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9:30 am – 12:30 am
Setting up Server part 1
- unpacked server yesterday
- collecting cables for new server: MORGAN.
- installed Windows 2012 Server edition.
- submitted purchase requests for Server 2012 R2 Standard license and 5 per user CAL remote desktop
- contacted IT about getting ethernet and Adobe and Office installed
- Alec will install wheels tomorrow
10:00 am – 11:00 pm
- prep slides for meeting with LM et al this evening
- running more progressive condensation BLUE simulations
- these work better than starting all sticky for the purposes of getting mixing.
Meetings & Seminars
- postdoc seminar at 4:00 pm
- discussion with ML and team: 5:30pm – 8:00pm
- follow up discussion with BB: 8 – 9pm.
Notes from discussion with ML
- should compute gyration tensors — radii of gyration along each principle component
- try computing pairwise distance distributions for all points
- would like theoretical framework for .2 scaling
- need to demonstrate entire range (show transitions from .5 at small scales to .33 at large scales)
- see notes
10:00 am – 9:00 pm,
remotely 10:00 pm – 1:00 am
- see post
- quick update team meeting
- XZ team meeting
- working on manuscript text
- do we see TAD like structure in black chromatin simulations?
9:30 am -5:50 pm, 7:30 pm – 12:00 am
- check simulation project
- Now black behaves properly but yellow and blue are giving issues
- yellow not equilibrating?
- not sure what’s going on with blue, will require further investigation. Possible that large domains are swallowing smaller ones and growing too fast.
- also possible that large domains are just splitting into multi-rosettes and small domains stay as singles.
- ‘WholeNucVOp5′ – 10% sticky blue, blue attraction 3.0 repulsion 3.0
- ‘WholeNucVOp6′ – yellow back to no stiffness, run for 200 steps.
- this does (as before) a good yellow black split.
- New approach — successively add more sticky sites to BLUE. see if we get a better saturated state if it folds in steps.
Discussion with Xiaowei
- XZ doesn’t like the yellow model as a faster equilibration to Eq. Globule from Fractal globule (due to energy or chain-crossing). Too much of a polymer explanation, not enough useful biology.
- probably right, I think the modeling is actually rewarding and complex enough just with the blue.