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Team:Aberdeen Scotland/modeling/combined model
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A schematic diagram of the model as it works in SimBiology is displayed below: | A schematic diagram of the model as it works in SimBiology is displayed below: | ||
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The dashed lines represent an enzymatic reaction, and the arrows represent the direction of chemical reaction. As stated before all mRNA productions must be modelled by an enzymatic production from DNA, and all protein productions must be modelled as enzymatic production from mRNA. This is useful as the repression and activation of gene networks can be modelled by mass action reactions between the unbound and bound form of the DNA or mRNA. | The dashed lines represent an enzymatic reaction, and the arrows represent the direction of chemical reaction. As stated before all mRNA productions must be modelled by an enzymatic production from DNA, and all protein productions must be modelled as enzymatic production from mRNA. This is useful as the repression and activation of gene networks can be modelled by mass action reactions between the unbound and bound form of the DNA or mRNA. | ||
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Our SimBiology model can be downloaded on the download page if you want to see how we modelled it exactly, and if you want to see the set of parameters we used. Below is a graph of the system turning on in response to input signals of quorum sensing and IPTG, and below that is one of the system reaching steady state without inputs: | Our SimBiology model can be downloaded on the download page if you want to see how we modelled it exactly, and if you want to see the set of parameters we used. Below is a graph of the system turning on in response to input signals of quorum sensing and IPTG, and below that is one of the system reaching steady state without inputs: | ||
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Revision as of 18:01, 21 October 2009
University of Aberdeen - Pico Plumber
Contents |
Combined Chemotaxis and Lysis Model
Introduction
Results
A schematic diagram of the model as it works in SimBiology is displayed below:
The dashed lines represent an enzymatic reaction, and the arrows represent the direction of chemical reaction. As stated before all mRNA productions must be modelled by an enzymatic production from DNA, and all protein productions must be modelled as enzymatic production from mRNA. This is useful as the repression and activation of gene networks can be modelled by mass action reactions between the unbound and bound form of the DNA or mRNA.
Our SimBiology model can be downloaded on the download page if you want to see how we modelled it exactly, and if you want to see the set of parameters we used. Below is a graph of the system turning on in response to input signals of quorum sensing and IPTG, and below that is one of the system reaching steady state without inputs:
References
[1] A.B. Goryachev, D.J. Toh, T. Lee. “Systems analysis of a quorum sensing network: Design constraints imposed by the functional requirements, network topology and kinetic constants”. BioSystems 83 (2006) 178–187
[2] Michail Stamatakis and Nikos V. Manttaris. “Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network” Biophysical Journal Volume 96 February 2009 887-906 887
 Back to Quorum Sensing Activation Point
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