Team:UNAM-Genomics Mexico/Modeling

So, here goes the Model!

Simbiology

So having Simbiolgy, we decided to model our interfaces using it's deterministic solvers. Some results are here:

Data for Blue Emission system with absolute photons	Data for Blue Emission system with photons per second	Data for Blue Reception system with Polymerases per second	Data for Green Emission system with photons per second
Data for Green Receptor system with absolute polymerases	Aberrant behavior with red receptor...

We chose to simulate the flux of output given a determined input. So we have for a wide range of inputs, the resultant outputs in a time manner.

Kappa

Also, having the Kappa binaries, we decided to model the system using Kappa as a stochastic modeling platform. Some preliminary results would be here if the Server didn't have an unexplainable aversion for .7z, .rar, or indigestion for .zip As soon as the Server decides to tolerate our files, we will upload them. In the mean time, here's a sample graph.

This graphs plots the PopS output of our Blue Receptor (lovTAP). The system begins in dark state, and at a given time (you can guess which one), there's a photon influx. This graph is however in arbitrary units. We wanted to make a more useful characterization, but these simulations required some extreme computing time. Should we finish them, we will upload them.

Neural Network

In Training... Having over a million data to map, our Levenberg-Marquandt algorithm is taking longer than expected.

Conclusions

A model that says nothing is not very useful. However, our model has revealed some very interesting phenomena.

Photomultiplier

All our simulations, data, and intuition show that our system will behave as a photomultiplier. We are very excited at this, since this is the very first synthetic-organic photomultiplier device.

Construction Issue

Had we been able to get Cph8 working, we would have found that the OmpR-P concentration was saturating the available plasmid slots, even with the kinase knocked off it was always superior to 120 molecules per cell. This behavior was revealed by our model, so for the construction we would recommend a high-copy number plasmid.