Difference between revisions of "Team:Queens Canada/Model"

 
(26 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
{{Queens Canada/Header}}
 
{{Queens Canada/Header}}
 
{{Queens Canada/Navbar}}
 
{{Queens Canada/Navbar}}
−
 
 
<html>
 
<html>
−
<head>
+
<meta name="viewport" content="width=device-width, initial-scale=1">
 
<style>
 
<style>
 +
 
body {
 
body {
 
     background-color: white;
 
     background-color: white;
Line 10: Line 10:
 
     margin-top: 20px;
 
     margin-top: 20px;
 
     position: relative;
 
     position: relative;
 +
    margin-left: auto;
 +
    margin-right: auto;
 
}
 
}
−
</style>
 
−
</head>
 
−
<body>
 
  
−
<p style="width:70%;margin-left:15%">At team Queens Canada, we believe that proper preparation is the best way to reach a desired outcome. Accordingly, we sought to model many aspects of our project which aided in making the right choices in the lab and receiving positive results. Through the help of student on our team specializing in biomedical computing, applied mathematics, and chemical engineering, we created a number of different models that were crucial to our project design.</p>
+
/* Create two equal columns that floats next to each other */
 +
.column {
 +
    float:left;
 +
    padding: 10px;
 +
    margin: 30px;
 +
    width: 28%;
 +
    border: 20px double #0485BF;
 +
    border-radius: 15px;
 +
    text-align: center;
 +
height: 630px;
 +
min-width: 450px;
  
 +
}
  
−
<h2 style="width:70%;margin-left:15%">Molecular Dynamic Simulations</h2>
+
/* Clear floats after the columns */
−
<p style="width:70%;margin-left:15%">
+
.row:after {
−
One of our constructs relied on linkers of sufficient length and flexibility to convert a conformational change, into signal transduction. We have achieved this through firstly modelling with <a href="https://2018.igem.org/Team:Queens_Canada/Linker_Development">PyMol</a> and then performing molecular dynamic simulations of the root-mean-square deviation of <a href="https://2018.igem.org/Team:Queens_Canada/Fluid_Dynamics"> atomic position </a>. </p>
+
    content: "";
 +
    display: table;
 +
    clear: both;
 +
}
  
−
<figure style="width:70%;margin-left:15%">
+
h1 {
−
<img src="https://static.igem.org/mediawiki/2018/b/b6/T--Queens_Canada--PyMOLNoLinker.jpg" alt='nolinker'/>
+
     text-align: center;
−
</figure>
+
}
−
<figure style="width:70%;margin-left:15%">
+
−
     <img src="https://static.igem.org/mediawiki/2018/f/f7/T--Queens_Canada--RMSDcartoon0.png" alt='RMSD0'/>
+
−
</figure>
+
−
<h3 style="width:70%;margin-left:15%">Michaelis - Menten kinetics</h3>
+
−
<p style="width:70%;margin-left:15%">Michaelis - Menten kinetics is a model used to examine enzyme kinetic. Luciferase's activity can be modeled by Michaelis-Menten kinetics as they perform the simple conversion of a substrate into a product and a photon. Our project relied on the light producing NanoLuc Luciferase as a signal in our devices. We were able to model this relationship with MATLAB. The governing equations
+
−
for this model were compiled in the MATLAB, with the goal of creating a generic calculator which teams may use in the future. Known
+
−
values for concentrations and reactions rates are used as inputs, and the file produces the various
+
−
rates of change with respect to the concentrations.</p>
+
  
−
<figure style="width:70%;margin-left:15%">
+
h2 {
−
<img style="width:70%;margin-left:15%" src="https://static.igem.org/mediawiki/2018/f/f9/T--Queens_Canada--NanoTimelapse.jpeg"/>
+
    text-align: center;
−
</figure>
+
}
−
<figure style="width:70%;margin-left:15%">
+
−
<img src="https://static.igem.org/mediawiki/2018/a/a0/T--Queens_Canada--examplemichaelismenten.png" alt='RMSD0'/>
+
−
</figure>
+
−
<p style="width:70%;margin-left:15%">An example Michaelis-Menten graph demonstrating the relationship between substrate concentration and enzyme activity</p>
+
  
