Thursday 12/12/13

10:45a – 11:00p

Ph Simulations

  • Troubleshooting extra along bonds.
  • Oops, actually just resulted from plotting the wrong attachment matrix for the given position list.
  • Simulations ran at subsaturating Ph — more total sites than available Ph. Hence there is a sligth effect of increasing the Ph concentration.
  • decreasing the binding energy or increasing the site density results in shifting the transition point of clustered to unclustered to higher PhM concentrations. Interesting…

Figure prep

  • assembling images into model figure
  • sent draft of model figure to Ajaz

New simulations

  • increased total Ph and set simulations to rerun. Should get stronger staturation effects this time. May not be necessary.
  • Also increased range of PhM to explore concentration, at 1000 max we just sampled the beginning of the PhM saturation (I think). Would be good to have more than two data points at saturation.

Bead test

  • washing out excess probe at 60C
  • test if beads remain crosslinked
  • both old and new EDAC reacted beads are abundantly still present after treatment
  • on the down side, neither sample has G03 staining. Don’t know if it’s just this probe batch failed (most likely?) or something with the hybe or a consequence of the EDAC.

Z calibrations

  • issues with fitting routine
  • can call ‘Robust’ ‘LAR’ or ‘Bicubic’
  • curves still don’t align neatly. suspect x-y dependent widths
  • no really obvious spatial pattern in the parameters…

Test staining

  • G01 P1 at 5 uL on straight new cells
  • G03 P1 at 5 uL on straight new cells
  • D12 P1 at 5 uL on straight new cells
  • E12 on EDAC treated cells
  • E12 on non-EDAC treated cells


  • Dentist Appointment, 2:50p – 4:50p
  • Meeting with XZ, discuss rotations, 5:00-5:20p
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