Minnesota/3 July 2009

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Got back all of the models today. I'll explain the results of each in comparison to the base model.


As can be seen when TetR2 decomposition is increased there is less TetR2 available and GFP production reaches its maximum (the assumed "basal" state, or state at which the cells would produce GFP is there was no repressor available) at a lower aTc concentration. When it is decreased there is more TetR2 and as aTc within the cell runs out (all of it is bound to the tetR2), GFP production becomes too slow and the GFP per cell is diluted. Dilution occurs at all aTc concentrations except for the highest, at 260 aTc molecules per cell.


When the rate was increased the supercomputer had an issue with running the program (I assume there was simply too make TetR2 molecules, and the simulation failed). I'll try increasing the rate by less to see the effects. As for the decrease, it had about the same effect as increasing the decomposition rate (as expected).


Here, as explained before, the equations governing how tightly tetO1 and tetO2 are bound to tetR2 (e.g. tetR2:tetO1 --> tetR2 + tetO1, increasing this rate means that tetO1 is bound less tightly to tetR2). Regardless, as can be seen, increasing or decreasing these kinetic constants does not have a significant affect on the graph.

smad_ttn_test1 and smad_ttn_test2

These two models were created simply to see if the time it took to achieve steady-state could be affected by increasing or decreasing the decomposition and synthesis of TetR2 together. As can be seen the results are consistent with those seen in Figures 2, 3, and 4 above.