Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes

Subnanosecond time‐resolved fluorescence depolarization has been used to monitor the reorientation of ethidium bromide intercalated in native DNA, synthetic polynucleotide complexes, and in supercoiled plasmid DNA. The fluorescence polarization anisotropy was successfully analyzed with an elastic model of DNA dynamics, including both torsion and bending, which yielded an accurate value for the torsional rigidity of the different DNA samples. The dependence of the torsional rigidity on the base sequence, helical structure, and tertiary structure was experimentally observed. The magnitude of the polyelectrolyte contribution to the torsional rigidity of DNA was measured over a wide range of ionic strength, and compared with polyelectrolyte theories for the persistence length. We also observed a rapid initial reorientation of the intercalated ethidium which had a much smaller amplitude in RNA than in DNA

LENS® and SFF: Enabling Technologies for Optimized Structures

Optimized, lightweight, high-strength structures are needed in many applications from aerospace to automotive. In pursuit of such structures, there have been proposed analytical solutions and some specialized FEA solutions for specific structures such as automobile frames. However, generalized 3D optimization methods have been unavailable for use by most designers. Moreover, in the cases where optimized structural solutions are available, they are often hollow, curving, thin wall structures that cannot be fabricated by conventional manufacturing methods. Researchers at Sandia National Laboratories and the University of Rhode Island teamed to solve these problems. The team has been pursuing two methods of optimizing models for generalized loading conditions, and also has been investigating the methods needed to fabricate these structures using Laser Engineered Net Shaping™ (LENS®) and other rapid prototyping methods. These solid freeform fabrication (SFF) methods offer the unique ability to make hollow, high aspect ratio features out of many materials. The manufacturing development required for LENS to make these complex structures has included the addition of rotational axes to Sandia’s LENS machine bringing the total to 5 controlled axes. The additional axes have required new efforts in process planning. Several of the unique structures that are only now possible through the use of SFF technology are shown as part of the discussion of this exciting new application for SFF.Mechanical Engineerin

Time-resolved spectroscopy of macromolecules: Effect of helical structure on the torsional dynamics of DNA and RNA

The torsional rigidity of DNA and RNA is measured via the fluorescence depolarization technique

String spectra near some null cosmological singularities

We construct cosmological spacetimes with null Kasner-like singularities as purely gravitational solutions with no other background fields turned on. These can be recast as anisotropic plane-wave spacetimes by coordinate transformations. We analyse string quantization to find the spectrum of string modes in these backgrounds. The classical string modes can be solved for exactly in these time-dependent backgrounds, which enables a detailed study of the near singularity string spectrum, (time-dependent) oscillator masses and wavefunctions. We find that for low lying string modes(finite oscillation number), the classical near-singularity string mode functions are non-divergent for various families of singularities. Furthermore, for any infinitesimal regularization of the vicinity of the singularity, we find a tower of string modes of ultra-high oscillation number which propagate essentially freely in the background. The resulting picture suggests that string interactions are non-negligible near the singularity.Comment: Latex, 30pgs; v2. minor clarifications, references adde

Humpback and Fin Whaling in the Gulf of Maine from 1800 to 1918

The history of whaling in the Gulf of Maine was reviewed primarily to estimate removals of humpback whales, Megaptera novaeangliae, especially during the 19th century. In the decades from 1800 to 1860, whaling effort consisted of a few localized, small-scale, shore-based enterprises on the coast of Maine and Cape Cod, Mass. Provincetown and Nantucket schooners occasionally conducted short cruises for humpback whales in New England waters. With the development of bomb-lance technology at mid century, the ease of killing humpback whales and fin whales, Balaenoptera physalus, increased. As a result, by the 1870’s there was considerable local interest in hunting rorquals (baleen whales in the family Balaenopteridae, which include the humpback and fin whales) in the Gulf of Maine. A few schooners were specially outfitted to take rorquals in the late 1870’s and 1880’s although their combined annual take was probably no more than a few tens of whales. Also in about 1880, fishing steamers began to be used to hunt whales in the Gulf of Maine. This steamer fishery grew to include about five vessels regularly engaged in whaling by the mid 1880’s but dwindled to only one vessel by the end of the decade. Fin whales constituted at least half of the catch, which exceeded 100 animals in some years. In the late 1880’s and thereafter, few whales were taken by whaling vessels in the Gulf of Maine

Infinite products involving binary digit sums

Let $(u_n)_{n\ge 0}$ denote the Thue-Morse sequence with values $\pm 1$. The Woods-Robbins identity below and several of its generalisations are well-known in the literature \begin{equation*}\label{WR}\prod_{n=0}^\infty\left(\frac{2n+1}{2n+2}\right)^{u_n}=\frac{1}{\sqrt 2}.\end{equation*} No other such product involving a rational function in $n$ and the sequence $u_n$ seems to be known in closed form. To understand these products in detail we study the function \begin{equation*}f(b,c)=\prod_{n=1}^\infty\left(\frac{n+b}{n+c}\right)^{u_n}.\end{equation*} We prove some analytical properties of $f$. We also obtain some new identities similar to the Woods-Robbins product.Comment: Accepted in Proc. AMMCS 2017, updated according to the referees' comment

Impact Ionization in ZnS

The impact ionization rate and its orientation dependence in k space is calculated for ZnS. The numerical results indicate a strong correlation to the band structure. The use of a q-dependent screening function for the Coulomb interaction between conduction and valence electrons is found to be essential. A simple fit formula is presented for easy calculation of the energy dependent transition rate.Comment: 9 pages LaTeX file, 3 EPS-figures (use psfig.sty), accepted for publication in PRB as brief Report (LaTeX source replaces raw-postscript file

Toward the End of Time

The null-brane space-time provides a simple model of a big crunch/big bang singularity. A non-perturbative definition of M-theory on this space-time was recently provided using matrix theory. We derive the fermion couplings for this matrix model and study the leading quantum effects. These effects include particle production and a time-dependent potential. Our results suggest that as the null-brane develops a big crunch singularity, the usual notion of space-time is replaced by an interacting gluon phase. This gluon phase appears to constitute the end of our conventional picture of space and time.Comment: 31 pages, reference adde

Non-equilibrium steady state of sparse systems

A resistor-network picture of transitions is appropriate for the study of energy absorption by weakly chaotic or weakly interacting driven systems. Such "sparse" systems reach a novel non-equilibrium steady state (NESS) once coupled to a bath. In the stochastic case there is an analogy to the physics of percolating glassy systems, and an extension of the fluctuation-dissipation phenomenology is proposed. In the mesoscopic case the quantum NESS might differ enormously from the stochastic NESS, with saturation temperature determined by the sparsity. A toy model where the sparsity of the system is modeled using a log-normal random ensemble is analyzed.Comment: 6 pages, 6 figures, EPL accepted versio

Contact area of rough spheres: Large scale simulations and simple scaling laws

We use molecular simulations to study the nonadhesive and adhesive atomic-scale contact of rough spheres with radii ranging from nanometers to micrometers over more than ten orders of magnitude in applied normal load. At the lowest loads, the interfacial mechanics is governed by the contact mechanics of the first asperity that touches. The dependence of contact area on normal force becomes linear at intermediate loads and crosses over to Hertzian at the largest loads. By combining theories for the limiting cases of nominally flat rough surfaces and smooth spheres, we provide parameter-free analytical expressions for contact area over the whole range of loads. Our results establish a range of validity for common approximations that neglect curvature or roughness in modeling objects on scales from atomic force microscope tips to ball bearings.Comment: 2 figures + Supporting Materia