Theoretical evidence for efficient p-type doping of GaN using beryllium

Ab initio calculations predict that Be is a shallow acceptor in GaN. Its thermal ionization energy is 0.06 eV in wurtzite GaN; the level is valence resonant in the zincblende phase. Be incorporation is severely limited by the formation of Be_3N_2. We show however that co-incorporation with reactive species can enhance the solubility. H-assisted incorporation should lead to high doping levels in MOCVD growth after post-growth annealing at about 850 K. Be-O co-incorporation produces high Be and O concentrations at MBE growth temperatures.Comment: revised Feb 24 199

Chemical abundances and ages of the bulge stars in APOGEE high-velocity peaks

A cold high-velocity (HV, $\sim$ 200 km/s) peak was first reported in several Galactic bulge fields based on the APOGEE commissioning observations. Both the existence and the nature of the high-velocity peak are still under debate. Here we revisit this feature with the latest APOGEE DR13 data. We find that most of the low latitude bulge fields display a skewed Gaussian distribution with a HV shoulder. However, only 3 out of 53 fields show distinct high-velocity peaks around 200 km/s. The velocity distribution can be well described by Gauss-Hermite polynomials, except the three fields showing clear HV peaks. We find that the correlation between the skewness parameter ($h_{3}$) and the mean velocity ($\bar{v}$), instead of a distinctive HV peak, is a strong indicator of the bar. It was recently suggested that the HV peak is composed of preferentially young stars. We choose three fields showing clear HV peaks to test this hypothesis using the metallicity, [$\alpha$/M] and [C/N] as age proxies. We find that both young and old stars show HV features. The similarity between the chemical abundances of stars in the HV peaks and the main component indicates that they are not systematically different in terms of chemical abundance or age. In contrast, there are clear differences in chemical space between stars in the Sagittarius dwarf and the bulge stars. The strong HV peaks off-plane are still to be explained properly, and could be different in nature.Comment: 13 pages, 10 figures, published in ApJ. Updated to match the final ApJ published version. Minor revisions to the text and Figure

On the dynamics of the glass transition on Bethe lattices

The Glauber dynamics of disordered spin models with multi-spin interactions on sparse random graphs (Bethe lattices) is investigated. Such models undergo a dynamical glass transition upon decreasing the temperature or increasing the degree of constrainedness. Our analysis is based upon a detailed study of large scale rearrangements which control the slow dynamics of the system close to the dynamical transition. Particular attention is devoted to the neighborhood of a zero temperature tricritical point. Both the approach and several key results are conjectured to be valid in a considerably more general context.Comment: 56 pages, 38 eps figure

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty

DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes

In C. elegans, the conserved transcription factor DAF-16/FOXO is a powerful aging regulator, relaying dire conditions into expression of stress resistance and longevity promoting genes. For some of these functions, including low insulin/IGF signaling (IIS), DAF-16 depends on the protein SMK-1/SMEK, but how SMK-1 exerts this role has remained unknown. We show that SMK-1 functions as part of a specific Protein Phosphatase 4 complex (PP4(SMK-1)). Loss of PP4(SMK-1) hinders transcriptional initiation at several DAF-16-activated genes, predominantly by impairing RNA polymerase II recruitment to their promoters. Search for the relevant substrate of PP4(SMK-1) by phosphoproteomics identified the conserved transcriptional regulator SPT-5/SUPT5H, whose knockdown phenocopies the loss of PP4(SMK-1). Phosphoregulation of SPT-5 is known to control transcriptional events such as elongation and termination. Here we also show that transcription initiating events are influenced by the phosphorylation status of SPT-5, particularly at DAF-16 target genes where transcriptional initiation appears rate limiting, rendering PP4(SMK-1) crucial for many of DAF-16's physiological roles

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Large-scale deep-coverage whole-genome sequencing (WGS) is now feasible and offers potential advantages for locus discovery. We perform WGS in 16,324 participants from four ancestries at mean depth >29X and analyze genotypes with four quantitative traits-plasma total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. Common variant association yields known loci except for few variants previously poorly imputed. Rare coding variant association yields known Mendelian dyslipidemia genes but rare non-coding variant association detects no signals. A high 2M-SNP LDL-C polygenic score (top 5th percentile) confers similar effect size to a monogenic mutation (~30 mg/dl higher for each); however, among those with severe hypercholesterolemia, 23% have a high polygenic score and only 2% carry a monogenic mutation. At these sample sizes and for these phenotypes, the incremental value of WGS for discovery is limited but WGS permits simultaneous assessment of monogenic and polygenic models to severe hypercholesterolemia

Compressible Navier-Stokes analysis of floating wind turbine rotor aerodynamics

The unsteady aerodynamics of floating offshore wind turbine rotors is more complex than that of fixed-bottom turbine rotors, due to additional rigid-body motion components enabled by the lack of rigid foundations; it is still unclear if low-fidelity aerodynamic models, such as the blade element momentum theory, provide sufficiently reliable input for floating turbine design requiring load data for a wide range of operating conditions. High-fidelity Navies-Stokes CFD has the potential to improve the understanding of FOWT rotor aerodynamics, and support the improvement of lower-fidelity aerodynamic analysis models. To accomplish these aims, this study uses an in-house compressible Navier-Stokes code and the NREL FAST engineering code to analyze the unsteady flow regime of the NREL 5 MW rotor pitching with amplitude of 4o and frequency of 0.2 Hz, and compares all results to those obtained with a commercial incompressible code and FAST in a previous independent study. The level of agreement of CFD and engineering analyses in each of these two studies is found to be quantitatively similar, but the peak rotor power of the compressible flow analysis is about 20 % higher than that of the incompressible analysis. This is possibly due to compressibility effects, as the instantaneous local Mach number is found to be higher than 0.4. Validation of the compressible flow analysis set-up, using an absolute frame formulation and low-speed preconditioning, is based on the analysis of the steady and yawed flow past the NREL Phase VI rotor