Difference between revisions of "Team:HUST-China/Modeling on Ecosystem Level"

Line 1: Line 1:
−
[[File:Pcons+RBS+PBAN_Biobrick.jpg|thumb|450px|link=|frameless|center|'''Fig.3-1''' P<sub>cons</sub>+RBS+PBAN''(Mamestra brassicae'')]]
+
<HTML>
 +
<head lang="en">
 +
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
 +
<meta charset="UTF-8">
 +
<meta name="viewport" content="width=device-width,initial-scale=1">
  
−
[[File:HUST-China_2015_results_1|600px|thumb|center|Table1]]
+
<title>Team:HUST-China:Modeling</title>
 +
<link href="http://cdn.bootcss.com/bootstrap/3.3.5/css/bootstrap.min.css"rel="stylesheet">
 +
<script src="http://cdn.bootcss.com/jquery/1.11.3/jquery.min.js"></script>
 +
<script src="http://cdn.bootcss.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
 +
 
 +
<style>
 +
  /*改默认设定*/
 +
#footer-box,#sponsor-box,.shadow3,#content,table,#catlinks {
 +
    background-color: transparent;
 +
}
 +
.mediawiki.ltr.ns-0.ns-subject.page-Team_HUST-China
 +
#globalWrapper #top-section #p-logo a img {
 +
    visibility:hidden;
 +
}
 +
 +
#contentSub, #footer-box, #catlinks, #search-controls, #p-logo, .printfooter, .firstHeading, .visualClear{display: none;}
 +
#globalWrapper, #content,#bodyContent { /*-- changes default wiki settings --*/
 +
    width: 100%;
 +
    height: 100%;
 +
    border: 0px;
 +
    background-color: transparent;
 +
    margin: 0px;
 +
    padding: 0px;
 +
  top: 0px;
 +
}
 +
#top_menu_under{height: 0px;}
 +
 
 +
html, .wrapper { /*-- changes default wiki settings --*/
 +
    width: 100%;
 +
    height: 100%;
 +
    background-color: transparent; 
 +
top: 0px;
 +
}
 +
 
 +
table{width: 780px;
 +
margin-top: 20px;
 +
margin-bottom: 20px;
 +
}
 +
table tr,th,td{ width: auto;
 +
padding: 5px;
 +
text-align: center;}
 +
.viewport, .container {
 +
max-width: 1349px;
 +
          top: 0px;}
 +
 
 +
.picture{ width: 700px;
 +
    height: auto;
 +
        margin-bottom:30px;
 +
        margin-left: 50px;}
 +
 
 +
 
 +
#mid{width: 1349px;
 +
margin: 0 auto;}
 +
 
 +
 
 +
 
 +
      body{ background-color: white;
 +
position: absolute;
 +
margin: 0;
 +
    font-family:Arial,Verdana,Sans-serif;
 +
color: black;
 +
z-index: 0}
 +
 
 +
.header{position: fixed;
 +
    width: 1348px;
 +
                            text-align:center;
 +
  height:200px;
 +
  margin-top: 0px;
 +
  padding-top: 5px;
 +
  background-image: url(https://static.igem.org/mediawiki/2015/d/d7/HUST_daohang.png);
 +
  background-size:100% 100%;
 +
    filter:alpha(opacity:30);opacity:0.95;  -moz-opacity:0.4; -khtml-opacity: 0.4;
 +
  z-index:1;}
 +
 
 +
.first-menu{float: left;
 +
margin-left: 1%;
 +
font-size:19px;
 +
    max-width: 22%;
 +
                padding-top:5px;}
 +
 
 +
.other-menu{float: left;
 +
margin-left:1.2%;
 +
font-size:19px;
 +
    max-width: 22%;
 +
                    padding-top:5px;}
 +
 
 +
.navbar .nav > li .dropdown-menu {margin: 0;}
 +
.navbar .nav > li:hover .dropdown-menu {display: block;}
 +
 
 +
a:link,a:visited {
 +
color:#002855;
 +
text-decoration:none;
 +
            }
 +
a:hover,a:active {
 +
color:#007fff;
 +
text-decoration:underline;
 +
}
 +
 
