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

CHANGING CONSUMER DEMAND AND ITS IMPACT ON CANADIAN AGRICULTURAL POLICY AND TRADE

The purpose of this paper is to discuss how consumers in Canada, like those in the United States and Europe, have changed over the last ten years and the impact this is having on how agricultural commodities are being produced, transformed, distributed and traded. It will also be important to discuss how governments in Canada and elsewhere have reacted and how policies are being adopted to help the agriculture and agri-food sector adjust to the new realities of a more demanding and sophisticated consumer, at home and abroad.Agricultural and Food Policy, Demand and Price Analysis, International Relations/Trade,

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

Stiffness of Contacts Between Rough Surfaces

The effect of self-affine roughness on solid contact is examined with molecular dynamics and continuum calculations. The contact area and normal and lateral stiffnesses rise linearly with the applied load, and the load rises exponentially with decreasing separation between surfaces. Results for a wide range of roughnesses, system sizes and Poisson ratios can be collapsed using Persson's contact theory for continuous elastic media. The atomic scale response at the interface between solids has little affect on the area or normal stiffness, but can greatly reduce the lateral stiffness. The scaling of this effect with system size and roughness is discussed.Comment: 4 pages, 3 figure

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

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

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

Classification of unit-vector fields in convex polyhedra with tangent boundary conditions

A unit-vector field n on a convex three-dimensional polyhedron P is tangent if, on the faces of P, n is tangent to the faces. A homotopy classification of tangent unit-vector fields continuous away from the vertices of P is given. The classification is determined by certain invariants, namely edge orientations (values of n on the edges of P), kink numbers (relative winding numbers of n between edges on the faces of P), and wrapping numbers (relative degrees of n on surfaces separating the vertices of P), which are subject to certain sum rules. Another invariant, the trapped area, is expressed in terms of these. One motivation for this study comes from liquid crystal physics; tangent unit-vector fields describe the orientation of liquid crystals in certain polyhedral cells.Comment: 21 pages, 2 figure

Cognitive performance in multiple system atrophy

The cognitive performance of a group of patients with multiple system atrophy (MSA) of striato-nigral predominance was compared with that of age and IQ matched control subjects, using three tests sensitive to frontal lobe dysfunction and a battery sensitive to memory and learning deficits in Parkinson's disease and dementia of the Alzheimer type. The MSA group showed significant deficits in all three of the tests previously shown to be sensitive to frontal lobe dysfunction. Thus, a significant proportion of patients from the MSA group failed an attentional set-shifting test, specifically at the stage when an extra-dimensional shift was required. They were also impaired in a subject-ordered test of spatial working memory. The MSA group showed deficits mostly confined to measures of speed of thinking, rather than accuracy, on the Tower of London task. These deficits were seen in the absence of consistent impairments in language or visual perception. Moreover, the MSA group showed no significant deficits in tests of spatial and pattern recognition previously shown to be sensitive to patients early in the course of probable Alzheimer's disease and only a few patients exhibited impairment on the Warrington Recognition Memory Test. There were impairments on other tests of visual memory and learning relative to matched controls, but these could not easily be related to fundamental deficits of memory or learning. Thus, on a matching-to-sample task the patients were impaired at simultaneous but not delayed matching to sample, whereas difficulties in a pattern-location learning task were more evident at its initial, easier stages. The MSA group showed no consistent evidence of intellectual deterioration as assessed from their performance on subtests of the Wechsler Adult Intelligence Scale (WAIS) and the National Adult Reading Test (NART). Consideration of individual cases showed that there was some heterogeneity in the pattern of deficits in the MSA group, with one patient showing no impairment, even in the face of considerable physical disability. The results show a distinctive pattern of cognitive deficits, unlike those previously seen using the same tests in patients with Parkinson's and Alzheimer's diseases, and suggesting a prominent frontal-lobe-like component. The implications for concepts of 'subcortical' dementia and 'fronto-striatal' cognitive dysfunction are considered