User:Steven J. Koch/MTC/April 21, 2011
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< User:Steven J. Koch | MTC
- 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
- Results from Larry's paper
- Methods
- Random number generation reminder
- _very inneficient_ bad idea
- Gillespie -- easy / efficient
- Why do we care?
- 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
- Begin with examples / description of red blood cell (use wikipedia article as launching point)
- 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.
