First-principles characterization of Mg low-index surfaces: Structure, reconstructions, and surface core-level shifts

In this paper, first-principles calculations provide structural characterization of three low-index Mg surfaces - Mg(0001), Mg(1010), and Mg(1120) - and their respective surface core-level shifts (SCLSs). Inspired by the close similarities between Be and Mg surfaces, we also explore the reconstruction of Mg(1120). Through the calculation of surface energies and the use of the angular-component decomposed density of states, we show that reconstructions are likely to occur at the Mg(1120) surface, similarly to what was found earlier for Be(1120). Indeed, the surface energy of some of the explored reconstructions is slightly lower than that of the unreconstructed surface. In addition, because of lattice symmetry, the morphology of the unreconstructed surface (1120) results in a steplike zig-zag chain packing, with topmost chains supporting a resonant, quasi-one-dimensional (1D), partially filled electronic state. As the presence of partially filled quasi-1D bands is a necessary condition for Peierls-like dimerization, we verify that the undimerized surface chain remains stable with respect to it. Some of the reconstructions, namely, the 2 71 and 3 71 added row reconstructions, induce a stronger relaxation of the topmost chains, increasing the coupling with lower layers and thus significantly damping the quasi-1D character of this state. The original approach followed offers a common and general framework to identify quasi-1D bands - even in the case of resonant electronic surface states - and to meaningfully compare calculated and measured SCLSs even in the presence of multicomponent peak contributions

Ab initio complex band structure of conjugated polymers: Effects of hydrid DFT and GW schemes

The non-resonant tunneling regime for charge transfer across nanojunctions is critically dependent on the so-called \beta{} parameter, governing the exponential decay of the current as the length of the junction increases. For periodic materials, this parameter can be theoretically evaluated by computing the complex band structure (CBS) -- or evanescent states -- of the material forming the tunneling junction. In this work we present the calculation of the CBS for organic polymers using a variety of computational schemes, including standard local, semilocal, and hybrid-exchange density functionals, and many-body perturbation theory within the GW approximation. We compare the description of localization and \beta{} parameters among the adopted methods and with experimental data. We show that local and semilocal density functionals systematically underestimate the \beta{} parameter, while hybrid-exchange schemes partially correct for this discrepancy, resulting in a much better agreement with GW calculations and experiments. Self-consistency effects and self-energy representation issues of the GW corrections are discussed together with the use of Wannier functions to interpolate the electronic band-structure.Comment: Accepted for publication on Physical Review B v2: fixed some typo

Collective dipole effects in ionic transport under electric fields

In the context of ionic transport in solids, the variation of a migration barrier height under electric fields is traditionally assumed to be equal to the classical electric work of a point charge that carries the transport charge. However, how reliable is this phenomenological model and how does it fare with respect to Modern Theory of Polarization? In this work, we show that such a classical picture does not hold in general as collective dipole effects may be critical. Such effects are unraveled by an appropriate polarization decomposition and by an expression that we derive, which defines the equivalent polarization-work charge. The equivalent polarization-work charge is not equal neither to the transported charge, nor to the Born effective charge of the migrating atom alone, but it is defined by the total polarization change at the transition state. Our findings are illustrated by oxygen charged defects in MgO and in SiO2

v-P 2 O 5 micro-clustering in P-doped silica studied by a first-principles Raman investigation

