User:Steven J. Koch/MTC/March 29 2011: Difference between revisions

Revision as of 05:22, 29 March 2011

Review last HW
Summary of Kramers' reaction rate theory (we'll discuss in detail following lectures, diffusion, etc.)
1. Group work: Given prefactor of 10^-9 per second, Calculate bond lifetimes for energy barriers of: 1, 10, 20, and 40 kT
Bond lifetime under force
1. Why do we care?
  1. Evan Evans: Everything about cells is kinetics, not equilibrium diffEQ
  2. Famous example: luekocyte rolling]
  3. RNA Polymerase II / nucleosome barriers
  4. Kinesin neck linker (see Larry's paper)
2. Set-up the problem
3. Group work: intuition
4. Solve expected PDF for bond "strength" assuming constant force ramp rate, other assumptions
5. Examples
Preview next HW

Articles added to Mendeley
- Easiest to follow: Evan Evans' Annual Review (2001): Evans, E. (2001). Probing the relation between force--lifetime--and chemistry in single molecular bonds. Annual review of biophysics and biomolecular structure, 30, 105-28. doi: 10.1146/annurev.biophys.30.1.105.
- Thorough: Hänggi, P., Talkner, P., & Borkovec, M. (1990). Reaction-rate theory: fifty years after Kramers. Reviews of Modern Physics, 62(2), 251-341. doi: 10.1103/RevModPhys.62.251.
- Bell, G. (1978). Models for the specific adhesion of cells to cells. Science, 200(4342), 618-627. doi: 10.1126/science.347575.
Wikipedia article on George Bell
Wikipedia article on Kramers (needs improvement!)

@@ Line 5: / Line 5: @@
 # Bond lifetime under force
 ## Why do we care?
+### Evan Evans:  Everything about cells is kinetics, not equilibrium diffEQ
 ### Famous example: [http://www.youtube.com/watch?v=WEGGMaRX8f0 luekocyte rolling]]
 ### RNA Polymerase II / [http://www.pnas.org/content/107/25/11325/F5.large.jpg nucleosome barriers]
+### Kinesin neck linker (see Larry's paper)
 ## Set-up the problem
 ## Group work: intuition