Difference between revisions of "Team:CCU Taiwan/Model"

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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://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</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://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1> Modeling</h1>
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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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            <div class="container">
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                <ul class="front">
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                    <div id="home_button" style="cursor:pointer;"  onclick="location.href=
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'https://2018.igem.org/Team:CCU_Taiwan';"> <img src="https://static.igem.org/mediawiki/2018/0/08/T--CCU_Taiwan--home_button.png"></img></div>
  
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                    <li class="title" style="cursor:pointer;" id="Home"><img class="img_title" src="https://static.igem.org/mediawiki/2018/2/24/T--CCU_Taiwan--aboutus.png"></img><a>About Us</a>
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<h3> Gold Medal Criterion #3</h3>
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                        <ul class="sub" id="sub_home" style="cursor:default;">
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<p>
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Team"><li class="list" id="home1">Team</li></a>
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.  
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Attributions"><li class="list" id="home2">Attributions</li></a>
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<br><br>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Medal"><li class="list" id="home3">Medals</li></a>
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Judge"><li class="list" id="home4">For Judges</li></a>
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</p>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Achievements"><li class="list" id="home5">Achievements</li></a>
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                    </li>
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                    <li class="title" style="cursor:pointer;" id="Project"><img class="img_title" src="https://static.igem.org/mediawiki/2018/6/6f/T--CCU_Taiwan--project.png"></img><a>Project</a>
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<ul class="sub" id="sub_project" style="cursor:default;">
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    <a href="https://2018.igem.org/Team:CCU_Taiwan/Description"><li class="list" id="project1">Description</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Applied_Design"><li class="list" id="project2">Design</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Results"><li class="list" id="project3">Results</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Demonstrate"><li class="list" id="project4">Demonstration</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/InterLab"><li class="list" id="project5">InterLab</li></a>
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</ul>
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</li>
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                    <li class="title" style="cursor:pointer;" id="Parts"><img class="img_title" src="https://static.igem.org/mediawiki/2018/1/17/T--CCU_Taiwan--part.png"></img><a>Parts</a>
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                        <ul class="sub" id="sub_parts" style="cursor:default;">
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Parts"><li class="list" id="parts1">Overview</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Basic_Part"><li class="list" id="parts1">Basic Part</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Composite_Part"><li class="list" id="parts2">Composite Part</li></a>
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                        </ul>
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                    </li>
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                    <li class="title" style="cursor:pointer;" id="Modeling"><img class="img_title" src="https://static.igem.org/mediawiki/2018/0/09/T--CCU_Taiwan--model.png"></img><a>Modeling</a>
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                        <ul class="sub" id="sub_modeling" style="cursor:default;">
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Model"><li class="list" id="model1">Overview</li></a>
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Binding"><li class="list" id="model2">Binding Model</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Polymer"><li class="list" id="model3">Polymer Model</li></a>
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                        </ul>
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                    </li>
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                    <li class="title" style="cursor:pointer;" id="Drylab"><img class="img_title" src="https://static.igem.org/mediawiki/2018/f/fc/T--CCU_Taiwan--Dry_lab.png"></img><a>Product</a>
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                        <ul class="sub" id="sub_drylab" style="cursor:default;">
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Our_Plan"><li class="list" id="drylab1">Analysis</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Engineering"><li class="list" id="drylab2">Production Line</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Safety"><li class="list" id="drylab3">Safety</li></a>
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                        </ul>
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                    </li>
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    <li class="title" style="cursor:pointer;" id="Human_Practice"><img class="img_title" src="https://static.igem.org/mediawiki/2018/9/96/T--CCU_Taiwan--humanpractice.png"></img><a>HP</a>
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                        <ul class="sub" id="sub_human_practice" style="cursor:default;">
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Human_Practices"><li class="list" id="human_practice1">Human Practice</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Public_Engagement"><li class="list" id="human_practice2">Public Engagement</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Entrepreneurship"><li class="list" id="human_practice3">Entrepreneurship</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/engaging_experts"><li class="list" id="human_practice4">Engaging Experts</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Integrate"><li class="list" id="human_practice5">Integrated HP</li></a>
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                        </ul>
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                    </li>
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    <li class="title" style="cursor:pointer;" id="Notebook"><img class="img_title" src="https://static.igem.org/mediawiki/2018/c/c9/T--CCU_Taiwan--notebook.png"></img><a>Notebook</a>
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                        <ul class="sub" id="sub_notebook" style="cursor:default;">
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                            <a href="https://2018.igem.org/Team:CCU_Taiwan/Notebook"><li class="list" id="notebook1">Overview</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Collaborations"><li class="list" id="notebook2">Collaborations</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Protocols"><li class="list" id="notebook3">Protocols</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Experiments"><li class="list" id="notebook4">Experiments</li></a>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Materials"><li class="list" id="notebook5">Materials</li></a>
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                        </ul>
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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Medals Page</a> for more information.
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<div class="pointerModeling" id="1"><a href="#ca1">Binding model</a></div>
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<h3>Best Model Special Prize</h3>
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<div class="pointerModeling" id="2"><a href="#ca2">Polymer model</a></div>
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<div class="backgroundModeling">
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To compete for the <a href="https://2018.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://2018.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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<div class="photoModeling"><h1 class="bigtitle">MODELING<h1></div>
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<br><br>
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      <div class="content">
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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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<br>
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</p>
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<p class="description">&emsp;&emsp;In the future, there will be fewer and fewer petrochemical resources on the planet, but plastic waste are keeping accumulating. When things change, what should we do? To solve the problem, we use LIGGREEN. We hope to establish a new production line for laminating paper products using biological materials. First, we use natural enzymes to synthesize the material. Through the synthetic reaction of enzymes and monolignols, we ensure our LIGGREEN structure is similar to natural compounds. This allows us to create a biological laminate which will not require petrochemicals and high energy consumption. Our modeling is mainly divided into two parts to prove the feasibility of our project: binding model and polymer model.</p><br>
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<p class="first" id="ca1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Binding">Binding model</a></p>
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<div class="row"> 
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<div id="halftext3">
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<p class="description">&emsp;&emsp;In our experiment, coniferyl alcohol would form resonance structure after dehydrogenation, these resonance structures would form dimers (β-5, β-O-4, β-β). These reactions are catalytic by the enzymes and the addition of water.<br>
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<strong>Modeling:</strong> we decided to confirm the feasibility of the reaction through Gibbs free energy calculation. (Calculation method using Spartan 16)
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</p></div>
  