Synthetic vitreous silica is currently the preferred material for the production of optical fibres because of the several excellent properties of this glass, e.g. high transmission in the visible and IR domains, high mechanical strength, chemical durability, and ease of doping with various materials. For instance, fiber lasers and amplifiers exploit the light amplification properties provided by rare-earth ions employed as dopants in the core of silica-based optical fibers. The structure and composition of the nearest neighbor shell surrounding rare-earth ions in silica-based optical fibers and amplifiers have been intensively debated in the last decade. To reduce aggregation effects between rare-earth ions, co-dopants such as phosphorus and aluminium are added as structural modifiers; phosphorus-doping, in particular, has proved to be very efficient in dissolving rare-earth ions. In this work, we provide further insights concerning the embedding of P atoms into the silica network, which may be relevant for explaining the ease of formation of a phosphorus pentoxide nearest-neighbor shell around a rare-earth dopant. In particular, by means of first-principles calculations, we discuss alternative models for an irradiation (UV, x\u2013, \u3b3-rays) induced paramagnetic center, i.e. the so called room-temperature phosphorus-oxygen-hole center, and its precursors. We report that the most likely precursor of a room-temperature phosphorus-oxygen-hole center comprises of a micro-cluster of a few (at least two) neighboring phosphate tetrahedra, and correspondingly that the occurrence of isolated [(O-) 2 P(=O) 2 ] 12 units is unlikely even at low P-doping concentrations. In fact, this work predicts that the symmetric stretching of P=O bonds in isolated [(O-) 2 P(=O) 2 ] 12 units appears as a Raman band at a frequency of ~1110 cm 121 , and only by including at least another corner-sharing phosphate tetrahedron, it is shown to shift to higher frequencies (up to ~40 cm 121 ) due to the shortening of P=O bonds, thereby leading to an improved agreement with the observed Raman band located at ~1145 cm 121

O2 Loaded Germanosilicate Optical Fibers: Experimental In Situ Investigation and Ab Initio Simulation Study of GLPC Evolution under Irradiation

In this work we present a combined experimental and ab initio simulation investigation concerning the Germanium Lone Pair Center (GLPC), its interaction with molecular oxygen (O2), and evolution under irradiation. First, O2 loading has been applied here to Ge-doped optical fibers to reduce the concentration of GLPC point defects. Next, by means of cathodoluminescence in situ experiments, we found evidence that the 10 keV electron irradiation of the treated optical fibers induces the generation of GLPC centers, while in nonloaded optical fibers, the irradiation causes the bleaching of the pre-existing GLPC. Ab initio calculations were performed to investigate the reaction of the GLPC with molecular oxygen. Such investigations suggested the stability of the dioxagermirane (DIOG) bulk defect, and its back conversion into GLPC with a local release of O2 under irradiation. Furthermore, it is also inferred that a remarkable portion of the O2 passivated GLPC may form Ge tetrahedra connected to peroxy bridges. Such structures may have a larger resistance to the irradiation and not be back converted into GLPC

Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn Source Package for Research in Electronic Structure, Simulation, and Optimization". It is freely available to researchers around the world under the terms of the GNU General Public License. Quantum ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively-parallel architectures, and a great effort being devoted to user friendliness. Quantum ESPRESSO is evolving towards a distribution of independent and inter-operable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte

Vibrational and structural properties of P2O5P_2O_5 glass: Advances from a combined modeling approach

We present experimental measurements and ab initio simulations of the crystalline and amorphous phases of $P_2O_5$. The calculated Raman, infrared, and vibrational density of states (VDOS) spectra are in excellent agreement with experimental measurements and contain the signatures of all the peculiar local structures of the amorphous phase, namely, bridging and nonbridging (double-bonded or terminal) oxygens and tetrahedral $PO_4$ units associated with $Q^2$, $Q^3$, and $Q^4$ species ($Q^n$ denotes the various types of $PO_4$ tetrahedra, with $n$ being the number of bridging oxygen atoms that connect the tetrahedra to the rest of the network). In order to reveal the internal structure of the vibrational spectrum, the characteristics of vibrational modes in different frequency ranges are investigated using a mode-projection approach at different symmetries based on the $T_d$ symmetry group. In particular, the VDOS spectrum in the range from $∼ 600$ to $870$ $cm^-$$^1$ is dominated by bending ($F_2$$_b$) motions related to bridging oxygen and phosphorus ($∼ 800$ $cm^-$$^1$ band) atoms, while the high-frequency doublet zone ($∼ 870 – 1250$ $cm^-$$^1$ is associated mostly with the asymmetric (($F_2$$_s$) and symmetric ($A_1$) stretching modes, and most prominent peak around $1400$ $cm^-$$^1$ (exp. $1380$ $cm^-$$^1$) is mainly due to asymmetric stretching vibrations supported by double-bonded oxygen atoms. The lower-frequency range below $600$ $cm^-$$^1$ is shown to arise from a mixture of bending ($E$ and ($F_2$$_b$) and rotation ($F_1$) modes. The scissors bending ($E$) and rotation ($F_1$) modes are well localized below $600$ $cm^-$$^1$, whereas the ($F_2$$_b$ bending modes spread further into the range $∼ 600 – 870$ $cm^-$$^1$. The projections of the eigenmodes onto $Q^2$, $Q^3$, and $Q^4$ species yield well-defined contributions at frequencies in striking correspondence with the positions of the Raman and infrared bands

