D3R grand challenge 4: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

Journal of Computer-Aided Molecular Design - The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and...     

THE ECONOMICS OF TIMBER SUPPLY: AN ANALYTICAL SYNTHESIS OF MODELING APPROACHES

The joint supply of timber and other services from forest environments plays a central role in most forest land debates. This paper defines a general conceptual model of timber supply that provides the context for discussing both individual harvest choice and aggregate supply models. While the structure and breadth of these models has developed considerably over the last twenty years, unresolved issues remain. Supply formulations that account for the quality and vintage distribution of forest capital will be necessary for improving medium- and long-run forecasts. This will be especially important for examining the potential impacts of structural changes in forest production and timber markets. In addition, consistent aggregation of individual owners to total supply will be required to address changing forest land ownership patterns.     

Surface curvature analyzed with a grid-reflection technique

A method to determine the curvature of a reflective surface is described. The image of a grid network reflected from the surface is photographed. The magnification of the grid is used to obtain the curvature over the entire reflective surface. Two practical examples are reported: a curved mirror with irregularities and a reinforced rubber slab.     

On the role of material and optical properties in complete photoelastic analysis

Consideration of the laws of elasticity and optics allows the classification of photoelastic materials into several categories. Two types of photoelastic materials are studied experimentally in compressible and incompressible forms to decide in which category they belong. Two epoxies and three polyurethane rubbers are reported. Both epoxies were calibrated for their response to frozen stress, and one under live load. The rubbers were all calibrated under live load at ambient temperature. The results support an earlier hypothesis that the photoelastic response of incompressible materials is strain sensitive and cannot be used directly in the general three-dimensional case to determine normal stress without additional data.     

Observations of Lorentzian lines with slits of finite widths

We present, in graphical form, the required integrals for observations of spectral lines with Lorentzian profiles through rectangular slit functions.     

Effect of the Radiation Power Density on the Sensitivity of a Diamond Detector

This paper presents the results of an experimental study of the sensitivity of a detector made of natural diamond of the IIa type as a function of the power density of the radiation of a pulsed xenon lamp. It has been shown that the sensitivity of the detector depends on the power density of the xenon lamp radiation and equals about (1–6)·10^–4 A/W. A monotonic decrease in sensitivity of the detector during a radiation pulse has been detected. The minimum resistance of the diamond crystal with an irradiated face of area 3 mm², placed 7 mm away from the axis of the xenon lamp, was 300 , which corresponds to a specific conductivity of 2.2 ^–1·m^–1.     

An investigation of the chemical stability of arsenosugars in basic environments using IC-ICP-MS and IC-ESI-MS/MS

This paper evaluates the chemical stability of four arsenosugars using tetramethylammonium hydroxide (TMAOH) as an extraction solvent. This solvent was chosen because of the near quantitative removal of these arsenicals from difficult to extract seafood (oysters and shellfish). Four arsenosugars (3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropylene glycol--As(328), 3-5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropanesulfonic acid--As(392), 3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropyl hydrogen sulfate--As(408), and 3-[5'-deoxy-5'-(dimethylarsinoyl)-beta-ribofuranosyloxy]-2-hydroxypropyl-2,3-hydroxypropyl phosphate--As(482)) were evaluated. The stability of these four arsenosugars were studied independently in a solution of 2.5% TMAOH at 60 degrees C over a period of up to 8 h. Two arsenosugars, As(328) and As(392), were found to be relatively stable in this solution for up to 8 h. However, As(408) and As(482) formed detectable quantities of dimethylarsinic acid (DMAA) and As(328) within 0.5 and 2 h, respectively. It was found that 97% of As(408) degrades after 8 h of treatment producing 3.4 times as much DMAA as As(328). This is contrary to As(482), which produces 13 times as much As(328) as DMAA and only 37% of the As(482) was converted by the 8 h treatment at 60 degrees C. These degradation products led to the investigation of weaker TMAOH extraction solvents. Three different concentrations (2.5%, 0.83% and 0.25%) were used to determine the effect of TMAOH concentration on the degradation rate of As(408). By reducing the TMAOH concentration to 0.83%, the conversion of the arsenosugar to As(328) and DMAA is nearly eliminated (less than 5% loss). Arsenosugars, As(408) and As(482), were also studied in 253 mM NaOH to verify the degradation products. The NaOH experiments were conducted to investigate a possible hydroxide based reaction mechanism. Similar degradation plots were found for each arsenosugar when compared to the 2.5% TMAOH data. A mechanism has been proposed for the formation of As(328) from As(408) and As(482) in base via an SN2 reaction (hydroxide attack) at the side chain carbon adjacent to the inorganic ester. The formation of DMAA is observed in all arsenosugars after prolonged exposure. This probably occurs via an SN2 attack at the arsenic atom.     

Local vibrational modes of isolated hydrogen in germanium

Two distinct isolated hydrogen defects are observed in crystalline Ge by in situ infrared absorption spectroscopy. Implantation of protons into Ge at cryogenic temperatures gives rise to two intense absorption lines at 745 and 1794 cm(-1). The lines originate from distinct defects, each of which contains one H atom located on a <111> axis. The 1794-cm(-1) line is assigned to bond center H in the positive charge state, whereas the 745-cm(-1) line is ascribed to negatively charged H located on a <111> axis close to the tetrahedral site.     

EPR Studies of Tl0.5Pb0.5Sr1.6Ba0.4CaCu2?xRuxO7?δ Superconductor

Bulk superconducting samples of type Tl_0.5Pb_0.5Sr_1.6Ba_0.4CaCu_2−x Ru _x O_7−δ, (Tl, Pb)/Sr-1212, with 0.0 ≤ x ≤ 0.525 were prepared by the conventional one-step solid-state reaction technique. The prepared samples were investigated using X-ray powder diffraction, electrical resistivity and electron paramagnetic resonance (EPR) measurements. Enhancement of the phase formation, superconducting transition temperature T _c and hole carriers concentration P was observed up to x = 0.075. For x > 0.075, a reverse trend was observed. EPR spectra were measured at different temperatures (120–290 K) for all prepared samples. The number of spins N participating in the resonance and the paramagnetic susceptibility χ were calculated as a function of both Ru-content and temperature. N and χ increased as the Ru-content increased. A linear relationship between logN and 1/T was established, from which the activation energy E _a was calculated as a function of the Ru-content. The temperature dependence of χ was fitted according to Curie–Weiss type of magnetic behavior. Curie constant C, Curie temperature θ, the effective magnetic moment μ and the electronic specific heat γ were estimated as a function of the Ru-content.