175 research outputs found
Coulomb-hole summations and energies for GW calculations with limited number of empty orbitals: a modified static remainder approach
Ab initio GW calculations are a standard method for computing the
spectroscopic properties of many materials. The most computationally expensive
part in conventional implementations of the method is the generation and
summation over the large number of empty orbitals required to converge the
electron self energy. We propose a scheme to reduce the summation over empty
states by the use of a modified static-remainder approximation, which is simple
to implement and yields accurate self energies for both bulk and molecular
systems requiring a small fraction of the typical number of empty orbitals
A molecular-MNIST dataset for machine learning study on diffraction imaging and microscopy
An image dataset of 10 different size molecules, where each molecule has 2,000 structural variants, is generated from the 2D cross-sectional projection of Molecular Dynamics trajectories. The purpose of this dataset is to provide a benchmark dataset for the increasing need of machine learning, deep learning and image processing on the study of scattering, imaging and microscopy
Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture
Denitrification is an anaerobic respiration process that is the
primary contributor of the nitrous oxide (N2O) produced
from grassland soils. Our objective was to gain insight into the
relationships between denitrifier community size, structure, and
activity for a range of pasture soils. We collected 10 dairy pasture
soils with contrasting soil textures, drainage classes, management
strategies (effluent irrigation or non-irrigation), and geographic
locations in New Zealand, and measured their physicochemical
characteristics. We measured denitrifier abundance by quantitative
polymerase chain reaction (qPCR) and assessed denitrifier diversity
and community structure by terminal restriction fragment length
polymorphism (T-RFLP) of the nitrite reductase (nirS,
nirK) and N2O reductase (nosZ) genes. We
quantified denitrifier enzyme activity (DEA) using an acetylene
inhibition technique. We investigated whether varied soil conditions lead
to different denitrifier communities in soils, and if so, whether
they are associated with different denitrification activities and
are likely to generate different N2O emissions. Differences in
the physicochemical characteristics of the soils were driven mainly
by soil mineralogy and the management practices of the farms. We
found that nirS and nirK communities were strongly
structured along gradients of soil water and phosphorus (P)
contents. By contrast, the size and structure of the nosZ
community was unrelated to any of the measured soil
characteristics. In soils with high water content, the richnesses and
abundances of nirS, nirK, and nosZ genes were
all significantly positively correlated with DEA. Our data suggest
that management strategies to limit N2O emissions through
denitrification are likely to be most important for dairy farms on
fertile or allophanic soils during wetter periods. Finally, our data
suggest that new techniques that would selectively target
nirS denitrifiers may be the most effective for limiting
N2O emissions through denitrification across a wide range of
soil types
Galactos: Computing the Anisotropic 3-Point Correlation Function for 2 Billion Galaxies
The nature of dark energy and the complete theory of gravity are two central
questions currently facing cosmology. A vital tool for addressing them is the
3-point correlation function (3PCF), which probes deviations from a spatially
random distribution of galaxies. However, the 3PCF's formidable computational
expense has prevented its application to astronomical surveys comprising
millions to billions of galaxies. We present Galactos, a high-performance
implementation of a novel, O(N^2) algorithm that uses a load-balanced k-d tree
and spherical harmonic expansions to compute the anisotropic 3PCF. Our
implementation is optimized for the Intel Xeon Phi architecture, exploiting
SIMD parallelism, instruction and thread concurrency, and significant L1 and L2
cache reuse, reaching 39% of peak performance on a single node. Galactos scales
to the full Cori system, achieving 9.8PF (peak) and 5.06PF (sustained) across
9636 nodes, making the 3PCF easily computable for all galaxies in the
observable universe.Comment: 11 pages, 7 figures, accepted to SuperComputing 201
Exciton-plasmon states in nanoscale materials: breakdown of the Tamm-Dancoff approximation
Within the Tamm-Dancoff approximation ab initio approaches describe excitons
as packets of electron-hole pairs propagating only forward in time. However, we
show that in nanoscale materials excitons and plasmons hybridize, creating
exciton--plasmon states where the electron-hole pairs oscillate back and forth
