Thursday 06/26/14

9:45 am – 1:30 am

Chromatin Modeling continued

Checking my simulation results from the polymer models I was running last night.

Simulation Results

BBv1 no attractive potential does give expected scaling:


Adding an attractive potential does increase clustering. Has more effect on large polymers.

Notes from meeting with Max

More coding

  • Fixed up openmm-polymer code
  • implemented extension script to import and build off the openmmlib (I called my function lib openmmlibExt).
  • with some difficulty (stupidity), finally implemented node specific interactions
  • simulating free polymers,
  • simulating uniformly sticky polymers
  • simulating periodically stick polymers

Primer ordering

  • Lib4 primers still had the same bug as the Lib3 primers. Now when back and editted old scripts to fix this bug (will be logged in GitScripts).
  • bug was in the export list of T7 rev primers, the sequences of the Fwd primers was used and not the rev primers.
  • wrote new functions to index 96 well plates and to convert fasta files to csv tables for ordering primers.
  • validated primers in quick test.
  • remembered (belatedly) to add T7 to project 2 L5 primers and strip off extra Gs
  • sent primer orders to Alec.


  • new cell stains: C09 C10 and C11 (tiny blue and black regions)
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