DNA unzipping is a powerful tool to study protein-DNA interactions at the single-molecule level. In this chapter, we provide a detailed and practical guide to performing this technique with an optical trap, using nucleosome studies as an example. We detail protocols for preparing an unzipping template, constructing and calibrating the instrument, and acquiring, processing, and analyzing unzipping data. We also summarize major results from utilization of this technique for the studies of nucleosome structure, dynamics, positioning, and remodeling. © 2012 Elsevier Inc.

Motivated by recent experiments on the finite temperature Mott transition in VO 2 films, we propose a classical coarse-grained dielectric breakdown model where each degree of freedom represents a nanograin which transitions from insulator to metal with increasing temperature and voltage at random thresholds due to quenched disorder. We describe the properties of the resulting nonequilibrium metal-insulator transition and explain the universal characteristics of the resistance jump distribution.

Proteins are known to undergo a dynamical transition at around 200 K but the underlying mechanism, physical origin, and relationship to water are controversial. Here we report an observation of a protein dynamical transition as low as 110 K. This unexpected protein dynamical transition precisely correlated with the cryogenic phase transition of water from a high-density amorphous to a low-density amorphous state. The results suggest that the cryogenic protein dynamical transition might be directly related to the two liquid forms of water proposed at cryogenic temperatures.

We have fabricated large (≤400 μm diameter) high tensile stress SiN membrane mechanical resonators and measured the resonant frequency and quality factors (Q) of different modes of oscillation using optical interferometric detection. We observe that the dissipation (Q -1) is limited by clamping loss for pure radial modes, but higher order azimuthal modes are limited by a mechanism which appears to be intrinsic to the material. The observed dissipation is strongly dependent on size of the membrane and mode type.

We develop the analysis of x-ray intensity correlations from dilute ensembles of identical particles in a number of ways. Firstly, we show that the three-dimensional (3D) particle structure can be determined if the particles can be aligned with respect to a single axis having a known angle with respect to the incident beam. Secondly, we clarify the phase problem in this setting and introduce a data reduction scheme that assesses the integrity of the data even before particle reconstruction is attempted.

We calculate the vortex structures of an elongated two-component Bose-Einstein condensate. We study how these structures depend on the intracomponent and intercomponent interaction strengths. We present analytical and numerical results respectively at weak and strong interactions; finding lattices with different interlocking geometries: triangular, square, rectangular, and double core. © 2011 American Physical Society.

An alternative measure of X-ray absorption spectroscopy (XAS) called inverse partial fluorescence yield (IPFY) has recently been developed that is both bulk sensitive and free of saturation effects. Here we show that the angle dependence of IPFY can provide a measure directly proportional to the total X-ray absorption coefficient, μ(E). In contrast, fluorescence yield (FY) and electron yield (EY) spectra are offset and/or distorted from μ(E) by an unknown and difficult to measure amount.

We introduce a systematic method for extracting multivariable universal scaling functions and critical exponents from data. We exemplify our insights by analyzing simulations of avalanches in an interface using simulations from a driven quenched Kardar-Parisi-Zhang (qKPZ) equation. We fully characterize the spatial structure of these avalanches-we report universal scaling functions for size, height, and width distributions, and also local front heights.

A striking feature of bilayer graphene is the induction of a significant band gap in the electronic states by the application of a perpendicular electric field. Thicker graphene layers are also highly attractive materials. The ability to produce a band gap in these systems is of great fundamental and practical interest. Both experimental and theoretical investigations of graphene trilayers with the typical ABA layer stacking have, however, revealed the lack of any appreciable induced gap.

Aristotle contended that (regular) tetrahedra tile space, an opinion that remained widespread until it was observed that non-overlapping tetrahedra cannot subtend a solid angle of 4π around a point if this point lies on a tetrahedron edge. From this 15th century argument, we can deduce that tetrahedra do not tile space but, more than 500 years later, we are unaware of any known non-trivial upper bound to the packing density of tetrahedra. In this article, we calculate such a bound.