 +
ul.ul{list-style-type:none;
 +
list-style-image: none;
 +
margin-bottom: 0px;
 +
padding-left: 0px;}
 +
li.li{margin-top: 0px;
 +
list-style-image: none;}
 +
 
 +
#maodian ul{list-style-type:none;
 +
margin-bottom: 0px;
 +
padding-left: 0px;
 +
                margin-left:0px;}
 +
 
 +
 +
#pic{  background-image: url(https://static.igem.org/mediawiki/2015/d/d6/HUST_modeling.jpg);
 +
                width:1349px;
 +
                height:650px;
 +
              float: left;
 +
              z-index: 0;
 +
          background-size: 100%,100%;
 +
          margin-top: 0px;}
 +
 
 +
.title{width: 900px; 
 +
                height:300px;
 +
              margin-left: 18%;
 +
                margin-top:80px;}
 +
    .pic_a img{width: 135px;
 +
    height: 120px;
 +
    }
 +
    .pic_a{float: left;
 +
            margin-top:50px;
 +
            width: 1349px;
 +
            text-align:center;
 +
              }
 +
 
 +
#maodian{float: left;
 +
              top: 50px;
 +
  position: fixed;
 +
  margin-top: 70px;  
 +
  z-index: -1;
 +
margin-left: 0px; }
 +
#maodian img{ padding-left: 2% ;
 +
width:150px;
 +
height: auto;
 +
}
 +
.btn
 +
{ background-color:#5d96a3;
 +
margin-left: 0px;
 +
width: 220px;
 +
font-size: 14px;
 +
padding-left: 1px;
 +
    }
 +
 
 +
.btn:hover,.btn:active {
 +
color:white;
 +
background-color:#004c6f;}
 +
 
 +
   
 +
    .description {margin-left: 20%;
 +
              margin-right: 20%;
 +
              margin-top: 50px;
 +
              text-align: left;
 +
              float: left;
 +
              font-size:16px;}
 +
    .description p{font-size: 16px;
 +
                        width:809px;}
 +
     
 +
    .dongxi{height:50px;}
 +
 
 +
 
 +
 +
      .scroll{
 +
width:100px;
 +
height:120px;
 +
background-image: url(https://static.igem.org/mediawiki/2015/8/87/Top.png);
 +
background-size: 100% 100%;
 +
position:fixed;
 +
right:10px;
 +
bottom:20px;
 +
cursor:pointer;
 +
opacity:0.6;
 +
}
 +
 +
 
 +
</style>
 +
<!--点击TOP回滚到顶部js如下：-->
 +
<script type="text/javascript">
 +
$(function(){
 +
showScroll();
 +
function showScroll(){
 +
$(window).scroll( function() {
 +
var scrollValue=$(window).scrollTop();
 +
scrollValue > 100 ? $('div[class=scroll]').fadeIn():$('div[class=scroll]').fadeOut();
 +
} );
 +
$('#scroll').click(function(){
 +
$("html,body").animate({scrollTop:0},500);
 +
});
 +
}
 +
})
 +
</script>
 +
<script type="text/javascript">
 +
$(function(){
 +
showdes();
 +
function showdes(){
 +
$('#to_des').click(function(){
 +
$("html,body").animate({scrollTop:750},800);
 +
});
 +
}
 +
})
 +
</script>
 +
</head>
 +
 
 +
<body >
 +
<div id="mid">
 +
<!--上栏-->
 +
 
 +
<div class="container header" >
 +
 +
<!--悬浮菜单-->
 +
<div class="navbar">
 +
    <div class="navbar-inner">
 +
      <div class="container">
 +
          <ul class="nav">
 +
              <li class="first-menu"><a href="https://2015.igem.org/Team:HUST-China">HOME</a>
 +
                </li>    
 +
                <li class="dropdown other-menu" id="accountmenu"><a href="https://2015.igem.org/Team:HUST-China/Background">PROJECT<b class="caret"></b></a>
 +
                <ul class="dropdown-menu">
 +
                                <li><a href="https://2015.igem.org/Team:HUST-China/Background">Background</a></li>
 +
                <li class="divider"></li>
 +
                <li><a href="https://2015.igem.org/Team:HUST-China/Description">Description</a></li>
 +
                <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Design">Design</a></li>         
 +
                    </ul>
 +
                        </li>
 +
 
