Thickness dependence of structure and optical properties of silver films deposited by magnetron sputtering

A series of silver films with different thickness were prepared under identical conditions by direct current magnetron sputtering. The optical properties of the silver films were measured using spectrophotometric techniques and the optical constants were calculated from reflection and transmission measurements made at near normal incidence. The results show that the optical properties and constants are affected by films' thickness. Below the critical thickness of 17 nm at which Ag film forms a continuous film, the optical properties and constants vary significantly as the thickness of films increases and then tends to a stable value which is reached at 41 nm. X-ray diffraction measurements were carried out to examine the structure and stress evolution of the Ag films as a function of films' thickness. It was found that the interplanar distance of (111) orientation decreases when the film thickness increases and tends to be close to that of bulk material. The compressive strains also decrease with increasing thickness. (C) 2007 Published by Elsevier B.V.

Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats

Pheromones are chemicals produced and detected by conspecifics to elicit social/sexual physiological and behavioral responses, and they are perceived primarily by the vomeronasal organ (VNO) in terrestrial vertebrates. Two large superfamilies of G protein-coupled receptors, V1rs and V2rs, have been identified as pheromone receptors in vomeronasal sensory neurons. Based on a computational analysis of the mouse and rat genome sequences, we report the first global draft of the V2r gene repertoire, composed of similar to 200 genes and pseudogenes. Rodent V2rs are subject to rapid gene births/deaths and accelerated amino acid substitutions, likely reflecting the species-specific nature of pheromones. Vertebrate V2rs appear to have originated twice prior to the emergence of the VNO in ancestral tetrapods, explaining seemingly inconsistent observations among different V2rs. The identification of the entire V2r repertoire opens the door to genomic-level studies of the structure, function, and evolution of this diverse group of sensory receptors. (c) 2005 Elsevier Inc. All rights reserved.

Population genetic structure and geographical differentiation of the Chinese catfish Hemibagrus macropterus (Siluriformes, Bagridae): Evidence for altered drainage patterns

National Natural Science Foundation of China (NSFC) [2007CB411600, 30530120]

Structure and optical properties of self-assembled InAs/GaAs quantum dots with In0.15Ga0.85As underlying layer

A high density of 1.02 x 10(11) cm(-2) of InAs islands with In(0.15)Gao(0.85)As underlying layer has been achieved on GaAs (10 0) substrate by solid source molecular beam epitaxy. Atomic force microscopy and PL spectra show the size evolution of InAs islands. A 1.3 mum photoluminescence (PL) from InAs islands with In(0.15)Gao(0.85)As underlying layer and InGaAs strain-reduced layer has been obtained. Our results provide important information for optimizing the epitaxial structures of 1.3 mum wavelength quantum dots devices. (C) 2002 Elsevier Science B.V. All rights reserved.

The crystal structure and drawing induced polymorphism in poly(aryl ether ketone)s .3. Crystallization during hot-drawing of poly(ether ether ketone ketone)

The evolution of crystallinity and polymorphism during hot-drawing of amorphous poly(ether ether ketone ketone) (PEEKK) as a function of strain rate, draw ratio, and temperature was investigated. In modification I, the competition of chain extension and molecular alignment is responsible for the strain rate and temperature dependence. Modification II crystallization is basically controlled by chain extension during stretching. The former can be transformed into the latter via relaxation during stretching or annealing at elevated temperature.

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Influence of molten-state annealing on the phase structure and crystallization behaviour of high impact polypropylene copolymer

