Difference between revisions of "Team:NUDT CHINA/Model"

(Prototype team page)
 
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{{NUDT_CHINA}}
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<!doctype html>
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<html>
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<html lang="en">
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<head>
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    <meta charset="utf-8">
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    <meta name="viewport" content="width=device-width, initial-scale=1.0">
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    <title>Team:NUDT_CHINA</title>
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 +
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 +
.pure-u-md-3-8,.pure-u-md-9-24{width:37.5%}
 +
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 +
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 +
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 +
.pure-u-md-1-2,.pure-u-md-12-24{width:50%}
 +
.pure-u-md-13-24{width:54.1667%}
 +
.pure-u-md-14-24,.pure-u-md-7-12{width:58.3333%}
 +
.pure-u-md-3-5{width:60%}
 +
.pure-u-md-15-24,.pure-u-md-5-8{width:62.5%}
 +
.pure-u-md-16-24,.pure-u-md-2-3{width:66.6667%}
 +
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−
<div class="column full_size judges-will-not-evaluate">
+
</style>
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<h3>★  ALERT! </h3>
+
<!-- for the menu and all-->
−
<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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    <style type="text/css"><!--
−
<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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−
</div>
+
−
<div class="clear"></div>
+
  
−
<div class="column full_size">
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.pure-menu {
−
<h1> Modeling</h1>
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    box-sizing: border-box;
 +
}
 +
.pure-menu-fixed {
 +
    position: fixed;
 +
    left: 0;
 +
    top: 0;
 +
    z-index: 3;
 +
}
 +
.pure-menu-list,
 +
.pure-menu-item {
 +
    position: relative;
 +
}
  
−
<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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.pure-menu-list {
 +
    list-style: none;
 +
    margin: 0;
 +
    padding: 0;
 +
}
  
−
</div>
+
.pure-menu-item {
−
<div class="clear"></div>
+
    padding: 0;
 +
    margin: 0;
 +
    height: 100%;
 +
}
  
−
<div class="column half_size">
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.pure-menu-link,
−
<h3> Gold Medal Criterion #3</h3>
+
.pure-menu-heading {
−
<p>
+
    display: block;
−
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.  
+
    text-decoration: none;
−
</p>
+
    white-space: nowrap;
 +
}
 +
.pure-menu-item .pure-menu-item {
 +
    display: block;
 +
}
 +
.pure-menu-heading {
 +
    text-transform: uppercase;
 +
    color: #565d64;
 +
}
 +
.pure-menu-link, {
 +
    color: #777;
 +
}
  
−
<p>
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.pure-menu-link,
−
Please see the <a href="https://2017.igem.org/Judging/Medals"> 2017 Medals Page</a> for more information.  
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.pure-menu-heading {
−
</p>
+
    padding: .5em 1em;
−
</div>
+
}
 +
.pure-menu-active > .pure-menu-link,
 +
.pure-menu-link:hover,
 +
.pure-menu-link:focus {
 +
    background-color: #eee;
 +
}
 +
.pure-menu-selected .pure-menu-link,
 +
.pure-menu-selected .pure-menu-link:visited {
 +
    color: #000;
 +
}
  
−
<div class="column half_size">
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body {
−
<h3>Best Model Special Prize</h3>
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    color: #777;
 +
}
  
−
<p>
+
.pure-img-responsive {
−
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.
+
    max-width: 100%;
−
<br><br>
+
    height: auto;
−
You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
+
}
−
</p>
+
  
−
</div>
+
#layout,
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<div class="clear"></div>
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#menu,
 +
.menu-link {
 +
    -webkit-transition: all 0.2s ease-out;
 +
    -moz-transition: all 0.2s ease-out;
 +
    -ms-transition: all 0.2s ease-out;
 +
    -o-transition: all 0.2s ease-out;
 +
    transition: all 0.2s ease-out;
 +
}
  
−
<div class="column full_size">
+
#layout {
−
<h5> Inspiration </h5>
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    position: relative;
−
<p>
+
    left: 0;
−
Here are a few examples from previous teams:
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    padding-left: 0;
 +
}
 +
    #layout.active #menu {
 +
        left: 175px;
 +
        width: 175px;
 +
    }
 +
 
 +
    #layout.active .menu-link {
 +
        left: 175px;
 +
    }
 +
 
 +
.content {
 +
    margin: 0 auto;
 +
    padding: 0 2em;
 +
    max-width: 800px;
 +
    margin-bottom: 50px;
 +
    line-height: 1.6em;
 +
}
 +
 
