IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/Results

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('''Our Results''')
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:* '''2D Model 1: Lotka – Volterra'''  
:* '''2D Model 1: Lotka – Volterra'''  
:::[[Image:Model1.PNG]]
:::[[Image:Model1.PNG]]
 +
::*Lotka-Volterra is the first (and most famous) model for prey-predator interactions. There are some very appealing properties.
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model1| Detail Analysis for Model 1]]</b>
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model1| Detail Analysis for Model 1]]</b>
-
::*Lotka-Volterra is the first (and most famous) model for prey-predator interactions. We detail  here some of its (very appealing) properties.
 
-
 
:* '''2D Model 2: Bounded Prey Growth'''  
:* '''2D Model 2: Bounded Prey Growth'''  
:::[[Image:Model2.PNG]]
:::[[Image:Model2.PNG]]
 +
::*Lotka-Volterra is far too simple to yield essential results on the complex 2D model.
 +
::*We start to investigate the influence of various components of the system, e.g. bounding of the growth of the preys.
 +
::*The prey (AHL) production is bounded by the limited number of promoters. The number of activated promoter is directly responsible for the rate of production.
 +
::*The rate of production will become linear once the number of promoters is saturated. This enzyme activation-site-limited like behaviours can be modelled similarly to the Michaels Menton model
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model2| Detail Analysis for Model 2]]</b>
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model2| Detail Analysis for Model 2]]</b>
-
::*Lotka-Volterra is far too simple a model to yield any valuable results on the complex 2D model we wish to study. We start to investigate the influence of the various components of the system here by bounding the growth of the preys.
 
-
::*The prey (AHL) production is limited by the limited number of promoters. The number of promoter is directly responsible for the production. The rate of production will becomes linear once the number of promoters is saturated. This enzyme activation-site like behaviours can be modelled similarly to the Michaels Menton model
 
:* '''2D Model 3: Bounded Predator and Prey Growth'''
:* '''2D Model 3: Bounded Predator and Prey Growth'''
:::[[Image:Model3.PNG]]
:::[[Image:Model3.PNG]]
 +
::*Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate.
 +
::*We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
 +
::*Similarly, the production of the predator is also limited by the number of promoters available
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model3| Detail Analysis for Model 3]]</b>
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model3| Detail Analysis for Model 3]]</b>
-
::*Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate. We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
 
-
::*Similarly, the production of the predator is also limited by the number of promoters
 
:* '''2D Model 3a: Bounded Predator and Prey Growth'''
:* '''2D Model 3a: Bounded Predator and Prey Growth'''
:::[[Image:Model3a.PNG]]
:::[[Image:Model3a.PNG]]
 +
::*We have studied this model in parallel with the previous model
 +
::*Instead of bounding the production of the predator, we bound the degradation of prey
 +
::*The degradation of prey(AHL) by predator(aiiA) is truely an enzyme reaction, hence the killing of prey can be modelled by Michaelis Menton directly
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model3a| Detail Analysis for Model 3a]]</b>
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model3a| Detail Analysis for Model 3a]]</b>
-
::*Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate. We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
 
-
::*Similarly, the production of the predator is also limited by the number of promoters
 
:* '''2D Model 4: Bounded Predator and Prey Growth with Controlled Killing of Preys'''
:* '''2D Model 4: Bounded Predator and Prey Growth with Controlled Killing of Preys'''
:::[[Image:Model4.PNG]]
:::[[Image:Model4.PNG]]
 +
::*Combining the previous two models
 +
::*Such combination introduces some undesirable properties in the system.
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model4| Detail Analysis for Model 4]]</b>
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model4| Detail Analysis for Model 4]]</b>
-
::*We have obtained oscillations but unfortunately the killing term for the preys remains unrealistic and need regulating. we show such regulation introduces in the system some undesirable properties.
 
-
::*The degradation of prey(AHL) by predator(aiiA) is truely an enzyme reaction, hence the killing of prey can be modelled by Michaelis Menton directly.
 
