Team:CityU HK/collaboration

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<div id="main">
<div id="main">
<img id="banner"  src="http://2014.igem.org/wiki/images/4/4b/CityU_HK_collaboration-banner.png" width=100%>
<img id="banner"  src="http://2014.igem.org/wiki/images/4/4b/CityU_HK_collaboration-banner.png" width=100%>
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<div id="content">
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<h2 id="title">CUHK : Computer simulation of the “Nitrogenase System”  </h2>
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<p> This year, the CityU HK iGEM team collaborated with the <a href="http://2014.igem.org/Team:Hong_Kong-CUHK">CUHK iGEM team.</a></p><br>
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<h2 style="color:black"> How did we help the CUHK iGEM team? </h2><br>
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<p>We met the CUHK iGEM team in early October 2014. At the meeting, each party presented our projects and we were impressed with each other’s project goals. Following our discussion, the CityU team agreed to collaborate with the CUHK iGEM team to perform computer simulation/modelling of the “<b><a href="http://2014.igem.org/Team:Hong_Kong-CUHK/home.html?page=link-modelling">Nitrogenase System</a></b>” that the CUHK team was working on. We succeeded in producing a modelling system for their Nitrogenase project.</p><br>
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</div>
<div class="container"><div class="row"><div class="col-md-12">
<div class="container"><div class="row"><div class="col-md-12">
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<h2>CUHK : Computer simulation of the “Nitrogenase System”  </h2>
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<div class="arrow-down" id="arrow2"></div>
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<p id="content"> This year, the CityU HK iGEM team collaborate with the <a href="http://2014.igem.org/Team:Hong_Kong-CUHK">CUHK iGEM team.</a> </p><br>
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</div></div></div>
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<h3>When did it start?</h3>
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<br>
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<p>We met up the CUHK iGEM team in October 2014. During our meet up, we presented our projects to each other and were really impressed by their project. After we had discussion, we were interested to see the result of the “Nitrogenase System” and provide assistance to the CUHK iGEM team.</p><br>
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<h3>How did we help CUHK iGEM team</h3>
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<h3>The Model</h3>
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<p> Our team provided assistance with the computer simulation of the “Nitrogenase System” project of the Chinese University of Hong Kong iGEM Team. </p><br>
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<p> The computer simulation works on two enzyme kinetic systems as shown below.</p>
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<h3>Result</h3>
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<br><center><img class="display" src="http://2014.igem.org/wiki/images/1/11/CityU_HK_collaboration-fig1.png" width="70%"></center>
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<p> The computer simulation works on two enzyme kinetic systems. </p><br>
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<table class="fig">
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  <tr>
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    <th>Fig. 1 </th>
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    <td>Two Enzyme Kinetic Systems. (a) System I-a single one. (b) System II-combination of two kinetic systems.</td>
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  </tr>
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</table>
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<br><br>
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<h3>Acknowledgement</h3>
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<p>The table below presents the Vmax and Km of both enzyme systems.</p><br>
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<p> Dr. Zhu Yuan, Department of Mathematics and Statistics, Guangdong University of
Finance and Economics, Guangzhou, 510320, P.R. China </p>
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</div></div></div>
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<center><table id="parameter">
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  <tr>
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      <td></td>
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      <td><h2>Nitrogenase (30 °C)</h2></td>
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      <td><h2>Hydrogenase (80 °C)</h2></td>
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  </tr>
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  <tr>
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      <td><h2>Vmax</h2></td>
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      <td><p>0.0175 nmol CH4/ nmol MoFe protein /sec</p></td>
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      <td><p>5.28x10-6 nmol H+/ nmol hydrogenase/ sec</p></td>
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  </tr>
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  <tr>
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      <td><h2>Km </h2></td>
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      <td><p>16 mM HCO3</p></td>
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      <td><p>0.037 mM H2</p></td>
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  </tr>
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</table></center>
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<br><br>
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<p>Based on the parameters provided, we compared the two enzyme kinetic systems using Matlab simulation.</p><br>
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<h3>Equations</h3>
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<center><img  class="display" src="http://2014.igem.org/wiki/images/7/7b/CityU_HK_collaboration-eqn.png"width="40%"></center><br><br>
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<h3>Results</h3>
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<p> A comparison of the two systems using Matlab simulation is shown in Fig. 2. The difference between the product output of the two systems are provided by the data in <a href="http://2014.igem.org/wiki/images/4/45/CityU_HK_collaboration-fig4.png">Fig.4</a> and <a href="http://2014.igem.org/wiki/images/0/09/CityU_HK_collaboration-fig5.png">Fig.5</a>. </p>
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<br><center><img style="border:solid #ebebeb" class="display" src="http://2014.igem.org/wiki/images/3/39/CityU_HK_collaboration-fig2.png"width="50%"></center><br>
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<table class="fig">
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  <tr>
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    <th>Fig. 2 </th>
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    <td>Matlab code. Input: V1max, K1m and A10 are the initial parameter settings of the system I. V2max, K2m are those of system II. t represents the time.</td>
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  </tr>
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</table><br><br>
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<br><center><img class="display" src="http://2014.igem.org/wiki/images/a/a6/CityU_HK_collaboration-fig3.png" width="70%"></center><br>
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<table class="fig">
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  <tr>
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    <th>Fig. 3 </th>
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    <td>A. Relationship between substrate [A] and product [C]. B. Relationship between substrate [A] and difference between [C3] and [C1] . </td>
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  </tr>
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</table>
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<br><br>
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<h3>Acknowledgement</h3>
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<p> The modelling was performed by <b>Dr. Zhu Yuan</b> of the Department of Biology and Chemistry, City University of Hong Kong. </p>
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<br><br><br>
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Latest revision as of 00:23, 18 October 2014

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CUHK : Computer simulation of the “Nitrogenase System”

This year, the CityU HK iGEM team collaborated with the CUHK iGEM team.


How did we help the CUHK iGEM team?


We met the CUHK iGEM team in early October 2014. At the meeting, each party presented our projects and we were impressed with each other’s project goals. Following our discussion, the CityU team agreed to collaborate with the CUHK iGEM team to perform computer simulation/modelling of the “Nitrogenase System” that the CUHK team was working on. We succeeded in producing a modelling system for their Nitrogenase project.



The Model

The computer simulation works on two enzyme kinetic systems as shown below.


Fig. 1 Two Enzyme Kinetic Systems. (a) System I-a single one. (b) System II-combination of two kinetic systems.


The table below presents the Vmax and Km of both enzyme systems.


Nitrogenase (30 °C)

Hydrogenase (80 °C)

Vmax

0.0175 nmol CH4/ nmol MoFe protein /sec

5.28x10-6 nmol H+/ nmol hydrogenase/ sec

Km

16 mM HCO3

0.037 mM H2



Based on the parameters provided, we compared the two enzyme kinetic systems using Matlab simulation.


Equations



Results

A comparison of the two systems using Matlab simulation is shown in Fig. 2. The difference between the product output of the two systems are provided by the data in Fig.4 and Fig.5.



Fig. 2 Matlab code. Input: V1max, K1m and A10 are the initial parameter settings of the system I. V2max, K2m are those of system II. t represents the time.




Fig. 3 A. Relationship between substrate [A] and product [C]. B. Relationship between substrate [A] and difference between [C3] and [C1] .


Acknowledgement

The modelling was performed by Dr. Zhu Yuan of the Department of Biology and Chemistry, City University of Hong Kong.




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