Correlation-based squence comparison:

Devise a PAM-based extension to the basic-correlogram method and
extend the Java implementation accordingly. Experiment with a few 
protein sequences comparing them with the dynamic-programming global 
alignment method.

Anjali Ram

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Protein structure prediction:

Device a function to convert hydrophobicity-based time series
corresponding to a peptide chain to a helix/coil-based step
function for the secondary structure. Experiment with secondary
structure prediction based on the function of a homologus
protein in pdb to the target protein.

Robert Asfer

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E-coli DNA replication simulation:

Complete the simulation program by implementing the appropriate
differential equations and integrating the code into the exisiting
simulation code and GUI. You may need to collect and read the
basic paper on the area.

Park