Structural and energetic properties of nickel clusters: 2≤N≤1502 \le N \le 150

The four most stable structures of Ni$_N$ clusters with $N$ from 2 to 150 have been determined using a combination of the embedded-atom method in the version of Daw, Baskes and Foiles, the {\it variable metric/quasi-Newton} method, and our own {\it Aufbau/Abbau} method. A systematic study of energetics, structure, growth, and stability of also larger clusters has been carried through without more or less severe assumptions on the initial geometries in the structure optimization, on the symmetry, or on bond lengths. It is shown that cluster growth is predominantly icosahedral with $islands$ of {\it fcc}, {\it tetrahedral} and {\it decahedral} growth. For the first time in unbiased computations it is found that Ni$_{147}$ is the multilayer (third Mackay) icosahedron. Further, we point to an enhanced ability of {\it fcc} clusters to compete with the icosahedral and decahedral structures in the vicinity of N=79. In addition, it is shown that conversion from the {\it hcp}/anti-Mackay kind of icosahedral growth to the {\it fcc}/Mackay one occurs within a transition layer including several cluster sizes. Moreover, we present and apply different analytical tools in studying structural and energetic properties of such a large class of clusters. These include means for identifying the overall shape, the occurrence of atomic shells, the similarity of the clusters with, e.g., fragments of the {\it fcc} crystal or of a large icosahedral cluster, and a way of analysing whether the $N$-atom cluster can be considered constructed from the $(N-1)$-atom one by adding an extra atom. In addition, we compare in detail with results from chemical-probe experiment. Maybe the most central result is that first for clusters with $N$ above 80 general trends can be identified.Comment: 37 pages, 11 figure

Methods for coastal monitoring and erosion risk assessment: two Portuguese case studies

