Translational nucleosome positioning: A computational study.

About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes. In this study we ask the question whether the latter can be predicted by a simple coarse-grained DNA model with sequence-dependent elasticity, the rigid base-pair model. Whereas this model is known to be rather robust in predicting rotational nucleosome positioning, we show that the translational positioning is a rather subtle effect that is dominated by the guanine-cytosine content dependence of entropy rather than energy. A correct qualitative prediction within the rigid base-pair framework can only be achieved by assuming that DNA elasticity effectively changes on complexation into the nucleosome complex. With that extra assumption we arrive at a model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally.

Colloidal Spherocylinders at an Interface: Flipper Dynamics and Bilayer Formation.

We study the response of a film of colloidal spherocylinders to compression by combining pressure-area isotherm measurements, microscopy, and computer simulations. We find that the behavior of the film depends strongly on the geometry of the particles. For a small aspect ratio, a uniform monolayer forms and then buckles. For a higher aspect ratio, particles flip to orient perpendicular to the interface; we show that flipping occurs in locations where the nematic ordering is low. Our experiments and simulations further demonstrate that the longest particles rearrange to self-assemble a colloidal bilayer, which is stable due to the unique geometry of spherocylinders at an interface.