User:TheLarry/Notebook/Larrys Notebook/2009/10/08

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Fixing Rate Constants

I now have the kinesin taking the right amount of steps before falling off. ~960 nm which comes to 120 steps. so sure i can lower it a bit but i'm happy to be in the ball park right now. The problem right now is that it takes too long to fall off. It goes for about 7 seconds before coming off the microtubule. Since i know the basic cycle of this simulation has a k effective of 110 or so then this prolonged cycle time must be coming from excursions into weird states. Possibly too many excursions or too long of a time. not sure yet but i can take a look at that tomorrow.

Steve Koch 00:52, 9 October 2009 (EDT): That's interesting. Is there a way of plotting the total time in each state? I can imagine a way of processing the data afterward that could make that kind of graph, even without listing the sates ahead of time. I can also imagine a 3-D plot, where x&y are the possible states of each head, and the 3rd dimension is time spent in that combined state.