User:TheLarry/Notebook/Larrys Notebook/2010/08/24: Difference between revisions

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*Results
*Results
**our stuff matches experimental data
**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
**core cycle
**most probable way to detach
**most probable way to detach

Revision as of 15:35, 24 August 2010

Monte Carlo Simulation <html><img src="/images/9/94/Report.png" border="0" /></html> 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

  • 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
      • 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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