My current work for Prof. Yang involves unfolding proteins using an Atomic Force Microscope (AFM) at different temperatures to estimate the roughness of their free energy landscape. For a brief overview of force spectroscopy, see my two second summary. For more detail, you can look at some of my papers.

I've written some experimental control software, a Monte Carlo simulation program (sawsim) for analyzing the unfolding sawtooth curves, as well as software for calibrating AFM cantilevers via the thermal tune method (calibcant), scaling the unfolding data, selecting good curves, and fitting those curves with wormlike chains (Hooke).

Along the way I've had to learn way too much about the internal workings of our MultiMode AFM.

I've also posted my notes for our Debian cluster.