Research Outputs

Examples of research outputs coming from work carried on Viper can be found below.

The HPC Steering Group has agreed that where appropriate, the use of Viper on a research project should be acknowledged in publications with the following statement:

“We acknowledge the Viper High Performance Computing facility of the University of Hull and its support team”

We are always interested to know of any output that features work carried out on Viper, please contact viper@hull.ac.uk

Publications (69 outputs)

2020 (11 outputs)

Zhiguo Zhang and Jia Chuan Khong and Billy Koe and Shifeng Luo and Shi Huang and Ling Qin and Silvia Cipiccia and Darren Batey and Andrew J. Bodey and Christoph Rau and Yu Lung Chiu and Zhu Zhang and Jean-Christophe Gebelin and Nick Green and Jiawei Mi, 2020-11, Multiscale characterization of the 3D network structure of metal carbides in a Ni superalloy by synchrotron X-ray microtomography and ptychography, Scripta Materialia, doi: 10.1016/j.scriptamat.2020.10.032

Abstract

Synchrotron X-ray microtomography and ptychography were used to characterize the 3D network structure, morphology and distribution of metal carbides in an as-cast IN713LC Ni superalloy. MC typed carbides were found to distribute mainly on the grain boundary between the matrix γ and γ’ phase. The differences in solidification cooling rate had a minor influence on the volume fraction of the MC type carbides, but significantly affected the carbide size, distribution and network morphology. Depending on the local composition of the remaining liquid phase and geometric constraints, the carbides can form either spherical or strip or network morphologies. The research demonstrated clearly the advantage and technical potential of using the two complementary tomography techniques synergistically to characterize non-destructively complex multiple-phase structures in three dimensional space with a spatial resolution of ~30 nm.


Clark, Victoria H.J. and Benoit, David M., 2020-10-12, The vibrational signatures of polyaromatic hydrocarbons on an ice surface, Proceedings of the International Astronomical Union, doi: 10.1017/S174392131900944X

Abstract

We use quantum chemical techniques to model the vibrational spectra of small aromatic molecules on a proton-ordered hexagonal crystalline water ice (XIh) model. We achieve a good agreement with experimental data by accounting for vibrational anharmonicity and correcting the potential energy landscape for known failures of density functional theory. A standard harmonic description of the vibrational spectra only leads to a broad qualitative agreement.


Gottschalk, Hannes C. and Poblotzki, Anja and Fatima, Mariyam and Obenchain, Daniel A. and Perez, Cristobal and Antony, Jens and Auer, Alexander A. and Baptista, Leonardo and Benoit, David M. and Bistoni, Giovanni and Bohle, Fabian and Dahmani, Rahma and Firaha, Dzmitry and Grimme, Stefan and Hansen, Andreas and Harding, Michael E. and Hochlaf, Majdi and Holzer, Christof and Jansen, Georg and Klopper, Wim and Kopp, Wassja A. and Krasowska, Malgorzata and Kroger, Leif C. and Leonhard, Kai and Mogren Al-Mogren, Muneerah and Mouhib, Halima and Neese, Frank and Pereira, Max N. and Prakash, Muthuramalingam and Ulusoy, Inga S. and Mata, Ricardo A. and Suhm, Martin A. and Schnell, Melanie, 2020-04-30, The first microsolvation step for furans: New experiments and benchmarking strategies, The Journal of Chemical Physics, doi: 10.1063/5.0004465

Abstract

The site-specific first microsolvation step of furan and some of its derivatives with methanol is explored to benchmark the ability of quantum-chemical methods to describe the structure, energetics, and vibrational spectrum at low temperature. Infrared and microwave spectra in supersonic jet expansions are used to quantify the docking preference and some relevant quantum states of the model complexes. Microwave spectroscopy strictly rules out in-plane docking of methanol as opposed to the top coordination of the aromatic ring. Contrasting comparison strategies, which emphasize either the experimental or the theoretical input, are explored. Within the harmonic approximation, only a few composite computational approaches are able to achieve a satisfactory performance. Deuteration experiments suggest that the harmonic treatment itself is largely justified for the zero-point energy, likely and by design due to the systematic cancellation of important anharmonic contributions between the docking variants. Therefore, discrepancies between experiment and theory for the isomer abundance are tentatively assigned to electronic structure deficiencies, but uncertainties remain on the nuclear dynamics side. Attempts to include anharmonic contributions indicate that for systems of this size, a uniform treatment of anharmonicity with systematically improved performance is not yet in sight.


Brook, Chris B and Kawata, Daisuke and Gibson, Brad K and Gallart, Carme and Vicente, Andres, 2020-04-15, Explaining the chemical trajectories of accreted and in-situ halo stars of the Milky Way, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/staa992

Abstract

The Milky Way underwent its last significant merger ten billion years ago, when the Gaia-Enceladus-Sausage (GES) was accreted. Accreted GES stars and progenitor stars born prior to the merger make up the bulk of the inner halo. Even though these two main populations of halo stars have similar durations of star formation prior to their merger, they differ in [./Fe]-[Fe/H] space, with the GES population bending to lower [./Fe] at a relatively low value of [Fe/H]. We use cosmological simulations of a ’Milky Way’ to argue that the different tracks of the halo stars through the [./Fe]-[Fe/H] plane are due to a difference in their star formation history and efficiency, with the lower mass GES having its low and constant star formation regulated by feedback whilst the higher mass main progenitor has a higher star formation rate prior to the merger. The lower star formation efficiency of GES leads to lower gas pollution levels, pushing [./Fe]-[Fe/H] tracks to the left. In addition, the increasing star formation rate maintains a higher relative contribution of Type II SNe to Type Ia SNe for the main progenitor population that formed during the same time period, thus maintaining a relatively high [./Fe]. Thus the different positions of the downturns in the [./Fe]-[Fe/H] plane for the GES stars are not reflective of different star formation durations, but instead reflect different star formation efficiencies.


Chatterjee, Joyjit and Dethlefs, Nina, 2020-04-13, Deep learning with knowledge transfer for explainable anomaly prediction in wind turbines, Wind Energy, doi: 10.1002/we.2510

Abstract

The last decade has witnessed an increased interest in applying machine learning techniques to predict faults and anomalies in the operation of wind turbines. These efforts have lately been dominated by deep learning techniques which, as in other fields, tend to outperform traditional machine learning algorithms given sufficient amounts of training data. An important shortcoming of deep learning models is their lack of transparency—they operate as black boxes and typically do not provide rationales for their predictions, which can lead to a lack of trust in predicted outputs. In this article, a novel hybrid model for anomaly prediction in wind farms is proposed, which combines a recurrent neural network approach for accurate classification with an XGBoost decision tree classifier for transparent outputs. Experiments with an offshore wind turbine show that our model achieves a classification accuracy of up to 97\%. The model is further able to generate detailed feature importance analyses for any detected anomalies, identifying exactly those components in a wind turbine that contribute to an anomaly. Finally, the feasibility of transfer learning is demonstrated for the wind domain by porting our “offshore” model to an unseen dataset from an onshore wind farm. The latter model achieves an accuracy of 65\% and is able to detect 85\% of anomalies in the unseen domain. These results are encouraging for application to wind farms for which no training data are available, for example, because they have not been in operation for long.


J. Silva-Rodriguez and M. Pineiro-Fiel and S. J. Archibald and P. Aguiar and N. Efthimiou, 2020-04-09, A SimSET-STIR hybrid Monte Carlo model for the Philips Vereos Digital PET, 2019 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), doi: 10.1109/NSS/MIC42101.2019.9059645

Abstract

The aim of this study was to develop an accurate simulation and reconstruction model for the Philips Vereos digital whole-body PET/CT scanner. The model was developed using the SimSET Monte Carlo (MC) simulation code, storing all detected photons in SimSET list-mode (LM) format (history files). LM processing, binning and image reconstruction were performed using STIR recently added LM capabilities. In order to accurately process the listmode files generated by SimSET, a new interface between SimSET and STIR was developed. The performance of our MC model was evaluated using the NEMA NU2-2012 standard. Spatial resolution was in good agreement with published results(±12%). Count-rate performance was accurate overall, with NEC rates accurate for both low (32.5% vs. 31.7% at ≈ 5 KBq/mL), and high counts (146.2 kcps vs 153.4 at ≈ 55 KBq/mL), and consistent prompts for all the activity concentrations. LM-MLEM reconstruction including scatter and attenuation correction was performed to validate the SimSET-STIR developed interface.


N. Efthimiou and A. C. Whitehead and M. Stockhoff and C. Thyssen and S. J. Archibald and S. Vandenberghe, 2020-04-09, Preliminary investigation of the impact of Axial Ring Splitting on Image Quality for the Cost Reduction of Total-Body PET, 2019 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), doi: 10.1109/NSS/MIC42101.2019.9059650

Abstract

Recently, the first TB-PET scanner was unveiled and the initial results were nevertheless impressive. However, the cost of a TB-PET scanner is prohibiting for many institutions around the globe. Therefore here we investigate a cost reduction strategy incorporating a flexible detector arrangement. The proposed arrangement increases the axial field of view while keeping the overall cost at lower levels. We propose the axial ring splitting, which separates the full rings, of a compact PET scanner, to an expanded scanner with rings having only even or only odd numbered detectors. In this paper some preliminary performance results using Monte Carlo simulations, will be presented. In this comparison three configurations were considered (a) full rings PET (b) half-split rings TB-PET (c) full-split rings TBPET. In addition in this investigation the effects of a varying coincidence window are demonstrated. The preliminary results suggest that Config.A demonstrated the highest Noise Equivalent count rate using either a fixed or a varying coincidence window. The main reasons were the absence of gaps and better handling of background radiation. However, reconstructed images for a single bed, from a whole body acquisition, suggested that due to the longer single bed acquisition of the full-split rings geometry the images present better noise properties.


Benjamin Wehmeyer and Carla Frohlich and Benoit Cote and Marco Pignatari and Friedrich-Karl Thielemann, 2020-03-27, Could Failed Supernovae Explain the High r-process Abundances in Some Low Metallicity Stars?, Proceedings of the 15th International Symposium on Origin of Matter and Evolution of Galaxies (OMEG15), doi: 10.7566/JPSCP.31.011063

Abstract

Rapid neutron capture process (r-process) elements have been detected in a large number of metal-poor halo stars. The observed large abundance scatter in these stars suggests that r-process elements have been produced in a site that is rare compared to core-collapse supernovae (CCSNe). Although being rare, neutron star mergers (NSM) alone have difficulties explaining the observations, especially at low metallicities. In this paper, we present a complementary scenario: Using black hole – neutron star mergers (BHNSMs) as additional r-process site. We show that both sites together are able to explain the observed r-process abundances in the Galaxy.


Benoit Cote, Samuel Jones, Falk Herwig and Marco Pignatari, 2020-03-27, Chromium Nucleosynthesis and Silicon–Carbon Shell Mergers in Massive Stars, The Astrophysical Journal, doi: 10.3847/1538-4357/ab77ac

Abstract

We analyze the production of the element Cr in galactic chemical evolution (GCE) models using the NuGrid nucleosynthesis yields set. We show that the unusually large [Cr/Fe] abundance at [Fe/H] . 0 reported by previous studies using those yields and predicted by our Milky Way model originates from the merging of convective Si-burning and C-burning shells in a 20 ${M}_{\odot }$ model at metallicity Z = 0.01, about an hour before the star explodes. This merger mixes the incomplete burning material in the Si shell, including 51V and 52Cr, out to the edge of the carbon/oxygen (CO) core. The adopted supernova model ejects the outer 2 ${M}_{\odot }$ of the CO core, which includes a significant fraction of the Cr-rich material. When including this 20 M . model at Z = 0.01 in the yields interpolation scheme of our GCE model for stars between 15 and 25 ${M}_{\odot }$, we overestimate [Cr/Fe] by an order of magnitude at [Fe/H] . 0 relative to observations in the Galactic disk. This raises a number of questions regarding the occurrence of Si–C shell mergers in nature, the accuracy of different simulation approaches, and the impact of such mergers on the presupernova structure and explosion dynamics. According to the conditions in this 1D stellar model, the substantial penetration of C-shell material into the Si shell could launch a convective–reactive global oscillation if a merger does take place. In any case, GCE provides stringent constraints on the outcome of this stellar evolution phase.


