User:TheLarry/Notebook/Larrys Notebook/2010/08/24

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Monte Carlo Simulation
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Michaelis Menten
I got the michaelis menten dependency i wanted from yesterday. I decreased the neck linker from 40 (total) amino acids to 30. Meaning the complete length is 10.5 nm, and in the normal state (D/U) it is 7 nm needing to transverse 4.5 nm or -11.5. This lowered the rate of transition from an U/U state to 5 1/s which is what allowed the michaelis menten constant to be low. This increased the off rate for ADP bound head dramatically, but it hasn't caused a problem yet. So i am happy with this.

The only thing left to do is deal with inorganic phosphate release value

Paper
with everything looking good again, i think i can go back to the paper. i think this paper is going to get a good overhaul now with the changes we made so it'll look like this

i am having a hard time ripping apart the old draft because that paper's focus was on the fact that we used all the states. we said often that this allowed us to view rare states and extract information from systems that weren't normal. that is well and good, and we should put it in the discussion at the end, but since this paper doesn't go into any abnormal conditions we shouldn't make that a point. i am not sure what our point is. it is easy to say that the neck linker controls the processiivty and directionality through the worm like chain force between the two heads.

if we do that then we should change the neck linker length and show how the processivity changes (changing the run time and possibly the directionality as well. i don't think it'll change the directionality since that is caused from a combination of atp concentration and neck linker.)
 * Introduction
 * Methods
 * Model Description
 * Setting the transition rates
 * getting them from publications
 * force pulling off head
 * Hanggi rate equation
 * monomer kinesin for single attached head
 * neck linker can't dock in D/U state so it acts like U/U
 * adjusting the rest for correct processivity and run time
 * Agent Based Model
 * Markov Analysis
 * Extracting velocity from simulations
 * software
 * Results
 * our stuff matches experimental data
 * velocity
 * processivity histogram
 * run time histogram
 * ATP consumption (ratio of 1 atp consumed/step taken)
 * Michaelis-Menten curve
 * core cycle
 * most probable way to detach
 * Discussion

I was thinking of taking out the markov stuff, and maybe making it a supplemental info. like it is also possible to analyze this model this way, because it doesn't really say anything new that we can't get out of the monte carlo method


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