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


 * Igor guest lecture week from today / part of class--please be on time!
 * HW Questions
 * ZamZar example (what software did Sheng use to create the truncated movie?)
 * Media example on FigShare (From Sheng): http://figshare.com/figures/index.php?title=Microtube_break_at_the_bright_spot


 * 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)
 * Red blood cell normal shape: http://en.wikipedia.org/wiki/File:Redbloodcells.jpg Properties in body
 * Red blood cell membrane: http://en.wikipedia.org/wiki/File:RBC_membrane_major_proteins.png
 * Lipid bilayer
 * Spectrin -- repeating protein http://en.wikipedia.org/wiki/Spectrin_repeat
 * Unfolding -- Reif et al. (1999 on Mendeley), Wong, Evans (2008 on Mendeley)
 * Re-folding
 * Heat-denaturation of spectrin (can't find video!)
 * EASY repeat of this experiment in D2O -- should do it!
 * 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

Resources

 * Wikipedia article on red blood cells -- tons of interesting physics in these images! We can use this for the framework for studying membrane physics, same as Evans did.