PHYS 320 / 420


Introduction to Biological Physics, Fall 2020

                


Lecture Notes


8-24-20: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life. PDF, Video.

8-26-20: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD). PDF, Video.

8-28-20: Lecture 3: Ballistic versus diffusive motion, master equation. PDF, Video.
    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. PDF, Video.

9-2-20: Lecture 5: Deriving the mean squared displacement, diffusion at different biological scales, the implausibility of giraffes. PDF, Video.
    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. PDF, Video.
    Slides: Turbulent diffusion of respiratory droplets in air flows

9-7-20: Lecture 7: Diffusion to capture, mean first passage time. PDF, Video.

9-9-20: Lecture 8: Deriving the mean first passage time, part I: escape times and probabilties, Frogger. PDF, Video.

9-11-20: Lecture 9: Deriving the mean first passage time, part II: discrete and continuum equations. PDF, Video.

9-14-20: Lecture 10: Finding a speed limit for chemistry: the Smoluchowski reaction rate. PDF, Video.

9-16-20: Lecture 11: Tradeoff between reaction speeds and cellular crowding. PDF, Video.
    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. 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)]

9-21-20: Lecture 13: Kinetics of chemical binding; modeling enzymes. PDF, Video.

9-23-20: Lecture 14: "Exact" chemical dynamics via the master equation. PDF, Video.

9-25-20: Lecture 15: Approximating chemical dynamics by ignoring fluctuations. PDF, Video.

9-28-20: Lecture 16: Connecting transition rates to energy exchange with the environment. Detailed balance and the definition of temperature. PDF, Video.

9-30-20: Lecture 17: Exploring the meaning of the detailed balance relation and its connection to probability currents in biochemical systems. PDF, Video.

10-2-20: Lecture 18: Probability currents, equilibrium and non-equilibrium stationary states, the Boltzmann distribution. PDF, Video.

10-5-20: Lecture 19: The nature of Boltzmann equilibrium. Does a system always equilibrate? PDF, Video.

10-7-20: Lecture 20: The "dynamics" in thermodynamics: irreversibility and the second law; minimization of Helmholtz free energy. PDF, Video.