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

10. System coupled to a thermal bath: microscopic reversibility and the definition of temperature

11. Probability currents, equilibrium versus nonequilibrium stationary states (death vs. life), the Boltzmann distribution,
      Tempus vincit omnia: all roads lead to equilibrium


12. Degeneracy, meso- vs. microstates, state entropy, chemical potential

13. Myosin motor protein as an example, rates and currents, irreversibility and the second law of thermodynamics
      Slides: Muscle contraction
       Movie: Muscle contraction process, Youtube link

14. Nonequilibrium stationary states, biological power inputs and outputs, efficiency

15. Slides: Thermodynamics and the origin of life, recent developments in prebiotic chemistry, the role of 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)]

16. Cycle of photosensitive protein, transport through membranes
      Slides: Membranes
       Movie: Dynamic hydrogen bond network in water, MP4
       Movie: Water molecule diffusing through lipid membrane, MP4 [credits: YouTube]

17. Ion transport through membranes, Poisson-Boltzmann equation, conductivity of an ion channel, sodium-potassium pumps
      Slides: Membrane pumps, famous nerves, voltage-gated sodium channels

18. Electrical model of an axon, cable equation, voltage-gated sodium channels, nerve signals as solitons, ionic equilibration after death

19. Copying DNA: modeling the speed and fidelity of DNA polymerases, energetic vs. kinetic discrimination in proofreading

20. Population genetics I: neutral Wright-Fisher model, coalescence, heterozygosity, effective population