Team:WLC-Milwaukee/Modeling

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<h2>Protein Modeling</h2>
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<p> We are currently undergoing protein data modeling which describes the kinetics of our catalytic enzymes.</p>
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<h1>Protein Modeling</h1>
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This code models Michaelis-Menten enzyme kinetics over a user inputted time duration. Product formation and enzyme-substrate complex formation are assumed irreversible. Initial concentrations of the E-S complex and product are assumed to be zero. And it does not account for the presence of inhibitors or activators.
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Using the law of mass action the enzyme substrate complex, and product formation chemical equations, are separated into a set of differential equations. The MATLAB ode45 function is used to solve the set of differential equations over the given time span.
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INPUT CODE AND DATA???
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<tr>
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<td style="border:1px solid black;" colspan="3" align="center" height="150px" bgColor=#FF404B>
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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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<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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<br>
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<p style="color:#E7E7E7"> <a href="https://2014.igem.org/wiki/index.php?title=Team:WLC-Milwaukee/Modeling&action=edit"style="color:#FFFFFF"> Click here  to edit this page!</a> </p>
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</br></br></br></br></br></br></br></br></br>
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<h1>XynA at pH 7.3</h1>
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<table  width="100%">
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</br>
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<tr heigth="75px">  
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4e/XynA7.3_2E_1s.jpg">
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<a href="https://2014.igem.org/Team:WLC-Milwaukee"style="color:#000000">Home </a> </td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/c/c3/XynA7.3_2E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg">
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<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Team"style="color:#000000"> Team </a> </td>
 
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<td style="border:1px solid black;" align="center"  height ="45px"  onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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<a href="https://igem.org/Team.cgi?year=2014&team_name=WLC-Milwaukee"style="color:#000000"> Official Team Profile </a></td>
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<td style="border:1px solid black" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7> 
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</br>
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Project"style="color:#000000"> Project</a></td>
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<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Parts"style="color:#000000"> Parts</a></td>
 
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<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Modeling"style="color:#000000"> Modeling</a></td>
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<td style="border:1px solid black;" align="center" height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/3/3c/XynA7.3_10E_1s.jpg">
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Notebook"style="color:#000000"> Notebook</a></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/e/e6/XynA7.3_10E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
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<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>
 
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Safety"style=" color:#000000"> Safety </a></td>
 
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<td style="border:1px solid black;" align="center"  height ="45px" onMouseOver="this.bgColor='#d3d3d3'" onMouseOut="this.bgColor='#e7e7e7'" bgColor=#e7e7e7>  
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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<a href="https://2014.igem.org/Team:WLC-Milwaukee/Attributions"style="color:#000000"> Attributions </a></td>
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</br>
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<td align ="center"> <a href="https://2014.igem.org/Main_Page"> <img src="https://static.igem.org/mediawiki/igem.org/6/60/Igemlogo_300px.png" width="55px"></a> </td>
 
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</table>
 
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</td>
 
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<h2>100:1 Substrate-Enzyme Concentration</h2>
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<tr> <td colspan="3" height="15px"> </td></tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/a/a6/100E_1s.jpg"></td>
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<tr><td bgColor="#e7e7e7" colspan="3" height="1px"> </tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/3/32/XynA7.3_100E_5s.jpg"></td>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg"></td>
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<!--modeling content -->
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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<tr><td colspan="3"> <h3>Modeling</h3></td></tr>
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</br>
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<td width="45%"  valign="top">
 
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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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</td>
 
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<td></td>
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<h2>Increased Substrate Concentration at 15 Seconds</h2>
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<td></td>
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</tr>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/9/9f/XynA7.3_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/84/XynA7.3_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/d/de/XynA7.3_100E_15s.jpg">
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</table>
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
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</br>
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<p>DISCUSSION</p>
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</br></br></br></br></br></br></br></br>
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<h1>XynA at pH 8.8</h1>
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</br>
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/10/XynA8.8_2E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/17/XynA8.8_2E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/0/01/XynA8.8_2E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/6/67/XynA8.8_10E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/6/66/XynA8.8_10E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_10E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>100:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7b/XynA8.8_100E_1s.jpg">
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<img width="33%" src=" https://static.igem.org/mediawiki/2014/8/8d/XynA8.8_100E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
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</br>
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<h2>Increased Substrate Concentration at 15 Seconds</h2>
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<img width="33%" src=" https://static.igem.org/mediawiki/2014/0/01/XynA8.8_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/74/XynA8.8_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/b/b6/XynA8.8_100E_15s.jpg">
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
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</br>
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<p>DISCUSSION</p>
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</br></br></br></br></br></br></br></br></br></br>
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<h1>YesZ at pH 7.0</h1>
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</br>
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<h2>2:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/5/55/YesZ_2E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/0/04/YesZ_2E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
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<h2>10:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/77/YesZ_10E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/2/25/YesZ_10E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg">
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
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<h2>100:1 Substrate-Enzyme Concentration</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/0/08/YesZ_100E_1s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/1/12/YesZ_100E_5s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg">
 +
 
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<p>As time progresses from 1 second to 15 seconds, the reaction moves to completion and almost all substrate has been catalyzed into product.</p>
 +
 
 +
</br>
 +
 
 +
<h2>Increased Substrate Concentration at 15 Seconds</h2>
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<img width="33%" src="https://static.igem.org/mediawiki/2014/7/7d/YesZ_2E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/4/4d/YesZ_10E_15s.jpg">
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<img width="33%" src="https://static.igem.org/mediawiki/2014/8/8f/YesZ_100E_15s.jpg">
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<p>Despite the increase in substrate concentration with a constant enzyme concentration, all substrate was catalyzed into product in similar amounts of time.</p>
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</br>
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<p>DISCUSSION</p>
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Latest revision as of 02:11, 18 October 2014


Protein Modeling

We are currently undergoing protein data modeling which describes the kinetics of our catalytic enzymes.

Retrieved from "http://2014.igem.org/Team:WLC-Milwaukee/Modeling"