Structural studies and influence of the structure on the electrical and optical properties of microcrystalline silicon thin films produced by RF sputtering

Microcrystalline silicon thin films were produced by reactive magnetron sputtering on glass substrates under several different conditions (RF power and gas mixture composition). The film structure was studied by X-ray diffractometry (XRD), transmission electron microscopy (TEM) and Raman spectroscopy, allowing the determination of crystal sizes, crystallinity and mechanical strain. These parameters were evaluated by fitting a pseudo-Voigt function to the X-ray data, and by the application of the strong phonon confinement model to the Raman spectra. The degree of crystallinity and the presence of single crystals or crystal agglomerates, which was confirmed by TEM, depends on the preparation conditions, and strongly affects the optical spectra and the electrical transport properties.Fundação para a Ciência e a Tecnologia (FCT) - PRAXIS XX

Influence of copper on the electronic properties of amorphous chalcogenides

We have studied the influence of alloying copper with amorphous arsenic sulfide on the electronic properties of this material. In our computer-generated models, copper is found in two-fold near-linear and four-fold square-planar configurations, which apparently correspond to Cu(I) and Cu(II) oxidation states. The number of overcoordinated atoms, both arsenic and sulfur, grows with increasing concentration of copper. Overcoordinated sulfur is found in trigonal planar configuration, and overcoordinated (four-fold) arsenic is in tetrahedral configuration. Addition of copper suppresses the localization of lone-pair electrons on chalcogen atoms, and localized states at the top of the valence band are due to Cu 3d orbitals. Evidently, these additional Cu states, which are positioned at the same energies as the states due to ([As4]-)-([S_3]+) pairs, are responsible for masking photodarkening in Cu chalcogenides

Optical modulation spectroscopy of hydrogenated microcrystalline silicon

The properties of microcrystalline silicon thin films prepared by RF sputtering were investigated by optical modulation spectroscopy at room temperature and the results were correlated with Raman and conductivity measurements. For comparative purposes, a number of good quality PECVD microc-Si:H samples were also investigated. For PECVD samples the OMS signal is very weak, and only measurable for probe beam energies comparable to the gap of amorphous silicon. This indicates the absence of gap states and therefore a very high crystalline fraction, as confirmed by Raman and TEM measurements. In what concerns RF-sputtered samples, different behaviors can be distinguished: Some samples show a low OMS signal which can be attributed either to a high crystallinity (low density of gap states) or to high recombination rates. These two cases can be distinguished by electrical conductivity values and analysis of the Raman spectra. Other samples exhibit a OMS signal similar to a-Si:H and have low conductivity values, consistent with a Raman spectrum typical of a-Si:H.FCT-grant from PRAXIS XX

Using signature genes as tools to assess environmental viral ecology and diversity

Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the Bacterial and Eukaryotic kingdoms, largely due to the absence of any ‘universal phylogenetic marker’. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for datasets of specific virus groups. Genes that have been used include those encoding structural proteins, portal protein, major capsid protein and tail sheath protein, auxiliary metabolism genes such as psbA, psbB and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal and seasonal variation and diversity in a wide range of habitats.http://aem.asm.orghb201

Modelling fish habitat preference with a genetic algorithm-optimized Takagi-Sugeno model based on pairwise comparisons

Species-environment relationships are used for evaluating the current status of target species and the potential impact of natural or anthropogenic changes of their habitat. Recent researches reported that the results are strongly affected by the quality of a data set used. The present study attempted to apply pairwise comparisons to modelling fish habitat preference with Takagi-Sugeno-type fuzzy habitat preference models (FHPMs) optimized by a genetic algorithm (GA). The model was compared with the result obtained from the FHPM optimized based on mean squared error (MSE). Three independent data sets were used for training and testing of these models. The FHPMs based on pairwise comparison produced variable habitat preference curves from 20 different initial conditions in the GA. This could be partially ascribed to the optimization process and the regulations assigned. This case study demonstrates applicability and limitations of pairwise comparison-based optimization in an FHPM. Future research should focus on a more flexible learning process to make a good use of the advantages of pairwise comparisons

High-level diversity of tailed phages, eukaryote-associated viruses, and virophage-like elements in the metaviromes of Antarctic soils

The metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularly Mycobacterium phages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae>Myoviridae>Podoviridae). No archaeal viruses were found. Unexpectedly, cyanophages were poorly represented in both metaviromes and were phylogenetically distant from currently characterized cyanophages. Putative phage genomes were assembled and showed a high level of unaffiliated genes, mostly from hypolithic viruses. Moreover, unusual gene arrangements in which eukaryotic and prokaryotic virus-derived genes were found within identical genome segments were observed. Phycodnaviridae and Mimiviridae viruses were the second-mostabundant taxa and more numerous within open soil. Novel virophage-like sequences (within the Sputnik clade) were identified. These findings highlight high-level virus diversity and novel species discovery potential within Antarctic hyperarid soils and may serve as a starting point for future studies targeting specific viral groups.IS