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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 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> | <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> | ||
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<h2 style="width:70%;margin-left:15%">Molecular Dynamic Simulations</h2> | <h2 style="width:70%;margin-left:15%">Molecular Dynamic Simulations</h2> | ||
<p style="width:70%;margin-left:15%"> | <p style="width:70%;margin-left:15%"> | ||
− | 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 | + | 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> |
<figure style="width:70%;margin-left:15%"> | <figure style="width:70%;margin-left:15%"> | ||
<img src="https://static.igem.org/mediawiki/2018/b/b6/T--Queens_Canada--PyMOLNoLinker.jpg" alt='nolinker'/> | <img src="https://static.igem.org/mediawiki/2018/b/b6/T--Queens_Canada--PyMOLNoLinker.jpg" alt='nolinker'/> | ||
+ | </figure> | ||
<figure style="width:70%;margin-left:15%"> | <figure style="width:70%;margin-left:15%"> | ||
<img src="https://static.igem.org/mediawiki/2018/f/f7/T--Queens_Canada--RMSDcartoon0.png" alt='RMSD0'/> | <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> | <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 | <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 |
Revision as of 01:16, 13 October 2018
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.
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 .
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.