Before you start, maybe those words could make you understand more quickly our project.

What do we model?

This modeling is about the simulation of FNR aero/anaerobic regulation system which we have successfully achieved in our experiments.

The FNR aero/anaerobic regulation system, briefly, we try to rebuild mathematically a system which can simulate the alternate expression of FNR in aerobic or anaerobic situation, from the translation of fnr to the production of reporter protein.

What’s our purpose for this modeling?

The main aim of our modeling is recreate the aero/anaerobic reporter protein expression system. By alternating the oxygen concentration, activated or inactivated FNR combine (or not) with potential sensor gene sequence and make blue or red color. Our job is to see if we can observe the alternating red and blue curve when we change the oxygen condition.

How do we model?

As the research of FNR regulation system is a well-studied territory, we found some excellent scientific paper in library especially [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2867928/ Regulation of Aerobic to Anaerobic Transitions by the FNR cycle in Escherichia coli by Dean A.Tolla and Michael A.Savageau]. This is a differential equation model. And in our modeling we decided to redo what they have done but use a different method: a stochastic system created by new modeling tool: Hsim. Hsim is a stochastic automation simulator, it simulate chemical or enzymatic reactions between molecules and based on reactions it can simulate whole system.