Billy Koe and Colin Abraham and Chris Bailey and Bob Greening and Martin Small and Thomas Connolley and Jiawei Mi, 2020-03-14, A novel electromagnetic apparatus for in-situ synchrotron X-ray imaging study of the separation of phases in metal solidification, HardwareX, doi: 10.1016/j.ohx.2020.e00104

Abstract

As a part of a research into new techniques for purifying recycled aluminium alloys, a novel electromagnetic apparatus had been developed for investigating in real-time the separation mechanisms of detrimental inclusions in aluminium alloy melts under alternating magnetic fields. The magnetic coil was designed based on the Helmholtz coil design. A viewing gap was designed for in-situ imaging studies using synchrotron X-rays. The gap was designed to maintain a uniform magnetic field in the central region where a sample is positioned. The current setup for the magnetic coil pair is able to produce a peak magnetic flux density of ~10 mT at a frequency of 25 kHz. A separate electrical resistance furnace, designed to concentrically fit within the magnetic coils, was used to control the heating (up to ~850°C) and cooling of the samples. After a series of systematic tests and commissioning, the apparatus was used in a number of in-situ and ex-situ experiments.


Somerville, Walter R. C. and Law, Adam D. and Rey, Marcel and Vogel, Nicolas and Archer, Andrew J. and Buzza, D. Martin A., 2020-03-11, Pattern formation in two-dimensional hard-core/soft-shell systems with variable soft shell profiles, Soft Matter, doi: 10.1039/D0SM00092B

Abstract

Hard-core/soft shell (HCSS) particles have been shown to self-assemble into a remarkably rich variety of structures under compression due to the simple interplay between the hard-core and soft-shoulder length scales in their interactions. Most studies in this area model the soft shell interaction as a square shoulder potential. Although appealing from a theoretical point of view{,} the potential is physically unrealistic because there is no repulsive force in the soft shell regime{,} unlike in experimental HCSS systems. To make the model more realistic{,} here we consider HCSS particles with a range of soft shell potential profiles beyond the standard square shoulder form and study the model using both minimum energy calculations and Monte Carlo simulations. We find that by tuning density and the soft shell profile{,} HCSS particles in the thin shell regime (i.e.{,} shell to core ratio ) can form a large range of structures{,} including hexagons{,} chains{,} squares{,} rhomboids and two distinct zig-zag structures. Furthermore{,} by tuning the density and r1/r0{,} we find that HCSS particles with experimentally realistic linear ramp soft shoulder repulsions can form honeycombs and quasicrystals with 10-fold and 12-fold symmetry. Our study therefore suggests the exciting possibility of fabricating these exotic 2D structures experimentally through colloidal self-assembly.


2019 (22 outputs)

Eva Tarazona, Christoph Hahn, Lluis Franch-Gras, Eduardo M. Garcia-Roger, Maria Jose Carmona and Africa Gomez, 2019-12-23, Ecological genomics of adaptation to unpredictability in experimental rotifer populations, Scientific Reports, doi: 10.1038/s41598-019-56100-y

Abstract

Elucidating the genetic basis of phenotypic variation in response to different environments is key to understanding how populations evolve. Facultatively sexual rotifers can develop adaptive responses to fluctuating environments. In a previous evolution experiment, diapause-related traits changed rapidly in response to two selective regimes (predictable vs unpredictable) in laboratory populations of the rotifer Brachionus plicatilis. Here, we investigate the genomic basis of adaptation to environmental unpredictability in these experimental populations. We identified and genotyped genome-wide polymorphisms in 169 clones from both selective regimes after seven cycles of selection using genotyping by sequencing (GBS). Additionally, we used GBS data from the 270 field clones from which the laboratory populations were established. This GBS dataset was used to identify candidate SNPs under selection. A total of 76 SNPs showed divergent selection, three of which are candidates for being under selection in the particular unpredictable fluctuation pattern studied. Most of the remaining SNPs showed strong signals of adaptation to laboratory conditions. Furthermore, a genotype-phenotype association approach revealed five SNPs associated with two key life-history traits in the adaptation to unpredictability. Our results contribute to elucidating the genomic basis for adaptation to unpredictable environments and lay the groundwork for future evolution studies in rotifers.


Molla, M.; Wekesa, S.; Cavichia, O.; Diaz, A. I.; Gibson, B. K.; Rosales-Ortega, F. F.; Ascasibar, Y.; Wamalwa, D. S.; Sanchez, S. F., 2019-11-01, 2D-Galactic chemical evolution: the role of the spiral density wave, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz2537

Abstract

We present a 2D chemical evolution code applied to a Milky Way type Galaxy, incorporating the role of spiral arms in shaping azimuthal abundance variations, and confront the predicted behaviour with recent observations taken with integral field units. To the usual radial distribution of mass, we add the surface density of the spiral wave and study its effect on star formation and elemental abundances. We compute five different models: one with azimuthal symmetry which depends only on radius, while the other four are subjected to the effect of a spiral density wave. At early times, the imprint of the spiral density wave is carried by both the stellar and star formation surface densities; conversely, the elemental abundance pattern is less affected. At later epochs, however, differences among the models are diluted, becoming almost indistinguishable given current observational uncertainties. At the present time, the largest differences appear in the star formation rate and/or in the outer disc (R ≥ 18 kpc). The predicted azimuthal oxygen abundance patterns for t ≤ 2 Gyr are in reasonable agreement with recent observations obtained with VLT/MUSE for NGC 6754.


Furness, Andrew I., Capellini, Isabella, 2019-10-17, The evolution of parental care diversity in amphibians, Nature Communications, doi: 10.1038/s41467-019-12608-5

Abstract

Parental care is extremely diverse across species, ranging from simple behaviours to complex adaptations, varying in duration and in which sex cares. Surprisingly, we know little about how such diversity has evolved. Here, using phylogenetic comparative methods and data for over 1300 amphibian species, we show that egg attendance, arguably one of the simplest care behaviours, is gained and lost faster than any other care form, while complex adaptations, like brooding and viviparity, are lost at very low rates, if at all. Prolonged care from the egg to later developmental stages evolves from temporally limited care, but it is as easily lost as it is gained. Finally, biparental care is evolutionarily unstable regardless of whether the parents perform complementary or similar care duties. By considering the full spectrum of parental care adaptations, our study reveals a more complex and nuanced picture of how care evolves, is maintained, or is lost.


Donatella Romano, Francesco Calura, Annibale D’Ercole and C. Gareth Few, 2019-10-08, High-resolution three-dimensional simulations of gas removal from ultrafaint dwarf galaxies, Astronomy & Astrophysics, doi: 10.1051/0004-6361/201935328

Abstract

Context. The faintest Local Group galaxies found lurking in and around the Milky Way halo provide a unique test bed for theories of structure formation and evolution on small scales. Deep Subaru and Hubble Space Telescope photometry demonstrates that the stellar populations of these galaxies are old and that the star formation activity did not last longer than 2 Gyr in these systems. A few mechanisms that may lead to such a rapid quenching have been investigated by means of hydrodynamic simulations, but these have not provided any final assessment so far.
Aims. This is the first in a series of papers aimed at analyzing the roles of stellar feedback, ram pressure stripping, host-satellite tidal interactions, and reionization in cleaning the lowest mass Milky Way companions of their cold gas using high-resolution, three-dimensional hydrodynamic simulations.
Methods. We simulated an isolated ultrafaint dwarf galaxy loosely modeled after Bootes I, and examined whether or not stellar feedback alone could drive a substantial fraction of the ambient gas out from the shallow potential well.
Results. In contrast to simple analytical estimates, but in agreement with previous hydrodynamical studies, we find that most of the cold gas reservoir is retained. Conversely, a significant amount of the metal-enriched stellar ejecta crosses the boundaries of the computational box with velocities exceeding the local escape velocity and is, thus, likely lost from the system.
Conclusions. Although the total energy output from multiple supernova explosions exceeds the binding energy of the gas, no galactic-scale outflow develops in our simulations and as such, most of the ambient medium remains trapped within the weak potential well of the model galaxy. It seems thus unavoidable that to explain the dearth of gas in ultrafaint dwarf galaxies, we will have to resort to environmental effects. This will be the subject of a forthcoming paper.


C. C. Roggatz, N. Fletcher, D. M. Benoit, A. C. Algar, A. Doroff, B. Wright, K. C. Wollenberg Valero & J. D. Hardege, 2019-10-07, Saxitoxin and tetrodotoxin bioavailability increases in future oceans, Nature Climate Change, doi: 10.1038/s41558-019-0589-3

Abstract

Increasing atmospheric CO2 levels are largely absorbed by the ocean, decreasing surface water pH1. In combination with increasing ocean temperatures, these changes have been identified as a major sustainability threat to future marine life2. Interactions between marine organisms are known to depend on biomolecules, although the influence of oceanic pH on their bioavailability and functionality remains unexplored. Here we show that global change substantially impacts two ecological keystone molecules3 in the ocean, the paralytic neurotoxins saxitoxin and tetrodotoxin. Increasing temperatures and declining pH increase the abundance of their toxic forms in the water. Our geospatial global model predicts where this increased toxicity could intensify the devastating impact of harmful algal blooms, for example through an increased incidence of paralytic shellfish poisoning. Calculations of future saxitoxin toxicity levels in Alaskan clams, Saxidomus gigantea, show critical exceedance of limits safe for consumption. Our findings for saxitoxin and tetrodotoxin exemplify potential consequences of changing pH and temperature on chemicals dissolved in the sea. This reveals major implications not only for ecotoxicology, but also for chemical signals that mediate species interactions such as foraging, reproduction or predation in the ocean, with unexplored consequences for ecosystem stability and ecosystem services.


Denissenkov, Pavel A; Herwig, Falk; Woodward, Paul; Andrassy, Robert; Pignatari, Marco; Jones, Samuel, 2019-09-21, The i-process yields of rapidly accreting white dwarfs from multicycle He-shell flash stellar evolution models with mixing parametrizations from 3D hydrodynamics simulations, Monthly notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz1921

Abstract

We have modelled the multicycle evolution of rapidly accreting CO white dwarfs (RAWDs) with stable H burning intermittent with strong He-shell flashes on their surfaces for 0.7 ≤ MRAWD/M⊙ ≤ 0.75 and [Fe/H] ranging from 0 to −2.6. We have also computed the i-process nucleosynthesis yields for these models. The i process occurs when convection driven by the He-shell flash ingests protons from the accreted H-rich surface layer, which results in maximum neutron densities Nn, max ≈ 1013–1015 cm−3. The H-ingestion rate and the convective boundary mixing (CBM) parameter ftop adopted in the one-dimensional nucleosynthesis and stellar evolution models are constrained through three-dimensional (3D) hydrodynamic simulations. The mass ingestion rate and, for the first time, the scaling laws for the CBM parameter ftop have been determined from 3D hydrodynamic simulations. We confirm our previous result that the high-metallicity RAWDs have a low mass retention efficiency (⁠η≲10 per cent⁠). A new result is that RAWDs with [Fe/H] ≲−2 have η≳20 per cent⁠; therefore, their masses may reach the Chandrasekhar limit and they may eventually explode as SNeIa. This result and the good fits of the i-process yields from the metal-poor RAWDs to the observed chemical composition of the CEMP-r/s stars suggest that some of the present-day CEMP-r/s stars could be former distant members of triple systems, orbiting close binary systems with RAWDs that may have later exploded as SNeIa.


den Hartogh, J. W. and Hirschi, R. and Lugaro, M. and Doherty, C. L. and Battino, U. and Herwig, F. and Pignatari, M. and Eggenberger, P., 2019-09-16, The s process in rotating low-mass AGB stars – Nucleosynthesis calculations in models matching asteroseismic constraints, Astronomy and Astrophysics, doi: 10.1051/0004-6361/201935476

Abstract

Aims. We investigate the s-process during the AGB phase of stellar models whose cores are enforced to rotate at rates consistent with asteroseismology observations of their progenitors and successors.
Methods. We calculated new 2 M. ,Z = 0.01 models, rotating at 0, 125, and 250 km s-1 at the start of main sequence. An artificial, additional viscosity was added to enhance the transport of angular momentum in order to reduce the core rotation rates to be in agreement with asteroseismology observations. We compared rotation rates of our models with observed rotation rates during the MS up to the end of core He burning, and the white dwarf phase.
Results. We present nucleosynthesis calculations for these rotating AGB models that were enforced to match the asteroseismic constraints on rotation rates of MS, RGB, He-burning, and WD stars. In particular, we calculated one model that matches the upper limit of observed rotation rates of core He-burning stars and we also included a model that rotates one order of magnitude faster than the upper limit of the observations. The s-process production in both of these models is comparable to that of non-rotating models.
Conclusions. Slowing down the core rotation rate in stars to match the above mentioned asteroseismic constraints reduces the rotationally induced mixing processes to the point that they have no effect on the s-process nucleosynthesis. This result is independent of the initial rotation rate of the stellar evolution model. However, there are uncertainties remaining in the treatment of rotation in stellar evolution, which need to be reduced in order to confirm our conclusions, including the physical nature of our approach to reduce the core rotation rates of our models, and magnetic processes.


