10:30 am – 6:20 pm, 10:30 pm – 12:00 am
Chromatin simulations
- Anaconda called from sbatch actually worked to get save data.
issues with current simulations
- black chromatin starts at .4 (and stays there).
- writing new template to do the the fractal globule 2 step formation first before starting simulation
- this is actually relatively slow, we may not want to do it fresh each time.
Summary of recent simulations
- WholeNucV6p15 – 30+ runs of basic blue/black/yellow
- yellow and black split off a bit too late, but with appropriate difference in slope
- both yellow and black a bit too relaxed — yellow .5 black .4
- blue is holding at correct Rg slope of .2 and a reasonable density, looks
New simulations
- running on Odyssey rpt of V6p15 with stiffer yellow and slightly fewer sticky blue
- testing on Monet new pipeline to generate and relax fractal globule all in same script (V7)
- V7p2 looking a bit better:
Running V8p1 — trying to get black to initialize closer to .3 than .4. I think this is because the Random Walk Polymer initiation starts entangled. Trying a simulation with a condensed regular coil.
Meeting Ajaz
- discuss PH project follow up