Linearized force constants method for lattice dynamics in mixed semiconductors

A simple and accurate method of calculating phonon spectra in mixed semiconductors alloys, on the basis of preliminarily (from first principles) relaxed atomic structure, is proposed and tested for (Zn,Be)Se and (Ga,In)As solid solutions. The method uses an observation that the interatomic force constants, calculated ab initio for a number of microscopic configurations in the systems cited, show a clear linear variation of the main (diagonal) values of the interatomic force constants with the corresponding bond length. We formulate simple rules about how to recover the individual 3x3 subblocks of the force constants matrix in their local (bonds-related) coordinate systems and how to transform them into a global (crystal cell-related) coordinate system. Test calculations done for 64-atom supercells representing different concentrations of (Zn,Be)Se and (Ga,In)As show that the phonon frequencies and compositions of eigenvectors are faithfully reproduced in a linearized force constants calculation, as compared to true ab initio calculations.Comment: to appear in the proceedings of the Phonons2007 conference (Paris, July 2007

Lattice dynamics of mixed semiconductors (Be,Zn)Se from first-principles calculations

Vibration properties of Zn(1-x)Be(x)Se, a mixed II-VI semiconductor haracterized by a high contrast in elastic properties of its pure constituents, ZnSe and BeSe, are simulated by first-principles calculations of electronic structure, lattice relaxation and frozen phonons. The calculations within the local density approximation has been done with the Siesta method, using norm-conserving pseudopotentials and localized basis functions; the benchmark calculations for pure endsystems were moreover done also by all-electron WIEN2k code. An immediate motivation for the study was to analyze, at the microscopic level, the appearance of anomalous phonon modes early detected in Raman spectra in the intermediate region (20 to 80%) of ZnBe concentration. This was early discussed on the basis of a percolation phenomenon, i.e., the result of the formation of wall-to-wall --Be--Se-- chains throughout the crystal. The presence of such chains was explicitly allowed in our simulation and indeed brought about a softening and splitting off of particular modes, in accordance with experimental observation, due to a relative elongation of Be--Se bonds along the chain as compared to those involving isolated Be atoms. The variation of force constants with interatomic distances shows common trends in relative independence on the short-range order.Comment: 11 pages, 10 figures, to be published in Phys. Rev.

Physiological response of the cold-water coral Desmophyllum dianthus to thermal stress and ocean acidification

Rising temperatures and ocean acidification driven by anthropogenic carbon emissions threaten both tropical and temperate corals. However, the synergistic effect of these stressors on coral physiology is still poorly understood, in particular for cold-water corals. This study assessed changes in key physiological parameters (calcification, respiration and ammonium excretion) of the widespread cold-water coral Desmophyllum dianthus maintained for ∼8 months at two temperatures (ambient 12 ◦C and elevated 15 ◦C) and two pCO2 conditions (ambient 390 ppm and elevated 750 ppm). At ambient temperatures no change in instantaneous calcification, respiration or ammonium excretion rates was observed at either pCO2 levels. Conversely, elevated temperature (15 ◦C) significantly reduced calcification rates, and combined elevated temperature and pCO2 significantly reduced respiration rates. Changes in the ratio of respired oxygen to excreted nitrogen (O:N), which provides information on the main sources of energy being metabolized, indicated a shift from mixed use of protein and carbohydrate/lipid as metabolic substrates under control conditions, to less efficient protein-dominated catabolism under both stressors. Overall, this study shows that the physiology of D. dianthus is more sensitive to thermal than pCO2 stress, and that the predicted combination of rising temperatures and ocean acidification in the coming decades may severely impact this cold-water coral species

A multi-approach survey as the most reliable tool to accurately assess biodiversity: an example of thai murine rodents

Wildlife surveys rely on an accurate taxonomic framework. Identification tools used to reach this goal are not equivalent and may depend on several objectives and constraints, including sampling conservation difficulties, the invasiveness of the sampling techniques, sampling capacity, the relevance of the results, materials needed, the cost and the user time required in the field and laboratory. This article presents and discusses the advantages and limits of each identification tool used in the Ceropath (Community ecology of rodents and their pathogens in South East Asia) program to reach a fast and relevant identification of the rodents sampled. It is concluded that there needs to be a combination of the results from different methods, including the most recent ones, to achieve an improvement in taxonomic identification

Preliminary morphologic and molecular study of teh Entoloma rusticoides group (Agaricales - Basidiomycota)

Es presenta un estudi sobre el grup rusticoides del gènere Entoloma subgènere Claudopus a la Península Ibérica. L'anàlisi filogenètica, sobre la base de 48 seqüències d'ITS i 45 seqüències de LSU, entre les quals, les dels tipus de 8 dels tàxons analitzats, mostra una marcada diversitat genètica que concorda amb la notable variabilitat observada en aquest grup. D'acord amb aquest fet, es descriuen els següents nous tàxons: E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum i E. phaeocarpum. A més, es tipifiquen E. phaeocyathus i E. rusticoides. S'inclouen claus provisionals d'identificació. S'aporten descripcions macro i microscòpiques, dibuixos i fotografies de la majoria dels tàxons estudiats.A study of the Entoloma rusticoides-group (subgenus Claudopus) in the Iberian peninsula is presented. Phylogenetic inference, based on 48 nrITS and 45 28S nrLSU sequences, including those of 8 type specimens, revealed a high genetic diversity, in accordance with the observed morphological variability in this group. In addition new taxa are proposed to accomodate independent lineages (E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum and E. phaeocarpum) and the typification of E. phaeocyathus and E. rusticoides is proposed. Preliminary taxonomic keys are included to help identification. For most species macro and microscopic descriptions, drawings and photographs are presented