Joan Garcia-Porta, Iker Irisarri, Martin Kirchner, Ariel Rodriguez, Sebastian Kirchhof, Jason L. Brown, Amy MacLeod, Alexander P. Turner, Faraham Ahmadzadeh, Gonzalo Albaladejo, Jelka Crnobrnja-Isailovic, Ignacio De la Riva, Adnane Fawzi, Pedro Galan, Bayram Gocmen, D. James Harris, Octavio Jimenez-Robles, Ulrich Joger, Olga Jovanovic Glavas, Mert Karis, Giannina Koziel, Sven Kunzel, Mariana Lyra, Donald Miles, Manuel Nogales, Mehmet Anil Oguz, Panayiotis Pafilis, Lois Rancilhac, Noemi Rodriguez, Benza Rodriguez Concepcion, Eugenia Sanchez, Daniele Salvi, Tahar Slimani, Abderrahim S’khifa, Ali Turk Qashqaei, Anamarija Zagar, Alan Lemmon, Emily Moriarty Lemmon, Miguel Angel Carretero, Salvador Carranza, Herve Philippe, Barry Sinervo, Johannes Muller, Miguel Vences & Katharina C. Wollenberg Valero, 2019-09-09, Environmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards, Nature Communications, doi: 10.1038/s41467-019-11943-x

Abstract

Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 lacertid species based on a supermatrix relying on novel phylogenomic datasets and fossil calibrations. Diversification of lacertids was accompanied by an increasing disparity among occupied bioclimatic niches, especially in the last 10 Ma, during a period of progressive global cooling. Temperate species also underwent a genome-wide slowdown in molecular substitution rates compared to tropical and desert-adapted lacertids. Evaporative water loss and preferred temperature are correlated with bioclimatic parameters, indicating physiological adaptations to climate. Tropical, but also some populations of cool-adapted species experience maximum temperatures close to their preferred temperatures. We hypothesize these species-specific physiological preferences may constitute a handicap to prevail under rapid global warming, and contribute to explaining local lizard extinctions in cool and humid climates.


M.P. Taggart and C. Akers and A.M. Laird and U. Hager and C. Ruiz and D.A. Hutcheon and M.A. Bentley and J.R. Brown and L. Buchmann and A.A. Chen and J. Chen and K.A. Chipps and A. Choplin and J.M. D’Auria and B. Davids and C. Davis and C.Aa. Diget and L. Erikson and J. Fallis and S.P. Fox and U. Frischknecht and B.R. Fulton and N. Galinski and U. Greife and R. Hirschi and D. Howell and L. Martin and D. Mountford and A.St.J. Murphy and D. Ottewell and M. Pignatari and S. Reeve and G. Ruprecht and S. Sjue and L. Veloce and M. Williams, 2019-08-28, A direct measurement of the 17O(.,.)21Ne reaction in inverse kinematics and its impact on heavy element production, Physics Letters B, doi: 10.1016/j.physletb.2019.134894

Abstract

uring the slow neutron capture process in massive stars, reactions on light elements can both produce and absorb neutrons thereby influencing the final heavy element abundances. At low metallicities, the high neutron capture rate of 16O can inhibit s-process nucleosynthesis unless the neutrons are recycled via the 17O(.,n)20Ne reaction. The efficiency of this neutron recycling is determined by competition between the 17O(.,n)20Ne and 17O(.,.)21Ne reactions. While some experimental data are available on the former reaction, no data exist for the radiative capture channel at the relevant astrophysical energies. The 17O(.,.)21Ne reaction has been studied directly using the DRAGON recoil separator at the TRIUMF Laboratory. The reaction cross section has been determined at energies between 0.6 and 1.6 MeV Ecm, reaching into the Gamow window for core helium burning for the first time. Resonance strengths for resonances at 0.63, 0.721, 0.81 and 1.122 MeV Ecm have been extracted. The experimentally based reaction rate calculated represents a lower limit, but suggests that significant s-process nucleosynthesis occurs in low metallicity massive stars.


Velez, Zelia and Roggatz, Christina C. and Benoit, David M. and Hardege, Jorg D. and Hubbard, Peter C., 2019-07-03, Short- and Medium-Term Exposure to Ocean Acidification Reduces Olfactory Sensitivity in Gilthead Seabream, Frontiers in Physiology, doi: 10.3389/fphys.2019.00731

Abstract

The effects of ocean acidification on fish are only partially understood. Studies on olfaction are mostly limited to behavioural alterations of coral reef fish; studies on temperate species and/or with economic importance are scarce. The current study evaluated the effects of short- and medium-term exposure to ocean acidification on the olfactory system of gilthead seabream (Sparus aurata), and attempted to explain observed differences in sensitivity by changes in the protonation state of amino acid odorants. Short-term exposure to elevated PCO2 decreased olfactory sensitivity to some odorants, such as L-serine, L-leucine, L-arginine, L-glutamate and conspecific intestinal fluid, but not to others, such as L-glutamine and conspecific bile fluid. Seabream were unable to compensate for high PCO2 levels in the medium-term; after four weeks’ exposure to high PCO2, the olfactory sensitivity remained lower in elevated PCO2 water. The decrease in olfactory sensitivity in high PCO2 water could be partly attributed to changes in the protonation state of the odorants and/or their receptor(s); we illustrate how protonation due to reduced pH causes changes in the charge distribution of odorant molecules, an essential component for ligand-receptor interaction. However, there are other mechanisms involved. At a histological level, the olfactory epithelium contained higher densities of mucus cells in fish kept in high CO2 water, and a shift in pH of the mucus they produced to more neutral. These differences suggest a physiological response of the olfactory epithelium to lower pH and/or high CO2 levels, but an inability to fully counteract the effects of acidification on olfactory sensitivity. Therefore, the current study provides evidence for a direct, medium-term, global effect of ocean acidification on olfactory sensitivity in fish, and possibly other marine organisms, and suggests a partial explanatory mechanism.


A Cote, Benoit; Lugaro, Maria; Reifarth, Rene; Pignatari, Marco; Vilagos, Blanka; Yague, Andres; Gibson, Brad K., 2019-06, Galactic Chemical Evolution of Radioactive Isotopes, The Astrophysical Journal, doi: 10.3847/1538-4357/ab21d1

Abstract

The presence of short-lived (̃Myr) radioactive isotopes in meteoritic inclusions at the time of their formation represents a unique opportunity to study the circumstances that led to the formation of the solar system. To interpret these observations, we need to calculate the evolution of radioactive-to-stable isotopic ratios in the Galaxy. We present an extension of the open-source galactic chemical evolution codes NuPyCEE and JINAPyCEE that enable the decay of radioactive isotopes in the interstellar medium to be tracked. We show how the evolution of the isotopic ratio depends on the star formation history and efficiency, star-to-gas mass ratio, and galactic outflows. Given the uncertainties in the observations used to calibrate our model, our predictions for isotopic ratios at the time of formation of the Sun are uncertain by a factor of 3.6. At that time, to recover the actual radioactive-to-stable isotopic ratios predicted by our model, one can multiply the steady-state solution (see Equation (1)) by {2.3}-0.7+3.4. However, in the cases where the radioactive isotope has a half-life longer than ̃200 Myr, or the target radioactive or stable isotopes have mass- and/or metallicity-dependent production rates, or they originate from different sources with different delay-time distributions, or the reference isotope is radioactive, our codes should be used for more accurate solutions. Our preliminary calculations confirm the dichotomy between radioactive nuclei in the early solar system with r- and s-process origin, and that 55Mn and 60Fe can be explained by galactic chemical evolution, while 26Al cannot.


Wehmeyer, B; Frohlich, C; Cote, B; Pignatari, M; Thielemann, F-K, 2019-05-16, Using failed supernovae to constrain the Galactic r-process element production, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz1310

Abstract

Rapid neutron capture process (r-process) elements have been detected in a large fraction of metal-poor halo stars, with abundances relative to iron (Fe) that vary by over two orders of magnitude. This scatter is reduced to less than a factor of 3 in younger Galactic disc stars. The large scatter of r-process elements in the early Galaxy suggests that the r-process is made by rare events, like compact binary mergers and rare sub-classes of supernovae. Although being rare, neutron star mergers alone have difficulties to explain the observed enhancement of r-process elements in the lowest metallicity stars compared to Fe. The supernovae producing the two neutron stars already provide a substantial Fe abundance where the r-process ejecta from the merger would be injected. In this work we investigate another complementary scenario, where the r-process occurs in neutron star-black hole mergers in addition to neutron star mergers. Neutron star-black hole mergers would eject similar amounts of r-process matter as neutron star mergers, but only the neutron star progenitor would have produced Fe. Furthermore, a reduced efficiency of Fe production from single stars significantly alters the age–metallicity relation, which shifts the onset of r-process production to lower metallicities. We use the high-resolution [(20 pc)3/cell] inhomogeneous chemical evolution tool ‘ICE’ to study the outcomes of these effects. In our simulations, an adequate combination of neutron star mergers and neutron star-black hole mergers qualitatively reproduces the observed r-process abundances in the Galaxy.


Cote, Benoit; Eichler, Marius; Arcones, Almudena; Hansen, Camilla J.; Simonetti, Paolo; Frebel, Anna; Fryer, Chris L.; Pignatari, Marco; Reichert, Moritz; Belczynski, Krzysztof; Matteucci, Francesca, 2019-04-22, Neutron star mergers might not be the only source of r-process elements in the Milky Way, The Astrophysical Journal, doi: 10.3847/1538-4357/ab10db

Abstract

Probing the origin of r-process elements in the universe represents a multidisciplinary challenge. We review the observational evidence that probes the properties of r-process sites, and address them using galactic chemical evolution simulations, binary population synthesis models, and nucleosynthesis calculations. Our motivation is to define which astrophysical sites have significantly contributed to the total mass of r-process elements present in our Galaxy. We found discrepancies with the neutron star (NS–NS) merger scenario. When we assume that they are the only site, the decreasing trend of [Eu/Fe] at [Fe/H] > −1 in the disk of the Milky Way cannot be reproduced while accounting for the delay-time distribution (DTD) of coalescence times (∝t −1) derived from short gamma-ray bursts (GRBs) and population synthesis models. Steeper DTD functions (∝t −1.5) or power laws combined with a strong burst of mergers before the onset of supernovae (SNe) Ia can reproduce the [Eu/Fe] trend, but this scenario is inconsistent with the similar fraction of short GRBs and SNe Ia occurring in early-type galaxies, and it reduces the probability of detecting GW170817 in an early-type galaxy. One solution is to assume an additional production site of Eu that would be active in the early universe, but would fade away with increasing metallicity. If this is correct, this additional site could be responsible for roughly 50% of the Eu production in the early universe before the onset of SNe Ia. Rare classes of supernovae could be this additional r-process source, but hydrodynamic simulations still need to ensure the conditions for a robust r-process pattern.


David Lauvergnat, Peter Felker, Yohann Scribano, David M. Benoit, Zlatko Bacic, 2019-04-15, H2, HD, and D2 in the small cage of structure II clathrate hydrate: Vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates, The Journal of Chemical Physics, doi: 10.1063/1.5090573

Abstract

We report the first fully coupled quantum six-dimensional (6D) bound-state calculations of the vibration-translation-rotation eigenstates of a flexible H2, HD, and D2 molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 H2O molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H2 in the hydrate domain, based on an ab initio 6D H2–H2O pair potential for flexible H2 and rigid H2O. They extend to the first excited (v = 1) vibrational state of H2, along with two isotopologues, providing a direct computation of vibrational frequency shifts. We show that obtaining a converged v = 1 vibrational state of the caged molecule does not require converging the very large number of intermolecular translation-rotation states belonging to the v = 0 manifold up to the energy of the intramolecular stretch fundamental (≈4100 cm−1 for H2). Only a relatively modest-size basis for the intermolecular degrees of freedom is needed to accurately describe the vibrational averaging over the delocalized wave function of the quantum ground state of the system. For the caged H2, our computed fundamental translational excitations, rotational j = 0 → 1 transitions, and frequency shifts of the stretch fundamental are in excellent agreement with recent quantum 5D (rigid H2) results [A. Powers et al., J. Chem. Phys. 148, 144304 (2018)]. Our computed frequency shift of −43 cm−1 for H2 is only 14% away from the experimental value at 20 K.