 +
                        <li class="dropdown other-menu" id="accountmenu"><a href="https://2015.igem.org/Team:HUST-China/Results">WETLAB<b class="caret"></b></a>
 +
                <ul class="dropdown-menu">
 +
<li><a href="https://2015.igem.org/Team:HUST-China/Results">Results</a></li>
 +
                        <li class="divider"></li>                      
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Experiments">Experiments&protocol</a></li>
 +
                        <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/InterLab Study">InterLab Study</a></li>
 +
                        <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Notebook">Notebook</a></li>     
 +
                    </ul>
 +
                        </li>
 +
 
 +
                        <li class="dropdown other-menu" id="accountmenu"><a href="https://2015.igem.org/Team:HUST-China/Basic_part">PARTS<b class="caret"></b></a>
 +
                <ul class="dropdown-menu">                        
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Basic_part">Basic Parts</a></li>
 +
                        <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Basic_part#2">Composite Parts</a></li> 
 +
                    </ul>
 +
                        </li>
 +
               
 +
                <li class="dropdown other-menu" id="accountmenu"><a href="https://2015.igem.org/Team:HUST-China/Modeling">MODELING<b class="caret"></b></a>
 +
                            <ul class="dropdown-menu">
 +
                          <li><a href="https://2015.igem.org/Team:HUST-China/Modeling on Cellular Level">Modeling on Cellular Level</a></li>
 +
                          <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Modeling on Ecosystem Level">Modeling on Ecosystem Level</a></li>
 +
                    </ul>
 +
                </li>
 +
 
 +
                               
 +
                 
 +
                <li class="dropdown other-menu" id="accountmenu">
 +
                    <a class="dropdown-toggle" data-toggle="dropdown" href="https://2015.igem.org/Team:HUST-China/Practices">HUMAN PRACTICES</a>
 +
                                         
 +
                </li>
 +
 
 +
              <li class="dropdown other-menu" id="accountmenu">
 +
                    <a class="dropdown-toggle" data-toggle="dropdown" href="https://2015.igem.org/Team:HUST-China/Safety">OTHERS<b class="caret"></b></a>
 +
                    <ul class="dropdown-menu">
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Safety">Safety</a></li>
 +
                        <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Collaborations">Collaborations</a></li>
 +
                        <li class="divider"></li>
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Attributions">Attributions</a></li>
 +
                        <li class="divider"></li>                   
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Team">Team</a></li>
 +
                        <li class="divider"></li>                   
 +
                        <li><a href="https://2015.igem.org/Team:HUST-China/Achievements">Achievements</a></li>
 +
                    </ul>
 +
              </li>
 +
          </ul>
 +
      </div>
 +
      </div>
 +
    </div>
 +
    <script type="text/javascript">
 +
        $(document).ready(function () {
 +
          $('.dropdown-toggle').dropdown(); }); </script>
 +
</div>
 +
<!--标题栏-->
 +
<div id="pic" >
 +
<img class="title" src="https://static.igem.org/mediawiki/2015/c/c4/HUST_MODELING.png"/>
 +
<br>
 +
<div class="pic_a" >
 +
    <img style="cursor:pointer;" id="to_des" src="https://static.igem.org/mediawiki/2015/8/80/White.png"/>
 +
</div>
 +
</div>
 +
 
 +
<!--锚点-->
 +
<div id="maodian">
 +
<img src="https://static.igem.org/mediawiki/2015/d/da/Maodian.png" >
 +
<ul class="ul" >
 +
<li class="li"><a href="#1" class="btn btn-default btn-lg">Modeling on Ecosystem Level</a></li>
 +
<li class="li"><a href="#2" class="btn btn-default btn-lg">The “wake-up” problem</a></li>
 +
<li class="li"><a href="#3" class="btn btn-default btn-lg">The permeation problem</a></li>
 +
<li class="li"><a href="#4" class="btn btn-default btn-lg">Robustness Analysis</a></li>
 +
</ul>
 +
</div>
 +
 
