User talk:Andy Maloney/Introduction to kinesin and microtubules

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If you do not have an account with Open Wet Ware, you can obtain one from here. I would like to have people format their questions and comments in the following manner:

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   • '''~~~~:''' The output of this looks like: Andy Maloney 12:29, 7 February 2011 (EST):.

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As much as I would like to keep my dissertation completely open and in the media wiki format, I will have to at some point format it to the guidelines dictated by my university. This will necessitate putting a final "snap shot" of the dissertation in a book format of which, all comments will have their own special appendix in each chapter.

Thanks for looking at my open dissertation!

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Steve

• Major
  • What kind of diffusion model did you use to calculate the 30 years for 1 meter diffusion? In 3-D free diffusion, assuming something like 1 micron^2/second, it'd be >100,000 years.
    • Andy Maloney 00:15, 6 April 2011 (EDT):
      • I was pressed for time so I just looked up the number. But, using the good old Stokes-Einstein [math]\displaystyle{ D=\frac{kT}{6\pi\eta R} }[/math] equation for one dimension and solving for time [math]\displaystyle{ t=\frac{x^2}{2D} }[/math], one would get around 2 years for a particle that's 100 nm in diameter at 40°C. If I'm remembering this correctly then in 3 dimensions [math]\displaystyle{ t=\frac{x^2}{6D} }[/math] which would make it half a year. What am I doing wrong or forgetting?
    • Andy Maloney 14:07, 6 April 2011 (EDT):
      • Argh! The damn numbers are wrong. Here's a classic example of me not making sure my units worked out correctly. The above answer is totally wrong. For linear diffusion in one dimension it should be somewhere around 2000 years for a particle of 100 nm diameter to go 1 m using the following numbers:
        • [math]\displaystyle{ k = 1.3806503 * 10^{-23} \frac{m^2kg}{s^2K} }[/math]
        • [math]\displaystyle{ T = 300 K }[/math]
        • [math]\displaystyle{ \eta = 0.653 * 10^{-3} N\frac{s}{m^2} }[/math]
        • [math]\displaystyle{ R = 50 * 10^{-9} m }[/math]
      • I've just reworded the text to state "thousands" of years as opposed to an actual number.
  • In addition to fundamental understanding of mechanochemistry, there are applications. You mention one, human disease, I think it's also worth mentioning the application some people care about for microdevices. Just briefly.
    • Andy Maloney 00:15, 6 April 2011 (EDT): You know, I've only read a couple of articles that use kinesin and microtubules as a means for microdevices. I suppose those references will be sufficient but if you can suggest any, by all means please do.
    • Andy Maloney 14:07, 6 April 2011 (EDT): Done.
• Minor
  • "THe first major component(s) to the kinesin molecule is / are the motor domains." (plural / singular match)
    • Andy Maloney 14:07, 6 April 2011 (EDT): Done.
• Consider including a figure of the kinetic cycle from Larry's paper (which is CC licensed), or drawing your own, to explain the paragraph that talks about stepping.
  • Andy Maloney 17:08, 6 April 2011 (EDT): Done.
• Switch "outer dimension" to "outer diameter" to be more specific
  • Andy Maloney 14:07, 6 April 2011 (EDT): Done.
• more to come...