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Main things our simulation can do that others can't
After reading through some of these other simulation papers, Kanada-Sasaki, Fisher et al, and Peskin-Oster, I came to the realization that simulation papers are brutally boring. Seriously every time i start i want to gauge my eyes out. Anyways i also came up with a list of things that makes our simulation unique from these three other models
I am sure there are 100% dynamic simulations but i haven't reached them yet. I just read 3 papers so far. This is going really slowly because of how boring they are, but it is important. And I feel that I am getting a better understanding of the simulations out there and where ours fits in. (Steve Koch 15:57, 30 October 2009 (EDT):You're right that this is really important and I'm really glad you're doing it. I like your conclusions above, it will definitely result in key text in our paper.)
TheLarry 16:23, 30 October 2009 (EDT): I started thinking about Block's unbound/bound time. I got something like 50% with more time spent in bound state. And i can't follow his argument for 93% of the time spent in an unbound state. Initially he says that they measure an average of 440 ms unbound and 320 ms bound but then says 93% of the time it is unbound. I don't know--it must make sense i just can't figure it out. If you use 440 and 320 my numbers aren't that far off. I can always do some adjutments to try to get to their numbers but i don't think i can get to 93% unbound without some serious work.
Interestingly, right now i am getting 450 ms for unbound and 540 ms for bound. so i almost have block's numbers from that paper except i am off by 200 ms for bound. but then his numbers give an expected walk time of .76 seconds while mine are closer to 1 second. So really i don't know what to make of it, but i think i'll be ok keeping it the same right now.
1. Derenyi I, Vicsek T. The kinesin walk: a dynamic model with elastically coupled heads [Internet]. Proc. Natl. Acad. Sci. USA. 1996 ;936775–6779.Available from: http://www.pnas.org/content/93/13/6775.full.pdf
This paper models kinesin with an inch worm motion so i think i can skip this guy