PHYS 320 / 420

Introduction to Biological Physics, Fall 2023


Lecture Notes

8-28-23: Lecture 1 [Course overview]: wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life. PDF, Video.

8-30-23: Lecture 2: Molecules diffusing in a volume, transition rates for random motion, probabilities, moments, mean squared displacement (MSD). PDF, Video.

9-1-23: Lecture 3: Master equation, deriving equations for the moments of the distribution, calculating the MSD. PDF, Video.
    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. 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

9-8-23: Lecture 5: Continuum approximation continued, solving the diffusion and Fokker-Planck equations, the problem of two molecules diffusing to meet in three dimensions. PDF, Video.

9-11-23: Lecture 6: Deriving the mean first passage time, part I: escape times and probabilties, Frogger, discrete recurrence equation. PDF, Video.

9-13-23: Lecture 7: Deriving the mean first passage time, part II: continuum equations, Smoluchowski rate limit. PDF, Video.

9-15-23: 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

9-18-23: Lecture 9: 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)]

9-20-23: Lecture 10: Modeling enzymes via the chemical master equation. PDF, Video.

9-22-23: Lecture 11: Approximating chemical dynamics by ignoring fluctuations. Connecting transition rates to energy exchange with the environment. PDF, Video.

9-25-23: Lecture 12: Defining temperature via local detailed balance. PDF, Video.

9-27-23: Lecture 13: Probability currents, equilibrium and non-equilibrium stationary states, Boltzmann equilibrium. PDF, Video.

9-29-23: Lecture 14: Boltzmann equilbrium; coupling system transitions to external work. PDF, Video.

10-2-23: Lecture 15: 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)]

10-4-23: Lecture 16: Defining thermodynamic production rates; irreversibility. PDF, Video.

10-6-23: Lecture 17: First and second laws of thermodynamics: energy conservation and entropy production. PDF, Video.

10-9-23: Lecture 18: Parallels between classical stochastic and quantum systems; the "Heisenberg picture" for the classical master equation. PDF, Video.

10-11-23: Lecture 19: Proving the existence of a stationary state; the necessity of dissipated power in nonequilibrium stationary states. PDF, Video.

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. PDF, 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. PDF, Video.

10-20-23: Lecture 23: Chemical potential in action: biochemical cycles driven by ATP hydrolysis. PDF, Video.

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. PDF, Video.

10-30-23: Lecture 26: Osmotic pressure and its implications for living cells. Charged molecules. PDF, Video.

11-1-23: Lecture 27: Cell membranes as capacitors. PDF, Video.

11-3-23: Lecture 28: Na and K channels, resting potential, Na/K pumps, total current through membrane. PDF, Video.

11-6-23: Lecture 29: Cells as circuits, modeling the axon. PDF, Video.

11-8-23: Lecture 30: Setting up the cable equation for neural signals along axons; the need for voltage-gated channels. PDF, Video.

11-10-23: Lecture 31: Nerves signals as solitons; the speed of signal propagation. PDF, Video.

11-13-23: Lecture 32: ``Wave of death'' in neural signaling; introduction to population genetics: the Wright-Fisher model. PDF, Video.
      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. PDF, Video.

11-17-23: Lecture 34: Effective population size, probability of coalescence going back in time. PDF, Video.

11-20-23: Lecture 35: Time-varying populations, mean time to coalescence, dynamics of mutations, substitution rate. PDF, Video.

11-27-23: Lecture 36: Dynamics of mutations; the Moran model; deriving Kimura's substitution rate formula. PDF, Video.

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. PDF, Video.