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

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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.)
  • 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