Deliverables: 


1. Some idea of what the 
folded protein T might and might not look like based on which 
amino acids may be near each other.  Draw some sketches. 

2. Realistic 1D, and, preferably, 2D 
folding funnels constructured and expolored using Mathematica. Good pictures. 

3. A good idea of which methods might and might not work on the real 
protein folding problem. Explore --relevant-- 
methods available to you in Mathematica, 
starting from what's available for FindMinimum[] (Newton, Conjugate gradient,
etc.) working your way up to more complex stuff implemented  in NMinimize[].
You need to read up on each of the methods (expect questions in-class), 
know the general idea and basic pros and cons. 
You must present pictures showing the minimization results on your funnels. 
Explore a minimum of 5 methods.