Difference between revisions of "Team:CHINA CD UESTC/Modeling"

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<h2> Modeling</h2>
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<h4>Note</h4>
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<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best Model award</a>, you must fill out this page.</p>
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<p>Mathematical models and computer simulations provide a great way to describe the function and operation of BioBrick Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior in conjunction with experiments in the wetlab.</p>
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#pic_title {
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Here are a few examples from previous teams:
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</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">ETH Zurich 2014</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">Waterloo 2014</a></li>
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<B>MODELING</B>
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&nbsp;&nbsp;We are a skillful and persistent group of nine Finns. We started as a group of students who didn't really know each other, assuming that we were going to spend our summer studying synthetic biology with strange colleagues. In the end we got a bunch of new friends and (in addition to studying synthetic biology) we just might have spent one of the best summers of our lives.
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<h3>Model</h3>
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<div id="content">
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<div class="grid_8">
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<p>
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Biological fuel cell (BFC) is a device with the use of enzymes or microorganisms as catalysts. According to the types of catalysts, it can be divided into microbial fuel cells（MFC）and enzymatic biofuel cell. Our project is focused on improving the catalytic efficiency of laccase in biofuel cell. Laccase, produced by higher plants, fungi, and some bacterial strains, is a multicopper oxidoreductase and oxidizes phenolic compounds while reducing oxygen to water directly without requiring H <sub>2</sub>
 +
O <sub>2</sub>
 +
or any other co-factors for its catalysis <sup>[1]</sup>
 +
. In addition to be applied in the biological fuel cells, it also has various applications containing pulp and paper industry, environmental applications, food industry, and biosensors.
 +
</p>
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</div>
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</div>
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<div class="container clearfix">
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<h3>The cathodic Potential prediction</h3>
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</div>
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<div class="clear"></div>
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<div id="content">
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<div class="grid_8">
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<p>
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One of the criteria of evaluating a microbial fuel cell is potential. We use the laccase as a bio-cathode to achieve electron transfer function from pole to oxygen.
 +
</p>
 +
<p>
 +
According to E. Laviron's article <sup>[2]</sup>
 +
, we can use the Laviron formula to estimate the cathodic peak potential:
 +
</p>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/b/bc/CHINA_CD_UESTC_MODELING01.png" width="60%"></div>
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<div class="project_pic">
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<p id="pic_title"></p>
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<img src="https://static.igem.org/mediawiki/2015/1/18/CHINA_CD_UESTC_MODELING02.png" width="60%"></div>
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<h3>Hypothesis condition</h3>
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<div id="content">
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<div class="grid_8">
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<p>
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If we want to do some analysis, hypothesis condition is necessary form existing literatures.
 +
</p>
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<div class="project_pic">
 +
<p id="pic_title"></p>
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<img src="https://static.igem.org/mediawiki/2015/a/a8/CHINA_CD_UESTC_MODELING03.png" width="60%"></div>
 +
<p>
 +
From the formula (1), we can judge that the electron transfer coefficient determines the potential size. In order to study the relationship between them, we use MATLAB for the operation. The results are as follows:
 +
</p>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/e/ee/CHINA_CD_UESTC_MODELING04.png" width="60%">
 +
<p id="pic_illustration">
 +
Figure 1：With the increase of electron transfer coefficient, cathodic peak potential is also increasing rapidly. But the value ofαis form 0.3 to 0.7 in general.
 +
</p>
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</div>
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</div>
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<h3>The conjecture of catalytic efficiency</h3>
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</div>
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<div class="clear"></div>
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 +
<div id="content">
 +
<div class="grid_8">
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<p>
 +
We want to improve the catalytic efficiency of laccase to make biological fuel cells more efficient. So we guess that enrichment of laccase in the electrode can improve the efficiency of electron transfer.The following figure 2 shows our conjecture:
 +
</p>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/e/e2/CHINA_CD_UESTC_MODELING05.png" width="60%">
 +
<p id="pic_illustration">
 +
Figure 2: We predict the enrichment of laccase will improve the efficiency of the BFC.
 +
</p>
 +
</div>
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 +
</div>
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</div>
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</div>
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</div>
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<div class="container clearfix">
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<div id="content" class="grid_12">
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<h3>Theoretical calculation</h3>
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</div>
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<div class="clear"></div>
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 +
<div id="content">
 +
<div class="grid_8">
 +
<p>
 +
The Michaelis–Menten curve describes the relationship between an enzyme (at constant concentration) and the concentration of enzyme’s substrate.
 +
</p>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/c/ce/CHINA_CD_UESTC_MODELING06.png" width="60%">
 +
<p id="pic_illustration">
 +
Figure 2: We predict the enrichment of laccase will improve the efficiency of the BFC.
 +
</p>
 +
</div>
 +
<p>
 +
Form figure 1, we learn about the electron transfer coefficient determines the potential. So what determines the electron transfer coefficient ? We think enzyme quantity per unit area and the distance between enzymes and electrodes are the main influence factors. So we establish the formula:
 +
</p>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/a/a8/CHINA_CD_UESTC_MODELING07.png" width="60%"></div>
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/5/5c/CHINA_CD_UESTC_MODELING08.png" width="60%"></div>
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<div class="container clearfix">
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<div id="content" class="grid_12">
 +
<h3>Ideal assumptions</h3>
 +
</div>
 +
<div class="clear"></div>
 +
 
