Managing the supercell approximation for charged defects in semiconductors: finite size scaling, charge correction factors, the bandgap problem and the ab initio dielectric constant

The errors arising in ab initio density functional theory studies of semiconductor point defects using the supercell approximation are analyzed. It is demonstrated that a) the leading finite size errors are inverse linear and inverse cubic in the supercell size, and b) finite size scaling over a series of supercells gives reliable isolated charged defect formation energies to around +-0.05 eV. The scaled results are used to test three correction methods. The Makov-Payne method is insufficient, but combined with the scaling parameters yields an ab initio dielectric constant of 11.6+-4.1 for InP. Gamma point corrections for defect level dispersion are completely incorrect, even for shallow levels, but re-aligning the total potential in real-space between defect and bulk cells actually corrects the electrostatic defect-defect interaction errors as well. Isolated defect energies to +-0.1 eV are then obtained using a 64 atom supercell, though this does not improve for larger cells. Finally, finite size scaling of known dopant levels shows how to treat the band gap problem: in less than about 200 atom supercells with no corrections, continuing to consider levels into the theoretical conduction band (extended gap) comes closest to experiment. However, for larger cells or when supercell approximation errors are removed, a scissors scheme stretching the theoretical band gap onto the experimental one is in fact correct.Comment: 11 pages, 3 figures (6 figure files). Accepted for Phys Rev

Density functional theory calculations of defect energies using supercells

Reliable calculations of defect properties may be obtained with density functional theory using the supercell approximation. We systematically review the known sources of error and suggest how to perform calculations of defect properties in order to minimize errors. We argue that any analytical error-correction scheme relying on electrostatic considerations is not appropriate to derive reliable defect formation energies, especially not for relaxed geometries. Instead we propose finite size scaling of the calculated defect formation energies, and compare the use of this with both fully converged and "Gamma" (Γ) point only k-point integration. We give a recipe for practical DFT calculations which will help to obtain reliable defect formation energies and demonstrate it using examples from III-V semiconductors

Innate Conformational Dynamics Drive Binding Specificity in Anti-Apoptotic Proteins Mcl-1 and Bcl-2

The structurally conserved B-cell lymphoma 2 (Bcl-2) family of protein function to promote or inhibit apoptosis through an exceedingly complex web of specific, intrafamilial protein–protein interactions. The critical role of these proteins in lymphomas and other cancers has motivated a widespread interest in understanding the molecular mechanisms that drive specificity in Bcl-2 family interactions. However, the high degree of structural similarity among Bcl-2 homologues has made it difficult to rationalize the highly specific (and often divergent) binding behavior exhibited by these proteins using conventional structural arguments. In this work, we use time-resolved hydrogen deuterium exchange mass spectrometry to explore shifts in conformational dynamics associated with binding partner engagement in the Bcl-2 family proteins Bcl-2 and Mcl-1. Using this approach combined with homology modeling, we reveal that Mcl-1 binding is driven by a large-scale shift in conformational dynamics, while Bcl-2 complexation occurs primarily through a classical charge compensation mechanism. This work has implications for understanding the evolution of internally regulated biological systems composed of structurally similar proteins and for the development of drugs targeting Bcl-2 family proteins for promotion of apoptosis in cancer

A Combined Signal Approach To Technical Analysis On The S&P 500

This paper examines the effectiveness of nine technical trading rules on the S&P 500 from January 1950 to March 2008 (14,646 daily observations).  The annualized returns from each trading rule are compared to a naïve buy-and-hold strategy to determine profitability. Over the 59 year period, only the moving-average cross-over (1,200) and (5,150) trading rules were able to outperform the buy-and-hold trading strategy after adjusting for transaction costs. However, excess returns were generated by employing a Combined Signal Approach (CSA) on the individual trading rules. Statistical significance was confirmed through bootstrap simulations and robustness through sub-period analysis.&nbsp

Loss of beta-catenin triggers oxidative stress and impairs hematopoietic regeneration

