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Team:KULeuven/Model/Diffusion
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Revision as of 17:06, 4 September 2008
Diffusion
The LuxI protein, output of our InverTimer, produces the long-lived 3OC6HSL molecules. These are in fact signaling molecules used by cells to communicate with each other by diffusing in the environment.
Even though HSL in our system is not really aimed at communication between cells, we still need to model diffusion in our system (we expect it to have a nice synchronising effect though). Most importantly because it significantly inluences the intracellular HSL concentration, modifying the timer function we're aiming for in our system.
Since the final destination of Dr. Coli would be the colon of a patient, we would like to model diffusion in a similar environment. We also want to model a dividing 'colony' of cells (see Multicell so we can not make the system too large or complex. A compromise between these two has been found in the form of a microchemostat. The use of this device has a couple of very interesting advantages for us.
- The first advantage is that in this device, we can have a continuous flow of new nutrients while old medium is removed, this can create an equilibrium state where the dilution rate is equal to the growth rate of the bacteria. This is a lot more similar to the situation in the gut of a patient than say, a petri-dish.
- Another advantage is the fact that the medium inside the chemostat can be considered to be quite homogeneous, making the precise working out of Fick's laws unnecessary. We still looked at this though, for example in a petri-dish. Output can be seen below.
- The microchemostat contains a relatively small number of cells, placing multi-cell modeling of the system within our grasp.
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Vcell | 7.0E-16 L | Cellular volume | |
| Vext | 1.0E-12 L | Volume of the microchemostat, 1000 µm3 | |
| σ.A | 2.1E-17 L.s-1 | Permeability of the entire E. coli cell wall | [http://www.pnas.org/content/101/30/10955.full link] |
| Ddilution | 8.0E-5 s-1 | Dilution rate in the microchemostat, can be adjusted of course | [http://www.nature.com/uidfinder/10.1038/msb.2008.24 link] |
