PHYS 320 / 420


Introduction to Biological Physics, Fall 2018

                


Lecture Notes


1. Slides: Wiggling and jiggling, the crowded cell, nonequilibrium processes and the origins of life

       Movie: Shaken, not stirred, MP4 [credits: Harvard BioVisions and Harry Belafonte]
       Movie: Viral capsid assembly, MP4 [credits: Perlmutter et al., eLife 2, e00632 (2013)]

2. Molecules diffusing in a volume, transition rates for random motion
    Slides: Random walk

3. Probabilities, moments, mean squared displacement (MSD), ballistic motion

4. Master equation
    Extra notes: Mastering the master equation - Part I: Writing it down
    Slides: Shake, rattle, and roll...
    Movie: Diffusion experiment
    Experimental apparatus design: Bob Sobin, Rick Bihary; thanks to Pete Kernan for the Rokenbok balls

5. Simple master equation example, diffusion constant
    Slides: Diffusion time scales in biology

6. Relative diffusion of two molecules, capture and escape times

7. Mean first passage time equation, diffusive capture in 1D and 3D

8. Smoluchowski reaction rate, searching for targets in the crowded cell, optimizing protein volume fraction
    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. Binding/unbinding dynamics, chemical master equation for enzyme catalysis, approximate rate equations, Michaelis-Menten kinetics