High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click-chemistry

pages, 7 figures.-- Data Availability Statement: Raw sequences are publicly available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena) under the accession number PRJEB63614. The datasets generated for this study are available on request to the corresponding authors.The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5 μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g., Chaetoceros, Thalassiosira, Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal, and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19–31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups, and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communitiesThis work was funded by the Spanish Ministry of Science, Innovation and Universities (MICINN) through the MIAU (RTI2018-101025-30-B-I00) and MICOLOR (PID2021-125469NB-C31) projects and the Ramon y Cajal contract to C.R.G. (RYC2019-026758-I), with funding from the Spanish Government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). C.M. was supported by the Juan de la Cierva-formación fellowship (FJC2021-047745-34 I), funded by the Spanish Ministry of Science and Innovation (MCIN/AEI) and the EU (“NextGenerationEU”/PRTR)Peer reviewe

Land- and water-based exercise intervention in women with fibromyalgia: the al-andalus physical activity randomised controlled trial

Background The al-Andalus physical activity intervention study is a randomised control trial to investigate the effectiveness of a land- and water-based exercise intervention for reducing the overall impact of fibromyalgia (primary outcome), and for improving tenderness and pain-related measures, body composition, functional capacity, physical activity and sedentary behaviour, fatigue, sleep quality, health-related quality of life, and cognitive function (secondary outcomes) in women with fibromyalgia. Methods/Design One hundred eighty women with fibromyalgia (age range: 35-65 years) will be recruited from local associations of fibromyalgia patients in Andalucía (Southern Spain). Patients will be randomly assigned to a usual care (control) group (n = 60), a water-based exercise intervention group (n = 60) or a land-based exercise intervention group (n = 60). Participants in the usual care group will receive general physical activity guidelines and participants allocated in the intervention groups will attend three non-consecutive training sessions (60 min each) per week during 24 weeks. Both exercise interventions will consist of aerobic, muscular strength and flexibility exercises. We will also study the effect of a detraining period (i.e., 12 weeks with no exercise intervention) on the studied variables. Discussion Our study attempts to reduce the impact of fibromyalgia and improve patients' health status by implementing two types of exercise interventions. Results from this study will help to assess the efficacy of exercise interventions for the treatment of fibromyalgia. If the interventions would be effective, this study will provide low-cost and feasible alternatives for health professionals in the management of fibromyalgia. Results from the al-Andalus physical activity intervention will help to better understand the potential of regular physical activity for improving the well-being of women with fibromyalgia.This study was supported by the Consejeria de Turismo, Comercio y Deporte (CTCD-201000019242-TRA), the Spanish Ministry of Science and Innovation (I + D + I DEP2010-15639, grants: BES-2009-013442, BES-2011-047133, RYC-2010-05957, RYC-2011-09011), the Swedish Heart-Lung Foundation (20090635), the Spanish Ministry of Education (AP-2009-3173), Granada Research of Excelence Initiative on Biohealth (GREIB), Campus BioTic, University of Granada, Spain and European University of Madrid. Escuela de Estudios Universitarios Real Madrid. 2010/04RM