Coastal zones are naturally dynamic and mobile systems exposed to natural (river flows, waves and storms) as well as human interventions that continuously reshape their morphology. Erosion phenomena related to extreme weather events and sediment scarcity are common, threatening buildings and infrastructures, as well as beaches, ecosystems and valuable wetland; conditions that pose challenges to coastal security and defence. Regular monitoring of coastal areas, assessment of their morphodynamics and identification of the processes influencing sediment transport are thus increasingly important for a better understanding of changes and evolutionary trends in coastal systems. This demands a multi-disciplinary approach involving researchers with expertise in coastal processes and state-of-the-art observation technologies. In this paper state-of-the-art surveying methods for an efficient quantification of changes in coastal environments are described and evaluated, and two NW-Portuguese case studies are presented. Survey methods included: topographic surveys based on terrestrial videogrammetric mobile mapping and aerial photogrammetry; sub-tidal bathymetry with sonar imagery using an Autonomous Surface Vehicle (ASV); as well as field observations, with sediment sampling and beach characterisation. In the first case study erosion/accretion patterns in the Douro estuary sand spit are analysed, considering its breakwater, river flow, wave and wind effects. Prior to the construction of a detached breakwater, the spitâ s morphodynamics was related to extreme river flow events, wave and wind conditions; afterwards the spit stabilized its shape and increased its area and volume. In the second case study the coast of Vila Nova de Gaia was broadly analysed, including the shoreface, foreshore and dunes, the characterization of major features and a short-period analysis of installed dynamics. Results obtained from field data, topographical surveys and numerical wave models were combined for the erosion risk assessment, using a methodology specifically developed for the study area. Both monitoring programs achieved their proposed objectives and provided valuable information to the local authorities, as gathered and processed information constitutes a valuable database for coastal planning and for ICZM purposes. They demonstrate the potential of several approaches, supported by advanced technologies, for the study of complex coastal morphodynamic processes.Zonas costeiras são sistemas naturalmente dinâmicos e móveis, expostos a fatores naturais (fluxos de rios, ondas e tempestades) e intervenções humanas, que alteram continuamente a sua morfologia. Fenómenos de erosão relacionados com temporais e escassez de sedimentos são comuns. Eles ameaçam construções e infraestruturas, praias, ecossistemas e zonas húmidas, o que constitui um desafio para a segurança e defesa costeiras. Uma monitorização regular de áreas costeiras, com avaliação da sua morfodinâmica e identificação dos processos que influenciam o transporte de sedimentos, visando uma melhor compreensão das alterações e tendências evolutivas nos sistemas costeiros, torna-se portanto cada vez mais importante. Para tal necessita-se de uma abordagem multidisciplinar e investigadores especializados em processos costeiros e tecnologias de observação de ponta. O presente trabalho descreve e avalia métodos de monitorização de última geração para uma quantificação eficiente de alterações em ambientes costeiros e apresenta dois estudos de caso Portugueses. Os métodos de observação incluem: levantamentos topográficos terrestres em modo cinemático baseados em videogrametria; levantamentos topográficos aéreos baseados em fotogrametria; batimetria sub-tidal e imagens de fundo obtidas com sonar a partir de um veículo autónomo de superfície; e observações de campo com análise de sedimentos e caracterização de praias. O primeiro caso de estudo referese à análise de padrões de erosão e acreção na restinga do estuário do Douro, tendo em conta efeitos causados pelo molhe, o caudal do rio, ondas e vento. Antes da construção de um molhe destacado, a morfodinâmica da restinga estava relacionada com eventos extremos de caudal, agitação marítima e vento. Após a construção, a forma da restinga estabilizou e observou-se um aumento da sua área e do seu volume. No segundo caso de estudo, a costa de Vila Nova de Gaia foi amplamente estudada, incluindo shoreface, foreshore e dunas, com a caracterização dos principais atributos e uma análise de curto-período da dinâmica instalada. Os resultados obtidos a partir de dados de campo, dos levantamentos topográficos e de modelos numéricos de ondas foram combinados numa análise de risco com métodos especificamente desenvolvidos para a área de estudos. Ambos os programas de monitorização atingiram os seus objetivos e geraram informação relevante para as autoridades locais. A informação recolhida e processada constitui uma base de dados valiosa para o planeamento costeiro e a Gestão Integrada de Zonas Costeiras. Os estudos demonstram o potencial das diversas abordagens, apoiadas por tecnologias avançadas, para o estudo dos processos complexos de morfodinâmica costeira.This research was partially supported by the European Regional Development Fund (ERDF) through the COMPETE – Operational Competitiveness Programme and national funds through FCT – Foundation for Science and Technology, under the project “Pest-C/ MAR/LA0015/2013”, and partially funded by the Project ECORISK (reference NORTE-07-0124-FEDER- 000054), co-financed by the North Portugal Regional Operational Programme (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF). Wave climate analyses were supported by the FCT-funded RAP project (PTDC/MAR/111223/2009)

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

Electrical transport between epitaxial manganites and carbon nanotubes

The possibility of performing spintronics at the molecular level may be realized in devices that combine fully spin polarized oxides such as manganites with carbon nanotubes. However, it is not clear whether electrical transport between such different material systems is viable. Here we show that the room temperature conductance of manganite-nanotube-manganite devices is only half the value recorded in similar palladium-nanotube-palladium devices. Interestingly, the former shows a pseudogap in the conductivity below the relatively high temperature of 200 K. Our results suggest the possibility of new spintronics heterostructures that exploit fully spin polarized sources and drains

Vibrational Properties of Nanoscale Materials: From Nanoparticles to Nanocrystalline Materials

The vibrational density of states (VDOS) of nanoclusters and nanocrystalline materials are derived from molecular-dynamics simulations using empirical tight-binding potentials. The results show that the VDOS inside nanoclusters can be understood as that of the corresponding bulk system compressed by the capillary pressure. At the surface of the nanoparticles the VDOS exhibits a strong enhancement at low energies and shows structures similar to that found near flat crystalline surfaces. For the nanocrystalline materials an increased VDOS is found at high and low phonon energies, in agreement with experimental findings. The individual VDOS contributions from the grain centers, grain boundaries, and internal surfaces show that, in the nanocrystalline materials, the VDOS enhancements are mainly caused by the grain-boundary contributions and that surface atoms play only a minor role. Although capillary pressures are also present inside the grains of nanocrystalline materials, their effect on the VDOS is different than in the cluster case which is probably due to the inter-grain coupling of the modes via the grain-boundaries.Comment: 10 pages, 7 figures, accepted for publication in Phys. Rev.

