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
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.
PDF,
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.
PDF,
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.
PDF,
Video.
10-1-25: Lecture 16: First and second laws of thermodynamics: energy conservation and entropy production; parallels between classical stochastic and quantum systems.
PDF,
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.
PDF,
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.
Slides: Thermodynamics and the origins of life (part 1).
10-8-25: Lecture 19: Primordial biochemistry. Fossil evidence of early life: stromatolites.
Video.
Movie:
Lake Untersee, Antarctica,
Youtube link
10-10-25: Lecture 20: Origins of life hypothesis #2: deep-sea vents. Generalizing the local detailed balance relation: work against pressure, enthalpy. Coarse-graining biological models: macro- vs micro-states.
PDF,
Video.
Slides: Thermodynamics and the origins of life (part 2).
Movie:
Lost City hydrothermal veents,
MP4
10-13-25: Lecture 21: Chemical potential.
PDF,
Video.
10-15-25: Lecture 22: Chemical potential in action: driving chemical cycles via ATP hydrolysis. Muscle proteins.
PDF,
Video.
Slides: Muscle myosin, ATP hydrolysis at the microscopic level, ATP synthase.
Movie:
Muscle contraction process,
Youtube link
10-17-25: Lecture 23: Flexible membranes, permeable and non-permeable molecules.
PDF,
Video.
Slides: Hydrophobic forces, phospholipid membranes.
Movie:
Water hydrogen bond network dynamics,
Youtube link
Movie:
Water permeation through phospholipid membrane,
Youtube link
10-22-25: Lecture 24: Osmotic pressure and its implications for living cells. Charged molecules.
PDF,
Video.
10-24-25: Lecture 25: Cell membranes as capacitors, ion channels, Nernst potential.
PDF,
Video.
10-27-25: Lecture 26: Cells as circuits, modeling the axon.
PDF,
Video.
10-29-25: Lecture 27: Setting up the cable equation for neural signals along axons; the need for voltage-gated channels.
PDF,
Video.
10-31-25: Lecture 28: Nerves signals as solitons; the speed of signal propagation; ``wave of death'' in neural signaling.
PDF,
Video.
Slides: Membrane pumps, voltage-gated sodium channels, ``wave of death''
11-3-25: Lecture 29: Introduction to population genetics: the Wright-Fisher model.
PDF,
Video.
11-5-25: Lecture 30: Neutral mutations, infinite allele model, heterozygosity, effective population size.
PDF,
Video.