth in the presence of NGF</h1><br>
 
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<p><i>In this part our goal is to determine the length of the neurite outgrowth (g(t)) in response to the gradient concentration of NGF.</i></p>
 
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<h3>Explanation of the model</h3>
 
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<h5 style="text-align: left">Baseline growth rate: </h5>
 
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<p>In our mathematical model, neurites grow at a constant growth rate defined as the baseline growth rate G0  when the concentration is below the threshold (assumed to be 995 ng.mL<SUP>-1</SUP>). Neurites stop growing when the NGF concentration is higher than the threshold concentration. The value for the baseline growth rate G0 has been fixed at 20 <FONT face="Raleway">&mu;</FONT>m.h<SUP>-1</SUP> for this model. </p>
 
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<h5 style="text-align: left">Concentration Gradient:</h5>
 
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<p>The extent of directional guidance is gradient steepness-dependent provided that the concentration gradient reaches the threshold value. The gradient factor k is a gradient steepness-dependent positive effect on the neurite growth rate. </p>
 
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<p>In this model we assume that the baseline growth rate and the growth rate in the presence of concentration gradient follow an additive rule. This can be explained by the fact that both the NGF concentration and the its gradient can both individually contribute to neurite extension. The equation governing neurite outgrowth thus becomes:<br><br>
 
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<span style="position: relative; display: inline-block; text-align: center; width: 100%">
 
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<span class="frac">
 
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<span>dg</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
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</span>
 
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= G<SUB>0</SUB> + k
 
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<span class="frac">
 
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<span><FONT face="Raleway">&part;</FONT>u</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
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|<SUB>(g(t),t)</SUB> &emsp; &emsp; &emsp; (4)</p>
 
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<div class="block full">
 
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<p>We can introduce a time parameter Tlag because the time taken to transmit the NGF signal is finite. The experiments show that the time lag for the cells to respond to NGF is approximately 1 day. The experiments show:<br>
 
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if t <FONT face="Raleway">&le;</FONT> T<SUB>lag</SUB> : &emsp; &emsp;
 
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<span class="frac">
 
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<span>dg</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
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</span> = 0<br>
 
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else, if: t <FONT face="Raleway">&ge;</FONT> T<SUB>lag</SUB> : &emsp; &emsp; 
 
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<span class="frac">
 
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<span>dg</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
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</span> = G<SUB>0</SUB> + k
 
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<span class="frac">
 
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<span><FONT face="Raleway">&part;</FONT>u</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
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</span>
 
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|<SUB>(g(t),t)</SUB>
 
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</p>
 
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</div>
 
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<div class="block full">
 
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<h3>Solving the model</h3>
 
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<div class="block full">
 
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<p>To solve the equation (4) we are using Euler’s method forward because the gradient concentration of NGF depends on the length of the neurite (since neurites consume NGF). <br><br>
 
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The Equation (4): &emsp; &emsp; <br>
 
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<span style="position: relative; display: inline-block; width: 100%; text-align: center;">
 
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<span class="frac">
 
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<span>dg</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
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</span> = G<SUB>0</SUB> + k
 
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<span class="frac">
 
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<span><FONT face="Raleway">&part;</FONT>u</span>
 
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<span class="symbol">/</span>
 
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<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
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</span>
 
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|<SUB>(g(t),t)</SUB>
 
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</span><br><br>
 
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Can be written as: &emsp; &emsp; <br><br>
 
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<span style="position: relative; display: inline-block; width: 100%; text-align: center;">
 
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g' = G<SUB>0</SUB> + k*f(g,t)
 
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</span><br><br>
 
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Which can be written as : &emsp; &emsp; <br><br>
 
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<span style="position: relative; display: inline-block; width: 100%; text-align: center;">
 
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<span class="frac">
 
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<span>g<SUB>n+1</SUB> - g<SUB>n</SUB></span>
 
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<span class="symbol">/</span>
 
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<span class="bottom">dt</span>
 
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</span>
 
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|<SUB>(g(t),t)</SUB> = G<SUB><FONT face= "Raleway">&theta;</FONT></SUB> + k
 
