Difference between revisions of "Team:XJTU-China/Model"

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      <h1 class="font-weight-bold text-center">Model</h1>
  
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      <h3>Overview</h3>
  
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<h1> Modeling</h1>
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        In our design, we aim to manufacture psicose, which has a lot of advantages over other sugar or sweetener as is mentioned in the research of the psicose. The advantages of psicose include low energy, benefit to diabetes and hyperlipidemia, making psicose become more and more popular in people. People can get a psicose sweetener or food rich in psicose, in which psicose is synthesized by biological ways, because using chemical ways is not a good choice to synthesize clear and edible psicose in a food grade for the containing of unhealthy and poisonous by-product in chemical synthesis methods.
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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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        Nevertheless, biological methods in producing psicose are inefficient due to the low enzyme efficiency of D-psicose 3-epimerase. The efficiency of D-psicose 3-epimerase is different due to the various environment system and the different concentration of substrate( sounds amazing due to the efficiency of enzyme irrelevant in most occasions). As a result, the temperature, PH value and the concentration are considered in our model to describe the efficiency of D-pisocose 3-epimerase, which is significant in our manufacture.
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$$|x_1-x_2|=\sqrt{x_1^2+x_2^2-2|x_1||x_2|\cos(x_1,x_2)}\,,\,\,x_1,x_2\in R^n$$
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$$|x_1-x_2| = \sqrt{1+1-2\cos(x_1,x_2)}\,,\,\,x_1,x_2\in R^n, |x_1|=|x_2|=1$$
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        Although the market size is estimated large enough from the market research we have made, modeling is needed to describe exactly how much is the efficiency of D-psicose 3-epimerase. we analysis the efficiency of D-psicose 3-epimerase is affected by the temperature, PH value and the concentration of substrate. In this way, we can predict the catalytic efficiency of D-psicose 3-epimerase by simulating the catalytic process.
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<h3> Gold Medal Criterion #3</h3>
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        The third model we would like to model is the market model for the application of psicose. From the research, the conclusion that the psicose is very much needed among public and patients is analyzed. By the statistics we get, the potential market and the value curve of psicose appear from our mind by running the market model.
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Convince the judges that your project's design and/or implementation is based on insight you have gained from modeling. This could be either a new model you develop or the implementation of a model from a previous team. You must thoroughly document your model's contribution to your project on your team's wiki, including assumptions, relevant data, model results, and a clear explanation of your model that anyone can understand.  
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The model should impact your project design in a meaningful way. Modeling may include, but is not limited to, deterministic, exploratory, molecular dynamic, and stochastic models. Teams may also explore the physical modeling of a single component within a system or utilize mathematical modeling for predicting function of a more complex device.
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          Psicose Synthesis Kinetic Model
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          Production Simulink Model
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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Medals Page</a> for more information.
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          Market and Price Model
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          Microfluidics Model
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<h3>Best Model Special Prize</h3>
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      <h3>Psicose synthesis kinetic model</h3>
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To compete for the <a href="https://2018.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://2018.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.
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        In our design, the DTE process is one of the most significant part in manufacturing psicose. The main process of psicose manufacture is catalyzed by D-psicose 3-epimerase. The models of device A, B, C and D are as follows.
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You must also delete the message box on the top of this page to be eligible for the Best Model Prize.
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      <img src="#" alt="DeviceA" />
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        In device A, extracellular concentration of <i>psicose</i> is higher than which is intracellular, so it can enter the cells by diffusion. As a small molecular, the <i>psicose</i> inside the cell can be combined with <i>pPsiR</i> to generate cci. <i>pPsiR</i> is a repressor, which can bind to promoters on DNA and block gene expression. After binding with <i>psicose</i>, <i>pPsiR</i> falls off from the promoter and the gene starts expressing, And eventually produce the produce <i>EGFP</i>.
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        For device A, the dynamic equation can be listed as follows:
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<h3> Inspiration </h3>
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         Concentrations of A and B are different inside and outside the cell, so the diffusion rate of  is proportional to the concentration difference between inside and outside of the cells.
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Here are a few examples from previous teams:
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      $$$$
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      <p>Where  is the diffusion coefficient.</p>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<li><a href="https://2014.igem.org/Team:ETH_Zurich/modeling/overview">2014 ETH Zurich</a></li>
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<li><a href="https://2014.igem.org/Team:Waterloo/Math_Book">2014 Waterloo</a></li>
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      Finally, based on the probability distribution function, the variation of production is defined and we can compare the psicose production in natural system and directed evolution system.
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      <h3>Results and Discussion</h3>
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      <h3>Strengths and Prospect</h3>
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      <h3>Reference</h3>
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      Schmidt F R. Optimization and scale up of industrial fermentation processes.[J]. Appl Microbiol Biotechnol, 2005, 68(4):425-435.<br>
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          <li class="nav-item"><a class="nav-link" href="#">HUMAN PRACTICE</a></li>
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      Lin P Y, Whang L M, Wu Y R, et al. Biological hydrogen production of the genus Clostridium: Metabolic study and mathematical model simulation[J]. International Journal of Hydrogen Energy, 2007, 32(12):1728-1735.<br>
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          <li class="nav-item"><a class="nav-link" href="#">TEAM</a></li>
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      Whang L M, Hsiao C J, Cheng S S. A dual-substrate steady-state model for biological hydrogen production in an anaerobic hydrogen fermentation process[J]. Biotechnology & Bioengineering, 2010, 95(3):492-500.<br>
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          <li class="nav-item"><a class="nav-link" href="#">AWARDS</a></li>
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      Rousu J, Elomaa T, Aarts R. Predicting the speed of beer fermentation in laboratory and industrial scale[J]. 1999, 1607.
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Revision as of 08:13, 14 October 2018

