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Since I won't be able to go to work tomorrow and I won't be here this weekend. I figure I'll hold off on changing the constants till Monday. So right now i'll make figures for Koch's talk. The first thing he wanted was the three graphs (force v velocity, concentration v velocity, and histogram of run length) and show it has the right form. Below are the graphs i'll send koch. first i gotta get Andy to make them pretty in Igor. But that's them in all their glory
Koch wants to compare these to real data. You can get run length histogram and force versus velocity from Guydosh and Block's "Direct Observation of the binding state of the kinesin head to microtubule." The graphs are in the supplementary data. There is a Michaelis Menten graph in"Kinesin hydrolyses one ATP per 8-nm step" by Schnitzer and Block. There is also a distance per time graph in this paper as well.
Steve Koch 22:42, 10 September 2009 (EDT): Thanks! And have a great trip! Oh, and I've already said it, but need to say again that those graphs are so fucking cool.
TheLarry 22:55, 10 September 2009 (EDT): Thanks Doc, I wish I could see your presentation tomorrow. You always make good slides and present everything well. I wish I could see how you introduce the simulation and stuff.
Oy I gotta e-mail Susan Atlas to ask her to be on my candidacy group.
Note to myself (and probably Andy who'll read this): Monday I want to start tackling the rate constant problem. And since organization is probably the best idea. We should write down papers that discuss the rate constants and if it is low or high. I figured we'd do this on like a white board or lots of pieces of papers. For example from Guydosh/Block we know that an unbound foot will have a low rate constant until the other foot has ATP bound to it. Then it becomes high