PHYS 320 / 420

8-24-26: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life. PDF, Video. 8-25-26: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD). PDF, Video 8-29-25: Lecture 3: Master equation, deriving equations for the moments of the distribution, calculating the MSD. PDF, Video.
8-31-26: Lecture 4: Measuring MSD, diffusion at different biological scales, the implausibility of giraffes, the continuum approximation. PDF, Video.
    Slides: Shake, rattle, and roll...
    Movie: Diffusion experiment
    Slides: Diffusion time scales in biology
    Experimental apparatus design: Bob Sobin, Rick Bihary; thanks to Pete Kernan for the Rokenbok balls 9-2-26: Lecture 5: Continuum approximation continued, solving the diffusion and Fokker-Planck equations, the problem of two molecules diffusing to meet in three dimensions. PDF, Video.
9-5-26: Lecture 6: Deriving the mean first passage time equation: escape times and probabilties, Frogger, discrete recurrence equation. PDF, Video.
9-9-26: Lecture 7: Continuum version of mean first passage time equation, deriving the Smoluchowski rate limit. PDF, Video. 9-11-26: Lecture 8: Tradeoff between reaction speeds and cellular crowding. PDF, Video.
    Slides: Crowding and the limits of cell size: parasitic bacteria, giant viruses, and seaweed
9-14-26: Lecture 9: Developing a theory of biochemical reaction kinetics. PDF, Video.
    Movie: Random search of a cancer drug for a protein binding site, AVI [credits: Shan et al., J. Am. Chem. Soc. 133, 9181 (2011)]