Noncollinear magnetic ordering in small Chromium Clusters

We investigate noncollinear effects in antiferromagnetically coupled clusters using the general, rotationally invariant form of local spin-density theory. The coupling to the electronic degrees of freedom is treated with relativistic non-local pseudopotentials and the ionic structure is optimized by Monte-Carlo techniques. We find that small chromium clusters (N \le 13) strongly favor noncollinear configurations of their local magnetic moments due to frustration. This effect is associated with a significantly lower total magnetization of the noncollinear ground states, ameliorating the disagreement between Stern-Gerlach measurements and previous collinear calculations for Cr_{12} and Cr_{13}. Our results further suggest that the trend to noncollinear configurations might be a feature common to most antiferromagnetic clusters.Comment: 9 pages, RevTeX plus .eps/.ps figure

Características físico-químicas de diferentes genótipos de café resistentes à ferrugem, em cafés integrais e torrados.

Uma das principais doenças do café é a ferrugem alaranjada, acarretando grandes perdas na produção e na qualidade. Nos últimos anos, a atividade cafeeira vem se adaptando para atender a demanda do mercado. Portanto, altas tecnologias têm sido aplicadas para o aumento da produtividade, resistência a doenças, redução de custos e restrição ao uso de agroquímicos. Vale ressaltar que, a qualidade do café depende da interação entre fatores genéticos, ambientais, métodos de colheita, processamento, armazenamento, torração e moagem que garantem ao grão as características de sabor e aroma desejados. Com isso, o conhecimento do potencial de cada cultivar melhorada geneticamente quanto a produtividade, qualidade de sementes e composição química são ferramentas importantes para complementar os trabalhos de melhoramento genético. Neste sentido, o objetivo no presente trabalho foi caracterizar sementes de diferentes genótipos de café resistentes à ferrugem por meio de analises físico-químicas em amostras integrais e torradas, afim de investigar as alterações sofridas após a torração

Qualidade fisiológica de sementes de diferentes cultivares de café com resistência à ferrugem.

A cultura do café é suscetível a inúmeras doenças. Dentre essas, a ferrugem é a que mais se destaca, podendo ocorrer em qualquer região produtora de café, causando grandes prejuízos na produção que podem chegar até 50%. Entretanto, a intensidade da ferrugem está associada ao ambiente, ao patógeno, ao hospedeiro e aos manejos culturais. O controle químico apresenta-se viável economicamente, mas apresenta várias desvantagens. A melhor alternativa para o controle da ferrugem é o uso de cultivares resistentes, por ser um método econômico e não prejudicial ao meio ambiente. Nesse sentido, no presente trabalho teve como objetivo caracterizar sementes de clones de cafés resistentes à ferrugem, por meio de análises fisiológicas

Hyperglycaemia and Pseudomonas aeruginosa acidify cystic fibrosis airway surface liquid by elevating epithelial monocarboxylate transporter 2 dependent lactate-H⁺ secretion

The cystic fibrosis (CF) airway surface liquid (ASL) provides a nutrient rich environment for bacterial growth including elevated glucose, which together with defective bacterial killing due to aberrant HCO3− transport and acidic ASL, make the CF airways susceptible to colonisation by respiratory pathogens such as Pseudomonas aeruginosa. Approximately half of adults with CF have CF related diabetes (CFRD) and this is associated with increased respiratory decline. CF ASL contains elevated lactate concentrations and hyperglycaemia can also increase ASL lactate. We show that primary human bronchial epithelial (HBE) cells secrete lactate into ASL, which is elevated in hyperglycaemia. This leads to ASL acidification in CFHBE, which could only be mimicked in non-CF HBE following HCO3− removal. Hyperglycaemia-induced changes in ASL lactate and pH were exacerbated by the presence of P. aeruginosa and were attenuated by inhibition of monocarboxylate lactate-H+ co-transporters (MCTs) with AR-C155858. We conclude that hyperglycaemia and P. aeruginosa induce a metabolic shift which increases lactate generation and efflux into ASL via epithelial MCT2 transporters. Normal airways compensate for MCT-driven H+ secretion by secreting HCO3−, a process which is dysfunctional in CF airway epithelium leading to ASL acidification and that these processes may contribute to worsening respiratory disease in CFRD