in Science on Frap, Diffusion, Simulation, Matlab, Biophysics
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.
Osmos is a game about being a blob in a void full of other blobs. Absorb something smaller and you grow; touch something larger and it eats you. You move by ejecting part of yourself in the opposite direction, which means every course correction makes you smaller. It is a beautiful game built on one rule of physics.
My friend Ryan Miller sent me an Excel spreadsheet with a game he’d invented called Territories. It had the satisfying quality of a good pencil-and-paper game: the rules fit in a sentence, but the strategy is unclear. It feels like a simplified Go.