DNA is tightly wrapped around histone proteins in nucleosome core particles (NCPs) yet must become accessible for processing in the cell. This accessibility, a key component of transcription regulation, is influenced by the properties of both the histone proteins and the DNA itself. Small angle x-ray scattering with contrast variation is used to examine how sequence variations affect DNA unwrapping from NCPs at different salt concentrations. Salt destabilizes NCPs, populating multiple unwrapped states as many possible unwrapping pathways are explored by the complexes. We apply coarse-grained Monte Carlo methods to generate realistic sequence-dependent unwrapped structures for the nucleosomal DNA with thermal variations. An ensemble optimization method is employed to determine the composition of the overall ensemble as electrostatic interactions are weakened. Interesting DNA-sequence-dependent differences are revealed in the unwrapping paths and equilibrium constants. These differences are correlated with specific features within the nucleic acid sequences.

The set of transition probabilities for a single neutrino emitted from a point proto-neutron source after passage through a turbulent supernova density profile have been found to be random variates drawn from parent distributions whose properties depend upon the stage of the explosion, the neutrino energy and mixing parameters, the observed channel, and the properties of the turbulence such as the amplitude C⋆. In this paper we examine the consequences of the recently measured mixing angle θ13 upon the neutrino flavor transformation in supernova when passing through turbulence, in order to provide some clarity as to what one should expect in the way of turbulence effects in the next supernova neutrino burst signal. We find the measurements of a relatively large value of θ13 means the neutrinos are relatively immune to small, C⋆ 1%, amplitude turbulence but as C⋆ increases the turbulence effects grow rapidly and spread to all mixing channels. For C⋆ 10% the turbulence effects in the high (H) density resonance mixing channels are independent of θ13 but non-resonant mixing channels are more sensitive to turbulence when θ13 is large.

Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS.

We study statistical properties of packings of monodisperse spheres in a flat box. After "gravitational" filling and appropriate agitation, a nearly regular (in plane) but frustrated (normal to the plane) triangular lattice forms, where beads at individual sites touch either the front or back wall. It has striking analogies to order in antiferromagnetic Ising spin models. When tilting the container, Earth's gravitational field mimics external forces similar to magnetic fields in the spin systems. While packings in vertical containers adopt a frustrated state with statistical correlations between neighboring sites, the configurations continuously approach the predictions of a random Ising model when the cell tilt is increased. Our experiments offer insights into both the influence of geometrical constraints on random granular packing and a descriptive example of frustrated ordering.

The transition probabilities describing the evolution of a neutrino with a given energy along some ray through a turbulent supernova are random variates unique to each ray. If the source of the neutrinos were a point then all neutrinos of a given energy and emitted at the same time which were detected in some far off location would have seen the same turbulent profile therefore their transition probabilities would be exactly correlated and would not form a representative sample of the underlying parent transition probability distributions. But if the source has a finite size then the profiles seen by neutrinos emitted from different points at the source will have seen different turbulence and the correlation of the transition probabilities will be reduced. In this paper we study the correlation of the neutrino transition probabilities through turbulent supernova profiles as a function of the separation δx between the emission points using an isotropic and an anisotropic power spectrum for the random field used to model the turbulence. We find that if we use an isotropic power spectrum for the random field, the correlation of the high (H) density resonance mixing channel transition probability is significant, greater than 0.5, for emission separations of δx = 10 km, typical of proto neutron star radii, only when the turbulence amplitude is less than C⋆ ∼ 10%; at larger amplitudes the correlation in this channel drops close to zero for this same separation of δx = 10 km. In contrast, there is significant correlation in the low (L) density resonant and non-resonant channels even for turbulence amplitudes as high as 50%. Switching to anisotropic spectra requires the introduction of an 'isotropy' parameter kI whose inverse defines the scale below which the field is isotropic. We find the correlation of all transition probabilities, especially the H resonance channel, strongly depends upon the choice of kI relative to the long wavelength radial cutoff k⋆. The spectral features in the H resonance mixing channel of the next Galactic supernova neutrino burst may be strongly obscured by large amplitude turbulence when it enters the signal due to the finite size of the source while the presence of features in the L and non resonant mixing channels may persist, the exact amount depending upon the degree of anisotropy of the turbulence.