Saturday 09/11/14

10:00 am – 8:00 pm

Modeling Calculations

fractions of chromatin types in genome

  • of the 120 Mb of classified sequence (some 60 Mb ‘other’ class)
  • estimate: from Pc track, 1 – 3% ‘Blue’
  • estimate: from yellow/red Filion data: 34% ‘Yellow’ (21% ‘Yellow’,13% ‘Red’).
  • estimate: from black and blue minus true blue: 64% ‘Black’

estimate monomer length and size

I estimate the intersection of three scaling laws to occur between 0.4 kb and 3.2 kb to ~95% confidence*.

*About the calculation:
I have 3 lines from our 3 scaling laws. Around each line I can plot the lower and upper uncertainty bounds and turn each line into a pair of lower and upper extema. If I compute the first time the lower extrema of the yellow crosses the upper extrema of the blue I call that the largest value possible for the intersection. But I think its wrong to compute this using the 95% bounds, because the probability all 3 of these datasets are at or outside their 95% limit is (0.05)^3 not (0.05). So instead I use the 63% bounds around the line and compute the earliest (and latest) time where they could all intersect and I get the above numbers.

The volume of the chromatin at the crossing point depends a little which crossing point in this range we look at.

  • at 0.4 kb it ranges from 10^5.4 to 10^5.8 nm
  • at 1 kb it ranges from 10^5.8 to 10^6.1 nm
  • at 3.2 kb it ranges from 10^6.3 10^6.7 nm
    based on the the confidence intervals.

Any one of the monomer lengths (0.4 to 3.2) can satisfy the constraint that the biggest blue has a volume fraction less than 1.0 if we chose its lower bound for the the monomer volume estimate. (the upper estimates all put the volume fraction way above 1).

Modeling to do

  • check convergence time:
    • run mulitple very long simulations, see how Rg changes at several subchain lengths for blue, black and yellow.
  • formalize computation of monomer size. Done. See above.
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