 +
 
 +
<!--描述-->
 +
 +
    <div align="center" class="description"><a name="1"></a><br>
 +
    <div class="dongxi"></div>
 +
    <h2 style="color:black" align="left"><b>Modeling on Ecosystem Level</b></h2><br>
 +
    <p>With the benefit of the DDEs model we built, we could acquire necessary data to move on to the Ecosystem level modeling based on Cellular Automaton. In this modeling, we attended to foresee the important points of the application, such as how do we release the strains, how would they spread and how much Euk.Cement do we need to produce the best result, and derive the best strategy to make full use of our strains.</p>
 +
    </div>
 +
 
 +
<div align="center" class="description"><a name="2"></a><br>
 +
    <div class="dongxi"></div>
 +
        <h2 style="color:black" align="left"><b>Part one: the “wake-up” problem</b></h2><br>
 +
            <p>Since it takes some time for the darkness induction system to shut down, we have to treat our strains in darkness to make sure they recover from the shut-down state. However, the problem is: How long should we put the strains into darkness? </p>
 +
            <p>As we can see from the DDEs model, our system has bi-stable state: the stable state in darkness and another stable state in light. The longer our strains are exposed to light, the longer it takes to convert them to the stable-state of darkness. Besides, our strains are more sensitive to light than darkness. In another words, if our strains are exposed to light for 10 minutes, it has to take 60 to 70 minutes for the strains to return to the original state.</p>
 +
            <p>For storage and transportation, we have to keep our strains exposed to light all the time to ensure they would not produce Si-tag or Mcfp-3. When we need them to work, we have to turn off the light and put them into darkness and wait for them to “wake up”. With the DDEs model, we can simulate the process of how do the strains “wake up”.</p>
 +
            <img class="picture" src=""/>
 +
          <h3 style="color:black" align="left"><b>Results</b></h3><br>
 +
          <p>The figure shows that it takes about 3600 minutes for Euk.Cement to “wake up” from the stable-state of light. Therefore, before releasing our kit into the sands, we should turn off the light and treat them for 60 hours. If some Euk.Cement drift away from the sands, they will be exposed to sunlight and their downstream systems would be shut down by darkness induction system.</p>
 +
    </div>
 +
 
 +
      <div align="center" class="description"><a name="3"></a><br>
 +
    <div class="dongxi"></div>
 +
        <h2 style="color:black" align="left"><b>Part two: the permeation problem</b></h2><br>
 +
            <p>After releasing Euk.Cement, it would permeate the sands and we intended to find out what’s the final outcome of its permeation and what strategy should we take to attain the best result. To achieve this goal, we built a permeation model with Lattice Method (Cellular Automaton). </p>
 +
       
 +
        <h3 style="color:black" align="left"><b>Hypothesis</b></h3><br>
 +
            <p>In order to build as well as simplify the model, we hypothesized the following prerequisites.<br>
 +
- There is no current in the sands.<br>
 +
- The total number of our yeast is constant. No yeast will be born or dead during the permeation process.<br>
 +
- The variability of temperature has no effect on our Euk.Cement or it could be ignored.<br>
 +
- The size of the sands and our Euk.Cement is constant.<br>
 +
- Every unit of sands has the same amount of silica.<br>
 +
The Cellular Automation simulated the process that our Euk.Cement expresses Si-tag and Mcfp-3 while it permeates in the sands. The PDEs (Partial Differential Equations) of this model are listed below.
 +
</p>
 +
 
 +
  <h3 style="color:black" align="left"><b>Parameters</b></h3><br>
 +
            <p>The description of parameters, their values and the references involved in this model are listed in a table.
 +
            <a href="#"><b>The parameters table (2) can be downloaded here.</b></a>
 +
</p>
 +
 
 +
    <h3 style="color:black" align="left"><b>Formulary</b></h3><br>
 +
            <img class="picture" src="">
 +
 
