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

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
('''Our Results''')
('''Our Results''')
Line 3: Line 3:
-
:During the run of the summer 2006, we had time to study six 2-dimensional Dynamical Systems. Unfortunately we lacked time to carry out a thorough analysis of the 3D model.  
+
:During the run of the summer 2006, we had time to study six 2-dimensional Dynamical Systems. Unfortunately we lacked time to carry out a thorough analysis of the 3D model.In order of complexity, the 2D models are:
-
:In order of complexity, the 2D models are:
+
<br><br>
<br><br>
:<font size="4"> '''2D Model 1: Lotka – Volterra''' </font size="4">
:<font size="4"> '''2D Model 1: Lotka – Volterra''' </font size="4">
Line 16: Line 15:
::*Lotka-Volterra is far too simple to yield essential results on the complex 2D model.  
::*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 by bounding the growth of the preys.
::*We start to investigate the influence of various components of the system by bounding the growth of the preys.
-
::*<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 with Bounded Prey Growth]]</b>
<br><br>
<br><br>
:<font size="4">  '''2D Model 3: Bounded Predator and Prey Growth'''</font size="4">  
:<font size="4">  '''2D Model 3: Bounded Predator and Prey Growth'''</font size="4">  
Line 22: Line 21:
::*Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate anymore.  
::*Bounding the growth of the preys only stabilises the system to the extent we cannot make it oscillate anymore.  
::*We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
::*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 with Bounded Growths]]</b>
-
::*<b>[[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical Analyses/2D Model3| Detail Analysis for Model 3]]</b>
+
<br><br>
-
 
+
:<font size="4">  '''2D Model 3a: Bounded Predator and Prey Growth'''</font size="4"> 
-
:* '''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
::*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
+
::*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>

Revision as of 09:05, 30 October 2006

Analysis of the Model of the Molecular Predation Oscillator


Our Results

During the run of the summer 2006, we had time to study six 2-dimensional Dynamical Systems. Unfortunately we lacked time to carry out a thorough analysis of the 3D model.In order of complexity, the 2D models are:



2D Model 1: Lotka – Volterra
Image:Model1.PNG
  • Lotka-Volterra is the first (and most famous) model for prey-predator interactions and is notoriously endowed with some very appealing properties. Lotka-Volterra also was a major inspiration for the design of the molecular predation oscillator.



2D Model 2: Bounded Prey Growth
Image:Model2.PNG



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 anymore.
  • We now seek ways to obtain oscillations by bounding the growth terms of both preys and predators.
  • Detail Analysis for Model with Bounded Growths



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
  • 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
Personal tools