For Christmas my brother gave me a toy robotic arm kit, a Raspberry Pi 3, and an Xbox controller. The gift was really the project: he studied electrical engineering in college, and the plan was that he would teach me how to design the circuit that connects those three things together. We spent the rest of the holiday on the couch building it.
Every family has a game. Growing up, we played a lot of Rummy 500, and over Christmas 2016 we played enough of it to develop standings, grievances, and a general reluctance to let the tournament end when everyone went home.
Our trip to Martinique. L’île est magnifique.
I came to kinetic Monte Carlo while studying how nucleosomes are arranged in budding yeast. Nucleosomes are proteins around which DNA is wrapped in eukaryotic cells (think the “spindle” in a “spool of (DNA) thread”).
I spent this semester in a Mathematical Modeling course, and I realized some of the techniques were relevant to work going on in the Lieb lab. I work on nucleosomes, where the standard question is where proteins sit on DNA. The complementary question—how long they stay there, and how fast they get there—is measured by a technique called FRAP, and turning a FRAP movie into a number requires solving a PDE. So I implemented three FRAP models of increasing complexity and fit them to a real recovery curve. The third and most detailed of them turned out not to be identifiable from the data, which is the part of the project I found most worth writing down.