 +
        <h3 style="color:black" align="left"><b>Monte Carlo Simulation</b></h3><br>
 +
            <p>To determine the values of some necessary parameters in the permeation model, we run the Monte Carlo simulation for a single lattice.<br>
 +
The Euk.Cement moves in the sands and has a certain possibility to bind the silica.  Besides, the motion of Euk.Cement includes the Brownian motion, the sedimentation due to gravity and the motion due to the current. We hypothesized that there is no water flow in the sands, and therefore the motion of Euk.Cement is largely depended on the former two.
 +
</p>
 +
 
 +
    <h3 style="color:black" align="left"><b>Monte Carlo Simulation</b></h3><br>
 +
        <img class="picture" src=""><br>
 +
            <p>We know that the speed of Brownian motion: <img class="picture2" src="">  is relevant to the value of free time. The average length of steps of Brownian motion has the same scale with the cracks of the sands. Hence, we can set the unit time of Monte Carlo Simulation as 1s (It’s not the unit time of permeation). And with this setting, we could derive that every yeast has one collision with the sands.</p>
 +
 
 +
        <h3 style="color:black" align="left"><b>Sedimentation due to Gravity</b></h3><br>
 +
            <img class="picture" src=""><br>
 +
            <p>and therefore</p>
 +
              <img class="picture" src=""><br>
 +
            <p>Comparing the effect of sedimentation due to gravity and the Brownian motion, we reach a conclusion that the latter one outweigh the former one (about 100 times). And therefore the most effective factor of the motion of Euk.Cement in the sands is Brownian motion.</p>
 +
           
 +
            <p><a href=""><b>The code of the Monte Carlo Simulation can be downloaded here.</b></a>Its flow chart is</p>
 +
            <img class="picture" src=""><br>
 +
            <p>After running the Monte Carlo Simulation with 106 yeasts for multiple times, we finally determine the values of the following parameters</p>
 +
            <img class="picture" src=""><br>
 +
 +
        <h3 style="color:black" align="left"><b>Lattices Method</b></h3><br>
 +
            <p>With sufficient parameters, we could finally simulate the permeation process.<a href=""><b> The code of our permeation model could be downloaded here.</b></a></p>
 +
            <p>We chose to use numerical solution to solve our Permeation model. We divided the space into the same lattices, and each lattice has only one phase. Hence, each variable in the same coordinate is considered the same. The timeline was divided into the minimum and discrete values. By calculating the variables in each lattice through the discretized timeline, we could attain the values of a(x,y,z,t),A(x,y,z,t)and C(x,y,z,t). If the lattices were small enough, the PDEs above could be replaced by Lattices Method. The equations of Lattices Method (Cellular Automaton) are listed below.</p>
 +
            <img class="picture" src=""><br>
 +
            <img class="picture" src=""><br>
 +
            <img class="picture" src=""><br>
 +
            <p>With the equations of Cellular Automaton as well as Boundary equations and Initial state equations, we could attain the values of the concentration of Mcfp-3, the number of fixed Euk.Cement and free Euk.Cement at any time and at any coordinate.</p>
 +
            <p>We ran the simulation with a server and printed a heat map</p>
 +
            <img class="picture" src=""><br>
 +
 
 +
        <h3 style="color:black" align="left"><b>Results</b></h3><br>
 +
            <p>From the permeation process shown in the heat map, we can derive the following conclusion:<br>
 +
- The Euk.Cement permeates very efficiently over a large space. Therefore, perhaps we have to enclose it.<br>
 +
- A rock (1000 cm3) is added to the sands. However, it’s not even noticeable from the outcome. Hence, the rocks or stone inside the sands have little effect on the permeation.<br>
 +
- The final shape of the permeation is approximately global and not sensitive to the initial input.<br>
 +
- The Euk.Cement distributed quite evenly in the whole space they spread but not densely at the surface of the sands.<br>
 +
- The Euk.Cement expressed sufficient amount of Mcfp-3.<br>
 +
</p>
 +
</div>
 +
   
