Minnesota/29 June 2009

From 2009.igem.org

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I switched over today to looking at making the "leakiness" equations for the TTN model. Initially I would represent the leakiness with two equations:

Rxn # Reaction Forward Kinetic Constant
46RNAp + lacP + tetO1:tetR2 + tetO2 -> RNAp:lacP1E+07
47RNAp + lacP + tetO1 + tetO2:tetR2 -> RNAp:lacP1E+07

The aTc complexes don't have to be represented since the leakiness is for aTc=0 in particular. Also a third leakiness equation could be made, one where both tetO1:tetR2 and tetO2:tetR2 exist, but I chose to add this later if necessary. I expect the results tomorrow.


Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + tetO1:tetR2 + lacP -> RNAp:lacP + tetR2310
RNAp + tetO1:aTc:tetR2 + lacP -> RNAp:lacP + tetR2310
RNAp + tetO1:aTc2:tetR2 + lacP -> RNAp:lacP + tetR2310

The table above shows the changes that were made from the base model inorder to produce the modeling graph shown above. This model was completed by the supercomputer the day after the previous model, by which time I knew this direction was not giving good results. The low kinetic constant for these three reactions simply produces low amounts of GFP in the system at all times except for when the system has no aTc in it.