PHYS 320 / 420


Introduction to Biological Physics, Fall 2020

                 


Syllabus

  • Setting the stage: "jiggling and wiggling" within the crowded cell
  • Molecules diffusing in a volume, transition rates for random motion
  • Probabilities and moments, mean squared displacement
  • The master equation: a unified framework for stochastic dynamics in complex biological systems
  • Diffusion, mean first passage times, Smoluchowski reaction rate
  • Searching for targets within the cell, optimizing protein volume fraction
  • Crowding and the limits of cell size: parasitic bacteria, giant viruses, and seaweed
  • Reaction dynamics, chemical master equation, approximate rate equations
  • Energy scales of biological interactions, self-assembly
  • Non-equilibrium vs. equilibrium stationary states (life vs. death)
  • Biological thermodynamics: detailed balance, temperature and the Boltzmann distribution
  • Degeneracy, meso- vs. microstates, state entropy, chemical potential
  • Myosin motor protein, rates and currents, irreversibility and the second law of thermodynamics
  • Biological power inputs and outputs, efficiency
  • Thermodynamics and the origin of life
  • Light-sensitive proteins
  • Ion transport through membranes, Poisson-Boltzmann equation, conductivity of an ion channel, sodium-potassium pumps
  • Neural signaling
  • Population genetics, evolution through the lens of statistical physics