Team:UT-Tokyo/Modeling

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<h1 id="Students">Students</h1>
 
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<h2>Background</h2>
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<p class="ini">Our concept of Multicellular Analog Clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our system can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation.</p>
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<h3>aaaaa</h3>
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<p class="ini">Genetic engineering has achieved numerous victories
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both in basic and applied biology. However, there still remains room
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for progress in the area, especially in developing new tools. For
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instance, although the importance of cell-cell interaction has been
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emphasized, there are limited number of tools in bioengineering to
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utilize it. Controlling interaction among microorganisms will help
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understanding living things and constructing completely novel
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multicellular systems.</p>
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<h2 id="Project_Summary">Project Summary</h2>
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<h2>DDE model derivation</h2>
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<p class="ini">aaaaaaaaaaaaaaa</p>
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<p class="ini">Using DDE (delay-differential equation) analysis, we can conduct gene network simulation which accounts for delayed production of proteins. It is true that ODE (ordinary differential equation) analysis enables us to simulate rough behavior of complex gene networks, but if you want to simulate temporally more detailed behavior, ODE analysis is insufficient. Since when cells produce proteins including transcription factors, they must pass through processes of transcription, translation, maturation, transcription rate of genes reflects production of transcription factor after these processes' time delay. For this reason, we derived delay-differential equation in reference to [1].</p>
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<p>For the reason stated above, we developed the model based on partial delay-differential equations with Hill functions that captured the activation and repression of protein synthesis, and Michaelis-Menten kinetics that captured enzyme catalysis. Finally we derived the following set of delay-differential equation model for concentrations of AiiA (A), TetR (T), LuxI (I), internal AHL (H<sub>i</sub>), and external AHL (H<sub>e</sub>):</p>
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Revision as of 04:05, 28 September 2013

           TEAM

Our concept of Multicellular Analog Clock is based on qualitative assumption such as how negative feedback loop behaves, how AHL diffuses, and so on. To ascertain our system can function as an analogue clock, namely, to confirm the feasibility of our cell-cell communication included gene circuit, and to deepen understanding of behavior of the system, we conducted the following simulation.

DDE model derivation

Using DDE (delay-differential equation) analysis, we can conduct gene network simulation which accounts for delayed production of proteins. It is true that ODE (ordinary differential equation) analysis enables us to simulate rough behavior of complex gene networks, but if you want to simulate temporally more detailed behavior, ODE analysis is insufficient. Since when cells produce proteins including transcription factors, they must pass through processes of transcription, translation, maturation, transcription rate of genes reflects production of transcription factor after these processes' time delay. For this reason, we derived delay-differential equation in reference to [1].

For the reason stated above, we developed the model based on partial delay-differential equations with Hill functions that captured the activation and repression of protein synthesis, and Michaelis-Menten kinetics that captured enzyme catalysis. Finally we derived the following set of delay-differential equation model for concentrations of AiiA (A), TetR (T), LuxI (I), internal AHL (Hi), and external AHL (He):

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