10:00 am – 2:45 am
Chromatin
Literature
- reading Mirny 2011 review
Simulations
Data for Bogdan
- send volume table to Bodgan to explore densities
- send table of internal volumes
- send table of intact Rgs
- send table of internal Rgs
To plot for XZ meeting
- blue internal scaling, just BX-C data. With .5 and .33 reference lines
- blue internal scaling, just ANT-C data. With .5 and .33 reference lines
- simulation of pure black chromatin.
Simulations
- got black working
- added yellow – too many holes? allows black to equilibrate?
- reduced yellow – seems to help, hard to tell when not a lot of yellow to go by.
- went back to all black – back to 0.4 scaling?
- went back to all black with Grosberg repulsion, still 0.4 scaling.
- reduced number of domains and increased min domain size (maybe the too smalls are getting in the way).
- this fixes things, back to 0.3. ‘YellowBlackAllK4_Rnd’
- switching back from Grosberg to tagged force. Seems to be okay. 0.32 ‘YellowBlackAllK5_Rnd’
- adding back 10% yellow ‘YellowBlackAllK6_Rnd’. Black seems to stay down at 0.3 to 0.35, though the data is supernoisy with this few points. Yellow with 3 points is useless to fit. showing 0.24 (-1,1.5)
- ‘YellowBlackAllK7_Rnd’ with more yellow poitns is still pretty even (0.32 black [.21 .42], 0.26 yellow [.13 .4])
- let’s try making yellow a bit more phantom than 5:50. ‘YellowBlackAllK8_Rnd’ looking at 2::50 comparison
- This looks a bit more promising, black is staying at .3, yellow is occassionally climbing above (though still very noise).
- running 200 step, more subchains, larger polymer, long run overnight ‘YellowBlackAllK11_Rnd’.
- overnight run looks decent. data is still very noisy, maybe this will average away if we use a random chain configuration to start instead of the deterministic wrapping, and we do we enough repeats. (current system of repeats doesn’t average away noise).
Project 2
- restart Cajal running on scans