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)]
9-16-26: Lecture 10: Chemical master equation in gory detail, building a dynamical description of a reaction system.
PDF,
Video.
9-18-26: Lecture 11: Approximating chemical kinetics by ignoring fluctuations, connecting transition rates to energy exchange with the environment.
PDF,
Video.
9-21-26: Lecture 12: Energy exchange as a diffusion process, deriving local detailed balance and the concept of temperature.
PDF,
Video.
9-23-26: Lecture 13: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium.
PDF,
Video.
9-28-26: Lecture 15: Modeling light-sensitive proteins.
PDF,
Video.
9-30-26: Lecture 16: General thermodynamic framework: edge properties, production rates, irreversibility.
PDF,
Video.
10-2-26: Lecture 17: First and second laws of thermodynamics: energy conservation and entropy production.
PDF,
Video (part 1),
Video (part 2, audio only due to technical glitch).
10-5-26: Lecture 18: Parallels between classical stochastic and quantum systems; the "Heisenberg picture" for the classical master equation.
PDF,
Video.
10-7-26: Lecture 19: Proving the existence of a stationary state; the necessity of dissipated power in nonequilibrium stationary states.
PDF,
Video.
10-9-26: Lecture 20: Dissipation in the light-sensitive protein example. Origins of life hypothesis #1: the role of UV photons.
PDF,
Video.
Slides: Thermodynamics and the origins of life (part 1).
10-12-26: Lecture 21: Fossil evidence of early life: stromatolites. Origins of life hypothesis #2: deep-sea vents.
Video.
Slides: Thermodynamics and the origins of life (part 2).
Movie:
Lake Untersee, Antarctica,
Youtube link