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Manhattan Metric
Software and Science in Equal Measure

Ph.D. Preliminary Exam

This is the paper I prepared as part of my Ph.D. preliminary examination. The topic is "The Importance of Side-Chain Entropy in Protein Folding"... I know, riveting stuff, right? If you're the sort of person that likes this kind of stuff, you can also get the LaTeX source for the paper here. I've released it all under a CC BY-NC license.

Ph.D. Thesis Dissertation

This is the full text of my Ph.D. Thesis Dissertation entitled "A Model for the Evolution of Nucleotide Polymerase Directionality". If you don't feel like slogging through a full thesis, you can also check out the slightly shorter version that I published as a paper in PLoS One. The LaTeX source is also available here and is also licensed under a CC BY-NC license.

Evolver

This is the "toy model" (that's a technical term) that I constructed and studied as the bulk of my Ph.D. Thesis work. It was originally written in Ruby (and the "master" branch represents the final version used for all of the work presented in my dissertation), but I've also begun experimenting with re-implementing it in other languages.