Jianguo Wang, Philip Rubini, Qin Qin, Brian Houston, 2019-04-04, A Model to Predict Acoustic Resonant Frequencies of Distributed Helmholtz Resonators on Gas Turbine Engines, Applied Sciences, doi: 10.3390/app9071419

Abstract

Helmholtz resonators, traditionally designed as a narrow neck backed by a cavity, are widely applied to attenuate combustion instabilities in gas turbine engines. The use of multiple small holes with an equivalent open area to that of a single neck has been found to be able to significantly improve the noise damping bandwidth. This type of resonator is often referred to as “distributed Helmholtz resonator”. When multiple holes are employed, interactions between acoustic radiations from neighboring holes changes the resonance frequency of the resonator. In this work, the resonance frequencies from a series of distributed Helmholtz resonators were obtained via a series of highly resolved computational fluid dynamics simulations. A regression analysis of the resulting response surface was undertaken and validated by comparison with experimental results for a series of eighteen absorbers with geometries typically employed in gas turbine combustors. The resulting model demonstrates that the acoustic end correction length for perforations is closely related to the effective porosity of the perforated plate and will be obviously enhanced by acoustic radiation effect from the perforation area as a whole. This model is easily applicable for engineers in the design of practical distributed Helmholtz resonators.


Alex Sheardown and Thomas M. Fish and Elke Roediger and Matthew Hunt and John ZuHone and Yuanyuan Su and Ralph P. Kraft and Paul Nulsen and Eugene Churazov and William Forman and Christine Jones and Natalya Lyskova and Dominique Eckert and Sabrina De Grandi, 2019-03-28, A New Class of X-Ray Tails of Early-type Galaxies and Subclusters in Galaxy Clusters: Slingshot Tails versus Ram Pressure Stripped Tails, The Astrophysical Journal, doi: 10.3847/1538-4357/ab0c06

Abstract

We show that there is a new class of gas tails—slingshot tails—that form as a subhalo (i.e., a subcluster or early-type cluster galaxy) moves away from the cluster center toward the apocenter of its orbit. These tails can point perpendicular or even opposite to the subhalo direction of motion, not tracing the recent orbital path. Thus, the observed tail direction can be misleading, and we caution against naive conclusions regarding the subhalo’s direction of motion based on the tail direction. A head-tail morphology of a galaxy’s or subcluster’s gaseous atmosphere is usually attributed to ram pressure stripping, and the widely applied conclusion is that gas stripped tail traces the most recent orbit. However, during the slingshot tail stage, the subhalo is not being ram pressure stripped (RPS) and the tail is shaped by tidal forces more than just the ram pressure. Thus, applying a classic RPS scenario to a slingshot tail leads not only to an incorrect conclusion regarding the direction of motion but also to incorrect conclusions regarding the subhalo velocity, expected locations of shear flows, instabilities, and mixing. We describe the genesis and morphology of slingshot tails using data from binary cluster merger simulations and discuss their observable features and how to distinguish them from classic RPS tails. We identify three examples from the literature that are not RPS tails but slingshot tails and discuss other potential candidates.


Alexander Turner and Stephen Hayes, 2019-02-21, The Classification of Minor Gait Alterations Using Wearable Sensors and Deep Learning, IEEE Transactions on Biomedical Engineering, doi: 10.1109/TBME.2019.2900863

Abstract

Objective: This paper describes how non-invasive wearable sensors can be used in combination with deep learning to classify artificially induced gait alterations without the requirement for a medical professional or gait analyst to be present. This approach is motivated by the goal of diagnosing gait abnormalities on a symptom by symptom basis, irrespective of other neuromuscular movement disorders patients may be affected by. This could lead to improvements in treatment and offer a greater insight into movement disorders. Methods: In-shoe pressure was measured for 12 able-bodied participants, each subject to 8 artificially induced gait alterations, achieved by modifying the underside of the shoe. The data were recorded at 100 Hz over 2520 data channels and was analysed using the deep learning architecture, long term short term memory networks. Additionally, the rationale for the decision-making process of these networks was investigated. Conclusion: Long term short term memory networks are applicable to the classification of gait function. The classifications can be made using only 2 seconds of sparse data (82.0% accuracy over 96,000 instances of test data) from participants who were not part of the training set. Significance: This work provides potential for gait function to be accurately classified using non-invasive techniques, and at more regular intervals, outside of a clinical setting without the need for healthcare professionals to be present.


Mishenina, T; Pignatari, M; Gorbaneva, T; Bisterzo, S; Travaglio, C; Thielemann, F. K.; Soubiran, C, 2019-02-08, Enrichment of the Galactic disc with neutron capture elements: Sr, Monthly notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz178

Abstract

The enrichment history of heavy neutron-capture elements in the Milky Way disc provides fundamental information about the chemical evolution of our Galaxy and about the stellar sources that made those elements. In this work we give new observational data for Sr, the element at the first neutron-shell closure beyond iron, N=50, based on the analysis of the high resolution spectra of 276 Galactic disc stars. The Sr abundance was derived by comparing the observed and synthetic spectra in the region of the Sr I 4607Ã…4607Ã… line, making use of the LTE approximation. NLTE corrections lead to an increase of the abundance estimates obtained under LTE, but for these lines they are minor near solar metallicity. The average correction that we find is 0.151 dex. The star that is mostly affected is HD 6582, with a 0.244 dex correction. The behavior of the Sr abundance as a function of metallicity is discussed within a stellar nucleosynthesis context, in comparison with the abundance of the heavy neutron-capture elements Ba (Z=56) and Eu (Z=63). The comparison of the observational data with the current GCE models confirm that the s-process contributions from Asymptotic Giant Branch stars and from massive stars are the main sources of Sr in the Galactic disc and in the Sun, while different nucleosynthesis sources can explain the high [Sr/Ba] and [Sr/Eu] ratios observed in the early Galaxy.


Keegans, James D.; Fryer, Chris L.; Jones, Samuel W.; Cote, Benoit; Belczynski, Krzysztof; Herwig, Falk; Pignatari, Marco; Laird, Alison M.; Diget, Christian Aa., 2019-02-06, Nucleosynthetic yields from neutron stars accreting in binary common envelopes, Monthly notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz368

Abstract

Massive-star binaries can undergo a phase where one of the two stars expands during its advanced evolutionary stage as a giant and envelops its companion, ejecting the hydrogen envelope and tightening its orbit. Such a common envelope phase is required to tighten the binary orbit in the formation of many of the observed X-ray binaries and merging compact binary systems. In the formation scenario for neutron star binaries, the system might pass through a phase where a neutron star spirals into the envelope of its giant star companion. These phases lead to mass accretion onto the neutron star. Accretion onto these common-envelope-phase neutron stars can eject matter that has undergone burning near to the neutron star surface. This paper presents nucleosynthetic yields of this ejected matter, using population synthesis models to study the importance of these nucleosynthetic yields in a galactic chemical evolution context. Depending on the extreme conditions in temperature and density found in the accreted material, both proton-rich and neutron-rich nucleosynthesis can be obtained, with efficient production of neutron rich isotopes of low Z material at the most extreme conditions, and proton rich isotopes, again at low Z, in lower density models. Final yields are found to be extremely sensitive to the physical modeling of the accretion phase. We show that neutron stars accreting in binary common envelopes might be a new relevant site for galactic chemical evolution, and therefore more comprehensive studies are needed to better constrain nucleosynthesis in these objects.


Donatus O. Onwuli and Sabrina Francesca Samuel and Pagona Sfyri and Kevin Welham and Martin Goddard and Yasir Abu-Omar and Mahmoud Loubani and Francisco Rivero and Antonios Matsakas and David M. Benoit and Mark Wade and John Greenman and Pedro Beltran-Alvarez, 2019-01-31, The inhibitory subunit of cardiac troponin (cTnI) is modified by arginine methylation in the human heart, International Journal of Cardiology, doi: 10.1016/j.ijcard.2019.01.102

Abstract

The inhibitory subunit of cardiac troponin (cTnI) is a gold standard cardiac biomarker and also an essential protein in cardiomyocyte excitation-contraction coupling. The interactions of cTnI with other proteins are fine-tuned by post-translational modification of cTnI. Mutations in cTnI can lead to hypertrophic cardiomyopathy.


Thielemann, F. K.; Mishenina, T.; Pignatari, M.; Gorbaneva, T.; Travaglio, C.; Cote, B.; Thielemann, F.K; Soubiran, C., 2019-01-01, Enrichment of the Galactic disc with neutron-capture elements: Mo and Ru, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stz2202

Abstract

We present new observational data for the heavy elements molybdenum (Mo, Z = 42) and ruthenium (Ru, Z = 44) in F-, G-, and K-stars belonging to different substructures of the Milky Way. The range of metallicity covered is -1.0 < [Fe/H] < + 0.3. The spectra of Galactic disc stars have a high resolution of 42 000 and 75 000 and signal-to-noise ratio better than 100. Mo and Ru abundances were derived by comparing the observed and synthetic spectra in the region of Mo I lines at 5506, 5533 Ã… for 209 stars and Ru I lines at 4080, 4584, 4757 Ã… for 162 stars using the LTE approach. For all the stars, the Mo and Ru abundance determinations are obtained for the first time with an average error of 0.14 dex. This is the first extended sample of stellar observations for Mo and Ru in the Milky Way disc, and together with earlier observations in halo stars it is pivotal in providing a complete picture of the evolution of Mo and Ru across cosmic time-scales. The Mo and Ru abundances were compared with those of the neutron-capture elements (Sr, Y, Zr, Ba, Sm, Eu). The complex nucleosynthesis history of Mo and Ru is compared with different Galactic Chemical Evolution (GCE) simulations. In general, present theoretical GCE simulations show underproduction ofMo and Ru at all metallicities compared to observations. This highlights a significant contribution of nucleosynthesis processes not yet considered in our simulations. A number of possible scenarios are discussed.


A Molla, M.; Diaz, A. I.; Cavichia, O.; Gibson, B. K.; Maciel, W. J.; Costa, R. D. D.; Ascasibar, Y.; Few, C. G., 2019-01, The time evolution of the Milky Way’s oxygen abundance gradient, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/sty2877

Abstract

We study the evolution of oxygen abundance radial gradients as a function of time for the Milky Way Galaxy obtained with our MULCHEM chemical evolution model. We review the recent data of abundances for different objects observed in our Galactic disc. We analyse with our models the role of the growth of the stellar disc, as well as the effect of infall rate and star formation prescriptions, or the pre-enrichment of the infall gas, on the time evolution of the oxygen abundance radial distribution. We compute the radial gradient of abundances within the disc, and its corresponding evolution, taking into account the disc growth along time. We compare our predictions with the data compilation, showing a good agreement. Our models predict a very smooth evolution when the radial gradient is measured within the optical disc with a slight flattening of the gradient from ̃-0.057 dex kpc-1 at z = 4 until values around ̃-0.015 dex kpc-1 at z = 1 and basically the same gradient until the present, with small differences between models. Moreover, some models show a steepening at the last times, from z = 1 until z = 0 in agreement with data which give a variation of the gradient in a range from -0.02 to -0.04 dex kpc-1 from t = 10 Gyr until now. The gradient measured as a function of the normalized radius R/Reff is in good agreement with findings by CALIFA and MUSE, and its evolution with redshift falls within the error bars of cosmological simulations.


2018 (20 outputs)

Lluis Franch-Gras, Christoph Hahn, Eduardo M. Garcia-Roger, Maria Jose Carmona, Manuel Serra & Africa Gomez, 2018-10-30, Genomic signatures of local adaptation to the degree of environmental predictability in rotifers, Scientific reports, doi: 10.1038/s41598-018-34188-y

Abstract

Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.


Cseh, B.; Lugaro, M.; D’Orazi, V.; de Castro, D. B.; Pereira, C. B.; Karakas, A. I.; Molnar, L.; Plachy, E.; Szabo, R.; Pignatari, M.; Cristallo, S., 2018-10-17, The s process in AGB stars as constrained by a large sample of barium stars, Astronomy & Astrophysics, doi: 10.1051/0004-6361/201834079

Abstract

Barium (Ba) stars are dwarf and giant stars enriched in elements heavier than iron produced by the slow neutron-capture process (s process). These stars belong to binary systems in which the primary star evolved through the asymptotic giant branch (AGB) phase. During this phase the primary star produced s-process elements and transferred them onto the secondary, which is now observed as a Ba star. Aims. We compare the largest homogeneous set of Ba giant star observations of the s-process elements Y, Zr, La, Ce, and Nd with AGB nucleosynthesis models to reach a better understanding of the s process in AGB stars. Methods. By considering the light-s (ls: Y and Zr) heavy-s (hs: La, Ce, and Nd) and elements individually, we computed for the first time quantitative error bars for the different hs-element to ls-element abundance ratios, and for each of the sample stars. We compared these ratios to low-mass AGB nucleosynthesis models. We excluded La from our analysis because the strong La lines in some of the sample stars cause an overestimation and unreliable abundance determination, as compared to the other observed hs-Type elements. Results. All the computed hs-Type to ls-Type element ratios show a clear trend of increasing with decreasing metallicity with a small spread (less than a factor of 3). This trend is predicted by low-mass AGB models in which 13C is the main neutron source. The comparison with rotating AGB models indicates the need for the presence of an angular momentum transport mechanism that should not transport chemical species, but significantly reduces the rotational speed of the core in the advanced stellar evolutionary stages. This is an independent confirmation of asteroseismology observations of the slow down of core rotation in giant stars, and of rotational velocities of white dwarfs lower than predicted by models without an extra angular momentum transport mechanism.


