8-28-23: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life.
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Video.
8-30-23: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD).
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Video.
9-1-23: Lecture 3: Master equation, deriving equations for the moments of the distribution, calculating the MSD.
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Slides: 1D random walk example
9-6-23: Lecture 4: Experimentally measuring MSD, diffusion at different biological scales, the implausibility of giraffes, the continuum approximation and the diffusion equation.
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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
9-8-23: Lecture 5: Continuum approximation continued, solving the diffusion and Fokker-Planck equations, the problem of two molecules diffusing to meet in three dimensions.
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9-11-23: Lecture 6: Deriving the mean first passage time, part I: escape times and probabilties, Frogger, discrete recurrence equation.
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9-13-23: Lecture 7: Deriving the mean first passage time, part II: continuum equations, Smoluchowski rate limit.
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9-15-23: Lecture 8: Tradeoff between reaction speeds and cellular crowding.
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Slides: Crowding and the limits of cell size: parasitic bacteria, giant viruses, and seaweed
9-18-23: Lecture 9: Developing a theory of biochemical reaction kinetics.
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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)]
9-20-23: Lecture 10: Modeling enzymes via the chemical master equation.
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Video.
9-22-23: Lecture 11: Approximating chemical dynamics by ignoring fluctuations. Connecting transition rates to energy exchange with the environment.
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9-25-23: Lecture 12: Defining temperature via local detailed balance.
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9-27-23: Lecture 13: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium.
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9-29-23: Lecture 14: Boltzmann equilbrium; coupling system transitions to external work.
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10-2-23: Lecture 15: Example of coupling to external work source: light-sensitive proteins.
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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)]
10-4-23: Lecture 16: Defining thermodynamic production rates; irreversibility.
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10-6-23: Lecture 17: First and second laws of thermodynamics: energy conservation and entropy production.
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10-9-23: Lecture 18: Parallels between classical stochastic and quantum systems; the "Heisenberg picture" for the classical master equation.
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10-11-23: Lecture 19: Proving the existence of a stationary state; the necessity of dissipated power in nonequilibrium stationary states.
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10-13-23: Lecture 20: Origins of life hypothesis #1: the role of UV photons. Recent advances in prebiotic chemistry. The fossil record: stromatolites.
Video.
Slides: Thermodynamics and the origins of life (part 1).
10-16-23: Lecture 21: Stromatolites continued. Origins of life hypothesis #2: deep-sea vents. Generalizing the local detailed balance relation: work against pressure, enthalpy, macro- vs. microstates.
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Video.
Slides: Thermodynamics and the origins of life (part 2).
Movie:
Lake Untersee, Antarctica,
Youtube link
Movie:
Lost City hydrothermal veents,
MP4
10-18-23: Lecture 22: Coarse-graining biological models, counting microstates, chemical potential.
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10-20-23: Lecture 23: Chemical potential in action: biochemical cycles driven by ATP hydrolysis.
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10-25-23: Lecture 24: Muscles and membranes.
Video.
Slides: Muscle myosin, ATP hydrolysis at the microscopic level, ATP synthase.
Movie:
Muscle contraction process,
Youtube link
Slides: Hydrophobic forces, phospholipid membranes.
Movie:
Water hydrogen bond network dynamics,
Youtube link
Movie:
Water permeation through phospholipid membrane,
Youtube link
10-27-23: Lecture 25: Flexible membranes, permeable and non-permeable molecules.
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10-30-23: Lecture 26: Osmotic pressure and its implications for living cells. Charged molecules.
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11-1-23: Lecture 27: Cell membranes as capacitors.
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11-3-23: Lecture 28: Na and K channels, resting potential, Na/K pumps, total current through membrane.
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11-6-23: Lecture 29: Cells as circuits, modeling the axon.
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11-8-23: Lecture 30: Setting up the cable equation for neural signals along axons; the need for voltage-gated channels.
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11-10-23: Lecture 31: Nerves signals as solitons; the speed of signal propagation.
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11-13-23: Lecture 32: ``Wave of death'' in neural signaling; introduction to population genetics: the Wright-Fisher model.
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Slides: Membrane pumps, famous nerves, voltage-gated sodium channels, ``wave of death''
11-15-23: Lecture 33: Coalescent theory, neutral mutations, infinite allele model, heterozygosity.
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11-17-23: Lecture 34: Effective population size, probability of coalescence going back in time.
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11-20-23: Lecture 35: Time-varying populations, mean time to coalescence, dynamics of mutations, substitution rate.
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11-27-23: Lecture 36: Dynamics of mutations; the Moran model; deriving Kimura's substitution rate formula.
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11-29-23: Lecture 37: Mapping evolution to statistical physics: Sella-Hirsh model; distribution of fitness effects, ratio of non-synonymous to synonymous substitution rates.
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