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

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<h1> Modeling</h1>
 
<h1> Modeling</h1>
  
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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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<h2> Why did we model?</h2>
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<p>Our goal of this part was to develop the dynamic model of the expression of our outputs, to precisely describe, predict and control the expression of the proteins and the generation of our colors. What’s more, our modelling also provided instructions for our experiments.</p>
  
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<h3> Gold Medal Criterion #3</h3>
 
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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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<h2>What have we done?</h2>
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Please see the <a href="https://2018.igem.org/Judging/Medals"> 2018
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<p>Although various actuators were used in our project, we finally chose fluorescent proteins to build our models because fluorescence could be measured easily by ELIASA (microplate reader) and flow cytometry to get quantitative results, and the expression period of fluorescent proteins is much shorter than those of chromoproteins and enzymes. Besides the modelling of the expression of proteins, we also modelled the light intensity distribution in our hardware, to further optimize our hardware to get evener light on the plates and 96-well plates.</p>
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Medals Page</a> for more information.  
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<p>Our model consisted of six parts. In part 1, we established model about free growth of bacteria. In part 2, we discussed the influence of light on the growth of bacteria. In part 3, the expression of fluorescent proteins over time was described. In part 4, the effect of illuminance on the expression of fluorescence was shown. In part 5, we combined the models in part 3 and part 4, drawing a general view about how the expression of fluorescence changed with time and illuminance. In part 6, we introduced how we built models about our hardware and optimize the design of our hardware. </p>
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<h3>Best Model Special Prize</h3>
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<h2>How did the models improve our project?</h2>
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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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<p>Our model was tightly combined with other parts of our project, especially our experiment and hardware. The part 2 of model provided methods for experiment to make the growth rate of bacterium on same plate even. The part 4 of model revealed how to get wanted R/G/B of color by changing the wavelength of projected light. The part 5 of model shew how to get wanted fluorescence intensity by adjusting the time and illuminance. The part 6 of model gave evidence on the feasibility of hardware improvement.</p>
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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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<h2>Part1 Dynamics of Free Growth</h2>
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<p>We created a model to simulate the process of bacteria’s free growth.</p>
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<p>Questions to answer:</p>
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<p>1. How fast the bacteria grow?</p>
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<p>2. Is there growth difference between bacteria carrying different plasmids of outputs?</p>
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<p>According to Logistic function [1]:</p>
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<h3> Inspiration </h3>
 
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Here are a few examples from previous teams:
 
Here are a few examples from previous teams:
 
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</p>

Revision as of 02:53, 17 October 2018

Modeling

Why did we model?

Our goal of this part was to develop the dynamic model of the expression of our outputs, to precisely describe, predict and control the expression of the proteins and the generation of our colors. What’s more, our modelling also provided instructions for our experiments.

What have we done?

Although various actuators were used in our project, we finally chose fluorescent proteins to build our models because fluorescence could be measured easily by ELIASA (microplate reader) and flow cytometry to get quantitative results, and the expression period of fluorescent proteins is much shorter than those of chromoproteins and enzymes. Besides the modelling of the expression of proteins, we also modelled the light intensity distribution in our hardware, to further optimize our hardware to get evener light on the plates and 96-well plates.

Our model consisted of six parts. In part 1, we established model about free growth of bacteria. In part 2, we discussed the influence of light on the growth of bacteria. In part 3, the expression of fluorescent proteins over time was described. In part 4, the effect of illuminance on the expression of fluorescence was shown. In part 5, we combined the models in part 3 and part 4, drawing a general view about how the expression of fluorescence changed with time and illuminance. In part 6, we introduced how we built models about our hardware and optimize the design of our hardware.

How did the models improve our project?

Our model was tightly combined with other parts of our project, especially our experiment and hardware. The part 2 of model provided methods for experiment to make the growth rate of bacterium on same plate even. The part 4 of model revealed how to get wanted R/G/B of color by changing the wavelength of projected light. The part 5 of model shew how to get wanted fluorescence intensity by adjusting the time and illuminance. The part 6 of model gave evidence on the feasibility of hardware improvement.

Part1 Dynamics of Free Growth

We created a model to simulate the process of bacteria’s free growth.

Questions to answer:

1. How fast the bacteria grow?

2. Is there growth difference between bacteria carrying different plasmids of outputs?

According to Logistic function [1]:

Here are a few examples from previous teams:

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