User:TheLarry/Notebook/Larrys Notebook/2009/10/28

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Things I want to add to the paper

Right now i am waiting for Koch to give me the revisions to the first draft. But I am looking through other papers for more references and filling in some weak sentences. Also I am adding .vis to better analyze the states being entered in the simulation. So a couple of things i want to add to the paper

  1. Kikkawa M. The role of microtubules in processive kinesin movement [Internet]. Trends in cell biology. 2008 ;(February):Available from: http://linkinghub.elsevier.com/retrieve/pii/S0962892408000251
    • This is a good paper that explores the connection between the microtubule, nucleotide and docking of the neck linker. Adding this to the paper means saying something like the docking is connected to the the nucleotide binding to the head as well as the head bound to the microtubule. Which I didn't see written down before but we do have that in the simulation since we don't have an interaction for unbound heads. This means that the unbound heads can't make the neck linker dock/undock which is what this paper states
  2. Fisher, Peskin, Kanada...
    • These are theoretical kinesin people and i am trying to read their papers to improve my understanding of previous work
    • Fisher as per my understanding has a stochastic simulation but he chooses a random waiting time. So his simulation waits then steps either forward or backwards depending on a rate constant, but that's it. So it doesn't analyze the sub steps like mine does.SJK 02:15, 29 October 2009 (EDT)
      02:15, 29 October 2009 (EDT)These will be crucial to cite, and I'm glad to hear that they're not addressing the things your simulation is getting at.  Good work today, I like the waiting time distribution too!
      02:15, 29 October 2009 (EDT)
      These will be crucial to cite, and I'm glad to hear that they're not addressing the things your simulation is getting at. Good work today, I like the waiting time distribution too!
  3. Waiting Time
    • I don't like waiting time since the kinesin is never really waiting: It just isn't moving. But the world loves this freaking thing. So I included now in the labview the ability to measure how much time elapses between steps. A histogram can then be made. I have to check this to known waiting distributions and hopefully it matches up.
  4. Time spend bound/unbound
    • On Koch's suggestions I added code to calculate the total time the head was bound/unbound to the microtubule as well as the percent of time it was

Waiting Distribution

The histogram i have looks awfully like a Poisson Distribution which from the limited amount of searching i have done i think is what it is supposed to look like

Here is the histogram of the waiting times between steps. An array of the summed waiting times between steps for 1000 sims of kinesin walking formed this histogram.
Here is the histogram of the waiting times between steps. An array of the summed waiting times between steps for 1000 sims of kinesin walking formed this histogram.

Bound/Unbound Times

I haven't run this over 1000 sims yet but it looks like the amount of time spent bound for a head is about 80% thus making time spent unbound 20%. This is interesting. I don't know what I expected it to be. So 20% of the time only 1 head is bound to the microtubule.

More interesting is that i ran the 1000 simulations and kept track of how many times both heads where bound and how many times they weren't (i.e. 1 head unbound or both heads unbound which happens once). And the percentages were 54.4% both heads were bound and 45.6% not. So almost 50% of the time that if you grab a kinesin it will have 1 head in the air. That is pretty interesting SJK 02:14, 29 October 2009 (EDT)
02:14, 29 October 2009 (EDT)I agree interesting and it's directly addressed in Guydosh and Block, but I don't yet know how to think about it clearly.  I can't see how to connect that 20% of the time it's in 1 head bound state (your results in previous paragraph) with the 54.4% both heads bound).  I remember being equally confused trying to read the Guydosh Block paper...but then I figured it out...and then forgot again.
02:14, 29 October 2009 (EDT)
I agree interesting and it's directly addressed in Guydosh and Block, but I don't yet know how to think about it clearly. I can't see how to connect that 20% of the time it's in 1 head bound state (your results in previous paragraph) with the 54.4% both heads bound). I remember being equally confused trying to read the Guydosh Block paper...but then I figured it out...and then forgot again.


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