Accidental or deliberate ionizing radiation exposure can be fatal due to widespread hematopoietic destruction. However, little is known about either the course of injury or the molecular pathways that regulate the subsequent regenerative response. Here we show that the Wnt signaling pathway is critically important for regeneration after radiation-induced injury. Using Wnt reporter mice, we show that radiation triggers activation of Wnt signaling in hematopoietic stem and progenitor cells. β-Catenin-deficient mice, which lack the ability to activate canonical Wnt signaling, exhibited impaired hematopoietic stem cell regeneration and bone marrow recovery after radiation. We found that, as part of the mechanism, hematopoietic stem cells lacking β-catenin fail to suppress the generation of reactive oxygen species and cannot resolve DNA double-strand breaks after radiation. Consistent with the impaired response to radiation, β-catenin-deficient mice are also unable to recover effectively after chemotherapy. Collectively, these data indicate that regenerative responses to distinct hematopoietic injuries share a genetic dependence on β-catenin and raise the possibility that modulation of Wnt signaling may be a path to improving bone marrow recovery after damage

Macroinvertebrate traits in Arctic streams reveal latitudinal patterns in physiology and habits that are strongly linked to climate

IntroductionArctic freshwater ecosystems are undergoing rapid environmental transformation because of climate change, which is predicted to produce fundamental alterations in river community structure and function.MethodsWe explored how climate change affects benthic invertebrate communities of Arctic streams by examining patterns of their biological traits along latitudinal and climatic gradients in eastern North America (Canada) and northwestern Europe (Sweden, Norway).ResultsDespite differences in taxonomic composition between continents, we identified similarities in the functional trait niche (FTN) of predominant macroinvertebrate taxonomic groups. Trait composition differed by latitude in eastern Canada, with a predominance of cold-tolerant taxa, tubular body shape, and cased and attached habits at the highest latitudes. Differences in trait composition were evident among ecoregions in Europe, with trait dominance at the highest latitudes that was comparable to North America. There was a similar increase in the relative abundance of cold tolerance and tubular body shape and a decrease in obligate shredders and trait richness with decreasing temperatures across both continents.DiscussionThese patterns are indicative of FTNs that include physiological traits and habits that are advantageous for the low temperatures, short ice-free period, and low riparian vegetation cover at the highest latitudes. We predict that climate change will lead to an increase in functional diversity at high latitudes, as organisms with trait modalities that are currently only found at lower latitudes move northward. However, this change in trait composition will be mediated by the effect of spatial connectivity on dispersal ability, with slower change occurring on Arctic islands. These findings can support modelling of future change in Arctic freshwater assemblages in response to ongoing climate change

Spatial and temporal variation in Arctic freshwater chemistry—Reflecting climate-induced landscape alterations and a changing template for biodiversity

Freshwater chemistry across the circumpolar region was characterised using a pan-Arctic data set from 1,032 lake and 482 river stations. Temporal trends were estimated for Early (1970-1985), Middle (1986-2000), and Late (2001-2015) periods. Spatial patterns were assessed using data collected since 2001.Alkalinity, pH, conductivity, sulfate, chloride, sodium, calcium, and magnesium (major ions) were generally higher in the northern-most Arctic regions than in the Near Arctic (southern-most) region. In particular, spatial patterns in pH, alkalinity, calcium, and magnesium appeared to reflect underlying geology, with more alkaline waters in the High Arctic and Sub Arctic, where sedimentary bedrock dominated.Carbon and nutrients displayed latitudinal trends, with lower levels of dissolved organic carbon (DOC), total nitrogen, and (to a lesser extent) total phosphorus (TP) in the High and Low Arctic than at lower latitudes. Significantly higher nutrient levels were observed in systems impacted by permafrost thaw slumps.Bulk temporal trends indicated that TP was higher during the Late period in the High Arctic, whereas it was lower in the Near Arctic. In contrast, DOC and total nitrogen were both lower during the Late period in the High Arctic sites. Major ion concentrations were higher in the Near, Sub, and Low Arctic during the Late period, but the opposite bulk trend was found in the High Arctic.Significant pan-Arctic temporal trends were detected for all variables, with the most prevalent being negative TP trends in the Near and Sub Arctic, and positive trends in the High and Low Arctic (mean trends ranged from +0.57%/year in the High/Low Arctic to -2.2%/year in the Near Arctic), indicating widespread nutrient enrichment at higher latitudes and oligotrophication at lower latitudes.The divergent P trends across regions may be explained by changes in deposition and climate, causing decreased catchment transport of P in the south (e.g. increased soil binding and trapping in terrestrial vegetation) and increased P availability in the north (deepening of the active layer of the permafrost and soil/sediment sloughing). Other changes in concentrations of major ions and DOC were consistent with projected effects of ongoing climate change. Given the ongoing warming across the Arctic, these region-specific changes are likely to have even greater effects on Arctic water quality, biota, ecosystem function and services, and human well-being in the future