−
<h3 style="width:70%;margin-left:15%">Fluid Dynamics</h3>
+
h3 {
−
<p style="width:70%;margin-left:15%">The ultimate application of our work from this year will be in the form of a diagnostic pacifier capable of collecting saliva, mixing with an internal biosensor and generating a signal for salivary hormone quantification. Therefore we sought to model many aspects of the pacifier including: saliva flow rate, flow turbulence, and particle mixing.
+
    text-align: center;
 +
}
  
−
<img src="https://static.igem.org/mediawiki/2018/0/06/T--Queens_Canada--BrownianSimulation2FD.png" alt='Diagram showing Brownian simulations in a tube' />
+
a:visited {
−
<figcaption>Figure 4: Simulations of Brownian motion within a cylinder</figcaption>
+
    color: black;
 +
    background-color: transparent;
 +
}
 +
a:hover {
 +
    color: #0485BF;
 +
    background-color: transparent;
 +
    text-decoration: underline;
 +
}
 +
footer {
 +
  position:fixed;
 +
  left:0px;
 +
  bottom:0px;
 +
  width:100%;
 +
}
  
−
<div class="column full_size" style="width:70%;margin-left:15%">
+
</style>
−
<h1>Computer Aided Design</h1>
+
−
We created relevant hardware for our project including a 3D printed pacifier to passively collect saliva samples. Before 3D printing any iterations of our design, we modeled our device on Computer Aided Design Software.
+
−
<p> <h2>Computer Aided Design and 3D Printing</h2>
+
−
    <h3>Attempt 1</h3>
+
−
    <!-- 3 pics -->
+
−
    <img src="https://static.igem.org/mediawiki/2018/d/d5/T--Queens_Canada--pacifier1.jpg"/>
+
−
    <img src="https://static.igem.org/mediawiki/2018/9/9b/T--Queens_Canada--pacifier2.jpg"/>
+
−
    <img src="https://static.igem.org/mediawiki/2018/f/f9/T--Queens_Canada--pacifier3.jpg" height="300"/>
+
−
    <h5>Results:</h5>
+
−
    <!-- 2 pics -->
+
−
    <img src="https://static.igem.org/mediawiki/2018/5/58/T--Queens_Canada--pacifier4.jpg"/>
+
−
    <img src="https://static.igem.org/mediawiki/2018/5/58/T--Queens_Canada--pacifier5.jpg"/>
+
−
</p>
+
−
</div>
+
−
<br>
+
  
 +
<body>
  
 +
<h2 style="width:70%;margin-left:15%">Modelling</h2>
  
 +
<p style="width:70%;margin-left:15%">At team Queens Canada, we believe that proper preparation is the best way to reach a desired outcome. Accordingly, we sought to model many aspects of our project
 +
which aided in making the right choices in the lab and receiving positive results. Through the help of student on our team specializing in biomedical computing, applied mathematics, and chemical
 +
engineering, we created a number of different models that were crucial to our project design.</p>
  
 +
 +
  <div class="column" style="background-color:#FFFFFF;">
 +
  <div style="margin:auto;">
 +
    <a href="https://2018.igem.org/Team:Queens_Canada/Molecular_Dynamic_Simulations"><img src="https://static.igem.org/mediawiki/2018/f/f7/T--Queens_Canada--RMSDcartoon0.png" alt='nolinker' style="height=50%"/></a>
 +
    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Molecular_Dynamic_Simulations">Molecular Dynamic Simulations</a></font>
 +
    <p>One of our constructs relied on linkers of sufficient length and flexibility to convert a conformational change, into signal transduction. We have achieved this through firstly modelling with <a href="https://2018.igem.org/Team:Queens_Canada/Linker_Development" target="_blank">PyMol</a> and then performing molecular dynamic simulations of the root-mean-square deviation of <a href="https://2018.igem.org/Team:Queens_Canada/Fluid_Dynamics" target="_blank"> atomic position.</p>
 +
    <br>
 +
</div>
 
