Difference between revisions of "Team:TU Darmstadt/Model/Kill Switch Modeling"

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                <a href="#Chapter1">EreB CM</a>
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                <a href="#Chapter2">EreB MD Simulation</a>
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                <a href="#Chapter3">Chapter 3</a>
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              EreB CM-Modeling
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                 Introduction  
 
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Revision as of 09:40, 14 October 2020

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EreB CM-Modeling

Introduction

This year presented us with several challenges. Due to the coronavirus outbreak and the resulting lockdown, we were not able to work in the wet lab and had to focus our work on the dry lab. Therefore, we decided to focus our resources in an all-round modelling effort. We used homology modelling to calculate a 3D structure of our laccase to improve our enzymes. The biofilm modelling simulated the growth of the biofilm and the third modelling branch was built around a MATLAB model of a kill switch. The latter will be described in the following. The kill switch model consists of three independent models which build upon each other . The first one describes the quorum sensing part, by simulating five individual cells and their interaction. The second one was built after the first model and describes one cell, to test different other parameters in the cell, whilst reducing its complexity. The third model improved the second one by describing two additional parameters. The circumstances allowed us to put more time into refining and testing our models, so we were able to build a more in-depth model of the kill switch. We also hypothesized that a good working model may theoretically prove our kill switch. With matching data from the lab, the model should be able to precisely fine-tune the kill-switch. Due to Limited lab access, we opted for a new strategy and devised the work to a conceptual model of our kill switch with MATLAB SimBiology and MATLAB SimBiology Analyzer. The model is based on ordinary differential equations which are solved with a numerical analyser. We developed three iterations of our models. In the following text, we would like to show you the process of the three m odels we created.