9:30 am -5:50 pm, 7:30 pm – 12:00 am
chromatin simulations
- check simulation project
Odyssey results
- Now black behaves properly but yellow and blue are giving issues
- yellow not equilibrating?
- not sure what’s going on with blue, will require further investigation. Possible that large domains are swallowing smaller ones and growing too fast.
- also possible that large domains are just splitting into multi-rosettes and small domains stay as singles.
New simulations
- ‘WholeNucVOp5’ – 10% sticky blue, blue attraction 3.0 repulsion 3.0
- ‘WholeNucVOp6’ – yellow back to no stiffness, run for 200 steps.
- this does (as before) a good yellow black split.
- New approach — successively add more sticky sites to BLUE. see if we get a better saturated state if it folds in steps.
Discussion with Xiaowei
- XZ doesn’t like the yellow model as a faster equilibration to Eq. Globule from Fractal globule (due to energy or chain-crossing). Too much of a polymer explanation, not enough useful biology.
- probably right, I think the modeling is actually rewarding and complex enough just with the blue.