Difference between revisions of "Team:Fujian United/Model"

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{{Fujian_United}}
 
 
<html>
 
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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 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. </p>
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<p>Please note you can compete for both the Gold Medal criterion #3 and the Best Model prize with this page. </p>
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<h3> Gold Medal Criterion #3</h3>
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<p>
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        <img src="https://static.igem.org/mediawiki/2021/9/94/T--Fujian_United--bg_1.png" alt="">
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Use modeling to gain insight into how your project works or should be implemented. Explain your model's assumptions, data, parameters, and results in a way that anyone could understand.
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<br><br>
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Please see the <a href="https://2021.igem.org/Judging/Medals">2021 Medals Page</a> for more information.
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</p>
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    <!--内容-->
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    <div class="content-middle-outer">
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        <div class="content-middle">
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            <section class="article p-t-30 p-b-54">
 +
                <h1 class="content-header">Modeling</h1>
  
−
<div class="column two_thirds_size">
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                <section>
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<h3>Best Model Special Prize</h3>
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                    <p>In order to find the optimal condition for alcohol production by our engineered yeast, we designed
 +
                        several control groups and collected samples respectively to detect the alcohol yield by Megazyme
 +
                        Ethanol Kit.</p>
  
−
<p>Models and computer simulations provide a great way to describe the functioning and operation of BioBrick Parts and Devices. Synthetic biology is an engineering discipline and part of engineering is simulation and modeling to determine system behavior before building your design. 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 before or in conjunction with experiments in the wetlab.
+
                    <p>Below is the initial data and there are two factors, enzyme concentration and fermentation hours
−
</p><p>
+
                        influencing the alcohol production of our engineered strains.</p>
−
To compete for the <a href="https://2021.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://2021.igem.org/Judging/Judging_Form">judging form</a>.
+
−
</p>
+
  
−
</div>
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                    <img src="https://static.igem.org/mediawiki/2021/6/60/T--Fujian_United--img_modeling_1.jpg" alt="">
 +
                    <img src="https://static.igem.org/mediawiki/2021/7/7e/T--Fujian_United--img_modeling_2.jpg" alt="">
  
 +
                    <p>After analyzing the scatterplots, we chose to use two-dimensional interpolation to construct models
 +
                        by MATLAB and we also give the coding below:</p>
  
−
<div class="column third_size">
+
                    <pre style="color: #0070C0">
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<div class="highlight decoration_A_full">
+
clear;clc;
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<h3> Inspiration </h3>
+
t0=[0 4 8 12 16 20 24];
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<p>You can look at what other teams did to get some inspiration! <br />
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x0=[0 0.3 0.6 1];
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Here are a few examples:</p>
+
−
<ul>
+
−
<li><a href="https://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
+
−
<li><a href="https://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
+
−
<li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
+
−
<li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</li>
+
−
<li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
+
−
<li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
+
−
<li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
+
−
</ul>
+
−
</div>
+
−
</div>
+
  
