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.