 +
      <div align="center" class="description"><a name="4"></a><br>
 +
    <div class="dongxi"></div>
 +
        <h2 style="color:black" align="left"><b>Robustness and Parameter Sensitivity Analysis</b></h2><br>
 +
            <p>The influential factors include noise of gene expression, variability of temperature, variability of the size of the sands and Euk.Cement, etc. However, our permeation model is most sensitive to the parameter α (the possibility of effective collision). Therefore, we focused on the analysis of the sensitivity of the parameter α. </p>
 +
            <p>When the α of MC = 0.001, the α of LM = 0.0282:<br>
 +
The total number of Euk.Cement bound with sands in 30s = 28224;<br>
 +
The total number of Euk.Cement drifted away in 30s = 74778;<br></p>
 +
<img class="picture" src=""><br><br>
 +
 +
<p>When the α of MC = 0.0013, the α of LM = 0.0365:<br>
 +
The total number of Euk.Cement bound with sands in 30s = 36464;<br>
 +
The total number of Euk.Cement drifted away in 30s = 74925;<br></p>
 +
<img class="picture" src=""><br><br>
 +
 +
<p>When the α of MC = 0.0015, the α of LM = 0.0421:<br>
 +
The total number of Euk.Cement bound with sands in 30s =42164;<br>
 +
The total number of Euk.Cement drifted away in 30s = 74661;<br></p>
 +
<img class="picture" src=""><br><br>
 +
 
 +
            <h3 style="color:black" align="left"><b>Results</b></h3><br>
 +
            <p>From the data above we could figure out that with about 83% addition of the α, the bound Euk.Cement had an increase of approximately 82%. This result indicates that the substance inside each lattice could be exchanged sufficiently to attain an even concentration of Euk.Cement as well as its secretions. Therefore, we could change theα by selecting different Si-tag to achieve different targets, such as the intensity of the sands and the scope of the permeation. </p>
 +
      </div>
 +
<!--下一页
 +
<a href="https://2015.igem.org/Team:HUST-China/Experiments" class="nextpage">
 +
Next >>
 +
</a>-->
 +
<!--top-->
 +
<div class="scroll" id="scroll" style="display:none;"></div>
 +
</div>
 +
 +
 +
</body>
 +
</html>

Revision as of 03:11, 15 September 2015

Team:HUST-China:Modeling



Modeling on Ecosystem Level


With the benefit of the DDEs model we built, we could acquire necessary data to move on to the Ecosystem level modeling based on Cellular Automaton. In this modeling, we attended to foresee the important points of the application, such as how do we release the strains, how would they spread and how much Euk.Cement do we need to produce the best result, and derive the best strategy to make full use of our strains.


Part one: the “wake-up” problem


Since it takes some time for the darkness induction system to shut down, we have to treat our strains in darkness to make sure they recover from the shut-down state. However, the problem is: How long should we put the strains into darkness?

As we can see from the DDEs model, our system has bi-stable state: the stable state in darkness and another stable state in light. The longer our strains are exposed to light, the longer it takes to convert them to the stable-state of darkness. Besides, our strains are more sensitive to light than darkness. In another words, if our strains are exposed to light for 10 minutes, it has to take 60 to 70 minutes for the strains to return to the original state.

For storage and transportation, we have to keep our strains exposed to light all the time to ensure they would not produce Si-tag or Mcfp-3. When we need them to work, we have to turn off the light and put them into darkness and wait for them to “wake up”. With the DDEs model, we can simulate the process of how do the strains “wake up”.

Results


The figure shows that it takes about 3600 minutes for Euk.Cement to “wake up” from the stable-state of light. Therefore, before releasing our kit into the sands, we should turn off the light and treat them for 60 hours. If some Euk.Cement drift away from the sands, they will be exposed to sunlight and their downstream systems would be shut down by darkness induction system.


Part two: the permeation problem


After releasing Euk.Cement, it would permeate the sands and we intended to find out what’s the final outcome of its permeation and what strategy should we take to attain the best result. To achieve this goal, we built a permeation model with Lattice Method (Cellular Automaton).

Hypothesis


In order to build as well as simplify the model, we hypothesized the following prerequisites.
- There is no current in the sands.
- The total number of our yeast is constant. No yeast will be born or dead during the permeation process.
- The variability of temperature has no effect on our Euk.Cement or it could be ignored.
- The size of the sands and our Euk.Cement is constant.
- Every unit of sands has the same amount of silica.
The Cellular Automation simulated the process that our Euk.Cement expresses Si-tag and Mcfp-3 while it permeates in the sands. The PDEs (Partial Differential Equations) of this model are listed below.

