User:Steven J. Koch/MTC/April 21, 2011

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  • More depth on kinetic simulation
    • Why do we care?
      • Results from Larry's paper
        • Agreement with experiments
        • Ability to "experiment" (show core cycle)
      • Protein-DNA example (PPT slide)
      • Kornberg example
        • Description of the system (nucleosome remodeling)
        • Great example of utility and contrast of both analytical MCA and stochastic simulation
        • (just show) Dill et al. maximum caliber
    • Methods
      • Random number generation reminder
      • _very inneficient_ bad idea
      • Gillespie -- easy / efficient

  • Introduction to membrane physics
    • Begin with examples / description of red blood cell (use wikipedia article as launching point)
    • Intuition building exercise -- what happens when we put lipids in water?
      • Find all the energies we need to worry about
      • End with Evans slides, showing the physics we'll need to consider -- next week, surface force apparatus, Langmuir trough, surface tension / pressure
  • PARP-1 or other interesting story