</div>
 
</div>
−
<footer style="background-color: #212121;height:90px ">
+
 
−
            <div class="container">
+
<div class="column" style="background-color:#FFFFFF;">
−
                <div class="row">
+
  <div style="margin:auto;">
−
                    <div class="col-md-4">
+
    <a href="http://https://2018.igem.org/Team:Queens_Canada/Linker_Development"><img src="https://static.igem.org/mediawiki/2018/b/b6/T--Queens_Canada--PyMOLNoLinker.jpg" alt='nolinker' style="height=50%"/></a>
−
                        <ul class="list-inline quicklinks">
+
    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Linker_Development">Linker Development</a></font>
−
                            <li><a href="https://igem.org/Main_Page" style="color:white; font-size:16pt">iGEM Headquarters</a>
+
    <p>As a part of our construct it is necessary to build linkers to connect the intein halves with the target receptor. The challenge in developing linkers for the system is that they must be of a specific length that will allow association of the intein halves in the bound conformation of the receptor but will not allow association of the intein halves in the unbound conformation of the receptor. In addition, the flexibility of the linkers must be adjusted for the same purpose. Therefore we performed extensive in-silico modelling of nuclear receptor Ligand Binding domains, and numerous purposed linkers</p>
−
                            </li>
+
    <br>
−
                        </ul>
+
</div>
−
                    </div>
+
</div>
−
                    <div class="col-md-4">
+
 
−
                        <ul class="list-inline social-buttons" style="margin-left:20%">
+
  <div class="column" style="background-color:#FFFFFF;">
−
                            <li><a href="https://twitter.com/iGEMQueens"style="   display: block;
+
  <div style="margin:auto;">
−
    background-color: #fff;
+
    <a href="https://2018.igem.org/Team:Queens_Canada/Michaelis-Menten_Kinetics"><img src="https://static.igem.org/mediawiki/2018/9/90/T--Queens_Canada--MichaelisM.png" style="height=50%"/></a>
−
    height: 40px;
+
    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Michaelis-Menten_Kinetics">Michaelis - Menten kinetics</a></font>
−
    width: 40px;
+
     <p>Michaelis - Menten kinetics is a model used to examine enzyme kinetic. Luciferase's activity can be modeled by Michaelis-Menten kinetics as they perform the simple conversion of a substrate into a product and a photon. Our project relied on the light producing NanoLuc Luciferase as a signal in our devices. We were able to model this relationship with MATLAB. The governing equations for this model were compiled in the MATLAB, with the goal of creating a generic calculator which teams may use in the future. Known
−
    border-radius: 100%;
+
values for concentrations and reactions rates are used as inputs, and the file produces the various
−
    font-size: 20px;
+
rates of change with respect to the concentrations.</p>
−
    line-height: 40px;
+
    <br>
−
    color: #000;
+
</div>
−
    outline: 0;
+
  </div>
−
    -webkit-transition: all .3s;
+
 
−
    -moz-transition: all .3s;
+
 
−
    transition: all .3;"><i class="fa fa-twitter"style="color:black; font-family:FontAwesome;margin-left:10.75px;"></i></a>
+
  <div class="column" style="background-color:#FFFFFF;">
−
                            </li>
+
  <div style="margin:auto;">
−
                            <li><a href="https://www.facebook.com/iGEMQueens/?fref=ts"style="    display: block;
+
     <a href="https://2018.igem.org/Team:Queens_Canada/Fluid_Dynamics"><img src="https://static.igem.org/mediawiki/2018/0/06/T--Queens_Canada--BrownianSimulation2FD.png" alt='Diagram showing Brownian simulations in a tube' style="width:50%"/></a>
−
    background-color: #fff;
+
    <br><br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Fluid_Dynamics">Fluid Dynamics</a></font>
−
    height: 40px;
+
     <p>The ultimate application of our work from this year will be in the form of a diagnostic pacifier capable of collecting saliva, mixing with an internal biosensor and generating a signal for salivary hormone quantification. Therefore we sought to model many aspects of the pacifier including: saliva flow rate, flow turbulence, and particle mixing.</p>
−
    width: 40px;
+
     <br>
−
    border-radius: 100%;
+
</div>
−
    font-size: 20px;
+
  </div>
−
     line-height: 40px;
+
 
−
    color: #000;
+
<div class="column" style="background-color:#FFFFFF;">
−
    outline: 0;
+
<div style="margin:auto;">
−
    -webkit-transition: all .3s;
+
     <a href="https://2018.igem.org/Team:Queens_Canada/Pacifier"><img src="https://static.igem.org/mediawiki/2018/8/81/T--Queens_Canada--CadofPac.png" style="height=50%"/></a>
−
    -moz-transition: all .3s;
+
<br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Pacifier">Computer Aided Design</a></font>
−
    transition: all .3;"><i class="fa fa-facebook"style="color:black;font-family:FontAwesome;margin-left:10.75px;"></i></a>
+
    <p>We created relevant hardware for our project including a 3D printed pacifier to passively collect saliva samples. Before 3D printing any iterations of our design, we modeled our device on Computer Aided Design Software.</p>
−
                            </li>
+
    <br>
−
                            <li><a href="mailto:director@qgemteam.com" style="   display: block;
+
</div>
−
    background-color: #fff;
+
  </div>
−
    height: 40px;
+
 
