Minnesota/25 June 2009

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I got back the analysis of the models submitted yesterday. I submitted a base model shown here:

I also changed the tendency for tetO1 to detach from the tetR2:tetO1:2aTc complex (k=100000 1/s initially) by lower or higher an order of magnitude:

None of the graphs were particularly interesting. I also submitted two more jobs: smad_tetRu/d which either increased or decreased the rate of synthesis of tetR2 (reaction 44, k = 1E-11 M/s initially) by an order of magnitude.

In order to try to improve the model, the following reaction constants were changed to try to see less leakiness in the model.

Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR21200000
RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR21200000
RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR21200000


This model does indeed show some different leakiness, which is definitely a good thing, although the leakiness is still too high for an accurate model. Still, the problem remains where the model peaks and decreases instead of reaching a steady state.