now if the bead on the central helix is the same at each crossover, an angle potential is applied instead of skipping the crossover

Slightly reorganized simulation protocol; added options to mrdna script and simulate.py for using twist in the coarsest step

First, ssDNA segments are now broken at crossovers
Second, ssDNA segments aren't allowed to stack intrahelically

Changed how particles are named so that it no longer reflects the number of nucleotides represented, but is more robust to clashes