Showing papers by "Argonne National Laboratory published in 2013"

Astropy: A community Python package for astronomy

Abstract: We present the first public version (v02) of the open-source and community-developed Python package, Astropy This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as flexible image transport system (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions Significant functionality is under activedevelopment, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Abstract: Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Sodium‐Ion Batteries

Abstract: The status of ambient temperature sodium ion batteries is reviewed in light of recent developments in anode, electrolyte and cathode materials. These devices, although early in their stage of development, are promising for large-scale grid storage applications due to the abundance and very low cost of sodium-containing precursors used to make the components. The engineering knowledge developed recently for highly successful Li ion batteries can be leveraged to ensure rapid progress in this area, although different electrode materials and electrolytes will be required for dual intercalation systems based on sodium. In particular, new anode materials need to be identified, since the graphite anode, commonly used in lithium systems, does not intercalate sodium to any appreciable extent. A wider array of choices is available for cathodes, including high performance layered transition metal oxides and polyanionic compounds. Recent developments in electrodes are encouraging, but a great deal of research is necessary, particularly in new electrolytes, and the understanding of the SEI films. The engineering modeling calculations of Na-ion battery energy density indicate that 210 Wh kg−1 in gravimetric energy is possible for Na-ion batteries compared to existing Li-ion technology if a cathode capacity of 200 mAh g−1 and a 500 mAh g−1 anode can be discovered with an average cell potential of 3.3 V.

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Abstract: High-throughput sequencing has revolutionized microbial ecology, but read quality remains a considerable barrier to accurate taxonomy assignment and α-diversity assessment for microbial communities. We demonstrate that high-quality read length and abundance are the primary factors differentiating correct from erroneous reads produced by Illumina GAIIx, HiSeq and MiSeq instruments. We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results.

GSAS-II: the genesis of a modern open-source all purpose crystallography software package

Abstract: The newly developed GSAS-II software is a general purpose package for data reduction, structure solution and structure refinement that can be used with both single-crystal and powder diffraction data from both neutron and X-ray sources, including laboratory and synchrotron sources, collected on both two- and one-dimensional detectors. It is intended that GSAS-II will eventually replace both the GSAS and the EXPGUI packages, as well as many other utilities. GSAS-II is open source and is written largely in object-oriented Python but offers speeds comparable to compiled code because of its reliance on the Python NumPy and SciPy packages for computation. It runs on all common computer platforms and offers highly integrated graphics, both for a user interface and for interpretation of parameters. The package can be applied to all stages of crystallographic analysis for constant-wavelength X-ray and neutron data. Plans for considerable additional development are discussed.

Astropy: A Community Python Package for Astronomy

Abstract: We present the first public version (v0.2) of the open-source and community-developed Python package, Astropy. This package provides core astronomy-related functionality to the community, including support for domain-specific file formats such as Flexible Image Transport System (FITS) files, Virtual Observatory (VO) tables, and common ASCII table formats, unit and physical quantity conversions, physical constants specific to astronomy, celestial coordinate and time transformations, world coordinate system (WCS) support, generalized containers for representing gridded as well as tabular data, and a framework for cosmological transformations and conversions. Significant functionality is under active development, such as a model fitting framework, VO client and server tools, and aperture and point spread function (PSF) photometry tools. The core development team is actively making additions and enhancements to the current code base, and we encourage anyone interested to participate in the development of future Astropy versions.

Crystal Growth of the Perovskite Semiconductor CsPbBr3: A New Material for High-Energy Radiation Detection

Abstract: The synthesis, crystal growth, and structural and optoelectronic characterization has been carried out for the perovskite compound CsPbBr3. This compound is a direct band gap semiconductor which meets most of the requirements for successful detection of X- and γ-ray radiation, such as high attenuation, high resistivity, and significant photoconductivity response, with detector resolution comparable to that of commercial, state-of-the-art materials. A structural phase transition which occurs during crystal growth at higher temperature does not seem to affect its crystal quality. Its μτ product for both hole and electron carriers is approximately equal. The μτ product for electrons is comparable to cadmium zinc telluride (CZT) and that for holes is 10 times higher than CZT.