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<span class="frac">
 
−
<span><FONT face="Raleway">&part;</FONT>u</span>
 
−
<span class="symbol">/</span>
 
−
<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
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</span>
 
−
|<SUB>(g(t),t)</SUB>
 
−
</span><br><br>
 
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We can therefore have an expression of g<SUB>n+1</SUB>: &emsp; &emsp; <br><br>
 
−
<span style="position: relative; display: inline-block; width: 100%; text-align: center;">
 
−
g<SUB>n+1</SUB> = g<SUB>n</SUB> + dt*[G<SUB>0</SUB> + k
 
−
<span class="frac">
 
−
<span><FONT face="Raleway">&part;</FONT>u</span>
 
−
<span class="symbol">/</span>
 
−
<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
−
</span>
 
−
|<SUB>(g(t),t)</SUB>]
 
−
</span><br><br>
 
−
With initial values of g<SUB><FONT face="Raleway">&theta;</FONT></SUB>, t<SUB><FONT face="Raleway">&theta;</FONT></SUB> and
 
−
<span class="frac">
 
−
<span><FONT face="Raleway">&part;</FONT>u</span>
 
−
<span class="symbol">/</span>
 
−
<span class="bottom"><FONT face="Raleway">&part;</FONT>x</span>
 
−
</span>
 
−
|<SUB>(g(t),t)</SUB>
 
−
  we can find all the values of the g </p>
 
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</div>
 
  
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</div>
 
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</div>
 
−
<div class="block separator"></div>
 
  
−
<div class="block title">
 
−
<h1 id="References">References</h1>
 
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</div>
 
−
<div class="block full">
 
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<p>[1] Defining the concentration gradient of nerve growth factor for guided neurite outgrowth, XCao M.SShoichet, March 2001</p>
 
−
<p>[2] Immobilized Concentration Gradients of Neurotrophic Factors Guide Neurite Outgrowth of Primary Neurons in Macroporous Scaffolds, Moore K, MacSween M, Shoichet M, feb 2006</p>
 
−
<p>[3] Mathematical Modeling of Guided Neurite Extension in an Engineered Conduit with Multiple Concentration Gradients of Nerve Growth Factor (NGF), Tse TH, Chan BP, Chan CM, Lam J, sep 2007</p>
 
−
<p>[4] Mathematical modelling of multispecies biofilms for wastewater treatment, Maria Rosaria Mattei, november 2005</p>
 
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Latest revision as of 19:32, 16 October 2018

""

Let's meet our team!

Students

Etienne Axelos




LinkedIn
Etienne is one of our designers. He studies at the ENSCI-les Ateliers in Paris. He is always wearing black and fluorescent colors, which is very convenient because you can’t miss him. He is also a big music fan, and has special skills in rock’n’roll dance (very impressive!). As you can imagine, he is one of our funniest team members, you are never bored with him. But he is as funny as he is a hard worker, and we can always count on his help.
By Emma

Alice Dejoux

Calm, determined, attentive and engaged: that’s how we see Alice. This young Parisian born in Marseille is currently studying at the prestigious school Chimie Paristech. Talented and always smiling she was one of the leaders of the Parisian meet up organisation and she also attended the Mediterranean meet up in Marseille. Her scientific experience made her show great involvement and perseverance in the lab while doing the modeling of the project. She is part of the 23 strong links of the team iGEM Paris Pasteur 2018.
By Florian



LinkedIn

Claire Dumont




LinkedIn
Claire is one of our three marvelous designers from ENSCi les Ateliers. But that’s not it! She is also the key to keeping calm and focused the other two designers, who are more extroverted. Yet, she still loves to make movie references and silly jokes. In the team, she works very hard to create amazing graphics and she co-developed our final 3D-printed interface. It wouldn’t be an easy task to count the hours she spent on Rhino software to achieve her great results.
By Jonathan

