User:TheLarry/Notebook/Larrys Notebook/2009/09/23

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Figuring out 160 Rate Constants
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Core Cycle
Andy and I are starting to figure out the constants in the core step cycle...basically no weird states.

So i have my Markov .vi that calculates the expectation value of t from the probability function described by Q in the continuous markov process, and i kept getting 10 as an answer when i made all the rate constants high. The reason was because i kept the step size the same .1 and i was skipping over the important parts of the graph. So a reminder when i make the rate constants huge make sure to bring down the step size.

So it turns out that you can have the values of rate constants that are given in the literature and get near a k effective of 100 1/s. Which would make 100 steps per second. We tweaked the stepping rate to be higher than the literature, and set ATP binding to be 1000 which in the literature it is 1-3 1/μMs. So this means something like 1 milliMoles of ATP in solution. So that's good news. I am procrastinating making this matrix huge.

See the problem is that in this matrix each state is a combination of each foot so empty behind ATP is not the same as ATP behind empty. So each one of these combinations needs another state. So if there are N combos then the matrix is NxN which could be huge. Probably something like 256 or something stupid like that. But then again this whole Markov excursion is to figure out the rate constants so not adding them all in is fine and then we can check it in the real simulation.


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