Team:UIUC Illinois/Modeling

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<center><p style="font-size: 400% ">Modeling</p></center>
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<center><p style="font-size: 150% "><i>"All science requires mathematics. The knowledge of mathematical things is almost innate in us.... This is the easiest of sciences, a fact which is obvious in that no one's brain rejects it; for laymen and people who are utterly illiterate know how to count and reckon."</i></p></center>
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<br><center>-Roger Bacon</br></center>
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<p><b>Overview:</b>
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  To predict the result of bioreactor, we used mathematica to solve differential using Michaelis-Menton equation. The strength of utilizing mathematica rather than matlab was that it allowed us to set up the value of several constants as varying rather than setting it as invariant. Kcat & Km values were obtained through research papers by Swati & Sathyanarayana (2006), and Ryan M.Summers (2010).
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This is caffeine demehtlyation pathway by demethlyase. It goes from Caffeine to theobromine to 7-methylxanthine to xanthine. The other pathway is caffeine dehydrogenase. It goes from Caffeine to Trimethyl Uric acid.
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<h2> Parameters </h2>
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<h1 >WELCOME TO iGEM 2014! </h1>
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<p>Your team has been approved and you are ready to start the iGEM season!
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<th>Name</th>
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<br>On this page you can document your project, introduce your team members, document your progress <br> and share your iGEM experience with the rest of the world! </p>
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<th>Description</th>
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<td>Vm</td>
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<td>Maximum rate of system</td>
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<td>Kcat</td>
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<td>Maximum number of substrate molecules converted into products</td>
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<td>Km</td>
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<td>Substrate concentration where the reaction rate is half of maximum (depend on both enzyme and substrate)</td>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:UIUC_Illinois/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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        <br><h2><center>Fig1. Caffeine Demethylation Pathway</center></h2>
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<center>Initial concentration of caffeine, 10 uM and decreases as it degrades to theobromine, 7-methylxanthine, and finally xanthine with final concentration of 10uM, only if our designed bacteria has efficiency of 100%. </center>
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        <br><h2><center>Fig2. Caffeine Dehydrogenase Pathway</center></h2>
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<center>Denotes initial concentration of caffeine 10 uM and gradually degrades to Trimethyl Uric Acid with final concentration of 10uM</center>
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<a href="https://2014.igem.org/Team:UIUC_Illinois"style="color:#000000">Home </a> </td>
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<h2>Modeling Dog's intestine </h2>
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<a href="https://2014.igem.org/Team:UIUC_Illinois/Team"style="color:#000000"> Team </a> </td>
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<p><b>Description:</b></p>
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K<sub>T</sub> is the rate of transfer, C<sub>i</sub> is concentration of caffeine in intestine of dog,
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C<sub>b</sub> is concentration of caffeine in blood which should be coming down from intestine.<br>
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A<sub>i</sub> is the surface area of the intestine, V<sub>i</sub> is the volume of the intestine, V<sub>b</sub> is the volume of blood.
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K<sub>cl</sub> is the clearance rate.
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<a href="https://igem.org/Team.cgi?year=2014&team_name=UIUC_Illinois"style="color:#000000"> Official Team Profile </a></td>
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<p>If you choose to create a model during your project, please write about it here. Modeling is not an essential part of iGEM, but we encourage any and all teams to model some aspect of their project. See previous "Best Model" awards for more information.</p>
 
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      <br><br><img src="https://static.igem.org/mediawiki/2014/3/3f/Intestine_caffeine_deg_model.jpg"/, width="98%"><br>
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        <h2><center>Fig3. Dog's Intestine & Blood Model</center></h2>
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<center>Initial Concentration of Caffeine decreases exponentially in the intestine as caffeine is delivered into the blood and degraded by bacteria. Concentration of caffeine increases in the blood then decreases due to the clearance factor K<sub>cl</sub> </center>
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Latest revision as of 03:45, 18 October 2014


Modeling

"All science requires mathematics. The knowledge of mathematical things is almost innate in us.... This is the easiest of sciences, a fact which is obvious in that no one's brain rejects it; for laymen and people who are utterly illiterate know how to count and reckon."


-Roger Bacon

Overview: To predict the result of bioreactor, we used mathematica to solve differential using Michaelis-Menton equation. The strength of utilizing mathematica rather than matlab was that it allowed us to set up the value of several constants as varying rather than setting it as invariant. Kcat & Km values were obtained through research papers by Swati & Sathyanarayana (2006), and Ryan M.Summers (2010).

This is caffeine demehtlyation pathway by demethlyase. It goes from Caffeine to theobromine to 7-methylxanthine to xanthine. The other pathway is caffeine dehydrogenase. It goes from Caffeine to Trimethyl Uric acid.

Parameters

Name Description
Vm Maximum rate of system
Kcat Maximum number of substrate molecules converted into products
Km Substrate concentration where the reaction rate is half of maximum (depend on both enzyme and substrate)




Fig1. Caffeine Demethylation Pathway

Initial concentration of caffeine, 10 uM and decreases as it degrades to theobromine, 7-methylxanthine, and finally xanthine with final concentration of 10uM, only if our designed bacteria has efficiency of 100%.





Fig2. Caffeine Dehydrogenase Pathway

Denotes initial concentration of caffeine 10 uM and gradually degrades to Trimethyl Uric Acid with final concentration of 10uM

Modeling Dog's intestine

Description:

KT is the rate of transfer, Ci is concentration of caffeine in intestine of dog, Cb is concentration of caffeine in blood which should be coming down from intestine.
Ai is the surface area of the intestine, Vi is the volume of the intestine, Vb is the volume of blood.
Kcl is the clearance rate.




Fig3. Dog's Intestine & Blood Model

Initial Concentration of Caffeine decreases exponentially in the intestine as caffeine is delivered into the blood and degraded by bacteria. Concentration of caffeine increases in the blood then decreases due to the clearance factor Kcl


The Institute for Genomic Biology
Biosystems Design, South wing, 2nd floor
University of Illinois at Urbana-Champaign
1206 West Gregory Drive
61801 Urbana, Illinois
illinoisigem@gmail.com
Copyright (c) 2014 igem.org. All rights reserved.

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