The theoretical DFT study of electronic structure of thin Si/SiO2 quantum nanodots and nanowires

The atomic and electronic structure of a set of proposed thin (1.6 nm in diameter) silicon/silica quantum nanodots and nanowires with narrow interface, as well as parent metastable silicon structures (1.2 nm in diameter), was studied in cluster and PBC approaches using B3LYP/6-31G* and PW PP LDA approximations. The total density of states (TDOS) of the smallest quasispherical silicon quantum dot (Si85) corresponds well to the TDOS of the bulk silicon. The elongated silicon nanodots and 1D nanowires demonstrate the metallic nature of the electronic structure. The surface oxidized layer opens the bandgap in the TDOS of the Si/SiO2 species. The top of the valence band and the bottom of conductivity band of the particles are formed by the silicon core derived states. The energy width of the bandgap is determined by the length of the Si/SiO2 clusters and demonstrates inverse dependence upon the size of the nanostructures. The theoretical data describes the size confinement effect in photoluminescence spectra of the silica embedded nanocrystalline silicon with high accuracy.Comment: 22 pages, 5 figures, 1 tabl

Boundary conditions for interfaces of electromagnetic (photonic) crystals and generalized Ewald-Oseen extinction principle

The problem of plane-wave diffraction on semi-infinite orthorhombic electromagnetic (photonic) crystals of general kind is considered. Boundary conditions are obtained in the form of infinite system of equations relating amplitudes of incident wave, eigenmodes excited in the crystal and scattered spatial harmonics. Generalized Ewald-Oseen extinction principle is formulated on the base of deduced boundary conditions. The knowledge of properties of infinite crystal's eigenmodes provides option to solve the diffraction problem for the corresponding semi-infinite crystal numerically. In the case when the crystal is formed by small inclusions which can be treated as point dipolar scatterers with fixed direction the problem admits complete rigorous analytical solution. The amplitudes of excited modes and scattered spatial harmonics are expressed in terms of the wave vectors of the infinite crystal by closed-form analytical formulae. The result is applied for study of reflection properties of metamaterial formed by cubic lattice of split-ring resonators.Comment: 15 pages, 8 figures, submitted to PR

Impact of climate change on the ground thermal regime in the lower Lena region, Arctic central Siberia

This paper presents the results of 30 years of permafrost thermal monitoring in the Tiksi area in the eastern Russian Arctic. At a stone ridge site, the mean annual temperatures in the upper 30 m of the ground have increased by 1–2.4 C compared to the first years of observations, with trends of C/yr. At the same time, its change was uneven. In the last 20 years, the rate of increase has increased compared with the first decade of observations. At wet tundra sites in the foothill plain, the mean annual temperatures at the top of permafrost have increased by 2.4–2.6 C between 2005 and 2022 at rates of 0.11–0.15 C/yr, and the active layer thicknesses have increased at rates of 0.05–0.41 cm/yr

Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time‑dependent density functional theory

Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460–470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein–substrate complex was optimized using a linear scaling quantum–mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified

An up-conversion luminophore with high quantum yield and brightness based on BaF2_{2}:Yb3+^{3+},Er3+^{3+} single crystals

Up-conversion (UC) of near-infrared radiation to visible light has received much attention because of its use in the conversion of solar radiation, luminescence thermometry, biosensing, and anti-counterfeiting applications. However, the main issue hindering the successful utilization of UC is the relatively low quantum efficiency of the process. In order to design new UC systems with high quantum yield (ϕ$_{UC}$) values, we synthesized two series of co-doped BaF$_{2}$ single crystals with nominal concentrations of Yb$^{3+}$ (2–15 mol%)/Er$^{3+}$ (2 mol%) as well as Yb$^{3+}$ (3 mol%)/Er$^{3+}$ (2–15 mol%). The highest ϕ$_{UC}$ value of 10.0% was demonstrated for the BaF$_{2}$:Er$^{3+}$ (2 mol%) and Yb$^{3+}$ (3 mol%) sample under 490 W cm$^{-2}$ of 976 nm excitation. To study the natural limit of UC efficiency, quantum yield values upon direct excitation (ϕ$_{DS}$) of the $^{4}$S$_{3/2}$ (ϕ$_{DS}$ ≤ 26%) levels were measured. Comparison of experimental values of quantum yields to the ones obtained using Judd–Ofelt theory reveals strong quenching of the $^{4}$S$_{3/2}$ state for all investigated compositions. In addition, we observed an unusually strong contribution of the Er$^{3+}$:4I$_{9/2}$ excited state to both UC and down-shifting luminescent processes. This contribution becomes possible due to the very low maximum phonon energy of BaF$_{2}$ crystals (240 cm$^{-1}$)

Report on Glaciological Observations in Suntar-Khayata Range by GRENE Project, 2012

第3回極域科学シンポジウム/特別セッション「これからの北極研究」11月28日（水） 国立極地研究所 2階大会議

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)

Ancient DNA suggests modern wolves trace their origin to a late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a dataset of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.L.L., K.D. and G.L. were supported by the Natural Environment Research Council, UK (grant numbers NE/K005243/1, NE/K003259/1); LL was also supported by the European Research Council grant (339941‐ADAPT); A.M. and A.E. were supported by the European Research Council Consolidator grant (grant number 647787‐LocalAdaptation); L.F. and G.L. were supported by the European Research Council grant (ERC‐2013‐StG 337574‐UNDEAD); T.G. was supported by a European Research Council Consolidator grant (681396‐Extinction Genomics) & Lundbeck Foundation grant (R52‐5062); O.T. was supported by the National Science Center, Poland (2015/19/P/NZ7/03971), with funding from EU's Horizon 2020 programme under the Marie Skłodowska‐Curie grant agreement (665778) and Synthesys Project (BETAF 3062); V.P., E.P. and P.N. were supported by the Russian Science Foundation grant (N16‐18‐10265 RNF); A.P. was supported by the Max Planck Society; M.L‐G. was supported by a Czech Science Foundation grant (GAČR15‐06446S)

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canisfamiliaris) lived(1-8). Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT8840,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.Peer reviewe

CATMoS: Collaborative Acute Toxicity Modeling Suite.

BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals. OBJECTIVES: The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg). METHODS: An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches. RESULTS: The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results. DISCUSSION: CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495