The Multi-object, Fiber-fed Spectrographs for the Sloan Digital Sky Survey and the Baryon Oscillation Spectroscopic Survey

Abstract: We present the design and performance of the multi-object fiber spectrographs for the Sloan Digital Sky Survey (SDSS) and their upgrade for the Baryon Oscillation Spectroscopic Survey (BOSS). Originally commissioned in Fall 1999 on the 2.5 m aperture Sloan Telescope at Apache Point Observatory, the spectrographs produced more than 1.5 million spectra for the SDSS and SDSS-II surveys, enabling a wide variety of Galactic and extra-galactic science including the first observation of baryon acoustic oscillations in 2005. The spectrographs were upgraded in 2009 and are currently in use for BOSS, the flagship survey of the third-generation SDSS-III project. BOSS will measure redshifts of 1.35 million massive galaxies to redshift 0.7 and Lyα absorption of 160,000 high redshift quasars over 10,000 deg2 of sky, making percent level measurements of the absolute cosmic distance scale of the universe and placing tight constraints on the equation of state of dark energy. The twin multi-object fiber spectrographs utilize a simple optical layout with reflective collimators, gratings, all-refractive cameras, and state-of-the-art CCD detectors to produce hundreds of spectra simultaneously in two channels over a bandpass covering the near-ultraviolet to the near-infrared, with a resolving power R = λ/FWHM ~ 2000. Building on proven heritage, the spectrographs were upgraded for BOSS with volume-phase holographic gratings and modern CCD detectors, improving the peak throughput by nearly a factor of two, extending the bandpass to cover 360 nm < λ < 1000 nm, and increasing the number of fibers from 640 to 1000 per exposure. In this paper we describe the original SDSS spectrograph design and the upgrades implemented for BOSS, and document the predicted and measured performances.

Spin Hall Effects in Metals

Abstract: Spin Hall effects convert charge currents into spin currents and vice versa even in nonmagnetic conductors due to spin orbit coupling. This enables spin Hall effects to be utilized both for the generation and detection of spin currents and magnetization dynamics. This paper reviews the experimental characterization of these effects in metallic systems, which have so far shown the highest efficiency in using spin Hall effects for charge-to-spin interconversion. The advantages and disadvantages of complimentary measurement techniques are discussed and in addition an outlook of the possible impact on applications is presented.

Polymer solar cells with enhanced fill factors

Abstract: New designs of donor polymers yield organic solar cells with fill factors approaching 80%, significantly higher than those of conventional cells. This enhanced performance is attributed to the close-packed and highly ordered structure of the polymers PTPD3T and PBT13T, which leads to efficient charge extraction and suppressed recombination.

Improving the hydrogen oxidation reaction rate by promotion of hydroxyl adsorption

Abstract: The development of hydrogen-based energy sources as viable alternatives to fossil-fuel technologies has revolutionized clean energy production using fuel cells However, to date, the slow rate of the hydrogen oxidation reaction (HOR) in alkaline environments has hindered advances in alkaline fuel cell systems Here, we address this by studying the trends in the activity of the HOR in alkaline environments We demonstrate that it can be enhanced more than fivefold compared to state-of-the-art platinum catalysts The maximum activity is found for materials (Ir and Pt₀₁Ru₀₉) with an optimal balance between the active sites that are required for the adsorption/dissociation of H₂ and for the adsorption of hydroxyl species (OHad) We propose that the more oxophilic sites on Ir (defects) and PtRu material (Ru atoms) electrodes facilitate the adsorption of OHad species Those then react with the hydrogen intermediates (Had) that are adsorbed on more noble surface sites

Cohabiting family members share microbiota with one another and with their dogs

Abstract: The human body is home to many different microorganisms, with a range of bacteria, fungi and archaea living on the skin, in the intestine and at various other sites in the body. While many of these microorganisms are beneficial to their human hosts, we know very little about most of them. Early research focused primarily on comparing the microorganisms found in healthy individuals with those found in individuals suffering from a particular illness. More recently researchers have become interested in more general issues, such as understanding how these collections of microorganisms, which are also known as the human microbiota or the human microbiome, become established, and exploring the causes of similarities and differences between the microbiota of individuals. We now know that the communities of microorganisms found in the intestines of genetically related people tend to be more similar than those of people who are not related. Moreover, the communities of microorganisms found in the intestines of non-related adults living in the same household are more similar than those of unrelated adults living in different households. We also know that the range of microorganisms found in the intestine changes dramatically between birth and the age of 3 years. However, these studies have focused on the intestine, and little is known about the effect of relatedness, cohabitation and age on the microbiota at other body sites. Song et al. compared the microorganisms found on the skin, on the tongue and in the intestines of 159 people—and 36 dogs—in 60 families. They found that co-habitation resulted in the communities of microorganisms being more similar to each other, with those on the skin being the most similar. This was true for all comparisons, including human pairs, dog pairs and human–dog pairs. This suggests that humans probably acquire many of the microorganisms on their skin through direct contact with their surroundings, and that humans tend to share more microbes with individuals, including their pets, with which they are in frequent contact. Song et al. also discovered that, unlike what happens in the intestine, the microbial communities on the skin and tongue of infants and children were relatively similar to those of adults. Overall, these findings suggest that the communities of microorganisms found in the intestine changes with age in a way that differs significantly from those found on the skin and tongue.

