10:00 am – 5:00 pm, 10:00 pm – 12:30 am

Lab stuff

Finally found and installed drivers for Cajal’s AMD Radeon 6900 graphics card (this card is still driving the monitors).
installed new NVIDIA Quadro K4000 for GPU computing (still need to install the CUDA SDK etc)
moved RAM from Tuck to Cajal. Tuck failed to boot (maybe just extremely slow, should give it an hour or so to attempt to sort itself out after windows updates, it doesn’t like these and they process very slowly).

Chromatin

clear exclusion issues revealed by sticky polymer sim. All polymers fit into the same volume. The expected volume of 500 monomers is 10E6, whereas the volume of the polymer (at all stages basically) is 10E4. Clearly an issue. (As is the negative scaling coefficient, since more monomers squeeze towards the center inside the volume. This is only expected in packing chains in tightly confined spaces).
attractive and repulsive energies built off of chain_a, which is the centroid-to-centroid distance between monomers, not the hard-sphere radius distance. This is probably a problem.
now running short sticky polymer simulations with simple change of radius for chain spacing in the energy functions.
Also exploring the alternative Grossberg energy functions used in the Minry polymer tools (in principle I should be able to import and call these rather than copy them since they are there own classes. Though figuring out the variable space is tricky since there’s essentially no documentation of it).
at first glance from the simulations this does not seem to have solved the problem.

‘GrossbergRepulsion’ energy function from Mirny lab openMM polymer doesn’t make sense to me as a repulsive energy. Why is this non-zero beyond the radius of the monomer?

Troubleshooting non-self avoiding behavior and wierd potentionals
believe repulsive force was targeted at all but the attractive nodes. Removed 1-index1*index2 part of repulsive force in polymer simulations (see GitScripts for code log)
Reducing potential energy magnitudes to minimize explosive behavior of polymer chains.

imaging sample D07. Not looking very strong staining, especially for a 150 kb region. Something has probably gone wrong.