−
     width: 40px;
+
<br>
−
    border-radius: 100%;
+
<br>
−
    font-size: 20px;
+
<br>
−
    line-height: 40px;
+
<br>
−
    color: #000;
+
<br>
−
    outline: 0;
+
−
    -webkit-transition: all .3s;
+
 
−
    -moz-transition: all .3s;
+
−
    transition: all .3;"><i class="fa fa-envelope"style="color:black;font-family:FontAwesome;margin-left:10.75px;"></i></a>
+
−
                            </li>
+
−
                            <li><a href="https://www.linkedin.com/company/1633448?trk=tyah&amp;trkInfo=clickedVertical%3Acompany%2CclickedEntityId%3A1633448%2Cidx%3A1-1-1%2CtarId%3A1464110668532%2Ctas%3Aqgem" style="    display: block;
+
−
     background-color: #fff;
+
−
     height: 40px;
+
−
    width: 40px;
+
−
    border-radius: 100%;
+
−
    font-size: 20px;
+
−
    line-height: 40px;
+
−
    color: #000;
+
−
    outline: 0;
+
−
     -webkit-transition: all .3s;
+
−
    -moz-transition: all .3s;
+
−
    transition: all .3;"><i class="fa fa-linkedin"style="color:black; font-family:FontAwesome;margin-left:10.75px;"></i></a>
+
−
                            </li>
+
−
                        </ul>
+
−
                    </div>
+
−
                    <div class="col-md-4">
+
−
                        <ul class="list-inline quicklinks" style="color: white;font-size:16pt;">
+
−
                            <li><a href="http://www.queensu.ca/" style="color:white;margin-left:100px;">Queen's University</a>
+
−
                            </li>
+
−
                        </ul>
+
−
                    </div>
+
−
                </div>
+
−
            </div>
+
−
        </footer>
+
 
</body>
 
</body>
 +
 
</html>
 
</html>

Latest revision as of 03:03, 16 October 2018

Modelling

At team Queens Canada, we believe that proper preparation is the best way to reach a desired outcome. Accordingly, we sought to model many aspects of our project which aided in making the right choices in the lab and receiving positive results. Through the help of student on our team specializing in biomedical computing, applied mathematics, and chemical engineering, we created a number of different models that were crucial to our project design.

nolinker
Molecular Dynamic Simulations

One of our constructs relied on linkers of sufficient length and flexibility to convert a conformational change, into signal transduction. We have achieved this through firstly modelling with PyMol and then performing molecular dynamic simulations of the root-mean-square deviation of atomic position.


nolinker
Linker Development

As a part of our construct it is necessary to build linkers to connect the intein halves with the target receptor. The challenge in developing linkers for the system is that they must be of a specific length that will allow association of the intein halves in the bound conformation of the receptor but will not allow association of the intein halves in the unbound conformation of the receptor. In addition, the flexibility of the linkers must be adjusted for the same purpose. Therefore we performed extensive in-silico modelling of nuclear receptor Ligand Binding domains, and numerous purposed linkers



Michaelis - Menten kinetics

Michaelis - Menten kinetics is a model used to examine enzyme kinetic. Luciferase's activity can be modeled by Michaelis-Menten kinetics as they perform the simple conversion of a substrate into a product and a photon. Our project relied on the light producing NanoLuc Luciferase as a signal in our devices. We were able to model this relationship with MATLAB. The governing equations for this model were compiled in the MATLAB, with the goal of creating a generic calculator which teams may use in the future. Known values for concentrations and reactions rates are used as inputs, and the file produces the various rates of change with respect to the concentrations.


Diagram showing Brownian simulations in a tube

Fluid Dynamics

The ultimate application of our work from this year will be in the form of a diagnostic pacifier capable of collecting saliva, mixing with an internal biosensor and generating a signal for salivary hormone quantification. Therefore we sought to model many aspects of the pacifier including: saliva flow rate, flow turbulence, and particle mixing.



Computer Aided Design

We created relevant hardware for our project including a 3D printed pacifier to passively collect saliva samples. Before 3D printing any iterations of our design, we modeled our device on Computer Aided Design Software.