User:TheLarry/Notebook/Larrys Notebook/2009/11/03

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Thinking of Simulation

1. Gillespie D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions [Internet]. Journal of computational physics. 1976 ;22(4):403–434.Available from:

I am in the middle of reading this paper which is the introduction of his SSA. And i keep thinking that it probably won't be tough to make a simulation for a gliding motility assay. I am not sure how thorough i would make it. But i can make a distribution of kinesin on a cover slip, make their orientation distributed and then step each kinesin molecule on a microtubule through a monte carlo method that is described in the above paper. Possibly keep track of ATP, ADP, P. I don't think this is paper worthy because it must have been done before. I haven't found it since I have only been searching kinesin kinetics and not a bulk assay simulation like this. I have to run it by Koch, but i think i can do it. If it's worth my time is something different. Just writing it here so i don't forget it.

Steve Koch 19:13, 3 November 2009 (EST): I think that's a very cool idea, but quite bit of a project. It's perfect for agent based modeling. But there'd be a ton of things you'd need to account for, and I'd think definitely you'd need to work on a lot of computational efficiency things. I don't think it's been done before. You'd also have to consider whether it's worth it too. There have been theoretical investigations of gliding motility assay, but I don't think stochastic simulation. An intermediate step (and much easier) would be to model kinesin molecules on a single, long protofilament. I have seen single-molecule fluorescence experiments monitoring a bunch of kinesin on one microtubule, so there would be data to look at. This would be more like what I did with polymerases on a single gene. So, really great idea, I like it, but you're right to wonder if it's worth your time. It would definitely be a topic of conversation for when you go up to visit LANL peeps.