The porin and the permeating antibiotic: A selective diffusion barrier in gram-negative bacteria

Gram-negative bacteria are responsible for a large proportion of antibiotic resistant bacterial diseases. These bacteria have a complex cell envelope that comprises an outer membrane and an inner membrane that delimit the periplasm. The outer membrane contains various protein channels, called porins, which are involved in the influx of various compounds, including several classes of antibiotics. Bacterial adaptation to reduce influx through porins is an increasing problem worldwide that contributes, together with efflux systems, to the emergence and dissemination of antibiotic resistance. An exciting challenge is to decipher the genetic and molecular basis of membrane impermeability as a bacterial resistance mechanism. This Review outlines the bacterial response towards antibiotic stress on altered membrane permeability and discusses recent advances in molecular approaches that are improving our knowledge of the physico-chemical parameters that govern the translocation of antibiotics through porin channel

Preliminary morphologic and molecular study of teh Entoloma rusticoides group (Agaricales - Basidiomycota)

Es presenta un estudi sobre el grup rusticoides del gènere Entoloma subgènere Claudopus a la Península Ibérica. L'anàlisi filogenètica, sobre la base de 48 seqüències d'ITS i 45 seqüències de LSU, entre les quals, les dels tipus de 8 dels tàxons analitzats, mostra una marcada diversitat genètica que concorda amb la notable variabilitat observada en aquest grup. D'acord amb aquest fet, es descriuen els següents nous tàxons: E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum i E. phaeocarpum. A més, es tipifiquen E. phaeocyathus i E. rusticoides. S'inclouen claus provisionals d'identificació. S'aporten descripcions macro i microscòpiques, dibuixos i fotografies de la majoria dels tàxons estudiats.A study of the Entoloma rusticoides-group (subgenus Claudopus) in the Iberian peninsula is presented. Phylogenetic inference, based on 48 nrITS and 45 28S nrLSU sequences, including those of 8 type specimens, revealed a high genetic diversity, in accordance with the observed morphological variability in this group. In addition new taxa are proposed to accomodate independent lineages (E. almeriense, E. graphitipes f. cystidiatum, E. halophilum, E. muscoalpinum and E. phaeocarpum) and the typification of E. phaeocyathus and E. rusticoides is proposed. Preliminary taxonomic keys are included to help identification. For most species macro and microscopic descriptions, drawings and photographs are presented

Environmental drivers of distribution and reef development of the Mediterranean coral Cladocora caespitosa

Cladocora caespitosa is the only Mediterranean scleractinian similar to tropical reef-building corals. While this species is part of the recent fossil history of the Mediterranean Sea, it is currently considered endangered due to its decline during the last decades. Environmental factors affecting the distribution and persistence of extensive bank reefs of this endemic species across its whole geographic range are poorly understood. In this study, we examined the environmental response of C. caespitosa and its main types of assemblages using ecological niche modeling and ordination analysis. We also predicted other suitable areas for the occurrence of the species and assessed the conservation effectiveness of Mediterranean marine protected areas (MPAs) for this coral. We found that phosphate concentration and wave height were factors affecting both the occurrence of this versatile species and the distribution of its extensive bioconstructions in the Mediterranean Sea. A set of factors (diffuse attenuation coefficient, calcite and nitrate concentrations, mean wave height, sea surface temperature, and shape of the coast) likely act as environmental barriers preventing the species from expansion to the Atlantic Ocean and the Black Sea. Uncertainties in our large-scale statistical results and departures from previous physiological and ecological studies are also discussed under an integrative perspective. This study reveals that Mediterranean MPAs encompass eight of the ten banks and 16 of the 21 beds of C. caespitosa. Preservation of water clarity by avoiding phosphate discharges may improve the protection of this emblematic species.Spanish Ministry of Economy and Competitiveness [CTM2014-57949-R]info:eu-repo/semantics/publishedVersio

Sublittoral soft bottom communities and diversity of Mejillones Bay in northern Chile (Humboldt Current upwelling system)

The macrozoobenthos of Mejillones Bay (23°S; Humboldt Current) was quantitatively investigated over a 7-year period from austral summer 1995/1996 to winter 2002. About 78 van Veen grab samples taken at six stations (5, 10, 20 m depth) provided the basis for the analysis of the distribution of 60 species and 28 families of benthic invertebrates, as well as of their abundance and biomass. Mean abundance (2,119 individuals m-2) was in the same order compared to a previous investigation; mean biomass (966 g formalin wet mass m-2), however, exceeded prior estimations mainly due to the dominance of the bivalve Aulacomya ater. About 43% of the taxa inhabited the complete depth range. Mean taxonomic Shannon diversity (H', Log e) was 1.54 ± 0.58 with a maximum at 20 m (1.95 ± 0.33); evenness increased with depth. The fauna was numerically dominated by carnivorous gastropods, polychaetes and crustaceans (48%). About 15% of the species were suspensivorous, 13% sedimentivorous, 11% detritivorous, 7% omnivorous and 6% herbivorous. Cluster analyses showed a significant difference between the shallow and the deeper stations. Gammarid amphipods and the polychaete family Nephtyidae characterized the 5-mzone, the molluscs Aulacomya ater, Mitrella unifasciata and gammarids the intermediate zone, while the gastropod Nassarius gayi and the polychaete family Nereidae were most prominent at the deeper stations. The communities of the three depth zones did not appear to be limited by hypoxia during non-El Niño conditions. Therefore, no typical change in community structure occurred during El Niño 1997–1998, in contrast to what was observed for deeper faunal assemblages and hypoxic bays elsewhere in the coastal Humboldt Current system