PHYS 320 / 420


Introduction to Biological Physics, Fall 2017

                


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
  • Ratchet potentials and the problem of one-directional motor protein motion
  • The second law and its biological consequences, nonequilibrium partition identity, entropy production
  • Photosensitive proteins as thermodynamic engines
  • Power output from a nonequilibrium stationary state, dissipated heat, the wonders of inefficiency
  • Fueling biological engines, chemical potential as a power source
  • Myosin motor cycle, muscle force-velocity relationship
  • Biological information engines, signaling receptors, re-interpreting the meaning of entropy
  • Modeling membrane receptors, the analogy between learning and mechanical work
  • Information thermodynamics, limits on sensing, designing a concentration-sensitive "learning engine"
  • Chemotaxis, flagellar motors
  • Swimming microorganisms, Stokes drag law, Einstein relation
  • Flagellar propulsion, Purcell scallop theorem, microswimmers
  • Origins of life: what are the constraints on abiogenesis from physical laws?