User:Steven J. Koch/MTC/April 19 2011

Tuesday April 19, 2011. Microtubule gliding assay / kinesin modeling


 * Apology for being sick / missing so much. Reiterate the goals of the class
 * Learn some molecular biophysics
 * More importantly: learn resources for doing molecular biophysics research (PDB, OpenWetWare, S30, Mendeley, Figshare, etc.)


 * Review of field trip -- watch movies!


 * Assignment due Tuesday April 26


 * What is going on in gliding assay?
 * Kinesin modeling (mostly Larry)
 * Guydosh and Block (2009) (On Mendeley) kinetic model & description of bad-ass experiment
 * Neck linker docking
 * What is best way to model tension in the neck linker (chain of amino acids)
 * GROUP WORK: In the two-headed bound state, does neck-linker docking INCREASE or DECREASE or KEEP SAME the tension
 * (A) Back head docks; (B) Front head docks
 * Discuss with partner and make answers for (A) and (B)
 * How do we analyze a kinetic model, even a simplified one?
 * Method of Gillespie
 * GROUP WORK For stochastic simulation, how would you choose paths in network as hinted at by Figure 3 (Herskowitz et al.)?
 * Discuss method
 * MCA
 * Describe. THINKING:  When / why is this appropriate for the model we've created?  When would it break down?
 * Cite sources, show method
 * CTMC / DiffEQ / Cellular network modeling example