 +
.header {
 +
    margin: 0;
 +
    color: #333;
 +
    text-align: center;
 +
    padding: 2.5em 2em 0;
 +
    border-bottom: 1px solid #eee;
 +
}
 +
    .header h1 {
 +
        margin: 0.2em 0;
 +
        font-size: 3em;
 +
        font-weight: 300;
 +
    }
 +
    .header h2 {
 +
        font-weight: 300;
 +
        color: #ccc;
 +
        padding: 0;
 +
        margin-top: 0;
 +
    }
 +
 
 +
.content-subhead {
 +
    margin: 50px 0 20px 0;
 +
    font-weight: 190;
 +
    color: #888;
 +
    font-size:200%;
 +
}
 +
.content-subsub{
 +
    margin: 50px 0 20px 0;
 +
    font-weight: 300;
 +
    color: #888;
 +
}
 +
 
 +
 
 +
#menu {
 +
    margin-left: -175px; /* "#menu" width */
 +
    width: 175px;
 +
    position: fixed;
 +
    top: 18px;
 +
    left: 0;
 +
    bottom: 0;
 +
    z-index: 1000; /* so the menu or its navicon stays above all content */
 +
    background: #000000;
 +
    overflow-y: auto;
 +
    -webkit-overflow-scrolling: touch;
 +
}
 +
    #menu a {
 +
        color: #999;
 +
        border: none;
 +
        padding: 0.6em 0 0.6em 0.6em;
 +
    }
 +
 
 +
    /*
 +
    Remove all background/borders, since we are applying them to #menu.
 +
    */
 +
    #menu .pure-menu,
 +
    #menu .pure-menu ul {
 +
        border: none;
 +
        background: transparent;
 +
    }
 +
 
 +
    #menu .pure-menu ul,
 +
    #menu .pure-menu .menu-item-divided {
 +
        border-top: 1px solid #333;
 +
    }
 +
        /*
 +
        Change color of the anchor links on hover/focus.
 +
        */
 +
        #menu .pure-menu li a:hover,
 +
        #menu .pure-menu li a:focus {
 +
            background: #333;
 +
        }
 +
       
 +
    #menu .pure-menu-selected,
 +
    #menu .pure-menu-heading {
 +
        background: #1f8dd6;
 +
    }
 +
        #menu .pure-menu-selected a {
 +
            color: #fff;
 +
        }
 +
 
 +
    #menu .pure-menu-heading {
 +
        color: #fff;
 +
    }
 +
 
 +
 
 +
.menu-link {
 +
    position: fixed;
 +
    display: block; /* show this only on small screens */
 +
    top: 18px;
 +
    left: 0; /* "#menu width" */
 +
    background: #000;
 +
    background: rgba(0,0,0,0.7);
 +
    font-size: 10px; /* change this value to increase/decrease button size */
 +
    z-index: 10;
 +
    width: 2em;
 +
    height: auto;
 +
    padding: 2.1em 1.6em;
 +
}
 +
 
 +
    .menu-link:hover,
 +
    .menu-link:focus {
 +
        background: #000;
 +
    }
 +
 
 +
    .menu-link span {
 +
        position: relative;
 +
        display: block;
 +
    }
 +
 
 +
    .menu-link span,
 +
    .menu-link span:before,
 +
    .menu-link span:after {
 +
        background-color: #fff;
 +
        width: 100%;
 +
        height: 0.2em;
 +
    }
 +
 
 +
        .menu-link span:before,
 +
        .menu-link span:after {
 +
            position: absolute;
 +
            margin-top: -0.6em;
 +
            content: " ";
 +
        }
 +
 
 +
        .menu-link span:after {
 +
            margin-top: 0.6em;
 +
        }
 +
@media (min-width: 88em) {
 +
 
 +
    .header,
 +
    .content {
 +
        padding-left: 2em;
 +
        padding-right: 2em;
 +
    }
 +
 
 +
    #layout {
 +
        padding-left: 175px; /* left col width "#menu" */
 +
        left: 0;
 +
    }
 +
    #menu {
 +
        left: 175px;
 +
    }
 +
 