 +
<div id="content">
 +
<div class="grid_8">
 +
<p>
 +
In order to verify whether our formula is correct. We need some ideal assumptions to meet calculation conditions.
 +
</p>
 +
 
 +
<div class="list_txt">
 +
<ul>
 +
<li>
 +
<p> <strong>◆ the EBFC can work well and smoothly.</strong>
 +
</p>
 +
</li>
 +
<li>
 +
<p> <strong>◆ the amount of substrate is enough</strong>
 +
</p>
 +
</li>
 +
<li>
 +
<p>
 +
<strong>◆ Laccases adhere to electrode strongly enough</strong>
 +
</p>
 +
</li>
 +
</ul>
 +
</div>
 +
<p>
 +
We calculate the equation (3), and simulate the results with MATLAB. The electron transfer coefficient variation tendency are as follows:
 +
</p>
 +
 
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/a/a6/CHINA_CD_UESTC_MODELING09.png" width="60%"></div>
 +
<p>
 +
There are many methods to fix laccase on the electrode. But we came up with a novel idea utilizing biology magnetotaxis. Magnetotactic bacterium(MTB) is a special microbe in nature which can be attracted by magnet . Magnetosome, some Fe3O4s nanocrystals covered by membrane, is the reason why MTB has the ability to be attracted. We design a expression system for E.coli expressing Magnetosomes., then connect laccase with Magnetosomes through structuring fusion protein with MamW. The ultimate goal is as the figure 4 showing:
 +
</p>
 +
 
 +
<div class="project_pic">
 +
<p id="pic_title"></p>
 +
<img src="https://static.igem.org/mediawiki/2015/1/1a/CHINA_CD_UESTC_MODELING10.png" width="60%">
 +
<p id="pic_illustration">
 +
Figure 4: Fixing laccase on the electrode with Magnetosome. It has the advantage of simple operation , environmental protection, as well as good biocompatibility.
 +
</p>
 +
</div>
 +
<p>
 +
According to previous experiments and papers, we verifiy our model by their experiment data. For exampe, Maryam Nazari et al
 +
<sup>[3]</sup>
 +
assembled a MFC with laccase. Detected voltage was 256 mV, and when =0.75, the result our model predicted was 0.238mV.In the error range, our model is correct!
 +
</p>
 +
 
 +
<div class="reference">
 +
<h4>Reference</h4>
 +
<p>
 +
[1] Alper Babadostu, Ozge Kozgus Guldu, Dilek Odaci Demirkol, et al. Affinity Based Laccase Immobilization on Modified Magnetic Nanoparticles: Biosensing Platform for the Monitoring of Phenolic Compounds [J]. Biocontrol Science and Technology, 2015, 64:260-266.
 +
</p>
 +
<p>
 +
[2] Laviron E. General expression of the linear potential sweep voltammogram in the case of diffusionless electrochemical systems[J]. Journal of Electroanalytical Chemistry, 1979, 101(1):19–28.
 +
</p>
 +
<p>
 +
[3] Nazari M, Kashanian S, Rafipour R. Laccase immobilization on the electrode surface to design a biosensor for the detection of phenolic compound such as catechol[J]. Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, 2015, 145:130–138.
 +
</p>
 +
 
 +
</div>
 +
 
 +
</div>
 +
</div>
 +
</div>
 +
</div>
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</div>
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Revision as of 03:23, 9 September 2015

<!DOCTYPE html>

MODELING

  We are a skillful and persistent group of nine Finns. We started as a group of students who didn't really know each other, assuming that we were going to spend our summer studying synthetic biology with strange colleagues. In the end we got a bunch of new friends and (in addition to studying synthetic biology) we just might have spent one of the best summers of our lives.