Parameters


The description of parameters, their values and the references involved in this model are listed in a table. The parameters table (2) can be downloaded here.

Formulary


Monte Carlo Simulation


To determine the values of some necessary parameters in the permeation model, we run the Monte Carlo simulation for a single lattice.
The Euk.Cement moves in the sands and has a certain possibility to bind the silica. Besides, the motion of Euk.Cement includes the Brownian motion, the sedimentation due to gravity and the motion due to the current. We hypothesized that there is no water flow in the sands, and therefore the motion of Euk.Cement is largely depended on the former two.

Monte Carlo Simulation



We know that the speed of Brownian motion: is relevant to the value of free time. The average length of steps of Brownian motion has the same scale with the cracks of the sands. Hence, we can set the unit time of Monte Carlo Simulation as 1s (It’s not the unit time of permeation). And with this setting, we could derive that every yeast has one collision with the sands.

Sedimentation due to Gravity



and therefore


Comparing the effect of sedimentation due to gravity and the Brownian motion, we reach a conclusion that the latter one outweigh the former one (about 100 times). And therefore the most effective factor of the motion of Euk.Cement in the sands is Brownian motion.

The code of the Monte Carlo Simulation can be downloaded here.Its flow chart is


After running the Monte Carlo Simulation with 106 yeasts for multiple times, we finally determine the values of the following parameters


Lattices Method


With sufficient parameters, we could finally simulate the permeation process. The code of our permeation model could be downloaded here.

We chose to use numerical solution to solve our Permeation model. We divided the space into the same lattices, and each lattice has only one phase. Hence, each variable in the same coordinate is considered the same. The timeline was divided into the minimum and discrete values. By calculating the variables in each lattice through the discretized timeline, we could attain the values of a(x,y,z,t),A(x,y,z,t)and C(x,y,z,t). If the lattices were small enough, the PDEs above could be replaced by Lattices Method. The equations of Lattices Method (Cellular Automaton) are listed below.




With the equations of Cellular Automaton as well as Boundary equations and Initial state equations, we could attain the values of the concentration of Mcfp-3, the number of fixed Euk.Cement and free Euk.Cement at any time and at any coordinate.

We ran the simulation with a server and printed a heat map


Results


From the permeation process shown in the heat map, we can derive the following conclusion:
- The Euk.Cement permeates very efficiently over a large space. Therefore, perhaps we have to enclose it.
- A rock (1000 cm3) is added to the sands. However, it’s not even noticeable from the outcome. Hence, the rocks or stone inside the sands have little effect on the permeation.
- The final shape of the permeation is approximately global and not sensitive to the initial input.
- The Euk.Cement distributed quite evenly in the whole space they spread but not densely at the surface of the sands.
- The Euk.Cement expressed sufficient amount of Mcfp-3.


Robustness and Parameter Sensitivity Analysis


The influential factors include noise of gene expression, variability of temperature, variability of the size of the sands and Euk.Cement, etc. However, our permeation model is most sensitive to the parameter α (the possibility of effective collision). Therefore, we focused on the analysis of the sensitivity of the parameter α.

When the α of MC = 0.001, the α of LM = 0.0282:
The total number of Euk.Cement bound with sands in 30s = 28224;
The total number of Euk.Cement drifted away in 30s = 74778;



When the α of MC = 0.0013, the α of LM = 0.0365:
The total number of Euk.Cement bound with sands in 30s = 36464;
The total number of Euk.Cement drifted away in 30s = 74925;



When the α of MC = 0.0015, the α of LM = 0.0421:
The total number of Euk.Cement bound with sands in 30s =42164;
The total number of Euk.Cement drifted away in 30s = 74661;



Results


From the data above we could figure out that with about 83% addition of the α, the bound Euk.Cement had an increase of approximately 82%. This result indicates that the substance inside each lattice could be exchanged sufficiently to attain an even concentration of Euk.Cement as well as its secretions. Therefore, we could change theα by selecting different Si-tag to achieve different targets, such as the intensity of the sands and the scope of the permeation.