 +
    .menu-link {
 +
        position: fixed;
 +
        left: 175px;
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        <div id="main">
 +
        <div class="header">
 +
            <h1>Model</h1>
 +
            <h2>Development of A Novel Blood-MicroRNA Handy Detection System with CRISPR</h2>
 +
        </div>
 +
 
 +
        <div class="content">
 +
            <h2 class="content-subhead">Abstract</h2>
 +
            <p>
 +
                This model is created to evaluate the effectiveness of initial design, and offers guidelines on how the system can (or must) be improved. (You can go to <a href="https://2016.igem.org/Team:NUDT_CHINA/Design">PROJECT. page</a> to see more
 +
            </p>
 +
            <h2 class="content-subhead">Introduction</h2>
 +
            <p>
 +
                We create mathematical models of two aspects of our project, a RCA model and a signal detection model.
 +
            </p>
 +
            <h2 class="content-subhead">Assumption and Justification</h2>
 +
            <h2 class="content-subsub">About model </h2>
 +
            <p>1. MiRNA is not degraded throughout the reaction process.</p>
 +
<p>2. The two fusion proteins of dCas9 and split-HRP fragments have the same ability to combine with the stem-loop structure, and only when two different proteins next to each other, can they have the ability to catalyze substrate and produce signal.</p>
 +
<p>3. The number of stem-loop structures in each RCA product is equal under a certain reaction time.</p>
 +
<p>4. The enzymatic activity remains unchanged with time under the premise of excessive amount of enzymes or a short-time reaction. </p>
 +
            <h2 class="content-subsub">About the data </h2>
 +
            <p>1. The data we obtain from wet-lab experiment are reliable.</p>
 +
<p>2. All the results are trustworthy in the process of statistical processing and data calculation.</p>
 +
 
 +
            <h2 class="content-subhead">Model</h2>
 +
            <h2 class="content-subsub">Notations</h2>
 +
           
 +
            <table class="MsoTableGrid" border="1" cellspacing="0" cellpadding="0" style="border:none;">
 +
<tbody>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">Symbol </span>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">Definition </span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">x</span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK7"></a><a name="OLE_LINK6"></a><span style="font-family:&quot;">The
 +
  concentration of</span><span style="font-family:&quot;"> miRNA (pM)</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">C<sub>1</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The
 +
  concentration of initiated probe (Abbreviated to iprobe)</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">k<sub>1</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK8"></a><span style="font-family:&quot;">A constant representing the scale factor</span><span style="font-family:&quot;"></span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">K<sub>m </sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">One
 +
  of the characteristic constants of phi29 DNA polymerase</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">V<sub>max</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">One
 +
  of the characteristic constants of phi29 DNA polymerase</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">k<sub>2</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">A
 +
  constant representing the scale factor</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">V</span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The initial
 +
  speed of RCA </span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK9"></a><i><span style="font-family:&quot;">n<sub>1</sub></span></i><i><sub><span style="font-family:&quot;"></span></sub></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The
 +
  moles of RCA product</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">n<sub>2</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK10"></a><span style="font-family:&quot;">The number of stem-loop structures in each RCA product</span><span style="font-family:&quot;"></span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">n</span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The total
 +
  amount of <a name="OLE_LINK23"></a><a name="OLE_LINK22"></a>stem-loop structures</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">N</span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK41"></a><a name="OLE_LINK16"></a><span style="font-family:&quot;">The
 +
  molecule number of the fusion protein of dCas9 and split-HRP fragments</span><span style="font-family:&quot;"></span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">k<sub>3</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">A
 +
  constant representing the scale factor</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">y<sub>1</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The fluorescence
 +
  intensity of DNA-dye-complex (RFU)</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">N<sub>1</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The
 +
  molecule number of the fusion protein of dCas9 and split-HRP fragments in the
 +
  solution</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">N<sub>2</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<a name="OLE_LINK45"></a><span style="font-family:&quot;">The molecule number of the fusion protein of dCas9 and
 +
  split-HRP fragments binding with stem-loop structure</span><span style="font-family:&quot;"></span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">k<sub>4</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">A
 +
  constant representing the scale factor</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">k<sub>5</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">A
 +
  constant representing the scale factor</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">ρ</span></i><i><span style="font-family:&quot;"></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">Signal
 +
  to noise ratio(Abbreviated to SNR)</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">I</span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The
 +
  molecule number of formed intact HRP proteins </span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">I<sub>1</sub></span></i>
 +
</p>
 +
</td>
 +
<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<span style="font-family:&quot;">The
 +
  molecule number of formed intact HRP proteins in the solution</span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
 +
<i><span style="font-family:&quot;">I<sub>2</sub></span></i>
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</p>
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</td>
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<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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<p class="MsoNormal">
 +
<a name="OLE_LINK43"></a><span style="font-family:&quot;">The molecule number of formed intact HRP proteins through
 +
  binding with stem-loop structure</span><span style="font-family:&quot;"></span>
 +
</p>
 +
</td>
 +
</tr>
 +
<tr>
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<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
 +
<p class="MsoNormal">
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<i><span style="font-family:&quot;">t</span></i>
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</p>
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</td>
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<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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<p class="MsoNormal">
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<span style="font-family:&quot;">Reaction
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  time</span>
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<td width="66" valign="top" style="border:solid windowtext 1.0pt;">
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<p class="MsoNormal">
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<i><span style="font-family:&quot;">y<sub>2</sub></span></i>
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</p>
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</td>
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<td width="487" valign="top" style="border:solid windowtext 1.0pt;">
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<p class="MsoNormal">
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<span style="font-family:&quot;">The
 +
  signal intensity (OD<sub>450</sub>)</span>
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</p>
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</td>
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</tbody>
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<div class="pure-g">
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                  <div class="pure-u-1-1">
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                    <img class="pure-img-responsive" src="https://static.igem.org/mediawiki/2017/0/0d/Show_test1.jpeg" alt="Peyto Lake">
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                </div>
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                </div>
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                <p><br>
 +
<span style="line-height:2;font-family:Perpetua;font-
 +
 
