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

 
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             <div class="container">
 
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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>
 
'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><hr>
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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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                         <ul class="sub" id="sub_home" style="cursor:default;">
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                             <li class="list" id="home1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Team">Team</a></li>
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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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<li class="list" id="home2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Attributions">Attributions</a></li>
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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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<li class="list" id="home2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Medal">Medal</a></li>
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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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<li class="list" id="home3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Judge">For Judge</a></li>
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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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<a href="https://2018.igem.org/Team:CCU_Taiwan/Achievements"><li class="list" id="home5">Achievements</li></a>
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<a>There's a home for us, always.</a>
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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><hr>
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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>
 
<ul class="sub" id="sub_project" style="cursor:default;">
 
<ul class="sub" id="sub_project" style="cursor:default;">
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    <li class="list" id="project1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Description">Description</a></li>
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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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<li class="list" id="project2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Design">Design</a></li>
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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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<li class="list" id="project3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Results">Results</a></li>
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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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<li class="list" id="project6"><a href="https://2018.igem.org/Team:CCU_Taiwan/Demonstrate">Demonstration</a></li>
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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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<li class="list" id="project5"><a href="https://2018.igem.org/Team:CCU_Taiwan/InterLab ">InterLab</a></li>
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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><hr>
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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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    <li class="list" id="parts1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Parts">Overview</a></li>
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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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<li class="list" id="parts2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Basic_Part">Basic Part</a></li>
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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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<li class="list" id="parts3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Composite_Part">Composite Part</a></li>
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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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<li class="list" id="parts4"><a href="https://2018.igem.org/Team:CCU_Taiwan/Improve">Improved Part</a></li>
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<hr>
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                         </ul>
 
                         </ul>
 
                     </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><hr>
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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>
 
                         <ul class="sub" id="sub_modeling" style="cursor:default;">
 
                         <ul class="sub" id="sub_modeling" style="cursor:default;">
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                             <li class="list" id="model1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Model">Overview</a></li>
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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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                            <li class="list" id="model2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Enzyme">Enzyme Model</a></li>
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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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<li class="list" id="model3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Lignin">Lignin Model</a></li>
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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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<li class="list" id="model4"><a href="https://2018.igem.org/Team:CCU_Taiwan/Tools">Tools</a></li>
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<hr>
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                         </ul>
 
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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>Drylab</a><hr>
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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>
 
                         <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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<li class="list" id="drylab2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Engineering">Engineering</a></li>
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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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<li class="list" id="drylab3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Safety">Safety</a></li>
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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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<hr>
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                         </ul>
 
                         </ul>
 
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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><hr>
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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>
 
                         <ul class="sub" id="sub_human_practice" style="cursor:default;">
 
                         <ul class="sub" id="sub_human_practice" style="cursor:default;">
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                             <li class="list" id="human_practice1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Human_Practices">Overview</a></li>
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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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<li class="list" id="human_practice2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Engagement">Public</a></li>
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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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<li class="list" id="human_practice3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Entrepreneurship">Entrepreneurship</a></li>
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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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<li class="list" id="human_practice4"><a href="https://2018.igem.org/Team:CCU_Taiwan/Intergrate">Intergrate</a></li>
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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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<hr>
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<a href="https://2018.igem.org/Team:CCU_Taiwan/Integrate"><li class="list" id="human_practice5">Integrated HP</li></a>
 
                         </ul>
 
                         </ul>
 
                     </li>
 
                     </li>
 
    <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>
 
    <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>
 
                         <ul class="sub" id="sub_notebook" style="cursor:default;">
 
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                             <li class="list" id="notebook1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Notebook">Overview</a></li>
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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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<li class="list" id="notebook2"><a href="https://2018.igem.org/Team:CCU_Taiwan/Collaborations">Collaborations</a></li>
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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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<li class="list" id="notebook3"><a href="https://2018.igem.org/Team:CCU_Taiwan/Experiments">Experiments</a></li>
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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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<li class="list" id="notebook4"><a href="https://2018.igem.org/Team:CCU_Taiwan/DATABASE">DATABASE</a></li>
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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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<hr>
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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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<!--<div class="scroll-line"></div>
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<div class="Quick-navigation">
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  <a href="#A" class="Quick-navigation-item">____Background</a>
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  <a href="#B" class="Quick-navigation-item">____Calibration 1</a>
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  <a href="#C" class="Quick-navigation-item">____Calibration 2</a>
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  <a href="#D" class="Quick-navigation-item">____Calibration 3</a>
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  <a href="#E" class="Quick-navigation-item">____Calibration 4</a>
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  <a href="#F" class="Quick-navigation-item">____Calibration 5</a>
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<div class="pointerModeling" id="1"><a href="#ca1">Binding model</a></div>
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<div class="pointerModeling" id="2"><a href="#ca2">Polymer model</a></div>
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</div>
 +
 
 +
<div class="backgroundModeling">
 +
<div class="photoModeling"><h1 class="bigtitle">MODELING<h1></div>
 
       <div class="content">
 
       <div class="content">
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<p class="first">Modeling Overview</p>
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<br>
−
<p class="description">In the future, there will be fewer and fewer petrochemical resources on the planet, and plastic waste will accumulate. When things change, what should we do? To solve the problem, we use Liggreen. We hope to establish a new production line of laminating coating through biological methods. First of all, we use natural enzyme to synthesize the material. Through the synthetic reaction of enzyme and monolignols, we make our Liggreen structure be close to natural vegetation. Then, we could create a biological coating which will not require petrochemicals and high energy consumption. Our modeling is mainly divided into three parts to prove our project – Enzyme production, Monomer polymerization, Molecular prediction.</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="second">Enzyme production:</p>
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<p class="first" id="ca1"><a href="https://2018.igem.org/Team:CCU_Taiwan/Binding">Binding model</a></p>
−
<p class="description">Transforming p.pastoris by synthetic biology. We want to make yeast produce the required enzymes – Lac1, Px16, Px18<br>Modeling: Proving the experiment by measuring the growth curve of p. pastoris and auto selection. Then using the different tag genes to design for western blot, proving the success of our overall enzyme production system.</p>
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<div class="row"> 
−
<p class="second">Monomer polymerization:</p>
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<div id="halftext3">
−
<p class="description"> The three enzymes are added into the monolignols. And the monolignols will generate free radicals and bond to each other.<br>Modeling: We use Spartan to simulate the monolignol and the primary product, and then the free energy is obtained. The experiment was used to verify the spontaneity of the reaction.</p>
+
<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>
−
<p class="second">Molecular prediction: </p>
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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)
−
<p class="description">When the polymerization reaction is carried out to a certain extent, we would measure the physicochemical properties and carry out the modification. So that lignin can be better used in the coating industry.<br>Modeling: In this part, because we can't complete the all of polymerization reaction, we refer to paper for the estimation of molecular polymerization products. The estimation is mainly based on three parts – monomer, bond and product molecular weight. Since we mainly use the monolignol G for the reaction first, the structural estimation is mainly based on the Epoxy Resin.</p>
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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">
 +
                    <p>Figure1: Activation energy diagram when reaction is spontaneous.</p>
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                  </div>
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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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<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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<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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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.