 +
z1=[0.16566911 0.158452214 0.151526625 0.182264212 0.178289281 0.180093505 0.199272782;...
 +
0.155877436 0.159194577 0.165697301 0.180394209 0.190777894 0.165969814 0.184500698;...
 +
0.160923625 0.151958887 0.141687966 0.174812391 0.163376242 0.183852305 0.169841378;...
 +
0.138944042 0.151883711 0.12808111 0.175648724 0.162624482 0.169634644 0.167388761];%1号样本
 +
 +
z2=[0.167116248 0.141349674 0.143915055 0.182828032 0.166223533 0.191557845 0.179604861;...
 +
0.185017533 0.150511749 0.158405229 0.185412207 0.181286924 0.192187444 0.180976823;...
 +
0.173384047 0.168469416 0.146555612 0.186755978 0.19386011 0.186229746 0.181521849;...
 +
0.15533241 0.157127237 0.154646429  0.19198071 0.175056713 0.174662039 0.182987781];%2号样本
 +
 +
z3=[0.150154663 0.148237675 0.137271376 0.198154539 0.196528858 0.186098188 0.166693383;...
 +
0.143229074 0.138934645 0.146471039 0.190721512 0.196735592 0.176362896 0.172453744;...
 +
0.150276824 0.14330425 0.146818728 0.183467028 0.184472507 0.181164763 0.173346459;...
 +
0.145709882 0.1465932 0.126145328 0.162304984 0.182095066 0.163000362 0.15570829];%3号样本
 +
 +
z4=[0.150878232 0.156281507 0.154308137 0.168760723 0.188231307 0.1738445 0.176898525;...
 +
0.155407586 0.171504647 0.139084997 0.188080955 0.19630333 0.182470946 0.178928277;...
 +
0.146048174 0.147927574 0.158771712 0.199629868 0.19113498 0.187141255 0.179961947;...
 +
0.156027788 0.149713004 0.149534461 0.175676915 0.198041775 0.170865651 0.180807677];%4号样本
 +
 +
t=0:0.5:24;%每间隔0.5小时取一个时刻
 +
x=0:0.01:1;%浓度间隔为0.01
 +
zA=interp2(t0,x0,z1,t,x','spline');%1号样本插值
 +
zB=interp2(t0,x0,z2,t,x','spline');%2号样本插值
 +
zC=interp2(t0,x0,z3,t,x','spline');%3号样本插值
 +
zD=interp2(t0,x0,z4,t,x','spline');%4号样本插值
 +
 +
subplot(2,2,1),surf(t,x,zA);
 +
subplot(2,2,2),surf(t,x,zB);
 +
subplot(2,2,3),surf(t,x,zC);
 +
subplot(2,2,4),surf(t,x,zD);
 +
zAmax=max(max(zA))
 +
zBmax=max(max(zB))
 +
zCmax=max(max(zC))
 +
zDmax=max(max(zD))
 +
[i1,j1]=find(zA==max(max(zA)));
 +
t1=t(j1)
 +
x1=x(i1)
 +
[i2,j2]=find(zB==max(max(zB)));
 +
t2=t(j2)
 +
x2=x(i2)
 +
[i3,j3]=find(zC==max(max(zC)));
 +
t3=t(j3)
 +
x3=x(i3)
 +
[i4,j4]=find(zD==max(max(zD)));
 +
t4=t(j4)
 +
x4=x(i4)
 +
                </pre>
 +
 +
                    <p>Finally, we obtained the interpolation curved surfaces of the 4 yeast groups as showing below:</p>
 +
 +
                    <div class="img-container m-t-12">
 +
                        <img src="https://static.igem.org/mediawiki/2021/d/de/T--Fujian_United--img_modeling_3.jpg" alt="">
 +
                        <span class="figure">Figure 1.  Alcohol production ability of 4 different engineered yeast against enzyme concentration and fermentation hours</span>
 +
                    </div>
 +
 +
                    <p>By MATLAB, it can be calculated that the highest value of alcohol concentration (g/L) and the
 +
                        corresponding fermentation conditions:</p>
 +
 +
                    <ul class="m-t-12 m-b-12" style="padding-left: 32px !important;">
 +
                        <li>For A strain, the highest value of alcohol concentration is 0.1993 g/L when enzyme concentration
 +
                            is given 0 and the fermentation time is 24 hours;
 +
                        </li>
 +
                        <li>For B strain, the highest value of alcohol concentration is 0.1991 g/L when enzyme concentration
 +
                            is given 0.01 and the fermentation time is 22 hours;
 +
                        </li>
 +
                        <li>For C strain, the highest value of alcohol concentration is 0.2049 g/L when enzyme concentration
 +
                            is given 0 and the fermentation time is 13.5 hours;
 +
                        </li>
 +
                        <li>For D strain, the highest value of alcohol concentration is 0.2018 g/L when enzyme concentration
 +
                            is given 0.56 and the fermentation time is 13 hours.
 +
                        </li>
 +
                    </ul>
 +
 +
                    <p>Overall consideration, we strongly recommend yeast C for alcohol industry use which requires
 +
                        less fermentation hours, less additional enzyme but higher yield.</p>
 +
                </section>
 +
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 +
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 +
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Latest revision as of 12:26, 20 October 2021

Modeling

In order to find the optimal condition for alcohol production by our engineered yeast, we designed several control groups and collected samples respectively to detect the alcohol yield by Megazyme Ethanol Kit.

Below is the initial data and there are two factors, enzyme concentration and fermentation hours influencing the alcohol production of our engineered strains.