in time. Then, as exemplified by the trans-azobenzene molecule and carbon
nanotubes, the Tamm-Dancoff approximation yields errors as large as the
accuracy claimed in ab initio calculations. Instead, we propose a general and
efficient approach that avoids the Tamm--Dancoff approximation, and correctly
describes excitons, plasmons and exciton-plasmon states
The Unique Origin of Colors of Armchair Carbon Nanotubes
The colors of suspended metallic colloidal particles are determined by their
size-dependent plasma resonance, while those of semiconducting colloidal
particles are determined by their size-dependent band gap. Here, we present a
novel case for armchair carbon nanotubes, suspended in aqueous medium, for
which the color depends on their size-dependent excitonic resonance, even
though the individual particles are metallic. We observe distinct colors of a
series of armchair-enriched nanotube suspensions, highlighting the unique
coloration mechanism of these one-dimensional metals.Comment: 4 pages, 3 figure
Applying the Roofline Performance Model to the Intel Xeon Phi Knights Landing Processor
The Roofline Performance Model is a visually intuitive method used to bound the sustained peak floating-point performance of any given arithmetic kernel on any given processor architecture. In the Roofline, performance is nominally measured in floating-point operations per second as a function of arithmetic intensity (operations per byte of data). In this study we determine the Roofline for the Intel Knights Landing (KNL) processor, determining the sustained peak memory bandwidth and floating-point performance for all levels of the memory hierarchy, in all the different KNL cluster modes.We then determine arithmetic intensity and performance for a suite of application kernels being targeted for the KNL based supercomputer Cori, and make comparisons to current Intel Xeon processors. Cori is the National Energy Research Scientific Computing Center’s (NERSC) next generation supercomputer. Scheduled for deployment mid-2016, it will be one of the earliest and largest KNL deployments in the world
Impacts of climate change on plant diseases – opinions and trends
There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods
Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities
Adaptive behaviour of plants, including rapid changes in physiology, gene regulation and defence response, can be altered when linked to neighbouring plants by a mycorrhizal network (MN). Mechanisms underlying the behavioural changes include mycorrhizal fungal colonization by the MN or interplant communication via transfer of nutrients, defence signals or allelochemicals. We focus this review on our new findings in ectomycorrhizal ecosystems, and also review recent advances in arbuscular mycorrhizal systems. We have found that the behavioural changes in ectomycorrhizal plants depend on environmental cues, the identity of the plant neighbour and the characteristics of the MN. The hierarchical integration of this phenomenon with other biological networks at broader scales in forest ecosystems, and the consequences we have observed when it is interrupted, indicate that underground ‘tree talk’ is a foundational process in the complex adaptive nature of forest ecosystems
Supplementation of Male Pheromone on Rock Substrates Attracts Female Rock Lizards to the Territories of Males: A Field Experiment
Background: Many animals produce elaborated sexual signals to attract mates, among them are common chemical sexual signals (pheromones) with an attracting function. Lizards produce chemical secretions for scent marking that may have a role in sexual selection. In the laboratory, female rock lizards (Iberolacerta cyreni) prefer the scent of males with more ergosterol in their femoral secretions. However, it is not known whether the scent-marks of male rock lizards may actually attract females to male territories in the field. Methodology/Principal Findings: In the field, we added ergosterol to rocks inside the territories of male lizards, and found that this manipulation resulted in increased relative densities of females in these territories. Furthermore, a higher number of females were observed associated to males in manipulated plots, which probably increased mating opportunities for males in these areas. Conclusions/Significance: These and previous laboratory results suggest that female rock lizards may select to settle in home ranges based on the characteristics of scent-marks from conspecific males. Therefore, male rock lizards might attract more females and obtain more matings by increasing the proportion of ergosterol when scent-marking their territories. However, previous studies suggest that the allocation of ergosterol to secretions may be costly and only high quality male
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