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

 
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Modeling</h1>
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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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<h3> Gold Medal Criterion #3</h3>
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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Medals Page</a> for more information.
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<h2 style="width:70%;margin-left:15%">Modelling</h2>
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<h3>Best Model Special Prize</h3>
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<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
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Model prize</a>, please describe your work on this page  and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>. Please note you can compete for both the gold medal criterion #3 and the best model prize with this page.  
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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
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engineering, we created a number of different models that were crucial to our project design.</p>
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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    <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>
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    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Molecular_Dynamic_Simulations">Molecular Dynamic Simulations</a></font>
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    <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>
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    <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>
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<h3> Inspiration </h3>
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    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Linker_Development">Linker Development</a></font>
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    <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>
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Here are a few examples from previous teams:
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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    <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>
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    <br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Michaelis-Menten_Kinetics">Michaelis - Menten kinetics</a></font>
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    <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
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values for concentrations and reactions rates are used as inputs, and the file produces the various
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rates of change with respect to the concentrations.</p>
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    <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>
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    <br><br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Fluid_Dynamics">Fluid Dynamics</a></font>
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    <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>
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    <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>
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<br><font size="6px"><a href="https://2018.igem.org/Team:Queens_Canada/Pacifier">Computer Aided Design</a></font>
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    <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>
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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.