 +
size:18px;"><b>Figure 1. Schematic diagram</b></span>
 
</p>
 
</p>
−
<ul>
 
−
<li><a href="https://2016.igem.org/Team:Manchester/Model">Manchester 2016</a></li>
 
−
<li><a href="https://2016.igem.org/Team:TU_Delft/Model">TU Delft 2016  </li>
 
−
<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
 
−
<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
 
−
</ul>
 
  
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Revision as of 14:52, 14 October 2017

<!doctype html> Team:NUDT_CHINA

Model

Development of A Novel Blood-MicroRNA Handy Detection System with CRISPR

Abstract

This model is created to evaluate the effectiveness of initial design, and offers guidelines on how the system can (or must) be improved. (You can go to PROJECT. page to see more

Introduction

We create mathematical models of two aspects of our project, a RCA model and a signal detection model.

Assumption and Justification

About model

1. MiRNA is not degraded throughout the reaction process.

2. The two fusion proteins of dCas9 and split-HRP fragments have the same ability to combine with the stem-loop structure, and only when two different proteins next to each other, can they have the ability to catalyze substrate and produce signal.

3. The number of stem-loop structures in each RCA product is equal under a certain reaction time.

4. The enzymatic activity remains unchanged with time under the premise of excessive amount of enzymes or a short-time reaction.

About the data

1. The data we obtain from wet-lab experiment are reliable.

2. All the results are trustworthy in the process of statistical processing and data calculation.

Model

Notations

Symbol

Definition

x

The concentration of miRNA (pM)

C1

The concentration of initiated probe (Abbreviated to iprobe)

k1

A constant representing the scale factor

Km

One of the characteristic constants of phi29 DNA polymerase

Vmax

One of the characteristic constants of phi29 DNA polymerase

k2

A constant representing the scale factor

V

The initial speed of RCA

n1

The moles of RCA product

n2

The number of stem-loop structures in each RCA product

n

The total amount of stem-loop structures

N

The molecule number of the fusion protein of dCas9 and split-HRP fragments

k3

A constant representing the scale factor

y1

The fluorescence intensity of DNA-dye-complex (RFU)

N1

The molecule number of the fusion protein of dCas9 and split-HRP fragments in the solution

N2

The molecule number of the fusion protein of dCas9 and split-HRP fragments binding with stem-loop structure

k4

A constant representing the scale factor

k5

A constant representing the scale factor

ρ

Signal to noise ratio(Abbreviated to SNR)

I

The molecule number of formed intact HRP proteins

I1

The molecule number of formed intact HRP proteins in the solution

I2

The molecule number of formed intact HRP proteins through binding with stem-loop structure

t

Reaction time

y2

The signal intensity (OD450)

Peyto Lake


Figure 1. Schematic diagram