The phase structure evolution of high impact polypropylene copolymer (IPC) during molten-state annealing and its influence on crystallization behaviour were studied. An entirely different architecture of the IPC melt was observed after being annealed, and this architecture resulted in variations of the crystallization behaviour. In addition, it was found that the core-shell structure of the dispersed phase was completely destroyed and the sizes of the dispersed domains increased sharply after being annealed at 200 degrees C for 200 min. Through examination of the coarseness of the phase morphology using phase contrast microscopy (PCM), it was found that a co-continuous structure and an abnormal 'sea-island' structure generally appeared with an increase in annealing time. The original matrix PP component appeared as a dispersed phase, whereas the copolymer components formed a continuous 'sea-island' structure. This change is ascribed to the large tension induced by solidification at the phase interface and the great content difference between the components. When the temperature was reduced the structure reverted to its original form. With increasing annealing time, the spherulite profiles became more defined and the spherulite birefringence changed from vague to clear. Overall crystallization rates and nucleation densities decreased, but the spherulite radial growth rates remained almost constant, indicating that molten-state annealing mainly affects the nucleation ability of IPC, due to a coarsened microstructure and decreased interface area. (C) 2011 Elsevier Ltd. All rights reserved.

The phylogeny, structure and function of trematode cysteine proteases, with particular emphasis on the Fasciola hepatica cathepsin L family

Helminth parasites (nematodes, flatworms and cestodes) infect over 1 billion of the world's population causing high morbidity and mortality. The large tissue-dwelling worms express papain-like cysteine peptidases, termed cathepsins that play important roles in virulence including host entry, tissue migration and the suppression of host immune responses. Much of our knowledge of helminth cathepsins comes from studies using flatworms or trematode (fluke) parasites. The developmentally-regulated expression of these proteases correlates with the passage of parasites through host tissues and their encounters with different host macromolecules. Recent phylogenetic, biochemical and structural studies indicate that trematode cathepsins exhibit overlapping but distinct substrate specificities due to divergence within the protease active site. Here we provide an overview of the evolution, biochemistry and structure of these important enzymes and highlight how recent advances in proteomics and gene silencing techniques are allowing researchers to probe their biological functions. We focus mainly on members of the cathepsin L gene family of the animal and human pathogen, Fasciola hepatica, because of our deep understanding of their function, biochemistry and structure.

A complete analytic theory for structure and dynamics of populations and communities spanning wide ranges in body size

The prediction and management of ecosystem responses to global environmental change would profit from a clearer understanding of the mechanisms determining the structure and dynamics of ecological communities. The analytic theory presented here develops a causally closed picture for the mechanisms controlling community and population size structure, in particular community size spectra, and their dynamic responses to perturbations, with emphasis on marine ecosystems. Important implications are summarised in non-technical form. These include the identification of three different responses of community size spectra to size-specific pressures (of which one is the classical trophic cascade), an explanation for the observed slow recovery of fish communities from exploitation, and clarification of the mechanism controlling predation mortality rates. The theory builds on a community model that describes trophic interactions among size-structured populations and explicitly represents the full life cycles of species. An approximate time-dependent analytic solution of the model is obtained by coarse graining over maturation body sizes to obtain a simple description of the model steady state, linearising near the steady state, and then eliminating intraspecific size structure by means of the quasi-neutral approximation. The result is a convolution equation for trophic interactions among species of different maturation body sizes, which is solved analytically using a novel technique based on a multiscale expansion.

The Vertical Distribution and Evolution of Slam Pressure on an Oscillating Wave Surge Converter

The accurate definition of the extreme wave loads which act on offshore structures represents a significant challenge for design engineers and even with decades of empirical data to base designs upon there are still failures attributed to wave loading. The environmental conditions which cause these loads are infrequent and highly non-linear which means that they are not well understood or simple to describe. If the structure is large enough to affect the incident wave significantly further non-linear effects can influence the loading. Moreover if the structure is floating and excited by the wave field then its responses, which are also likely to be highly non-linear, must be included in the analysis. This makes the description of the loading on such a structure difficult to determine and the design codes will often suggest employing various tools including small scale experiments, numerical and analytical methods, as well as empirical data if available.
Wave Energy Converters (WECs) are a new class of offshore structure which pose new design challenges, lacking the design codes and empirical data found in other industries. These machines are located in highly exposed and energetic sites, designed to be excited by the waves and will be expected to withstand extreme conditions over their 25 year design life. One such WEC is being developed by Aquamarine Power Ltd and is called Oyster. Oyster is a buoyant flap which is hinged close to the seabed, in water depths of 10 to 15m, piercing the water surface. The flap is driven back and forth by the action of the waves and this mechanical energy is then converted to electricity.
It has been identified in previous experiments that Oyster is not only subject to wave impacts but it occasionally slams into the water surface with high angular velocity. This slamming effect has been identified as an extreme load case and work is ongoing to describe it in terms of the pressure exerted on the outer skin and the transfer of this short duration impulsive load through various parts of the structure.
This paper describes a series of 40th scale experiments undertaken to investigate the pressure on the face of the flap during the slamming event. A vertical array of pressure sensors are used to measure the pressure exerted on the flap. Characteristics of the slam pressure such as the rise time, magnitude, spatial distribution and temporal evolution are revealed. Similarities are drawn between this slamming phenomenon and the classical water entry problems, such as ship hull slamming. With this similitude identified, common analytical tools are used to predict the slam pressure which is compared to that measured in the experiment.