Antoine Ehret

He is one of our dearest physicists studying at ESPCI Paris. He may seem like a shy person, but believe us: he is a man capable of wonders and knows a thing or two about inspirationnal speechs. In fact, you could consider him as our never ending source of encouragement. Each word that comes out of him fills you with determination. " You have to push back your limits each and everyday!"
By Aymen



LinkedIn

Andreas Fyrillas




LinkedIn
Behind his calm and hard-working look, Andreas Fyrillas will not hesitate to throw a punchline at you. His studies at the engineering school ESPCI Paris give him the skills to be an expert on microfluidic chips. Not only does he work the oscilloscope like no other, but he also has a secret talent in the kitchen that he uses to delight us from time to time. Apart from coding the wiki, he enjoys sharing his self-made dubstep music with us.
By Alice

Aymen Ghaneme

Aymen, currently a second-year student at CentraleSupelec, is a smiling Morrocan who is always in for a break and above all a great fruit sugar-free ice cream (in fact, after a while, we realized the break is only a pretext for the icecream). However, when he gets sufficient sleep, this hyper-active guy can use all his mathematical abilities on making models and will work for hours to solve any software bug.
By Thomas



LinkedIn

Léa Guerassimoff




LinkedIn
Léa is our little chemist from Chimie ParisTech who specializes in making everything she does, cute. Her kindness and good mood always delight everyone. She is a real ray of sunshine even when she blows a fuse on the Wiki. She is very organized and serious in what she undertakes, but don’t bother her if she is watching a video of a toy goat: toy goats make her crazy, like really crazy. Regardless, she is one of the best people I have met, thanks to iGEM. We are now bosom buddies, that’s why people nickname us Tic & Tac.
By Ellyn

Samuel Jaoui

Samuel is a 20 year-old engineering student from Chimie ParisTech. Despite being the youngest member of our team, Samuel was the first person to imagine and believe in this ambitious project and convinced us to create NeuronArch. His skills in biological engineering and programming help us to model scientific concepts of our project.
By Etienne



LinkedIn

Manon Madelenat




LinkedIn
Behind her strong character, Manon hides a very big heart! She is studying biotechnologies at Sup’Biotech Paris. She is in her last year of study and she actually works in health and production fields. Her next step is to work in neuroscience and understand neurodegenerative diseases! She is an essential member of the team and is the queen of mini and midi prep! Manon is truly as beautiful on the inside as she is on the outside, trust me!
By Léa

Jonathan Naccache

Jon is really motivated and commited to the lab work! Studying biotechnologies at Sup’Biotech Paris for the past five years, he is very passionate about synthetic biology and would like to continue in this field of study by getting his Master of research next year. In the team, he spends a lot of time in the lab but also on illustrator to make amazing explanatory schemes!
By Manon



LinkedIn

Éléa Paillares




LinkedIn
Motivated and always smiling, Éléa always sets a happy mood in the room and never misses an occasion to crack you up. Although she spends her days locked in the laboratory working hard, making use of the skills she learned at Sup’Biotech, she has the spirit of a true traveler. Sometimes, she likes to go on spontaneous trips, not even bothering to book a hotel beforehand. She looks forward to the Giant Jamboree: she has never been to the United States!
By Andreas

Emma Picaud-Lucet

What is more important to Emma than her cat’s happiness? IGEM of course! As a law student from the Faculté Jean Monnet, she is one of the members in charge of all of the legal aspects of the project. Never afraid of giving her opinions on various matters, she often deals with subjects beyond law, such as the human practices collaboration with other iGEM teams. Her secret talent: she’s a very talented cartoonist!
By Samuel



LinkedIn

Sarah Porte




LinkedIn
Sarah is a biology major getting her Master’s at the sorbonne-Université Pierre et Marie Curie. She is highly organized and is very good at multi-tasking, which is very useful. Sarah appreciates her independence as she works best this way, but will lend a helping hand if she is needed. She will also gladly borrow other people’s sweaters if it helps her stay warm!
By Deshmukh

