Friday 06/20/14

10:00 am – 11:55 pm


  • simulations with more nodes (1 every 300 bp) of blue regions don’t ‘work’,
  • simulation time not long enough for distributions to converge.
  • too many nodes such that larger regions never experience bonding interactions. Maybe bonding energy too low relative the entropy states for this number of molecules.




Closer look at original simulations

  • these behave very well
  • also working out plotting of polymers


initial rough version fig

New code

  • PlotTubes.m — for visualizing polymers
  • PlotSpheres.m — for visualizing polymers

RC computing, matlab MC simulations

  • in calling matlab from terminal, need to omit the .m part of the filename to get a matlab script to run.
  • also need to omit the filepath — all the slashes no good. just change to the target folder and launch from there.
  • This caused all my code to not launch properly yesterday.
  • finally running and saving data (after fixing a few other small bugs)


  • rpt G06 copied to: ProbBox4:N:\2014-06-17_L3E11toF01, needs to be analyzed
  • Needs analysis: ProBox7: Q:\2014-03-28_L2F02
  • copied from ProBox7 to ProBox5: 2014-01-12_G04
  • copied from STORM2 to ProBox7: L3D01 and L3D02.
  • Started analysis
    • 2014-06-17_L3E11toF01
    • 2014-03-28-L2F02


  • remove objective heater, clean up cart, transfer system back to Hao
  • new bioptics chamber to arrive by the end of next week (hopefully).
  • recentered beam on camera
  • flattened field using laser adjust mirrors
  • tried to get 561 and 647 centered.

To do

  • stain more black domains! (D04 to D08)
  • Analyze Hao’s cluster data
  • # Analyze cluster data for Ajaz
  • # order primers for my lib 4
  • # order primers for Hao Lib 5
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