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                <div id="Model1" class="polaroid" style="display:inline-block">
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                  <img src="https://static.igem.org/mediawiki/2018/b/be/T--CCU_Taiwan--CCUmodel111.png" width="100%">
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                  <div class="container">
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                    <p>Figure1: Activation energy diagram when reaction is spontaneous.</p>
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                  </div>
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<p class="first" id="ca2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Polymer">Polymer model</a></p>
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<div class="highlight decoration_A_full">
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<p class="description"> &emsp;&emsp;We produce three enzymes, Px16, Px18 and Lac1. LIGGREEN is produced by coniferyl alcohol and enzymes. The goal of Polymer model is to estimate the polymerization between coniferyl alcohol and enzymes.<br>
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<h3> Inspiration </h3>
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<strong>Modeling:</strong> We use Flory-Stockmayer theory to estimate the polymerization. Through the theory, we can control some conditions to do the oligomerization and let LIGGREEN be more biodegradation and chain-like.
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<p>
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</p>
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Here are a few examples from previous teams:
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</p>
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<br><br><br>
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<ul>
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      </div>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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</ul>
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</div>
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Latest revision as of 08:48, 1 December 2018

MODELING


  In the future, there will be fewer and fewer petrochemical resources on the planet, but plastic waste are keeping accumulating. When things change, what should we do? To solve the problem, we use LIGGREEN. We hope to establish a new production line for laminating paper products using biological materials. First, we use natural enzymes to synthesize the material. Through the synthetic reaction of enzymes and monolignols, we ensure our LIGGREEN structure is similar to natural compounds. This allows us to create a biological laminate which will not require petrochemicals and high energy consumption. Our modeling is mainly divided into two parts to prove the feasibility of our project: binding model and polymer model.


Binding model

  In our experiment, coniferyl alcohol would form resonance structure after dehydrogenation, these resonance structures would form dimers (β-5, β-O-4, β-β). These reactions are catalytic by the enzymes and the addition of water.
Modeling: we decided to confirm the feasibility of the reaction through Gibbs free energy calculation. (Calculation method using Spartan 16)

Figure1: Activation energy diagram when reaction is spontaneous.

Polymer model

  We produce three enzymes, Px16, Px18 and Lac1. LIGGREEN is produced by coniferyl alcohol and enzymes. The goal of Polymer model is to estimate the polymerization between coniferyl alcohol and enzymes.
Modeling: We use Flory-Stockmayer theory to estimate the polymerization. Through the theory, we can control some conditions to do the oligomerization and let LIGGREEN be more biodegradation and chain-like.