Friday 05/16/14

Chromatin Project

• Analyzing E06+ E07 data: chr2R:19726615-19888410__YELLOW_D12 a + b
• 4Tb hard-drive in Kangaroo mount died. All data from F03-F02 and F04-F02 lost. Drive recovery services probably not worth it. Damn it.
• chkdsk ‘recovered’ the files by deleting all the dax files ‘orphan segments’ (now 0 bits, just perfect windows. and not even a warning). should try TestDisk next time.

Literature

• continuing to read Halverson … Grosberg 2014 review melt of rings to chromosome territories
  1. Pt 1: if pre-arranged in unentagled territories, no additional mechanisms required to maintain un-entangled territoreis
  2. Scaling of chromatin random walk polymer melt of non-concatentated rings goes like $R ~ b N^v$ with $v = 2/5$ (Cates and Deutsch) based on balance of entropy loss do to small size rather than preferred ‘Gaussian’ (not really true for self-avoiding melt but anyway) and loss of entropy on large size do to topological constraint of loop tentacle protrusions.
  • more generally expect $v = (1+a)/(2+3a)$ rather than assuming cohabiting rings produce entropy loss of order unity.
    1. Crumpled / fractal globule — self similar, free of knots, dents, has $\Beta = 2/3$. where Beta is the easily accessible fraction of the surface, $ ns = N^\Beta$. $r(s)~s^v$ with $v= 1/3$, every subchain of sufficient length $s$ is collapsed in itself.
  • contact probability – defined as $P(s) ~ s^{-\gamma}$ gamma can get arbitrarily close to one from above and Beta arbitrarily close to 1 from below. common space-filling curves though have gamma = 4/3 Beta = 2/3.
    1. FISH and HiC. First, relating $r(s)=b s^v$ FISH/radius gyration to P(s) contact probability $P(s) ~ s^{-\gamma}$ .
  • $ gamma = 3v$
  • r(s) in equilibrium globules (dense) goes like $s^{1/2}$ for s up to around $N^{2/3}$ and there-after scales like $N^{1/3}.
  • Observation — if a black domain is its own independent globule, then globule size goes like $N^{1/3}$ i.e. constant volume, which is what we see, and volume of internal domains should grow like 3/2 or area like 1, which is — the opposite direction of the change that we see.
    1. Very interesting potential: “the second virial coefficient of two nonconcatenated rings in dilute solution is close to R_g^3 and is practically independent, at least in the scaling sense, of the real excluded volume of their monomers [129]”. i.e. to make two domains not mix in dilute solution, it sufficient to tie them off at their ends. Note later comments about cohesins etc. argue that any transient release of the rings allows complete mixing.