8-26-24: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life.
PDF,
Video.
8-28-24: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD).
PDF,
Video.
8-30-24: Lecture 3: Master equation, deriving equations for the moments of the distribution, calculating the MSD.
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Video.
9-4-24: Lecture 4: Experimentally measuring MSD, diffusion at different biological scales, the implausibility of giraffes, the continuum approximation and the diffusion equation.
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
9-6-24: 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.
9-9-24: Lecture 6: Deriving the mean first passage time equation: escape times and probabilties, Frogger, discrete recurrence equation.
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Video.
9-11-24: Lecture 7: Continuum version of mean first passage time equation, deriving the Smoluchowski rate limit.
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Video.
9-13-24: 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
Movie:
Random search of a cancer drug for a protein binding site,
AVI [credits:
Shan et al., J. Am. Chem. Soc. 133, 9181 (2011)]
9-16-24: Lecture 9: Developing a theory of biochemical reaction kinetics, the chemical master equation.
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Video.
9-18-24: Lecture 10: Chemical master equation in gory detail, approximating chemical dynamics by ignoring fluctuations.
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Video.
9-20-24: Lecture 11: Connecting transition rates to energy exchange with the environment.
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Video.
9-23-24: Lecture 12: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium, coupling system transitions to external work.
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Video.
9-25-24: Lecture 13: Example of coupling to external work source: 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)]
Movie:
Optogenetics,
MP4 [credits:
Nature Methods 8, 1 (2011)]
9-27-24: Lecture 14: Edge and state properties, defining thermodynamic production rates, irreversibility.
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Video.
9-30-24: Lecture 15: First and second laws of thermodynamics: energy conservation and entropy production; parallels between classical stochastic and quantum systems.
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Video.
10-2-24: Lecture 16: 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.
10-4-24: Lecture 17: Dissipation in the light-sensitive protein example. Origins of life hypothesis #1: the role of UV photons. Recent advances in prebiotic chemistry.
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Video.
Slides: Thermodynamics and the origins of life (part 1).
10-7-24: Lecture 18: Fossil evidence of early life: stromatolites. Origins of life hypothesis #2: deep-sea vents.
PDF,
Video.
Slides: Thermodynamics and the origins of life (part 2).
Movie:
Lake Untersee, Antarctica,
Youtube link
Movie:
Lost City hydrothermal veents,
MP4
10-9-24: Lecture 19: Generalizing the local detailed balance relation: work against pressure, enthalpy. Coarse-graining biological models: macro- vs micro-states.
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Video.
10-11-24: Lecture 20: Chemical potential.
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Video.
10-14-24: Lecture 21: Chemical potential in action: driving chemical cycles via ATP hydrolysis. Muscle proteins.
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Video.
Slides: Muscle myosin, ATP hydrolysis at the microscopic level, ATP synthase.
Movie:
Muscle contraction process,
Youtube link
10-16-24: Lecture 22: Flexible membranes, permeable and non-permeable molecules.
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Video.
Slides: Hydrophobic forces, phospholipid membranes.
Movie:
Water hydrogen bond network dynamics,
Youtube link
Movie:
Water permeation through phospholipid membrane,
Youtube link
10-18-24: Lecture 23: Osmotic pressure and its implications for living cells. Charged molecules.
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Video.
10-25-24: Lecture 24: Cell membranes as capacitors, ion channels, Nernst potential.
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Video.
10-28-24: Lecture 25: Cells as circuits, modeling the axon.
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Video.
10-30-24: Lecture 26: Setting up the cable equation for neural signals along axons; the need for voltage-gated channels.
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Video.