8-25-25: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life.
PDF,
Video.
8-27-25: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD).
PDF,
Video (Because of a technical glitch that prevented recording, this is a video from last year. We covered up through about the 39:30 minute mark.)
8-29-25: Lecture 3: Master equation, deriving equations for the moments of the distribution, calculating the MSD.
PDF,
Video.
9-3-25: Lecture 4: Measuring MSD, diffusion at different biological scales, the implausibility of giraffes, the continuum approximation.
PDF,
Video.
Slides: 1D random walk example
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
9-5-25: 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.
9-8-25: Lecture 6: Deriving the mean first passage time equation: escape times and probabilties, Frogger, discrete recurrence equation.
PDF,
Video.
9-10-25: Lecture 7: Continuum version of mean first passage time equation, deriving the Smoluchowski rate limit.
PDF,
Video.
9-12-25: 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