Deshmukh, Harshal and Papageorgiou, Maria and Kilpatrick, Eric S. and Atkin, Stephen L. and Sathyapalan, Thozhukat, 2018-10, Development of a novel risk prediction and risk stratification score for polycystic ovary syndrome, Clinical Endocrinology, doi: 10.1111/cen.13879

Abstract

Summary Objective The aim of this study was to develop a simple phenotypic algorithm that can capture the underlying clinical and hormonal abnormalities to help in the diagnosis and risk stratification of polycystic ovary syndrome (PCOS). Methods The study consisted of 111 women with PCOS fulfilling the Rotterdam diagnostic criteria and 67 women without PCOS. A Firth’s penalized logistic regression model was used for independent variable section. Model optimism, discrimination and calibration were assessed using bootstrapping, area under the curve (AUC) and Hosmer-Lemeshow statistics, respectively. The prognostic index (PI) and risk score for developing PCOS were calculated using independent variables from the regression model. Results Firth penalized logistic regression model with backward selection identified four independent predictors of PCOS namely free androgen index [β 0.30 (0.12), P = 0.008], 17-OHP [β = 0.20 (0.01), P = 0.026], anti-mullerian hormone [AMH; β = 0.04 (0.01) P < 0.0001] and waist circumference [β = 0.08 (0.02), P < 0.0001]. The model estimates indicated high internal validity (minimal optimism on 1000-fold bootstrapping), good discrimination ability (bias corrected c-statistic = 0.90) and good calibration (Hosmer-Lemeshow χ2 = 3.7865). PCOS women with a high-risk score (q1 + q2 + q3 vs q4) presented with a worse metabolic profile characterized by a higher 2-hour glucose (P = 0.01), insulin (P = 0.0003), triglycerides (P = 0.0005), C-reactive protein (P < 0.0001) and low HDL-cholesterol (P = 0.02) as compared to those with lower risk score for PCOS. Conclusions We propose a simple four-variable model, which captures the underlying clinical and hormonal abnormalities in PCOS and can be used for diagnosis and metabolic risk stratification in women with PCOS.


Deshmukh, Harshal and Barker, Emma and Ambarasan, Thineshkrishna and Levin, Daniel and Bell, Samira and Witham, Miles D and George, Jacob, 2018-10, Calcium channel blockers are associated with improved survival and lower cardiovascular mortality in patients with renovascular disease, Cardiovascular Therapeutics, doi: 10.1111/1755-5922.12474

Abstract

Background and objective Results of interventional trials in renovascular hypertension have been disappointing and medical therapy is the current recommended gold standard. However, the comparative long-term benefits of different antihypertensive drug classes in atherosclerotic renal artery stenosis are not known. We aim to assess the effect of different antihypertensive drug classes on outcomes in renovascular hypertension Design, setting, participants, and measurements Using Tayside Health Informatics Centre database, anonymised data over a 6-year period was analysed. Biochemistry, prescribing data, morbidity, mortality and demographic data were accessed via hospital medical records and electronic data stored in the Tayside Health Informatics Centre Safe Haven. General Registrar’s Office data was used to identify patients who died from cardiovascular disease. Independent predictors of survival in each group were analyzed using Kaplan-Meier survival curves and Cox proportional hazard models, adjusted for a range of covariates, using Time-Updated Drug Analysis. Blood pressure data was obtained from primary and secondary care clinic blood pressure records for each patient. Adjustments for mean systolic blood pressure over the follow-up period and baseline blood pressure were made. Results 579 patients with Atherosclerotic Renal Artery Stenosis were identified. In the unilateral renal artery stenosis cohort, Calcium Channel Blockers but not ACE inhibitors/ARBs, were associated with a significant reduction in all-cause (HR=0.45, CI= 0.31, 0.65; P=<0.0001) and Cardiovascular ((HR= 0.51, CI =0.29-0.90 P=0.019). This was maintained after adjustment for blood pressure. In the bilateral renal artery stenosis cohort, both classes of drugs reduced all-cause but not cardiovascular mortality. Patients with moderate disease benefitted more than those with mild or severe disease. Conclusions Calcium Channel Blockers are associated with significantly increased survival and lower cardiovascular mortality particularly in patients with moderate RAS disease. This article is protected by copyright. All rights reserved.


Alex Sheardown and Elke Roediger and Yuanyuan Su and Ralph P. Kraft and Thomas Fish and John A. ZuHone and William R. Forman and Christine Jones and Eugene Churazov and Paul E. J. Nulsen, 2018-09-28, The Recent Growth History of the Fornax Cluster Derived from Simultaneous Sloshing and Gas Stripping: Simulating the Infall of {NGC} 1404, American Astronomical Society, doi: 10.3847/1538-4357/aadc0f

Abstract

We derive the recent growth history of the Fornax Cluster, in particular the recent infall of the giant elliptical galaxy NGC 1404. We show, using a simple cluster minor merger simulation tailored to Fornax and NGC 1404, that a second or more likely third encounter between the two reproduces all the main merger features observed in both objects; we firmly exclude a first infall scenario. Our simulations reveal a consistent picture: NGC 1404 passed by NGC 1399 about 1.1–1.3 Gyr ago from the northeast to the southwest and is now almost at the point of its next encounter from the south. This scenario explains the sloshing patterns observed in Fornax—a prominent northern cold front and an inner southern cold front. This scenario also explains the truncated atmosphere, the gas-stripping radius of NGC 1404, and its faint gas tail. Independent of the exact history, we can make a number of predictions. A detached bow shock south of NGC 1404 should exist, which is a remnant of the galaxy’s previous infall at a distance from NGC 1404 between 450 and 750 kpc with an estimated Mach number between 1.3 and 1.5. The wake of NGC 1404 also lies south of the galaxy with enhanced turbulence and a slight enhancement in metallicity compared to the undisturbed regions of the cluster. Southwest of NGC 1404, there is likely evidence of old turbulence originating from the previous infall. No scenario predicts enhanced turbulence outside of the cold front northwest of the cluster center.


W.R.C. Somerville, J.L. Stokes, A.M., T.S. Horozov, A.J. Archer and D.M.A. Buzza, 2018-09-13, Density functional theory for the crystallization of two-dimensional dipolar colloidal alloys, Journal of Physics: Condensed Matter, doi: 10.1088/1361-648X/aaddc9

Abstract

Two-dimensional mixtures of dipolar colloidal particles with different dipole moments exhibit extremely rich self-assembly behaviour and are relevant to a wide range of experimental systems, including charged and super-paramagnetic colloids at liquid interfaces. However, there is a gap in our understanding of the crystallization of these systems because existing theories such as integral equation theory and lattice sum methods can only be used to study the high temperature fluid phase and the zero-temperature crystal phase, respectively. In this paper we bridge this gap by developing a density functional theory (DFT), valid at intermediate temperatures, in order to study the crystallization of one and two-component dipolar colloidal monolayers. The theory employs a series expansion of the excess Helmholtz free energy functional, truncated at second order in the density, and taking as input highly accurate bulk fluid direct correlation functions from simulation. Although truncating the free energy at second order means that we cannot determine the freezing point accurately, our approach allows us to calculate ab initio both the density profiles of the different species and the symmetry of the final crystal structures. Our DFT predicts hexagonal crystal structures for one-component systems, and a variety of superlattice structures for two-component systems, including those with hexagonal and square symmetry, in excellent agreement with known results for these systems. The theory also provides new insights into the structure of two-component systems in the intermediate temperature regime where the small particles remain molten but the large particles are frozen on a regular lattice.


Al-Qaissi, Ahmed and Papageorgiou, Maria and Deshmukh, Harshal and Madden, Leigh A. and Rigby, Alan and Kilpatrick, Eric S. and Atkin, Stephen L. and Sathyapalan, Thozhukat, 2018-09, Effects of acute insulin-induced hypoglycaemia on endothelial microparticles in adults with and without type 2 diabetes, Diabetes, Obesity and Metabolism, doi: 10.1111/dom.13548

Abstract

Aims To assess whether endothelial microparticles (EMPs), novel surrogate markers of endothelial injury and dysfunction, are differentially produced in response to acute insulin-induced hypoglycaemia in adults with and without type 2 diabetes. Materials and methods A prospective, parallel study was conducted in individuals with type 2 diabetes (n = 23) and controls (n = 22). Hypoglycaemia (<2.2 mmoL/L: <40 mg/dL) was achieved by intravenous infusion of soluble insulin. Blood samples were collected at baseline and at 0, 30, 60, 120, 240 minutes and 24 hours after hypoglycaemia and analysed for CD31+ (platelet endothelial cell adhesion molecule-1), CD54+ (intercellular adhesion molecule 1), CD62-E+ (E-selectin), CD105+ (endoglin), CD106+ (vascular cell adhesion molecule 1) and CD142+ (tissue factor) EMPs by flow cytometry. The peak elevations (\% rise from 0 minutes after hypoglycaemia) in EMP within 240 minutes after insulin-induced hypoglycaemia were modelled using a regression model, with adjustment for relevant covariates. All EMPs were expressed as percentage from 0 minutes hypoglycaemia for each time point and total areas under the curve (AUC0min–24h) were calculated. Results Following insulin-induced hypoglycaemia, levels of circulating EMPs were maximal at 240 minutes (P < 0.001) and returned to baseline values within 24 hours for both groups. The peak elevations (\% rise from 0 minutes following hypoglycaemia) seen in CD31+, CD54+, CD62-E+, CD105+ and CD142+ EMPs within 240 minutes were associated with diabetes status after adjustments for all relevant covariates. Individuals with type 2 diabetes showed increased CD31+ EMPs AUC0min–24h (P = 0.014) and CD105+ EMPs AUC0min–24h (P = 0.006) compared with controls, but there were no differences for CD54+ (P = 0.91), CD62-E+ (P = 0.14), CD106+ (P = 0.36) or CD142+ (P = 0.77) EMPs AUC0min–24h. Conclusions The associations between peak elevations within 240 minutes after insulin-induced hypoglycaemia for CD31+, CD54+, CD62-E+, CD105+ and CD142+ and diabetes status indicate that the assessment of a panel of EMPs within this timeframe would identify a hypoglycaemic event in this population. The greater overall responses over time (AUCs) for apoptosis-induced CD31+ and CD105+ EMPs suggest that hypoglycaemia exerts greater endothelial stress in type 2 diabetes.


Annika M Schoene and Nina Dethlefs, 2018-08-20, Unsupervised suicide note classification, Proceedings of the 7th KDD Workshop on Issues of Sentiment Discovery and Opinion Mining (WISDOM), doi:

Abstract

With the greater availability of linguistic data from public social media platforms and the advancements of natural language processing, a number of opportunities have arisen for researchers to analyse this type of data. Research efforts have mostly focused on detecting the polarity of textual data, evaluating whether there is positive, negative or sometimes neutral content. Especially the use of neural networks has recently yielded significant results in polarity detection experiments. In this paper we present a more fine-grained approach to detecting sentiment in textual data, particularly analysing a corpus of suicide notes, depressive notes and love notes. We achieve a classification accuracy of 71.76% when classifying based on text and sentiment features, and an accuracy of 69.41% when using the words present in the notes alone. We discover that while emotions in all three datasets overlap, each of them has a unique ‘emotion profile’ which allows us to draw conclusions about the potential mental state that is reflects. Using the emotion sequences only, we achieve an accuracy of 75.29%. The results from unannotated data, while worse than the other models, nevertheless represent an encouraging step towards being able to flag potentially harmful social media posts online and in real time. We provide a high-level corpus analysis of the data sets in order to demonstrate the grammatical and emotional differences.


