Modeling

We have modeled several aspects of the project to answer some key questions about our project:

• Kinetic Model -- How long will it take to convert ammonia into nitrous oxide?

In order to determine the practicality of our solution, we are applying kinetic modeling to investigate how much time our engeneered E. coli cells will take to convert a certain amount of ammonia to nitrous oxide. For ammonia concentrations typically encountered in wastewater, our modelling shows that our transformed E. coli cells will be able to do this within less than 10 minutes.

• Reactor Model -- How large a reactor will we need?

We want to get a first estimate of how large a reactor filled with our transformed E. coli cells must be to treat ammonia polluted wastewater. Since Mutant 2 requires anaerobic conditions, we plan to build two reactors in series. With our model, we find that the second should be around 10 times the size of the first. This is under the assumption that all transformed proteins will be expressed at the same level, so expressing proteins at different levels is something we should look into if we want to avoid a large difference in reactor sizes.

• Codon Optimization -- Will we need to codon optimize the Nitrosomonas europaea and Pseudomonas aeruginosa genes we are expressing in E. coli?
• Model of Periplasmic Contents for Hello World Pilot Project -- What fluorescence cross section will the cell have when we express GFP in the periplasm and RFP in the cytoplasm?
• Protein Models -- What are the structures of the proteins we are expressing in E. coli?