8-24-20: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life.
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8-26-20: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD).
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8-28-20: Lecture 3: Ballistic versus diffusive motion, master equation.
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Slides: Shake, rattle, and roll...
Movie: Diffusion experiment
Experimental apparatus design: Bob Sobin, Rick Bihary; thanks to Pete Kernan for the Rokenbok balls
8-31-20: Lecture 4: General form of master equation, transition matrix, equations for the moments of the distribution, simple Poisson life vs. death example.
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9-2-20: Lecture 5: Deriving the mean squared displacement, diffusion at different biological scales, the implausibility of giraffes.
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Slides: Diffusion time scales in biology
9-4-20: Lecture 6: Continuum approximation to the master equation: deriving the diffusion and Fokker-Planck equations. Digression on airborne infectious droplet dynamics.
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Slides: Turbulent diffusion of respiratory droplets in air flows
9-7-20: Lecture 7: Diffusion to capture, mean first passage time.
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9-9-20: Lecture 8: Deriving the mean first passage time, part I: escape times and probabilties, Frogger.
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9-11-20: Lecture 9: Deriving the mean first passage time, part II: discrete and continuum equations.
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9-14-20: Lecture 10: Finding a speed limit for chemistry: the Smoluchowski reaction rate.
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9-16-20: Lecture 11: 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
9-18-20: Lecture 12: The porous boundary between life and non-life. Developing a theory of biochemical reaction kinetics.
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Movie:
Random search of a cancer drug for a protein binding site,
AVI [credits:
Shan et al., J. Am. Chem. Soc. 133, 9181 (2011)]
9-21-20: Lecture 13: Kinetics of chemical binding; modeling enzymes.
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9-23-20: Lecture 14: "Exact" chemical dynamics via the master equation.
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9-25-20: Lecture 15: Approximating chemical dynamics by ignoring fluctuations.
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9-28-20: Lecture 16: Connecting transition rates to energy exchange with the environment. Detailed balance and the definition of temperature.
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9-30-20: Lecture 17: Exploring the meaning of the detailed balance relation and its connection to probability currents in biochemical systems.
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10-2-20: Lecture 18: Probability currents, equilibrium and non-equilibrium stationary states, the Boltzmann distribution.
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10-5-20: Lecture 19: The nature of Boltzmann equilibrium. Does a system always equilibrate?
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10-7-20: Lecture 20: The "dynamics" in thermodynamics: irreversibility and the second law; minimization of Helmholtz free energy.
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