Model

Overview

In our design, we aim to manufacture psicose, which has a lot of advantages over other sugar or sweetener as is mentioned in the research of the psicose. The advantages of psicose include low energy, benefit to diabetes and hyperlipidemia, making psicose become more and more popular in people. People can get a psicose sweetener or food rich in psicose, in which psicose is synthesized by biological ways, because using chemical ways is not a good choice to synthesize clear and edible psicose in a food grade for the containing of unhealthy and poisonous by-product in chemical synthesis methods.

Nevertheless, biological methods in producing psicose are inefficient due to the low enzyme efficiency of D-psicose 3-epimerase. The efficiency of D-psicose 3-epimerase is different due to the various environment system and the different concentration of substrate( sounds amazing due to the efficiency of enzyme irrelevant in most occasions). As a result, the temperature, PH value and the concentration are considered in our model to describe the efficiency of D-pisocose 3-epimerase, which is significant in our manufacture.

Although the market size is estimated large enough from the market research we have made, modeling is needed to describe exactly how much is the efficiency of D-psicose 3-epimerase. we analysis the efficiency of D-psicose 3-epimerase is affected by the temperature, PH value and the concentration of substrate. In this way, we can predict the catalytic efficiency of D-psicose 3-epimerase by simulating the catalytic process.

The third model we would like to model is the market model for the application of psicose. From the research, the conclusion that the psicose is very much needed among public and patients is analyzed. By the statistics we get, the potential market and the value curve of psicose appear from our mind by running the market model.

  • Psicose Synthesis Kinetic Model
  • Production Simulink Model
  • Market and Price Model
  • Microfluidics Model

Psicose synthesis kinetic model

In our design, the DTE process is one of the most significant part in manufacturing psicose. The main process of psicose manufacture is catalyzed by D-psicose 3-epimerase. The models of device A, B, C and D are as follows.

DeviceA

In device A, extracellular concentration of psicose is higher than which is intracellular, so it can enter the cells by diffusion. As a small molecular, the psicose inside the cell can be combined with pPsiR to generate cci. pPsiR is a repressor, which can bind to promoters on DNA and block gene expression. After binding with psicose, pPsiR falls off from the promoter and the gene starts expressing, And eventually produce the produce EGFP.

For device A, the dynamic equation can be listed as follows:

Concentrations of A and B are different inside and outside the cell, so the diffusion rate of is proportional to the concentration difference between inside and outside of the cells.

$$$$

Where is the diffusion coefficient.






Finally, based on the probability distribution function, the variation of production is defined and we can compare the psicose production in natural system and directed evolution system.

Results and Discussion

Strengths and Prospect

Reference

Schmidt F R. Optimization and scale up of industrial fermentation processes.[J]. Appl Microbiol Biotechnol, 2005, 68(4):425-435.
Lin P Y, Whang L M, Wu Y R, et al. Biological hydrogen production of the genus Clostridium: Metabolic study and mathematical model simulation[J]. International Journal of Hydrogen Energy, 2007, 32(12):1728-1735.
Whang L M, Hsiao C J, Cheng S S. A dual-substrate steady-state model for biological hydrogen production in an anaerobic hydrogen fermentation process[J]. Biotechnology & Bioengineering, 2010, 95(3):492-500.
Rousu J, Elomaa T, Aarts R. Predicting the speed of beer fermentation in laboratory and industrial scale[J]. 1999, 1607.

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