User:J. C. Martinez-Garcia/Notebook/HMS Activities/2008/11/15

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On the AKT Model
Today I finish the text and the graphics concerning the model of the modified AKT signaling pathway. In qualitative terms the model is very good, since provides a good explanation of the experimentally observed phenomena. At least the model suggest that the observed behavior is associated to bi-stability. The model does not take into account desensitization and maybe it would be good to say something about this question in the final report of this project. Moreover, the model lies in two strong assumptions:
 * 1) Time scale separation of the dynamical behavior of the two involved variables.
 * 2) Self activation (positive feedback) associated to one of the two variables.

These two assumptions must be argued in a good way. However, if the model is constrained to be a qualitative description the assumptions are justified. The assumptions opens then a via to new experiments.

I include in here the ZIP file which includes all the figures as well as the LaTeX file and the simulink and mathematica code for the computer-based experiments ([[Media:AKT_model_sontag.zip]]).

Tasks for tomorrow

 * 1) Print all the notebook files and include them in my hardcopy files.
 * 2) Read the Jablonka paper and send my comments.
 * 3) Review the Pilpel files.
 * 4) Review the Sontag papers on robustness (and maybe predictive control).
 * 5) Consider the possibility of invite Sontag to collaborate with Tzachi and me.
 * 6) Review all my notebook to track the evolution of my ideas and to reorganize them.
 * 7) Finish the Jablonka Book.
 * 8) Explain the project to Rafael (the AKT signaling pathway).
 * 9) Write to Kitano in order to have his comments about robustness as a conserved quantity.
 * 10) Write to Carson and review this thinh concerning supercriticality.
 * 11) Write something about the networks project with Pablo (sciende and the edge collapse of innovation). Maybe it would be nice to discuss this thing in the meeting with Maja.


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