PHYS 320 / 420


Introduction to Biological Physics, Fall 2024

                


Lecture Notes


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. PDF, 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. PDF, Video.

9-11-24: Lecture 7: Continuum version of mean first passage time equation, deriving the Smoluchowski rate limit. PDF, Video.

9-13-24: 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
    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. PDF, Video.

9-18-24: Lecture 10: Chemical master equation in gory detail, approximating chemical dynamics by ignoring fluctuations. PDF, Video.

9-20-24: Lecture 11: Connecting transition rates to energy exchange with the environment. PDF, Video.

9-23-24: Lecture 12: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium, coupling system transitions to external work. PDF, Video.

9-25-24: Lecture 13: Example of coupling to external work source: 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)]
       Movie: Optogenetics, MP4 [credits: Nature Methods 8, 1 (2011)]

9-27-24: Lecture 14: Edge and state properties, defining thermodynamic production rates, irreversibility. PDF, Video.

9-30-24: Lecture 15: First and second laws of thermodynamics: energy conservation and entropy production; parallels between classical stochastic and quantum systems. PDF, 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. PDF, 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. PDF, Video.
       Slides: Thermodynamics and the origins of life (part 1).