Model

Biological fuel cell (BFC) is a device with the use of enzymes or microorganisms as catalysts. According to the types of catalysts, it can be divided into microbial fuel cells（MFC）and enzymatic biofuel cell. Our project is focused on improving the catalytic efficiency of laccase in biofuel cell. Laccase, produced by higher plants, fungi, and some bacterial strains, is a multicopper oxidoreductase and oxidizes phenolic compounds while reducing oxygen to water directly without requiring H 2 O 2 or any other co-factors for its catalysis [1] . In addition to be applied in the biological fuel cells, it also has various applications containing pulp and paper industry, environmental applications, food industry, and biosensors.

The cathodic Potential prediction

One of the criteria of evaluating a microbial fuel cell is potential. We use the laccase as a bio-cathode to achieve electron transfer function from pole to oxygen.

According to E. Laviron's article [2] , we can use the Laviron formula to estimate the cathodic peak potential:

Hypothesis condition

If we want to do some analysis, hypothesis condition is necessary form existing literatures.

From the formula (1), we can judge that the electron transfer coefficient determines the potential size. In order to study the relationship between them, we use MATLAB for the operation. The results are as follows:

Figure 1：With the increase of electron transfer coefficient, cathodic peak potential is also increasing rapidly. But the value ofαis form 0.3 to 0.7 in general.

The conjecture of catalytic efficiency

We want to improve the catalytic efficiency of laccase to make biological fuel cells more efficient. So we guess that enrichment of laccase in the electrode can improve the efficiency of electron transfer.The following figure 2 shows our conjecture:

Figure 2: We predict the enrichment of laccase will improve the efficiency of the BFC.

Theoretical calculation

The Michaelis–Menten curve describes the relationship between an enzyme (at constant concentration) and the concentration of enzyme’s substrate.

Figure 2: We predict the enrichment of laccase will improve the efficiency of the BFC.

Form figure 1, we learn about the electron transfer coefficient determines the potential. So what determines the electron transfer coefficient ? We think enzyme quantity per unit area and the distance between enzymes and electrodes are the main influence factors. So we establish the formula:

Ideal assumptions

In order to verify whether our formula is correct. We need some ideal assumptions to meet calculation conditions.

  • ◆ the EBFC can work well and smoothly.

  • ◆ the amount of substrate is enough

  • ◆ Laccases adhere to electrode strongly enough

We calculate the equation (3), and simulate the results with MATLAB. The electron transfer coefficient variation tendency are as follows:

There are many methods to fix laccase on the electrode. But we came up with a novel idea utilizing biology magnetotaxis. Magnetotactic bacterium(MTB) is a special microbe in nature which can be attracted by magnet . Magnetosome, some Fe3O4s nanocrystals covered by membrane, is the reason why MTB has the ability to be attracted. We design a expression system for E.coli expressing Magnetosomes., then connect laccase with Magnetosomes through structuring fusion protein with MamW. The ultimate goal is as the figure 4 showing:

Figure 4: Fixing laccase on the electrode with Magnetosome. It has the advantage of simple operation , environmental protection, as well as good biocompatibility.

According to previous experiments and papers, we verifiy our model by their experiment data. For exampe, Maryam Nazari et al [3] assembled a MFC with laccase. Detected voltage was 256 mV, and when =0.75, the result our model predicted was 0.238mV.In the error range, our model is correct!

Reference

[1] Alper Babadostu, Ozge Kozgus Guldu, Dilek Odaci Demirkol, et al. Affinity Based Laccase Immobilization on Modified Magnetic Nanoparticles: Biosensing Platform for the Monitoring of Phenolic Compounds [J]. Biocontrol Science and Technology, 2015, 64:260-266.

[2] Laviron E. General expression of the linear potential sweep voltammogram in the case of diffusionless electrochemical systems[J]. Journal of Electroanalytical Chemistry, 1979, 101(1):19–28.

[3] Nazari M, Kashanian S, Rafipour R. Laccase immobilization on the electrode surface to design a biosensor for the detection of phenolic compound such as catechol[J]. Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, 2015, 145:130–138.