Difference between revisions of "Team:BNU-China/Model"

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                <title>BNU-China</title>
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                <meta name="author" content="Ziyu Liu（刘梓钰）,Zhaodong Wang（王兆栋）,Xizong Zhang（张溪棕）"/>
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                  <li id="w_menu2"><a class="w_a" href="https://2017.igem.org/Team:BNU-China/Model/microtubule">Microtubule</a></li>
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<h1>Overview</h1>
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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://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</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://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<p>Although there has been a lot of previous work focusing on the in vitro assembly of microtubules and flagellar filaments, no attempt has been made to assemble them on a cell’s surface. Therefore, we developed mathematical models to explore the possible dynamics of this process and to guide the experiments in wet lab.</p>
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<h1> Modeling</h1>
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<p>One key problem in both the microtubule part and flagellar filament part of our design is the competition between the assembly of monomers on the yeast surface and that in the solution. How can we adjust our experimental parameters such as initial monomer concentration to promote the polymerization on the yeast surface as much as possible and avoid the same process in the solution? Will we be able to obtain enough polymers on the yeast surface to satisfy our needs? Our models gave a positive answer and also provided guidance to optimize the outcome in experiments.</p>
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<p>There are differences between these two kinds of polymers as well. The most significant one is that depolymerization is prominent in the assembly of microtubule, but does not play an important role in the assembly of flagellar filaments. This led us to use different models to describe them. To capture the dynamic instability of microtubules, we used the stochastic chemical reaction model combined with Monte Carlo simulation method. The polymerization of flagellar filaments can be described with the law of mass action and Michaelis-Menten kinetics, so we chose ordinary differential equations to model it.</p>
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<p>Another key difference between the two polymers is our purpose. We want to use the displayed microtubules to screen microtubule-stabilizing agents (which inhibit microtubule depolymerization by curbing GTP hydrolysis), so we closely examined the effect of different GTP hydrolysis rate on microtubule assembly. We plan to use flagellar filaments to expand the yeasts’ capacity to display enzymes, so we used our model to predict the possible magnitude of this expansion.</p>
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<p>Please click on the sidebar to the left to view our modeling work of microtubules and flagellar filaments.</p>
  
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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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    <p style="text-align: center;color: #e5b051;padding-top: 5px;margin-top:75px;">Copyright © 2017 <a href="https://2017.igem.org/Team:BNU-China" style="color: #9E2B20;text-decoration: none;opacity:0.8;">BNU-China</a>&nbsp;All rights reserved.</p>
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    <p style="text-align: center;color: #e5b051;margin-bottom:-20px;">If you like this page, you can contact us: <span style="color:#9E2B20;text-decoration: none;opacity:0.8;">bnu_igem@163.com</a></span>
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<h3> Gold Medal Criterion #3</h3>
 
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To complete for the gold medal criterion #3, please describe your work on this page and fill out the description on your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a>. To achieve this medal criterion, you must convince the judges that your team has gained insight into your project from modeling. You may not convince the judges if your model does not have an effect on your project design or implementation.
 
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Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.
 
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<h3>Best Model Special Prize</h3>
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To compete for the <a href="https://2017.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://2017.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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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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<h5> Inspiration </h5>
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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">Manchester 2016</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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Latest revision as of 14:54, 31 October 2017

BNU-China ">

Overview

Although there has been a lot of previous work focusing on the in vitro assembly of microtubules and flagellar filaments, no attempt has been made to assemble them on a cell’s surface. Therefore, we developed mathematical models to explore the possible dynamics of this process and to guide the experiments in wet lab.

One key problem in both the microtubule part and flagellar filament part of our design is the competition between the assembly of monomers on the yeast surface and that in the solution. How can we adjust our experimental parameters such as initial monomer concentration to promote the polymerization on the yeast surface as much as possible and avoid the same process in the solution? Will we be able to obtain enough polymers on the yeast surface to satisfy our needs? Our models gave a positive answer and also provided guidance to optimize the outcome in experiments.

There are differences between these two kinds of polymers as well. The most significant one is that depolymerization is prominent in the assembly of microtubule, but does not play an important role in the assembly of flagellar filaments. This led us to use different models to describe them. To capture the dynamic instability of microtubules, we used the stochastic chemical reaction model combined with Monte Carlo simulation method. The polymerization of flagellar filaments can be described with the law of mass action and Michaelis-Menten kinetics, so we chose ordinary differential equations to model it.

Another key difference between the two polymers is our purpose. We want to use the displayed microtubules to screen microtubule-stabilizing agents (which inhibit microtubule depolymerization by curbing GTP hydrolysis), so we closely examined the effect of different GTP hydrolysis rate on microtubule assembly. We plan to use flagellar filaments to expand the yeasts’ capacity to display enzymes, so we used our model to predict the possible magnitude of this expansion.

Please click on the sidebar to the left to view our modeling work of microtubules and flagellar filaments.

Copyright © 2017 BNU-China All rights reserved.

If you like this page, you can contact us: bnu_igem@163.com