Difference between revisions of "Team:UI Indonesia/Modeling"

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{{UI_Indonesia}}
 
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<h2> Modeling</h2>
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<h4>Note</h4>
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body {
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</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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/* Creates the container for the content */
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Here are a few examples from previous teams:
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width: 814px;
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<div id="bannerContainer">
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<h2> Add a banner to your wiki! </h2>
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<p>You can make the image 980px by  200px</p>
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<p> Remember to call the file: "<i>Team_UI_Indonesia_banner.jpg</i>" </p>-->
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                        <img src="">
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<div style="width:900px;border: 2px solid #6D5417;margin-top:20px;margin-bottom:20px;padding-left:20px;padding-right:20px;margin-left:20px;background-image: url('https://static.igem.org/mediawiki/2015/1/10/UI_Indonesia_opacity.png');">
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<center><h1 id="judul"><p style="font-size:22px;">Modelling of Bacterial Contraception</p></h1></center>
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<p>Subtance which has spremicidal effect in Bacterial Contraception is SboA (Substlosin A), a kind of protein. On our project, there’re several part of theoritical modelling that we do :<br><br><b>A. SboA Struture</b></p>
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<img width="600px"src="https://static.igem.org/mediawiki/2015/d/da/UI_Indonesia_model_a.jpg">
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<p><b>(A)</b> Amino acid sequence of subtilosin A and subtilosin A1. The backbone cyclization of the peptide via an amide bond is represented by a solid line between the N and C termini. The positions of the sulfur-to-α-carbon thioether linkages are represented by solid lines connected to S. The arrow indicates the position of the single-amino-acid substitution (T6I) in subtilosin A1.<br><br><b>(B)</b> Backbone coil structure of subtilosin A as determined by solution NMR (10). The three sulfur-to-α-carbon thioether bridges are shown, and the location of the N- to C-terminal cyclization is indicated by the arrow. The side chain and backbone of threonine 6 are marked by the bracket.
 
</p>
 
</p>
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<ul>
 
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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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</ul>
 
  
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<img width="300px"src="https://static.igem.org/mediawiki/2015/0/09/UI_Indonesia_model_b.jpg">
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<img width="300px"src="https://static.igem.org/mediawiki/2015/4/4e/UI_Indonesia_model_c.jpg">
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<br><br><br><b>B. SboAConcentrationNeeded for ImmobilizingSperm</b>
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<img width="600px"src="https://static.igem.org/mediawiki/2015/9/99/UI_Indonesia_model_d.jpg">
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<br><br><br><b>C. Toggle Switch Logic</b><br>
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<img width="300px"src="https://static.igem.org/mediawiki/2015/0/0d/UI_Indonesia_model_e.jpg">
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<img width="300px"src="https://static.igem.org/mediawiki/2015/7/7f/UI_Indonesia_model_f.jpg">
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<br><br><br><b>D. Toggle switch mass action kinetic equation</b><br>
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<img width="300px"src="https://static.igem.org/mediawiki/2015/f/f2/UI_Indonesia_model_g.jpg">
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<br><br><br><b>E. Toggle switch mass action kinetic equation</b><br>
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<img width="300px"src="https://static.igem.org/mediawiki/2015/0/02/UI_Indonesia_model_h.jpg">
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<br><br><br><b>F. Toggle switch mass action kinetic equation</b><br>
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<img width="300px"src="https://static.igem.org/mediawiki/2015/3/3f/UI_Indonesia_model_i.jpg">
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<br><br><br><b>G. Toggle switch mass action kinetic equation</b><br>
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<img width="300px"src="https://static.igem.org/mediawiki/2015/3/3d/UI_Indonesia_model_j.jpg">
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<img width="300px"src="https://static.igem.org/mediawiki/2015/b/b9/UI_Indonesia_model_k.jpg">
  
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<p>Thats all the thoritical modelling that made by our team. We can’t do the “Real” modelling because our wet lab project haven’t done yet when I made this.<br><br>References :<br>
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• Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives<br>• Kawulka KE, Sprules T, Diaper CM, Whittal RM, McKay RT, Mercier P, Zuber P, Vederas JC
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</p>
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<div style="width:100%;height:100px">
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<img src="https://static.igem.org/mediawiki/2015/5/57/UI_Indonesia_kalbe.jpg" style="float:left;">
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<img src="https://static.igem.org/mediawiki/2015/a/a8/UI_Indonesia_bioneer.gif" style="float:left;margin-left:65px;">
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<img src="https://static.igem.org/mediawiki/2015/9/93/UI_Indonesia_dikti.jpg" style="float:left;margin-left:65px;">
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<div style="width:100%;height:90px">
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<img src="https://static.igem.org/mediawiki/2015/a/a3/UI_Indonesia_pakraden.png" style="float:left;margin-left:20px;">
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<img src="https://static.igem.org/mediawiki/2015/9/9b/UI_Indonesia_igemui.png" style="float:left;margin-left:70px;">
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<div style="width:110px;height:90px;float:left;margin-left:70px;">
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<a href="https://twitter.com/ui_synbio" target="_blank"><img src="https://static.igem.org/mediawiki/2015/2/26/UI_Indonesia_twitter.png"></a>
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<a href="https://instagram.com/igem_ui" target="_blank"><img src="https://static.igem.org/mediawiki/2015/d/da/UI_Indonesia_insta.png"></a>
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<img src="https://static.igem.org/mediawiki/2015/b/b0/UI_Indonesia_fk.png" style="float:left;margin-left:80px;">
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<img src="https://static.igem.org/mediawiki/2015/f/f8/UI_Indonesia_ft.jpg" style="float:left;margin-left:80px;">
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<img src="https://static.igem.org/mediawiki/2015/7/74/UI_Indonesia_ui.png" style="float:left;margin-left:80px;">
 
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Revision as of 21:59, 18 September 2015

Modelling of Bacterial Contraception

Subtance which has spremicidal effect in Bacterial Contraception is SboA (Substlosin A), a kind of protein. On our project, there’re several part of theoritical modelling that we do :

A. SboA Struture

(A) Amino acid sequence of subtilosin A and subtilosin A1. The backbone cyclization of the peptide via an amide bond is represented by a solid line between the N and C termini. The positions of the sulfur-to-α-carbon thioether linkages are represented by solid lines connected to S. The arrow indicates the position of the single-amino-acid substitution (T6I) in subtilosin A1.

(B) Backbone coil structure of subtilosin A as determined by solution NMR (10). The three sulfur-to-α-carbon thioether bridges are shown, and the location of the N- to C-terminal cyclization is indicated by the arrow. The side chain and backbone of threonine 6 are marked by the bracket.




B. SboAConcentrationNeeded for ImmobilizingSperm


C. Toggle Switch Logic



D. Toggle switch mass action kinetic equation



E. Toggle switch mass action kinetic equation



F. Toggle switch mass action kinetic equation



G. Toggle switch mass action kinetic equation

Thats all the thoritical modelling that made by our team. We can’t do the “Real” modelling because our wet lab project haven’t done yet when I made this.

References :
• Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives
• Kawulka KE, Sprules T, Diaper CM, Whittal RM, McKay RT, Mercier P, Zuber P, Vederas JC