The study of RNA tertiary interactions in tRNA structure and function

Le rôle des deux paires de bases universelles inverse Hoogsteen U : A ( RHUAs ) présentent chez les ARNt standards , une dans la boucle T et l'autre dans le noyau de la forme en L , a été étudiée. Pour chacun des RHUAs , un criblage génétique spécialisé in vivo chez les bactéries , le système suppresseur ambre ( pour l'étude de la RHUA dans la boucle T ) et le système d'ARNt de la sélénocystéine ( tRNASec ) ( pour l'étude de la RHUA dans le noyau ) , ont été utilisé pour générer des variants fonctionnels à partir de multiples librairies combinatoires . Ces variants ont ensuite été séquencé et soumis à une analyse systématique qui comprend la modélisation informatique et un type d'analyse phylogénétique. Les résultats du système suppresseur ambre ont montré un ensemble de variants fonctionnels qui ne nécessitent pas le motif RHUA dans la boucle T et qui ont remplacé la méthode standard de l'interaction entre les boucles D et T avec une double hélice interboucle , ILDH . D'autres études ont abouti à la détermination d'un modèle In silico de l'alternative à la norme standard de la boucle T, sous le nom de type III . Les résultats du système tRNASec ont révélé que pour cette ARNt exceptionnel, l'absence de RHUA ( dans le noyau ) assure une flexibilité accrue qui est spécifiquement nécessaire pour la fonction de tRNASec . Ainsi, les ARNt standards , à la différence de tRNASec , avec la présence universelle de RHUA dans le noyau , a été naturellement sélectionnée pour être rigide . Pris ensemble, la RHUA joue un rôle essentiel dans la stabilisation des interactions tertiaires.

Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Evaluating the structure and magnitude of the ash plume during the initial phase of the 2010 Eyjafjallajökull eruption using lidar observations and NAME simulations

The Eyjafjallajökull volcano in Iceland erupted explosively on 14 April 2010, emitting a plume of ash into the atmosphere. The ash was transported from Iceland toward Europe where mostly cloud-free skies allowed ground-based lidars at Chilbolton in England and Leipzig in Germany to estimate the mass concentration in the ash cloud as it passed overhead. The UK Met Office's Numerical Atmospheric-dispersion Modeling Environment (NAME) has been used to simulate the evolution of the ash cloud from the Eyjafjallajökull volcano during the initial phase of the ash emissions, 14–16 April 2010. NAME captures the timing and sloped structure of the ash layer observed over Leipzig, close to the central axis of the ash cloud. Relatively small errors in the ash cloud position, probably caused by the cumulative effect of errors in the driving meteorology en route, result in a timing error at distances far from the central axis of the ash cloud. Taking the timing error into account, NAME is able to capture the sloped ash layer over the UK. Comparison of the lidar observations and NAME simulations has allowed an estimation of the plume height time series to be made. It is necessary to include in the model input the large variations in plume height in order to accurately predict the ash cloud structure at long range. Quantitative comparison with the mass concentrations at Leipzig and Chilbolton suggest that around 3% of the total emitted mass is transported as far as these sites by small (<100 μm diameter) ash particles.