10:00 am – 7:30 pm, 11:20 pm – 12:10 am
Post-doc candidate visit
- see notes
Chromatin project figure making
internal domains
- need examples for figures
Multi-color region analysis
- Black:Yellow
- F01 :: F02
- F07 :: F06
- F11 :: F12
- G08 :: G06
- Blue :: Black
- G08 :: G09
- Blue :: Yellow
- F03 :: F02
- F05 :: F06
- G01 :: F12
- G05 :: G06
- Blue :: Blue
- G01 :: G02
- G02 :: G03
- F03 :: F04
- F04 :: F05
- Yellow :: Yellow
- L3E06 :: L3E07
- L3E07 :: L3E08 (?)
- Black :: Black
- L3D11 :: L3D12
Analysis methods
- want an Rg analog for overlap — we don’t want differences in the fringes of scattered particles to make a difference in the ‘volume’ fraction overlap.
- to be Rg analog, metric should treat localizations as density
- We could also make this independent of binning — which was an annoying free parameter last time.
- Proposal:
- fraction of localizations in one channel with at least N localization within distance D (relative to total localizations making up domain).
New simulations
- Free polymer with spherical confinement to a default density of 0.3 particles per cubic nanometer (if bond size is 1 nm).