:* '''Final 2D Model : 2D Model 5'''
:* '''Final 2D Model : 2D Model 5'''
:::[[Image:Model5.PNG]]
:::[[Image:Model5.PNG]]
-
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model5| Detail Analysis for Model 5]]</b>
+
::*Model 4 can be made to oscillate but exhibit some very unrealistic properties. Fortunately experimental conditions lead us to introduce a final dissipative term –eU to the derivative of the prey population.
-
::*Model 4 can be made to oscillate. However, it also exhibits some very unwelcome properties. Fortunately experimental conditions lead us to introduce a final dissipative term –eU to the derivative of the prey population.
+
::*We investigate the properties of this final 2D model and prove that the new dissipative term confers it some very interesting characteristics –among other things it prevents all the problems that may be encountered with Model 4.
-
 
+
-
::*We investigate the properties of the final 2D model and prove that the new dissipative term confers it some very interesting characteristics –among other things it prevents all the problems that may be encountered with Model 4.
+
-
 
+
::*The "-eU" term here is the "natural" decay rate of AHL. However, this is not mainly due to the half-life of the AHL since AHL is quite stable itself. The dominant contribution to this decay rate is the "wash-out" rate in the chemostat.  
::*The "-eU" term here is the "natural" decay rate of AHL. However, this is not mainly due to the half-life of the AHL since AHL is quite stable itself. The dominant contribution to this decay rate is the "wash-out" rate in the chemostat.  
::*AHL is small molecules that are free to move in the cells and medium. Hence it will be "wash-out" when we pump out the medium from the chemostat
::*AHL is small molecules that are free to move in the cells and medium. Hence it will be "wash-out" when we pump out the medium from the chemostat
::*This will allow us to have a extra feature to change the magnitude of the parameter "e" and maybe give us a better control of the system
::*This will allow us to have a extra feature to change the magnitude of the parameter "e" and maybe give us a better control of the system
 +
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model5| Detail Analysis for Model 5]]</b>

Revision as of 05:11, 30 October 2006

Analysis of the Model of the Molecular Predation Oscillator


Our Results

We had time to study the following five Dynamical Systems. In order of complexity:
  • 2D Model 1: Lotka – Volterra
Image:Model1.PNG
  • Lotka-Volterra is the first (and most famous) model for prey-predator interactions. There are some very appealing properties.
  • Detail Analysis for Model 1
  • 2D Model 2: Bounded Prey Growth
Image:Model2.PNG
  • Lotka-Volterra is far too simple to yield essential results on the complex 2D model.
  • We start to investigate the influence of various components of the system, e.g. bounding of the growth of the preys.
  • The prey (AHL) production is bounded by the limited number of promoters. The number of activated promoter is directly responsible for the rate of production.
  • The rate of production will become linear once the number of promoters is saturated. This enzyme activation-site-limited like behaviours can be modelled similarly to the Michaels Menton model
  • Detail Analysis for Model 2
  • 2D Model 3: Bounded Predator and Prey Growth
Image:Model3.PNG
  • Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate.
  • We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
  • Similarly, the production of the predator is also limited by the number of promoters available
  • Detail Analysis for Model 3
  • 2D Model 3a: Bounded Predator and Prey Growth
Image:Model3a.PNG
  • We have studied this model in parallel with the previous model
  • Instead of bounding the production of the predator, we bound the degradation of prey
  • The degradation of prey(AHL) by predator(aiiA) is truely an enzyme reaction, hence the killing of prey can be modelled by Michaelis Menton directly
  • Detail Analysis for Model 3a
  • 2D Model 4: Bounded Predator and Prey Growth with Controlled Killing of Preys
Image:Model4.PNG
  • Final 2D Model : 2D Model 5
Image:Model5.PNG
  • Model 4 can be made to oscillate but exhibit some very unrealistic properties. Fortunately experimental conditions lead us to introduce a final dissipative term –eU to the derivative of the prey population.
  • We investigate the properties of this final 2D model and prove that the new dissipative term confers it some very interesting characteristics –among other things it prevents all the problems that may be encountered with Model 4.
  • The "-eU" term here is the "natural" decay rate of AHL. However, this is not mainly due to the half-life of the AHL since AHL is quite stable itself. The dominant contribution to this decay rate is the "wash-out" rate in the chemostat.
  • AHL is small molecules that are free to move in the cells and medium. Hence it will be "wash-out" when we pump out the medium from the chemostat
  • This will allow us to have a extra feature to change the magnitude of the parameter "e" and maybe give us a better control of the system
  • Detail Analysis for Model 5
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