Please excuse any typographical issues as this is going up right after lunch. I’ll proofread and remove this message later.
The morning session was mostly computational/simulation studies. Ibáňez talked about threshold networks and how they can be used to simulate complex reactions and biological regulation.
Hajiaghayi and Doty talked about stochastic and differential equation based simulators. The limitations of using a formal language to describe reactions and reaction networks are that it makes assumptions about concentrations and that it is limited to rather small numbers of molecules. The advantage is that the reaction (number of molecules of each chemical species) can be highly precisely defined in time. I have always taken an ODE approach; the stochastic nature of this approach makes me nervous. Both approaches are reasonable and highlight a fundamental, interesting distinction that all nano-scientists need to make: deal with such large numbers of molecules that you can treat them as a fungible quantity, or deal with small numbers of molecules on a discrete basis.
Dr. Peter B Allen - Lab Blog 
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