Submitted by Nicholas C. Darnton (inactive) on Friday, 1/23/2009, at 11:42 PM
  1. Equilibrium in living cells.
    1. Thermodynamics and energy reserves in cells.
    2. Entropy considerations in binding problems; ligand / receptor binding and DNA / RNA polymerase binding.
  2. Two-state systems and cooperativity.
    1. Ion channels.
    2. Hemoglobin.
  3. Random walks in biology.
    1. Polymer theory, gambling and the drunkard's walk; DNA as a random chain.
    2. Protein structures as minima of free energy; the HP model.
  4. Water.
    1. Diffusion: 1D, 2D and 3D diffusion and search strategies; physics limits on diffusion-driven uptake.
    2. pH, screening and hydro-phobicity; protein denaturation.
    3. Viscosity and propulsion; strategies for locomotion; taxis and the biased random walk.
  5. Rates and dynamics.
    1. Bimolecular reaction rates; coupled reactions.
    2. Molecular motors; rectified Brownian motion and translocation ratchets; powered motors: linear and rotary motors.
  6. Regulation and networks.
    1. Control theory in biology; positive and negative feedback; branching instabilities.
    2. Oscillations in space and time; symmetry breaking and rhythms
    3. Small versus large numbers; epigenetics, prions and individuality; noise and sensitivity
  7. Experimental techniques
    1. X-ray and NMR structure determination; visualization software
    2. Optical spectroscopy, fluorescence, and FRET
    3. FRAP, FCS and microscopic measurements of diffusion
    4. Biofluidics; patterned surfaces and volumes
    5. Atomic force microscopy
    6. Single molecule techniques
    7. Optical tweezers.