T.L. Lee, J. Mi, S. Ren, S. Zhao, J. Fan, S. Kabra, S. Zhang, and P.S. Grant, 2018-05-26, Modelling and neutron diffraction characterization of the interfacial bonding of spray formed dissimilar steels, Acta Materialia, doi: 10.1016/j.actamat.2018.05.055

Abstract

The spray forming of thick, dissimilar steel clad tubes with the objective of achieving a high integrity metallurgical bond across the cladding-substrate interface able to withstand residual stresses and subsequent thermo-mechanical processing was investigated by large scale experiments, modelling and extensive microstructural characterization including microscopy, X-ray tomography, neutron scattering and mechanical testing. The simulated residual stress distributions across the cladding-substrate interface, accounting for any as-sprayed porosity and the distribution of martensitic and retained austenite phases, were compared with neutron diffraction measurements and differences used to infer the load transfer behaviour and thus the mechanical integrity of the interface. The mechanical properties of the interfaces were then also measured directly by shear testing. The link between substrate pre-heating, the spray forming temperature, and the resulting preform temperature, porosity, phase fractions, residual stress, strength and integrity of the interface were established and quantified explicitly.


Benoit, David M. and Lauvergnat, David and Scribano, Yohann, 2018-05-25, Does cage quantum delocalisation influence the translation-rotational bound states of molecular hydrogen in clathrate hydrate?, Faraday Discussions, doi: 10.1039/C8FD00087E

Abstract

In this study, we examine the effect of a flexible description of the clathrate hydrate framework on the translation-rotation (TR) eigenstates of guest molecules such as molecular hydrogen. Traditionally, the water cage structure is assumed to be rigid, thus ignoring the quantum nature of hydrogen nuclei in the water framework. However, it has been shown that protons in a water molecule possess a marked delocalised character in many situations, ranging from water clusters to proton transfer in the bulk. In the case of water clathrates, all previous TR bound-state calculations of guest molecules consider that the caging water molecules are fixed at their equilibrium geometry. Only recently, a static investigation of the role of proton configurations was performed by Bacic and co-workers by sampling a very large number of different static structures of water clathrates. Here, we investigate the importance of the rotational degrees of freedom of the water cage on the TR levels of the guest molecule using an efficient adiabatic decoupling scheme. Our approach combines rigid body diffusion Monte Carlo calculations for the description of the rotational degree of freedom of water molecules surrounding the guest molecular hydrogen to an efficient Smolyak sparse-grid technique for the calculation of the TR levels. This approach allows us to take into account the highly anharmonic nature of the rotational water motions in a high-dimensional system. The clathrate-induced splittings of the j = 1 rotational levels are much more sensitive to the quantum hydrogen delocalisation than the translational transitions. This result is in good agreement with the previous static study of Bacic and co-workers.


Daniela Carollo and Patricia B. Tissera and Timothy C. Beers and Dmitrii Gudin and Brad K. Gibson and Ken C. Freeman and Antonela Monachesi, 2018-05-18, The Origin of the Milky Way{\textquotesingle}s Halo Age Distribution, The Astrophysical Journal, doi: 10.3847/2041-8213/aac2dc

Abstract

We present an analysis of the radial age gradients for the stellar halos of five Milky Way (MW) mass-sized systems simulated as part of the Aquarius Project. The halos show a diversity of age trends, reflecting their different assembly histories. Four of the simulated halos possess clear negative age gradients, ranging from approximately .7 to .19 Myr kpc.1, shallower than those determined by recent observational studies of the Milky Way’s stellar halo. However, when restricting the analysis to the accreted component alone, all of the stellar halos exhibit a steeper negative age gradient with values ranging from .8 to .32 Myr kpc.1, closer to those observed in the Galaxy. Two of the accretion-dominated simulated halos show a large concentration of old stars in the center, in agreement with the Ancient Chronographic Sphere reported observationally. The stellar halo that best reproduces the current observed characteristics of the age distributions of the Galaxy is that formed principally by the accretion of small satellite galaxies. Our findings suggest that the hierarchical clustering scenario can reproduce the MW’s halo age distribution if the stellar halo was assembled from accretion and the disruption of satellite galaxies with dynamical masses less than ~109.5 M ., and a minimal in situ contribution.


Chen, Long; Vivier, Elodie; Eling, Charlotte J.; Babra, Tahkur S.; Bouillard, Jean Sebastien G.; Adawi, Ali M.; Benoit, David M.; Hartl, Frantisek; Colquhoun, Howard M.; Efremova, Olga A.; Greenland, Barnaby W., 2018-04-07, Conjugated, rod-like viologen oligomers: Correlation of oligomer length with conductivity and photoconductivity, Synthetic Metals, doi: 10.1016/j.synthmet.2018.03.019

Abstract

An iterative synthesis has been used to produce conjugated, monodisperse, viologen-based aromatic oligomers containing up to 12 aromatic/heterocyclic rings. The methoxy-substituted oligomers were soluble in common organic solvents and could be processed by spin coating. The conductivities of the resulting films (30–221 nm thick) increased by more than one order of magnitude as the oligomer length increased from unimer (1, 2.20 × 10 −11 S cm- 1 ) through dimer (2) to trimer (3, 6.87 × 10 -10 S cm -1 ). The bandgaps of the materials were estimated from the absorption spectra of these thin films. The longest oligomer, 3, exhibited a noticeably narrower bandgap (2.3 eV) than the shorter oligomers (1 and 2 both 2.7 eV). Oligomer 3 also showed photoconductivity under irradiation across a wide range of wavelengths in the visible spectral region. In conjunction with DFT calculations of these systems our results suggest that structurally related viologen-type oligomers may find use in optoelectronic devices.


Chalupa, David and Hawick, Ken A. and Walker, James A., 2018-04, Hybrid Bridge-Based Memetic Algorithms for Finding Bottlenecks in Complex Networks, Big Data Research, doi: 10.1016/j.bdr.2018.04.001

Abstract

We propose a memetic approach to find bottlenecks in complex networks based on searching for a graph partitioning with minimum conductance. Finding the optimum of this problem, also known in statistical mechanics as the Cheeger constant, is one of the most interesting NP-hard network optimisation problems. The existence of low conductance minima indicates bottlenecks in complex networks. However, the problem has not yet been explored in depth in the context of applied discrete optimisation and evolutionary approaches to solve it. In this paper, the use of a memetic framework is explored to solve the minimum conductance problem. The approach combines a hybrid method of initial population generation based on bridge identification and local optima sampling with a steady-state evolutionary process with two local search subroutines. These two local search subroutines have complementary qualities. Efficiency of three crossover operators is explored, namely one-point crossover, uniform crossover, and our own partition crossover. Experimental results are presented for both artificial and real-world complex networks. Results for Barabási–Albert model of scale-free networks are presented, as well as results for samples of social networks and protein–protein interaction networks. These indicate that both well-informed initial population generation and the use of a crossover seem beneficial in solving the problem in large-scale.”


Roggatz, Christina C. and Lorch, Mark and Benoit, David M., 2018-03-22, Influence of Solvent Representation on Nuclear Shielding Calculations of Protonation States of Small Biological Molecules, Journal of Chemical Theory and Computation, doi: 10.1021/acs.jctc.7b01020

Abstract

In this study, we assess the influence of solvation on the accuracy and reliability of isotropic nuclear magnetic shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for different protonation states, as biological molecules occur almost exclusively in aqueous solution and are subject to protonation with pH. We identify significant shortcomings of current implicit solvent models and present a hybrid solvation approach that improves agreement with experimental data by taking into account the presence of direct interactions between amino acid protonation state and water molecules.


Y. Zhao and W. Du and B. Koe and T. Connolley and S. Irvine and P.K. Allan and C.M. Schleputz and W. Zhang and F. Wang and D.G. Eskin and J. Mi, 2018-03-15, 3D characterisation of the Fe-rich intermetallic phases in recycled Al alloys by synchrotron X-ray microtomography and skeletonisation, Scripta Materialia, doi: 10.1016/j.scriptamat.2017.12.010

Abstract

Synchrotron X-ray microtomography and skeletonisation method were used to study the true 3D network structures and morphologies of the Fe-rich intermetallic phases in recycled Al-5.0%Cu-0.6%Mn alloys with 0.5% and 1.0% Fe. It was found that, the Fe-phases in the 1.0%Fe alloy have node lengths of 5–25μm; while those in the 0.5%Fe alloy are of 3–17μm. The Fe-phases in the 1.0%Fe alloy also developed sharper mean curvature with wider distribution than those in the 0.5%Fe alloy. Combining SEM studies of the deeply-etched samples, the true 3D structures of 4 different type Fe phases in both alloys are also revealed and demonstrated.


Travaglio, C.; Rauscher, T.; Heger, A.; Pignatari, M.; West, C., 2018-02-07, Role of core-collapse supernovae in explaining Solar System abundances of p nuclides, The Astrophysical journal, doi: 10.3847/1538-4357/aaa4f7

Abstract

The production of the heavy stable proton-rich isotopes between 74Se and 196Hg—the p nuclides—is due to the contribution from different nucleosynthesis processes, activated in different types of stars. Whereas these processes have been subject to various studies, their relative contributions to Galactic chemical evolution (GCE) are still a matter of debate. Here we investigate for the first time the nucleosynthesis of p nuclides in GCE by including metallicity and progenitor mass-dependent yields of core-collapse supernovae (ccSNe) into a chemical evolution model. We used a grid of metallicities and progenitor masses from two different sets of stellar yields and followed the contribution of ccSNe to the Galactic abundances as a function of time. In combination with previous studies on p-nucleus production in thermonuclear supernovae (SNIa), and using the same GCE description, this allows us to compare the respective roles of SNeIa and ccSNe in the production of p-nuclei in the Galaxy. The γ process in ccSN is very efficient for a wide range of progenitor masses (13 M ⊙–25 M ⊙) at solar metallicity. Since it is a secondary process with its efficiency depending on the initial abundance of heavy elements, its contribution is strongly reduced below solar metallicity. This makes it challenging to explain the inventory of the p nuclides in the solar system by the contribution from ccSNe alone. In particular, we find that ccSNe contribute less than 10% of the solar p nuclide abundances, with only a few exceptions. Due to the uncertain contribution from other nucleosynthesis sites in ccSNe, such as neutrino winds or α-rich freeze out, we conclude that the light p-nuclides 74Se, 78Kr, 84Sr, and 92Mo may either still be completely or only partially produced in ccSNe. The γ-process accounts for up to twice the relative solar abundances for 74Se in one set of stellar models and 196Hg in the other set. The solar abundance of the heaviest p nucleus 196Hg is reproduced within uncertainties in one set of our models due to photodisintegration of the Pb isotopes 208,207,206Pb. For all other p nuclides, abundances as low as 2% of the solar level were obtained.


Bing Wang and Dongyue Tan and Tung Lik Lee and Jia Chuan Khong and Feng Wang and Dmitry Eskin and Thomas Connolley and Kamel Fezzaa and Jiawei Mi, 2018-02-01, Ultrafast synchrotron X-ray imaging studies of microstructure fragmentation in solidification under ultrasound, Acta Materialia, doi: 10.1016/j.actamat.2017.10.067

Abstract

Ultrasound processing of metal alloys is an environmental friendly and promising green technology for liquid metal degassing and microstructural refinement. However many fundamental issues in this field are still not fully understood, because of the difficulties in direct observation of the dynamic behaviours caused by ultrasound inside liquid metal and semisolid metals during the solidification processes. In this paper, we report a systematic study using the ultrafast synchrotron X-ray imaging (up to 271,554 frame per second) technique available at the Advanced Photon Source, USA and Diamond Light Source, UK to investigate the dynamic interactions between the ultrasonic bubbles/acoustic flow and the solidifying phases in a Bi-8%Zn alloy. The experimental results were complimented by numerical modelling. The chaotic bubble implosion and dynamic bubble oscillations were revealed in-situ for the first time in liquid metal and semisolid metal. The fragmentation of the solidifying Zn phases and breaking up of the liquid-solid interface by ultrasonic bubbles and enhanced acoustic flow were clearly demonstrated and agreed very well with the theoretical calculations. The research provides unambiguous experimental evidence and robust theoretical interpretation in elucidating the dominant mechanisms of microstructure fragmentation and refinement in solidification under ultrasound.


Marco Pignatari and Peter Hoppe and Reto Trappitsch and Chris Fryer and F.X. Timmes and Falk Herwig and Raphael Hirschi, 2018-01-15, The neutron capture process in the He shell in core-collapse supernovae: Presolar silicon carbide grains as a diagnostic tool for nuclear astrophysics, Geochimica et Cosmochimica Acta, doi: 10.1016/j.gca.2017.06.005

Abstract

Carbon-rich presolar grains are found in primitive meteorites, with isotopic measurements to date suggesting a core-collapse supernovae origin site for some of them. This holds for about 1–2% of presolar silicon carbide (SiC) grains, so-called Type X and C grains, and about 30% of presolar graphite grains. Presolar SiC grains of Type X show anomalous isotopic signatures for several elements heavier than iron compared to the solar abundances: most notably for strontium, zirconium, molybdenum, ruthenium and barium. We study the nucleosynthesis of zirconium and molybdenum isotopes in the He-shell of three core-collapse supernovae models of 15, 20 and 25 M☉ with solar metallicity, and compare the results to measurements of presolar grains. We find the stellar models show a large scatter of isotopic abundances for zirconium and molybdenum, but the mass averaged abundances are qualitatively similar to the measurements. We find all models show an excess of 96Zr relative to the measurements, but the model abundances are affected by the fractionation between Sr and Zr since a large contribution to 90Zr is due to the radiogenic decay of 90Sr. Some supernova models show excesses of 95,97Mo and depletion of 96Mo relative to solar. The mass averaged distribution from these models shows an excess of 100Mo, but this may be alleviated by very recent neutron-capture cross section measurements. We encourage future explorations to assess the impact of the uncertainties in key neutron-capture reaction rates that lie along the n-process path.


