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.
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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.
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Video.
Slides: Crowding and the limits of cell size: parasitic bacteria, giant viruses, and seaweed
9-15-25: Lecture 9: Developing a theory of biochemical reaction kinetics, the chemical master equation.
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)]
9-17-25: Lecture 10: Chemical master equation in gory detail, approximating chemical dynamics by ignoring fluctuations.
PDF,
Video.
9-19-25: Lecture 11: Connecting transition rates to energy exchange with the environment.
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Video.
9-22-25: Lecture 12: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium.
PDF,
Video.
9-24-25: Lecture 13: Coupling system transitions to external work, light-sensitive proteins.
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Video.
Slides: Light-sensitive proteins
Movie:
Photoactive yellow protein in action,
AVI [credits:
Schotte et al., Proc. Natl. Acad. Sci. 109, 19256 (2012)]
9-26-25: Lecture 14: Modeling light-sensitive proteins, general thermodynamic framework: state properties.
PDF,
Video.
9-29-25: Lecture 15: General thermodynamic framework: edge properties, production rates, irreversibility.
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Video.
10-1-25: Lecture 16: First and second laws of thermodynamics: energy conservation and entropy production; parallels between classical stochastic and quantum systems.
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Video.
10-3-25: Lecture 17: The "Heisenberg picture" for the classical master equation; proving the existence of a stationary state; the necessity of dissipated power in nonequilibrium stationary states.
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Video.
10-6-25: Lecture 18: Dissipation in the light-sensitive protein example. Origins of life hypothesis #1: the role of UV photons.
PDF,
Video.