User:Steven J. Koch/MTC/April 19 2011
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< User:Steven J. Koch | MTC
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!
- 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
- Method of Gillespie
