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Team:SCUT/Modeling
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<h1>Diacetyl Producer</h1> | <h1>Diacetyl Producer</h1> | ||
| - | <p class="text"> | + | <p class="text">Our pathway model for diacetyl producer consists of two parts: ODE pathway analysis and parameter sensitivity analysis. ODE pathway analysis is to examine the feasibility of our pathway. It is the foundation of model analysis. |
</p> | </p> | ||
<div class="imgC"> | <div class="imgC"> | ||
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<div id="tblock2"> | <div id="tblock2"> | ||
<h1>Modelling of Oscillation</h1> | <h1>Modelling of Oscillation</h1> | ||
| - | <p class="text"> | + | <p class="text">To describe the mechanisms of oscillation, we developed a deterministic and “degrade-and-fire” model, using delayed differential equations for protein and LuxI concentrations. Although the nature of oscillations is related to the degrade-and-fire oscillations observed in a dual delayed feedback circuit, an important difference in our model is the coupling in different cells through extracellular AHL. The model of this coupling, and the related cell-density dependence, allowed us to explain most of the oscillation mechanisms. |
</p> | </p> | ||
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<div id="tblock3"> | <div id="tblock3"> | ||
<h1>Pathway model of odr-10</h1> | <h1>Pathway model of odr-10</h1> | ||
| - | <p class="text"> | + | <p class="text">Our pathway model for odr-10 consists of four parts: ODE pathway analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. ODE pathway analysis is to examine the feasibility of our odr-10 pathway. It also provides the foundation for next 3 sections of analysis.<br> |
Through parameter sensitivity analysis, it can distinguish the important parameters for the pathway system. And we can figure out the best parameter set of our system by parameter sweep. Finally, noise analysis based on Gillespie algorithm of the important parameters. The analysis can simulate the influence effects of real conditions in vivo. | Through parameter sensitivity analysis, it can distinguish the important parameters for the pathway system. And we can figure out the best parameter set of our system by parameter sweep. Finally, noise analysis based on Gillespie algorithm of the important parameters. The analysis can simulate the influence effects of real conditions in vivo. | ||
</p> | </p> | ||
Revision as of 17:34, 25 September 2013
Diacetyl Producer
Our pathway model for diacetyl producer consists of two parts: ODE pathway analysis and parameter sensitivity analysis. ODE pathway analysis is to examine the feasibility of our pathway. It is the foundation of model analysis.
Figure 1.
Figure 2.
Modelling of Oscillation
To describe the mechanisms of oscillation, we developed a deterministic and “degrade-and-fire” model, using delayed differential equations for protein and LuxI concentrations. Although the nature of oscillations is related to the degrade-and-fire oscillations observed in a dual delayed feedback circuit, an important difference in our model is the coupling in different cells through extracellular AHL. The model of this coupling, and the related cell-density dependence, allowed us to explain most of the oscillation mechanisms.
Pathway model of odr-10
Our pathway model for odr-10 consists of four parts: ODE pathway analysis, parameter sensitivity analysis, parameter sweep, stochastic analysis. ODE pathway analysis is to examine the feasibility of our odr-10 pathway. It also provides the foundation for next 3 sections of analysis.
Through parameter sensitivity analysis, it can distinguish the important parameters for the pathway system. And we can figure out the best parameter set of our system by parameter sweep. Finally, noise analysis based on Gillespie algorithm of the important parameters. The analysis can simulate the influence effects of real conditions in vivo.