Ellyn Redheuil

Nicknamed Tic because of her inseparable bond with Léa (aka Tac), Ellyn lit up our summer with her continuous smiles, laughter, and amazing ideas and animations for our wiki page! She is an engineer student at ESPCI Paris, and you would be impressed by the range of her abilities: from coding the wiki to transforming bacteria. Whether in the lab or behind her computer, she seems to know how to do anything and everything. Her best specialty is her delicious cookies which are better than anyone else’s!
By Charlotte



LinkedIn

Charlotte Richard




LinkedIn
Engineer, biologist, adventurer and athlete, Charlotte has it all ! She is in her second year at Ecole Polytechnique, a military engineer school, and wants to specialize in Biology. In the lab, she is the best at Mini-preps, but she is also involved in the modeling part. In her spare time, she likes scouting and teaching the youth how to survive in the wild. That’s why she has the best BBQ skills!
By Gabriela

Gabriela Sachet

Studying biology at Sup’Biotech, Gabriela has played a key part in the laboratory. She has also contributed a lot to the bibliography, which helped keep the project on track. She has had the privilege of living in many different countries, which has made her a modern adventurer, always seeking new experiences. She recently participated in the 4L Rally (France to Morocco in a French retro car) before focusing on the iGEM competition !
By Claire



LinkedIn

Thomas Starck




LinkedIn
Spirit-son of Tony Stark, great defender of planet Earth and member of the Avengers, Thomas Starck chose a different path. Full of imagination and a practical spirit, Thomas is in his second year in Ecole Polytechnique, a military engineer school. In addition to his lab work, he also dedicated his time to the making of this wiki page. In his free time, he loves to help his “dad” save the world, but also go out and enjoy life.
By Sarah

Florian Thomas

Florian has many skills in his designer toolbox, he studied cabinet-making and he is now finishing his studies at ENSCi les Ateliers. He enjoys the beauty of raw material and well made products, which is reflected in his work. While being a calm and thoughtful person, Florian still knows how to make his point, especially when it comes to the topic of the use of animals in research. Do not let his backwards cap and youthful smile fool you, Florian is actually our oldest team member!
By Éléa



LinkedIn

Kelly Trang




LinkedIn

Don’t let her fool you, behind her cute smile and freckles Kelly is actually a big fan of hardcore heavy metal. A first year Master’s student studying intellectual property law at the Faculté Jean Monnet, she is also a true scientist at heart and loves to follow the scientists around in the lab. When she is not baking something delicious or stealing food from her team members, she is very responsible and in charge of the legal work.


By Antoine

Supervisors

Deshmukh Gopaul




LinkedIn
Deshmukh Gopaul, researcher and Head of Design in Biology at the Institut Pasteur, has been coaching the iGEM Pasteur Paris teams for 4 years now. Although he specializes in Biology, he is well versed in a variety of topics, allowing him to always have an interesting anecdote to share. He is very meticulous and although working with him may take a lot of time, patience, and tears, we know that it’s worth it in the end!
By Kelly

Guillian Graves

Guillian is an industrial designer specialized in biomimicry, working in Paris at his design studio BIG BANG Project. He also teaches at ENSCI-Les Ateliers (National School for Advanced Studies in Design). His professionalism and his high expectations go hand in hand with his sympathy. He helps our team think about the design of our device and uses his expertise to support our designers in creating a global project.
By Claire



LinkedIn

Serena Petracchini




LinkedIn
Serena has been the key to answering many of our question, thanks to her extensive experience in microbiology. Her major contribution to the project as a coach has been in the Interlab, along with the many great ideas she has! When she doesn’t agree with something you will hear her Italian come out as she says “ma no!” followed, of course, by some hand motion. If still you disagree with her, try her delicious tiramisu. I am sure she (it) will convince you!
By Anna

Anna Segú Cristina

With a true catalan heart and a great french accent, Anna is putting the best of her energies in her tutoring role for iGem Pasteur. A soon-to-be second year PhD student, she finds time between a neuron an a miniprep to do sports and other extracurriculars, always leaving her friends astonished. Full of board game evenings and genetic engineering, she’s able to enjoy the best of Parisian life!
By Serena



LinkedIn