Difference between revisions of "Team:JNFLS/Model"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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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 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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<h3>Our Model </h3>
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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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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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<h3>Best Model Special Prize</h3>
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<p>We generally realized that, along with the increasing development of synthetic biology, a well-established model ought to be derived from the experiment and used in the experiment, which means to make assumption according to the data, and then use the principle we have learned (chemistry, biology, etc.) to establish a model that is able to reflect the essence of the phenomenon and add accuracy to the result; this is the principle and the reason for our modeling. </p>
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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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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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<p>We wanted to understand the effects of different concentrations of HCVC7 aptamer on the result of HCVC protein detection in our system, and we hoped that the inspirational result will help our experiment and contribute to the further application of our system in the real world. </p>
  
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<p>To achieve this goal, we decided to employ Hill equation to establish our model. Hill equation is commonly used to study the kinetics of reactions that exhibit a sigmoidal behavior in synthetic biology. The rate of many processes, such as the binding process of HCVC7 aptamer and HCVC protein in our system, can be analyzed by the Hill equation.</p>
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<p>The common form of Hill equation is shown below:</p>
  
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<p>And the adjusted form, based on the condition of our system, can be shown below:</p>
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<h3> Inspiration </h3>
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<img src="https://static.igem.org/mediawiki/2018/4/44/T--JNFLS--M2.jpg"style="width:50%">
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<p>R: The velocity of the binding process of HCVC7 aptamer and HCVC protein.</p>
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Here are a few examples from previous teams:
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<p>V_max: The maximum velocity of the reaction. It has the same units as the reaction velocity (R).</p>
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<p> [K_aptamer]: The concentration of HCVC7 aptamer. </p>
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<p>C_(1/2 aptamer): The half-maximal concentration constant; it is the concentration of HCVC7 aptamer that gives rise to a reaction velocity that is 50% of V_max. </p>
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<li><a href="https://2016.igem.org/Team:Manchester/Model">2016 Manchester</a></li>
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<p>n: The Hill coefficient, which provides a measure of the cooperativity of HCVC7 aptamer binding to the HCVC protein. </p>
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<li><a href="https://2016.igem.org/Team:TU_Delft/Model">2016 TU Delft</li>
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<p>Model of HCVC7 aptamer and HCVC protein binding</p>
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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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<p>This model indicates that as the concentration of HCVC7 aptamer increase, the binding rate of HCVC7 aptamer and HCVC protein increase as well; also, it predicts how the system will work in the real life, which encourages further applications of our device. In addition, it was really consequential that this model also enabled us to understand our device better, to improve our experiment, and to assess potential values of our device.  </p>
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<p>Reference:</p>
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<p>[1] Hill, A. V. (1910-01-22). "The possible effects of the aggregation of the molecules of hemoglobin on its dissociation curves". J.Physiol. 40 (Suppl): iv-vii. doi:10.1113/jphysiol.1910.sp001386</p>
 
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Latest revision as of 00:42, 18 October 2018



Our Model

We generally realized that, along with the increasing development of synthetic biology, a well-established model ought to be derived from the experiment and used in the experiment, which means to make assumption according to the data, and then use the principle we have learned (chemistry, biology, etc.) to establish a model that is able to reflect the essence of the phenomenon and add accuracy to the result; this is the principle and the reason for our modeling.

We wanted to understand the effects of different concentrations of HCVC7 aptamer on the result of HCVC protein detection in our system, and we hoped that the inspirational result will help our experiment and contribute to the further application of our system in the real world.

To achieve this goal, we decided to employ Hill equation to establish our model. Hill equation is commonly used to study the kinetics of reactions that exhibit a sigmoidal behavior in synthetic biology. The rate of many processes, such as the binding process of HCVC7 aptamer and HCVC protein in our system, can be analyzed by the Hill equation.

The common form of Hill equation is shown below:

And the adjusted form, based on the condition of our system, can be shown below:

R: The velocity of the binding process of HCVC7 aptamer and HCVC protein.

V_max: The maximum velocity of the reaction. It has the same units as the reaction velocity (R).

[K_aptamer]: The concentration of HCVC7 aptamer.

C_(1/2 aptamer): The half-maximal concentration constant; it is the concentration of HCVC7 aptamer that gives rise to a reaction velocity that is 50% of V_max.

n: The Hill coefficient, which provides a measure of the cooperativity of HCVC7 aptamer binding to the HCVC protein.

Model of HCVC7 aptamer and HCVC protein binding

This model indicates that as the concentration of HCVC7 aptamer increase, the binding rate of HCVC7 aptamer and HCVC protein increase as well; also, it predicts how the system will work in the real life, which encourages further applications of our device. In addition, it was really consequential that this model also enabled us to understand our device better, to improve our experiment, and to assess potential values of our device.

Reference:

[1] Hill, A. V. (1910-01-22). "The possible effects of the aggregation of the molecules of hemoglobin on its dissociation curves". J.Physiol. 40 (Suppl): iv-vii. doi:10.1113/jphysiol.1910.sp001386