Friday 06/20/14

Posted on June 20, 2014 by admin

10:00 am – 11:55 pm

Simulations

  • 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.

PHOpeaksSimulate200bpNodeV2

TooMuchExlcusionEffect

PHOpeaksSimulate200bpNode

Closer look at original simulations

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

SimulationVsDataPHOblue

initial rough version fig
PHOblueFig

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)

Data

  • 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

STORM

  • 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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