Biodiversity patterns of Arctic diatom assemblages in lakes and streams : Current reference conditions and historical context for biomonitoring

1. Comprehensive assessments of contemporary diatom distributions across the Arctic remain scarce. Furthermore, studies tracking species compositional differences across space and time, as well as diatom responses to climate warming, are mainly limited to paleolimnological studies due to a lack of routine monitoring in lakes and streams across vast areas of the Arctic. 2. The study aims to provide a spatial assessment of contemporary species distributions across the circum-Arctic, establish contemporary biodiversity patterns of diatom assemblages to use as reference conditions for future biomonitoring assessments, and determine pre-industrial baseline conditions to provide historical context for modern diatom distributions. 3. Diatom assemblages were assessed using information from ongoing regulatory monitoring programmes, individual research projects, and from surface sediment layers obtained from lake cores. Pre-industrial baseline conditions as well as the nature, direction and magnitude of changes in diatom assemblages over the past c.200 years were determined by comparing surface sediment samples (i.e. containing modern assemblages) with a sediment interval deposited prior to the onset of significant anthropogenic activities (i.e. containing pre-1850 assemblages), together with an examination of diatoms preserved in contiguous samples from dated sediment cores. 4. We identified several biotypes with distinct diatom assemblages using contemporary diatom data from both lakes and streams, including a biotype typical for High Arctic regions. Differences in diatom assemblage composition across circum-Arctic regions were gradual rather than abrupt. Species richness was lowest in High Arctic regions compared to Low Arctic and sub-Arctic regions, and higher in lakes than in streams. Dominant diatom taxa were not endemic to the Arctic. Species richness in both lakes and streams reached maximum values between 60°N and 75°N but was highly variable, probably reflecting differences in local and regional environmental factors and possibly sampling effort. 5. We found clear taxon-specific differences between contemporary and pre-industrial samples that were often specific to both ecozone and lake depth. Regional patterns of species turnover (β-diversity) in the past c.200 years revealed that regions of the Canadian High Arctic and the Hudson Bay Lowlands to the south showed most compositional change, whereas the easternmost regions of the Canadian Arctic changed least. As shown in previous Arctic diatom studies, global warming has already affected these remote high latitude ecosystems. 6. Our results provide reference conditions for future environmental monitoring programmes in the Arctic. Furthermore, diatom taxa identification and harmonisation require improvement, starting with circum-Arctic intercalibrations. Despite the challenges posed by the remoteness of the Arctic, our study shows the need for routine monitoring programmes that have a wide geographical coverage for both streams and lakes

Quantum Computing for High-Energy Physics: State of the Art and Challenges. Summary of the QC4HEP Working Group

Quantum computers offer an intriguing path for a paradigmatic change of computing in the natural sciences and beyond, with the potential for achieving a so-called quantum advantage, namely a significant (in some cases exponential) speed-up of numerical simulations. The rapid development of hardware devices with various realizations of qubits enables the execution of small scale but representative applications on quantum computers. In particular, the high-energy physics community plays a pivotal role in accessing the power of quantum computing, since the field is a driving source for challenging computational problems. This concerns, on the theoretical side, the exploration of models which are very hard or even impossible to address with classical techniques and, on the experimental side, the enormous data challenge of newly emerging experiments, such as the upgrade of the Large Hadron Collider. In this roadmap paper, led by CERN, DESY and IBM, we provide the status of high-energy physics quantum computations and give examples for theoretical and experimental target benchmark applications, which can be addressed in the near future. Having the IBM 100 x 100 challenge in mind, where possible, we also provide resource estimates for the examples given using error mitigated quantum computing