9:30 am – 5:00 pm, 9:00 pm – 12:15 am
PH project
- replotting all histograms — no more collecting all the big stuff into the last bin, this was confusing.
- made new figure-producing figs (actually just histograms, the images are separate code still).
- sent updated histograms (8 total) to Ajaz, along with some comments on the fig 2 layout and captions (can we please include more labels on the figures!)
project 2, team meeting
- My tasks for next week:
- cluster analysis for formamide titration data
- cluster analysis of E4 data
Chromatin simulations
- test polymer simulations with greater spacing (10 nm between molecules)
- it looks like these all relax to 1, nI thought the nodes were supposed to be 10nm.
- This is probably another good question for the authors if they ever write back.
Hacking an attractive force.
- lets just build a quadratic or quartic well
- outside the well we have the energy as 1 kT here. I have since changed it to zero.
- This finally appears to be working with the code that Bogdan started ( see image below).
- there’s this weird dip at the beginning, which could be due to the added stiffness of my polymer, it takes a while before the nodes can start interacting, but I’m not sure that’s it. Should probably investigate this more.
- But for molecules of length 100+ we are closer to the expected 1/3rd scaling exponent.
- My hacked version of a free polymer using openmmlib seems to ignore my force though. Maybe its a distance issue. Still has a 0.6 free polymer type scaling.