After analyzing the scatterplots, we chose to use two-dimensional interpolation to construct models by MATLAB and we also give the coding below:

clear;clc;
t0=[0 4 8 12 16 20 24];
x0=[0 0.3 0.6 1];

z1=[0.16566911 0.158452214 0.151526625 0.182264212 0.178289281 0.180093505 0.199272782;...
0.155877436	0.159194577	0.165697301	0.180394209	0.190777894	0.165969814	0.184500698;...
0.160923625	0.151958887	0.141687966	0.174812391	0.163376242	0.183852305	0.169841378;...
0.138944042	0.151883711	0.12808111	0.175648724	0.162624482	0.169634644	0.167388761];%1号样本

z2=[0.167116248 0.141349674 0.143915055 0.182828032 0.166223533 0.191557845 0.179604861;...
0.185017533	0.150511749	0.158405229	0.185412207	0.181286924	0.192187444	0.180976823;...
0.173384047	0.168469416	0.146555612	0.186755978	0.19386011	0.186229746	0.181521849;...
0.15533241 0.157127237 0.154646429  0.19198071	0.175056713	0.174662039	0.182987781];%2号样本

z3=[0.150154663 0.148237675 0.137271376 0.198154539 0.196528858 0.186098188 0.166693383;...
0.143229074	0.138934645	0.146471039	0.190721512	0.196735592	0.176362896	0.172453744;...
0.150276824	0.14330425	0.146818728	0.183467028	0.184472507	0.181164763	0.173346459;...
0.145709882	0.1465932 0.126145328 0.162304984 0.182095066 0.163000362 0.15570829];%3号样本

z4=[0.150878232 0.156281507 0.154308137 0.168760723 0.188231307 0.1738445 0.176898525;...
0.155407586	0.171504647	0.139084997	0.188080955	0.19630333	0.182470946	0.178928277;...
0.146048174	0.147927574	0.158771712	0.199629868	0.19113498	0.187141255	0.179961947;...
0.156027788	0.149713004	0.149534461	0.175676915	0.198041775	0.170865651	0.180807677];%4号样本

t=0:0.5:24;%每间隔0.5小时取一个时刻
x=0:0.01:1;%浓度间隔为0.01
zA=interp2(t0,x0,z1,t,x','spline');%1号样本插值
zB=interp2(t0,x0,z2,t,x','spline');%2号样本插值
zC=interp2(t0,x0,z3,t,x','spline');%3号样本插值
zD=interp2(t0,x0,z4,t,x','spline');%4号样本插值

subplot(2,2,1),surf(t,x,zA);
subplot(2,2,2),surf(t,x,zB);
subplot(2,2,3),surf(t,x,zC);
subplot(2,2,4),surf(t,x,zD);
zAmax=max(max(zA))
zBmax=max(max(zB))
zCmax=max(max(zC))
zDmax=max(max(zD))
[i1,j1]=find(zA==max(max(zA)));
t1=t(j1)
x1=x(i1)
[i2,j2]=find(zB==max(max(zB)));
t2=t(j2)
x2=x(i2)
[i3,j3]=find(zC==max(max(zC)));
t3=t(j3)
x3=x(i3)
[i4,j4]=find(zD==max(max(zD)));
t4=t(j4)
x4=x(i4)

Finally, we obtained the interpolation curved surfaces of the 4 yeast groups as showing below:

Figure 1. Alcohol production ability of 4 different engineered yeast against enzyme concentration and fermentation hours

By MATLAB, it can be calculated that the highest value of alcohol concentration (g/L) and the corresponding fermentation conditions:

  • For A strain, the highest value of alcohol concentration is 0.1993 g/L when enzyme concentration is given 0 and the fermentation time is 24 hours;
  • For B strain, the highest value of alcohol concentration is 0.1991 g/L when enzyme concentration is given 0.01 and the fermentation time is 22 hours;
  • For C strain, the highest value of alcohol concentration is 0.2049 g/L when enzyme concentration is given 0 and the fermentation time is 13.5 hours;
  • For D strain, the highest value of alcohol concentration is 0.2018 g/L when enzyme concentration is given 0.56 and the fermentation time is 13 hours.

Overall consideration, we strongly recommend yeast C for alcohol industry use which requires less fermentation hours, less additional enzyme but higher yield.

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