User:TheLarry/Notebook/Larrys Notebook/2010/08/13

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Diffusion with wlc

I said in my last posting Igor showed me a way to solve the smoluchowski equation. I've been having some trouble with instability, but i now know a little bit more of it.

the instability arises because the ratio of delta x and delta y and the maximum force from the wlc have to be less than a certain value. I don't know what that value is per say, but i do know what knobs to turn to get rid of the instability.

With that said check this shit out

That't the pdf of a head reaching the point to bind to the microtubule. I haven't put this in the simulation yet, but the rate constant i get from this is ~300. Which is great news. If it was something like 15/s then it would not work in the simulation at all. But at least it is on par with something it should be. So i am happy.

Note that i still have to change some constants to make sure they are good values. I mean persistence length, diffusivity, and distance to binding spot, but i am happy it is on par with something i want.