Peter Hoppe and Marco Pignatari and Janos Kodolanyi and Elmar Groner and Sachiko Amari, 2018-01-15, NanoSIMS isotope studies of rare types of presolar silicon carbide grains from the Murchison meteorite: Implications for supernova models and the role of 14C, Geochimica et Cosmochimica Acta, doi: 10.1016/j.gca.2017.01.051

Abstract

We have conducted a NanoSIMS ion imaging survey of about 1800 presolar silicon carbide (SiC) grains from the Murchison meteorite. A total of 21 supernova (SN) X grains, two \{SN\} C grains, and two putative nova grains were identified. Six particularly interesting grains, two X and C grains each and the two putative nova grains were subsequently studied in greater detail, namely, for C-, N-, Mg-Al-, Si-, S-, and Ca-Ti-isotopic compositions and for the initial presence of radioactive 26Al (half life 716,000 yr), 32Si (half life 153 yr), and 44Ti (half life 60 yr). Their isotope data along with those of three X grains from the literature were compared with model predictions for 15 M⊙ and 25 M⊙ Type \{II\} supernovae (SNe). The best fits were found for 25 M⊙ \{SN\} models that consider for the He shell the temperature and density of a 15 M⊙ \{SN\} and ingestion of H into the He shell before the explosion. In these models a C- and Si-rich zone forms at the bottom of the He burning zone (C/Si zone). The region above the C/Si zone is termed the O/nova zone and exhibits the isotopic fingerprints of explosive H burning. Satisfactory fits of measured C-, N-, and Si-isotopic compositions and of 26Al/27Al ratios require small-scale mixing of matter originating from a region extending over 0.2 M⊙ for X and C grains and over 0.4 M⊙ for one of the putative nova grains, involving matter from a thin Si-rich layer slightly below the C/Si zone, the C/Si zone, and the O/nova zone. Simultaneous fitting of 14N/15N and 26Al/27Al requires a C-N fractionation of a factor of 50 during SiC condensation. This leads to preferential incorporation of radioactive 14C (half life 5700 yr) over directly produced 14N and can account for the 14N/15N along with 26Al/27Al ratios as observed in the SiC grains. The good fit for one of the putative nova grains along with its high 26Al/27Al points towards a \{SN\} origin and supports previous suggestions that some grains classified as nova grains might be from SNe. Apparent problems with the small-scale mixing scheme considered here are C/O ratios that are mostly <1 if C-, N-, and Si-isotopic compositions and 26Al/27Al ratios are simultaneously matched, underproduction of 32Si, and overproduction of 44Ti. This confirms the limitations of one-dimensional hydrodynamical models for H ingestion and stresses the need to better study the convective-boundary mixing mechanisms at the bottom of the convective He shell in massive star progenitors. This is crucial to define the effective size of the C/Si zone formed by the \{SN\} shock. The comparison between the Si isotope data of the \{SN\} grains and the models gives a hint that the predicted 30Si is too high at the bottom of the He burning shell.


Hannes C. Gottschalk and Anja Poblotzki and Martin A. Suhm and Muneerah M. Al-Mogren and Jens Antony and Alexander A. Auer and Leonardo Baptista and David M. Benoit and Giovanni Bistoni and Fabian Bohle and Rahma Dahmani and Dzmitry Firaha and Stefan Grimme and Andreas Hansen and Michael E. Harding and Majdi Hochlaf and Christof Holzer and Georg Jansen and Wim Klopper and Wassja A. Kopp and Leif C. Kroger and Kai Leonhard and Halima Mouhib and Frank Neese and Max N. Pereira and Inga S. Ulusoy and Axel Wuttke and Ricardo A. Mata, 2018-01-01, The furan microsolvation blind challenge for quantum chemical methods: First steps, The Journal of Chemical Physics, doi: 10.1063/1.5009011

Abstract

Herein we present the results of a blind challenge to quantum chemical methods in the calculation of dimerization preferences in the low temperature gas phase. The target of study was the first step of the microsolvation of furan, 2-methylfuran and 2,5-dimethylfuran with methanol. The dimers were investigated through IR spectroscopy of a supersonic jet expansion. From the measured bands, it was possible to identify a persistent hydrogen bonding OH–O motif in the predominant species. From the presence of another band, which can be attributed to an OH-π interaction, we were able to assert that the energy gap between the two types of dimers should be less than or close to 1 kJ/mol across the series. These values served as a first evaluation ruler for the 12 entries featured in the challenge. A tentative stricter evaluation of the challenge results is also carried out, combining theoretical and experimental results in order to define a smaller error bar. The process was carried out in a double-blind fashion, with both theory and experimental groups unaware of the results on the other side, with the exception of the 2,5-dimethylfuran system which was featured in an earlier publication.


2017 (14 outputs)

Vorotnikova, Natalya A. and Vorotnikov, Yuri A. and Novozhilov, Igor N. and Syrokvashin, Mikhail M. and Nadolinny, Vladimir A. and Kuratieva, Natalia V. and Benoit, David M. and Mironov, Yuri V. and Walton, Richard I. and Clarkson, Guy J. and Kitamura, Noboru and Sutherland, Andrew J. and Shestopalov, Michael A. and Efremova, Olga A., 2017-12-22, 23-Electron Octahedral Molybdenum Cluster Complex [{Mo6I8}Cl6]−, Inorganic Chemistry, doi: 10.1021/acs.inorgchem.7b02760

Abstract

Photoactive transition metal compounds that are prone to reversible redox reactions are important for myriad applications, including catalysis, optoelectronics, and sensing. This article describes chemical and electrochemical methods to prepare cluster complex (Bu4N)[{Mo6I8}Cl6], a rare example of a 23 e– cluster complex within the family of octahedral clusters of Mo, W, and Re. The low temperature and room temperature crystal structures; electronic structure; and the magnetic, optical, and electrochemical properties of this complex are described.


Ruiz-Lara, T., Few, C. G., Florido, E., Gibson, B. K., Perez, I., Sanchez-Blazquez, P., 2017-12-15, The role of stellar radial motions in shaping galaxy surface brightness profiles, Astronomy & Astrophysics, doi: 10.1051/0004-6361/201731485

Abstract

Aims: The physics driving features such as breaks observed in galaxy surface brightness (SB) profiles remains contentious. Here, we assess the importance of stellar radial motions in shaping their characteristics. Methods: We use the simulated Milky Way-mass cosmological discs from the Ramses Disc Environment Study (RaDES) to characterise the radial redistribution of stars in galaxies displaying type-I (pure exponentials), II (downbending), and III (upbending) SB profiles. We compare radial profiles of the mass fractions and the velocity dispersions of different sub-populations of stars according to their birth and current location. Results: Radial redistribution of stars is important in all galaxies regardless of their light profiles. Type-II breaks seem to be a consequence of the combined effects of outward-moving and accreted stars. The former produce shallower inner profiles (lack of stars in the inner disc) and accumulate material around the break radius and beyond, strengthening the break; the latter can weaken or even convert the break into a pure exponential. Further accretion from satellites can concentrate material in the outermost parts, leading to type-III breaks that can coexist with type-II breaks, but situated further out. Type-III galaxies would be the result of an important radial redistribution of material throughout the entire disc, as well as a concentration of accreted material in the outskirts. In addition, type-III galaxies display the most efficient radial redistribution and the largest number of accreted stars, followed by type-I and II systems, suggesting that type-I galaxies may be an intermediate case between types II and III. In general, the velocity dispersion profiles of all galaxies tend to flatten or even increase around the locations where the breaks are found. The age and metallicity profiles are also affected, exhibiting different inner gradients depending on their SB profile, being steeper in the case of type-II systems (as found observationally). The steep type-II profiles might be inherent to their formation rather than acquired via radial redistribution.


Szitenberg A, Salazar-Jaramillo L, Blok VC, Laetsch DR, Joseph S, Williamson VM, et al., 2017-09-25, Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change., Genome Biology and Evolution, doi: 10.1093/gbe/evx201

Abstract

The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the apomictic MIG species are hypotriploids, with a proportion of one genome present in a second copy. The hypotriploid proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.


Thompson, B. B. and Few, C. G. and Bergemann, M. and Gibson, B. K. and MacFarlane, B. A. and Serenelli, A. and Gilmore, G. and Randich, S. and Vallenari, A. and Alfaro, E. J. and Bensby, T. and Francois, P. and Korn, A. J. and Bayo, A. and Carraro, G. and Casey, A. R. and Costado, M. T. and Donati, P. and Franciosini, E. and Frasca, A. and Hourihane, A. and Jofré, P. and Hill, V. and Heiter, U. and Koposov, S. E. and Lanzafame, A. and Lardo, C. and de Laverny, P. and Lewis, J. and Magrini, L. and Marconi, G. and Masseron, T. and Monaco, L. and Morbidelli, L. and Pancino, E. and Prisinzano, L. and Recio-Blanco, A. and Sacco, G. and Sousa, S. G. and Tautvaisiene, G. and Worley, C. C. and Zaggia, S., 2017-09-11, The Gaia-ESO Survey: Matching Chemo-Dynamical Simulations to Observations of the Milky Way, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stx2316

Abstract

The typical methodology for comparing simulated galaxies with observational surveys is usually to apply a spatial selection to the simulation to mimic the region of interest covered by a comparable observational survey sample. In this work we compare this approach with a more sophisticated post-processing in which the observational uncertainties and selection effects (photometric, surface gravity and effective temperature) are taken into account. We compare a ‘solar neighbourhood analogue’ region in a model Milky Way-like galaxy simulated with RAMSES-CH with fourth release Gaia-ESO survey data. We find that a simple spatial cut alone is insufficient and that observational uncertainties must be accounted for in the comparison. This is particularly true when the scale of uncertainty is large compared to the dynamic range of the data, e.g. in our comparison, the [Mg/Fe] distribution is affected much more than the more accurately determined [Fe/H] distribution. Despite clear differences in the underlying distributions of elemental abundances between simulation and observation, incorporating scatter to our simulation results to mimic observational uncertainty produces reasonable agreement. The quite complete nature of the Gaia-ESO survey means that the selection function has minimal impact on the distribution of observed age and metal abundances but this would become increasingly more important for surveys with narrower selection functions.


R. J. deBoer, J. Gorres, M. Wiescher, R. E. Azuma, A. Best, C. R. Brune, C. E. Fields, S. Jones, M. Pignatari, D. Sayre, K. Smith, F. X. Timmes, and E. Uberseder, 2017-09-07, The 12C(alpha,gamma)16O reaction and its implications for stellar helium burning, Reviews of Modern Physics, doi: 10.1103/RevModPhys.89.035007

Abstract

The creation of carbon and oxygen in our Universe is one of the forefront questions in nuclear astrophysics. The determination of the abundance of these elements is key to our understanding of both the formation of life on Earth and to the life cycles of stars. While nearly all models of different nucleosynthesis environments are affected by the production of carbon and oxygen, a key ingredient, the precise determination of the reaction rate of 12C(α,γ)16O, has long remained elusive. This is owed to the reaction’s inaccessibility, both experimentally and theoretically. Nuclear theory has struggled to calculate this reaction rate because the cross section is produced through different underlying nuclear mechanisms. Isospin selection rules suppress the E1 component of the ground state cross section, creating a unique situation where the E1 and E2 contributions are of nearly equal amplitudes. Experimentally there have also been great challenges. Measurements have been pushed to the limits of state-of-the-art techniques, often developed for just these measurements. The data have been plagued by uncharacterized uncertainties, often the result of the novel measurement techniques that have made the different results challenging to reconcile. However, the situation has markedly improved in recent years, and the desired level of uncertainty ≈10% may be in sight. In this review the current understanding of this critical reaction is summarized. The emphasis is placed primarily on the experimental work and interpretation of the reaction data, but discussions of the theory and astrophysics are also pursued. The main goal is to summarize and clarify the current understanding of the reaction and then point the way forward to an improved determination of the reaction rate.


Hahn, Christoph and Genner, Martin J and Turner, George F and Joyce, Domino A, 2017-08-29, The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi, Evolution Letters, doi: 10.1002/evl3.20

Abstract

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population-level RAD-seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome-level specialization for life at depth as an important process in cichlid radiation.


Dethlefs, Nina, 2017-07-18, Domain Transfer for Deep Natural Language Generation from Abstract Meaning Representations, IEEE Computational Intelligence Magazine, doi: 10.1109/MCI.2017.2708558

Abstract

Stochastic natural language generation systems that are trained from labelled datasets are often domain-specific in their annotation and in their mapping from semantic input representations to lexical-syntactic outputs. As a result, learnt models fail to generalize across domains, heavily restricting their usability beyond single applications. In this article, we focus on the problem of domain adaptation for natural language generation. We show how linguistic knowledge from a source domain, for which labelled data is available, can be adapted to a target domain by reusing training data across domains. As a key to this, we propose to employ abstract meaning representations as a common semantic representation across domains. We model natural language generation as a long short-term memory recurrent neural network encoder-decoder, in which one recurrent neural network learns a latent representation of a semantic input, and a second recurrent neural network learns to decode it to a sequence of words. We show that the learnt representations can be transferred across domains and can be leveraged effectively to improve training on new unseen domains. Experiments in three different domains and with six datasets demonstrate that the lexical-syntactic constructions learnt in one domain can be transferred to new domains and achieve up to 75-100% of the performance of in-domain training. This is based on objective metrics such as BLEU and semantic error rate and a subjective human rating study. Training a policy from prior knowledge from a different domain is consistently better than pure in-domain training by up to 10%.


Nan Liu and Larry R. Nittler and Marco Pignatari and Conel M. O’D. Alexander and Jianhua Wang, 2017-06-06, Stellar Origin of 15 N-rich Presolar SiC Grains of Type AB: Supernovae with Explosive Hydrogen Burning, The Astrophysical Journal Letters, doi: 10.3847/2041-8213/aa74e5

Abstract

We report C, N, and Si isotopic data for 59 highly 13 C-enriched presolar submicron- to micron-sized SiC grains from the Murchison meteorite, including eight putative nova grains (PNGs) and 29 15 N-rich ( 14 N/ 15 N ≤ solar) AB grains, and their Mg–Al, S, and Ca–Ti isotope data when available. These 37 grains are enriched in 13 C, 15 N, and 26 Al with the PNGs showing more extreme enhancements. The 15 N-rich AB grains show systematically higher 26 Al and 30 Si excesses than the 14 N-rich AB grains. Thus, we propose to divide the AB grains into groups 1 ( 14 N/ 15 N < solar) and 2 ( 14 N/ 15 N ≥ solar). For the first time, we have obtained both S and Ti isotopic data for five AB1 grains and one PNG and found 32 S and/or 50 Ti enhancements. Interestingly, one AB1 grain had the largest 32 S and 50 Ti excesses, strongly suggesting a neutron-capture nucleosynthetic origin of the 32 S excess and thus the initial presence of radiogenic 32 Si ( t 1/2 = 153 years). More importantly, we found that the 15 N and 26 Al excesses of AB1 grains form a trend that extends to the region in the N–Al isotope plot occupied by C2 grains, strongly indicating a common stellar origin for both AB1 and C2 grains. Comparison of supernova models with the AB1 and C2 grain data indicates that these grains came from supernovae that experienced H ingestion into the He/C zones of their progenitors.


Dethlefs, Nina and Turner, Alexander, 2017-05-27, Deep Text Generation — Using Hierarchical Decomposition to Mitigate the Effect of Rare Data Points, Language, Data, and Knowledge: First International Conference, LDK 2017, Galway, Ireland, June 19-20, 2017, Proceedings, doi: 10.1007/978-3-319-59888-8_25

Abstract

The generation of in situ sp2–sp3 diboron adducts has revolutionised the synthesis of organoboranes. Organocatalytic diboration reactions have represented a milestone in terms of unpredictable reactivity of these adducts. However, current methodologies have limitations in terms of substrate scope, selectivity and functional group tolerance. Here a new methodology based on the use of simple amines as catalyst is reported. This methodology provides a completely selective transformation overcoming current substrate scope and functional/protecting group limitations. Mechanistic studies have been included in this report.


Mishenina, T. and Pignatari, M. and Cote, B. and Thielemann, F.-K. and Soubiran, C. and Basak, N. and Gorbaneva, T. and Korotin, S. A. and Kovtyukh, V. V. and Wehmeyer, B. and Bisterzo, S. and Travaglio, C. and Gibson, B. K. and Jordan, C. and Paul, A. and Ritter, C. and Herwig, F., 2017-05-11, Observing the metal-poor solar neighbourhood: a comparison of galactic chemical evolution predictions, Monthly Notices of the Royal Astronomical Society, doi: 10.1093/mnras/stx1145

Abstract

Atmospheric parameters and chemical compositions for 10 stars with metallicities in the region of −2.2 < [Fe/H] < −0.6 were precisely determined using high-resolution, high signal-to-noise, spectra. For each star, the abundances, for 14–27 elements, were derived using both local thermodynamic equilibrium (LTE) and non-LTE (NLTE) approaches. In particular, differences by assuming LTE or NLTE are about 0.10 dex; depending on [Fe/H], Teff, gravity and element lines used in the analysis. We find that the O abundance has the largest error, ranging from 0.10 and 0.2 dex. The best measured elements are Cr, Fe, and Mn; with errors between 0.03 and 0.11 dex. The stars in our sample were included in previous different observational work. We provide a consistent data analysis. The data dispersion introduced in the literature by different techniques and assumptions used by the different authors is within the observational errors, excepting for HD103095. We compare these results with stellar observations from different data sets and a number of theoretical galactic chemical evolution (GCE) simulations. We find a large scatter in the GCE results, used to study the origin of the elements. Within this scatter as found in previous GCE simulations, we cannot reproduce the evolution of the elemental ratios [Sc/Fe], [Ti/Fe], and [V/Fe] at different metallicities. The stellar yields from core-collapse supernovae are likely primarily responsible for this discrepancy. Possible solutions and open problems are discussed.


Makina, Y. and Mahjoubi, K. and Benoit, D. M. and Jaidane, N.-E. and Al-Mogren, M. Mogren and Hochlaf, M., 2017-05-09, Periodic Dispersion-Corrected Approach for Isolation Spectroscopy of N2 in an Argon Environment: Clusters, Surfaces, and Matrices, The Journal of Physical Chemistry A, doi: 10.1021/acs.jpca.7b00093

Abstract

Ab initio and Perdew, Burke, and Ernzerhof (PBE) density functional theory with dispersion correction (PBE-D3) calculations are performed to study N2–Arn (n ≤ 3) complexes and N2 trapped in Ar matrix (i.e., N2@Ar). For cluster computations, we used both Møller–Plesset (MP2) and PBE-D3 methods. For N2@Ar, we used a periodic-dispersion corrected model for Ar matrix, which consists on a slab of four layers of Ar atoms. We determined the equilibrium structures and binding energies of N2 interacting with these entities. We also deduced the N2 vibrational frequency shifts caused by clustering or embedding compared to an isolated N2 molecule. Upon complexation or embedding, the vibrational frequency of N2 is slightly shifted, while its equilibrium distance remains unchanged. This is due to the weak interactions between N2 and Ar within these compounds. Our calculations show the importance of inclusion of dispersion effects for the accurate description of geometrical and spectroscopic parameters of N2 isolated, in interaction with Ar surfaces, or trapped in Ar matrices.


Siri Chongchitnan and Matthew Hunt, 2017-03-27, On the abundance of extreme voids II: a survey of void mass functions, Journal of Cosmology and Astroparticle Physics, doi: 10.1088/1475-7516/2017/03/049

Abstract

The abundance of cosmic voids can be described by an analogue of halo mass functions for galaxy clusters. In this work, we explore a number of void mass functions: from those based on excursion-set theory to new mass functions obtained by modifying halo mass functions. We show how different void mass functions vary in their predictions for the largest void expected in an observational volume, and compare those predictions to observational data. Our extreme-value formalism is shown to be a new practical tool for testing void theories against simulation and observation.


Dethlefs, Nina and Hawick, Ken, 2017-02-04, DEFIne: A Fluent Interface DSL for Deep Learning Applications, Proceedings of the 2nd International Workshop on Real World Domain Specific Languages, doi: 10.1145/3039895.3039898

Abstract

Recent years have seen a surge of interest in deep learning models that outperform other machine learning algorithms on benchmarks across many disciplines. Most existing deep learning libraries facilitate the development of neural nets by providing a mathematical framework that helps users implement their models more efficiently. This still represents a substantial investment of time and effort, however, when the intention is to compare a range of competing models quickly for a specific task. We present DEFIne, a fluent interface DSL for the specification, optimisation and evaluation of deep learning models. The fluent interface is implemented through method chaining. DEFIne is embedded in Python and is build on top of its most popular deep learning libraries, Keras and Theano. It extends these with common operations for data pre-processing and representation as well as visualisation of datasets and results. We test our framework on three benchmark tasks from different domains: heart disease diagnosis, hand-written digit recognition and weather forecast generation. Results in terms of accuracy, runtime and lines of code show that our DSL achieves equivalent accuracy and runtime to state-of-the-art models, while requiring only about 10 lines of code per application.


Uberseder, E.; Heil, M.; Kaeppeler, F.; Lederer, C.; Mengoni, A.; Bisterzo, S.; Pignatari, M.; Wiescher, M.;, 2017-02-02, Stellar (n ,gamma) cross sections of 23Na, Physical Review C, doi: 10.1103/PhysRevC.95.025803

Abstract

The cross section of the 23Na(n ,γ )24Na reaction was measured via the activation method at the Karlsruhe 3.7 MV Van de Graaff accelerator. NaCl samples were exposed to quasistellar neutron spectra at k T =5.1 and 25 keV produced via the 18O(p,n )18F and 7Li(p ,n )7Be reactions, respectively. The derived capture cross sections <σ> kT=5 keV=9.1 ±0.3 mb and <σ> kT =25keV=2.03 ±0.05 mb are significantly lower than reported in literature. These results were used to substantially revise the radiative width of the first 23Na resonance and to establish an improved set of Maxwellian average cross sections. The implications of the lower capture cross section for current models of s-process nucleosynthesis are discussed.


2016 (2 outputs)

Farre, Albert and Soares, Kaline and Briggs, Rachel A. and Balanta, Angelica and Benoit, David M. and Bonet, Amadeu, 2016-10-26, Amine Catalysis for the Organocatalytic Diboration of Challenging Alkenes, Chemistry – A European Journal, doi: 10.1002/chem.201603979

Abstract

The generation of in situ sp2–sp3 diboron adducts has revolutionised the synthesis of organoboranes. Organocatalytic diboration reactions have represented a milestone in terms of unpredictable reactivity of these adducts. However, current methodologies have limitations in terms of substrate scope, selectivity and functional group tolerance. Here a new methodology based on the use of simple amines as catalyst is reported. This methodology provides a completely selective transformation overcoming current substrate scope and functional/protecting group limitations. Mechanistic studies have been included in this report


Szitenberg, Amir; Cha, Soyeon; Opperman, Charles H.; Bird, David M.; Blaxter, Mark L.; Lunt, David H., 2016-09, Genetic drift, not life history or RNAi, determine long term evolution of transposable elements, Genome biology and evolution, doi: 10.1093/gbe/evw208

Abstract

Transposable elements (TEs) are a major source of genome variation across the branches of life. Although TEs may play an adaptive role in their host’s genome, they are more often deleterious, and purifying selection is an important factor controlling their genomic loads. In contrast, life history, mating system, GC content, and RNAi pathways, have been suggested to account for the disparity of TE loads in different species. Previous studies of fungal, plant, and animal genomes have reported conflicting results regarding the direction in which these genomic features drive TE evolution. Many of these studies have had limited power, however, because they studied taxonomically narrow systems, comparing only a limited number of phylogenetically independent contrasts, and did not address long-term effects on TE evolution. Here we test the long-term determinants of TE evolution by comparing 42 nematode genomes spanning over 500 million years of diversification. This analysis includes numerous transitions between life history states, and RNAi pathways, and evaluates if these forces are sufficiently persistent to affect the long-term evolution of TE loads in eukaryotic genomes. Although we demonstrate statistical power to detect selection, we find no evidence that variation in these factors influence genomic TE loads across extended periods of time. In contrast, the effects of genetic drift appear to persist and control TE variation among species. We suggest that variation in the tested factors are largely inconsequential to the large differences in TE content observed between genomes, and only by these large-scale comparisons can we distinguish long-term and persistent effects from transient or random changes.