Formation Of The Spinel Phase In The Layered Composite Cathode Used In Li-Ion Batteries

Abstract: Pristine Li-rich layered cathodes, such as Li1.2Ni0.2Mn0.6O2 and Li1.2Ni0.1Mn0.525Co0.175O2, were identified to exist in two different structures: LiMO2R3m and Li2MO3C2/m phases. Upon 300 cycles of charge/discharge, both phases gradually transform to the spinel structure. The transition from LiMO2R3m to spinel is accomplished through the migration of transition metal ions to the Li site without breaking down the lattice, leading to the formation of mosaic structured spinel grains within the parent particle. In contrast, transition from Li2MO3C2/m to spinel involves removal of Li+ and O2-, which produces large lattice strain and leads to the breakdown of the parent lattice. The newly formed spinel grains show random orientation within the same particle. Cracks and pores were also noticed within some layered nanoparticles after cycling, which is believed to be the consequence of the lattice breakdown and vacancy condensation upon removal of lithium ions. The AlF3-coating can partially relieve the spinel f...

Observation of a new boson with mass near 125 GeV in pp collisions at $ \sqrt{s}=7 $ and 8 TeV

Abstract: A detailed description is reported of the analysis used by the CMS Collaboration in the search for the standard model Higgs boson in pp collisions at the LHC, which led to the observation of a new boson. The data sample corresponds to integrated luminosities up to 5.1 inverse femtobarns at sqrt(s) = 7 TeV, and up to 5.3 inverse femtobarns at sqrt(s) = 8 TeV. The results for five Higgs boson decay modes gamma gamma, ZZ, WW, tau tau, and bb, which show a combined local significance of 5 standard deviations near 125 GeV, are reviewed. A fit to the invariant mass of the two high resolution channels, gamma gamma and ZZ to 4 ell, gives a mass estimate of 125.3 +/- 0.4 (stat) +/- 0.5 (syst) GeV. The measurements are interpreted in the context of the standard model Lagrangian for the scalar Higgs field interacting with fermions and vector bosons. The measured values of the corresponding couplings are compared to the standard model predictions. The hypothesis of custodial symmetry is tested through the measurement of the ratio of the couplings to the W and Z bosons. All the results are consistent, within their uncertainties, with the expectations for a standard model Higgs boson.

Origin of additional capacities in metal oxide lithium-ion battery electrodes

Abstract: Metal fluorides/oxides (MF(x)/M(x)O(y)) are promising electrodes for lithium-ion batteries that operate through conversion reactions. These reactions are associated with much higher energy densities than intercalation reactions. The fluorides/oxides also exhibit additional reversible capacity beyond their theoretical capacity through mechanisms that are still poorly understood, in part owing to the difficulty in characterizing structure at the nanoscale, particularly at buried interfaces. This study employs high-resolution multinuclear/multidimensional solid-state NMR techniques, with in situ synchrotron-based techniques, to study the prototype conversion material RuO2. The experiments, together with theoretical calculations, show that a major contribution to the extra capacity in this system is due to the generation of LiOH and its subsequent reversible reaction with Li to form Li2O and LiH. The research demonstrates a protocol for studying the structure and spatial proximities of nanostructures formed in this system, including the amorphous solid electrolyte interphase that grows on battery electrodes.

Mixed-integer nonlinear optimization

Abstract: Many optimal decision problems in scientific, engineering, and public sector applications involve both discrete decisions and nonlinear system dynamics that affect the quality of the final design or plan. These decision problems lead to mixed-integer nonlinear programming (MINLP) problems that combine the combinatorial difficulty of optimizing over discrete variable sets with the challenges of handling nonlinear functions. We review models and applications of MINLP, and survey the state of the art in methods for solving this challenging class of problems.Most solution methods for MINLP apply some form of tree search. We distinguish two broad classes of methods: single-tree and multitree methods. We discuss these two classes of methods first in the case where the underlying problem functions are convex. Classical single-tree methods include nonlinear branch-and-bound and branch-and-cut methods, while classical multitree methods include outer approximation and Benders decomposition. The most efficient class of methods for convex MINLP are hybrid methods that combine the strengths of both classes of classical techniques.Non-convex MINLPs pose additional challenges, because they contain non-convex functions in the objective function or the constraints; hence even when the integer variables are relaxed to be continuous, the feasible region is generally non-convex, resulting in many local minima. We discuss a range of approaches for tackling this challenging class of problems, including piecewise linear approximations, generic strategies for obtaining convex relaxations for non-convex functions, spatial branch-and-bound methods, and a small sample of techniques that exploit particular types of non-convex structures to obtain improved convex relaxations.We finish our survey with a brief discussion of three important aspects of MINLP. First, we review heuristic techniques that can obtain good feasible solution in situations where the search-tree has grown too large or we require real-time solutions. Second, we describe an emerging area of mixed-integer optimal control that adds systems of ordinary differential equations to MINLP. Third, we survey the state of the art in software for MINLP.

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies

Abstract: The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. Phys. Rev. Lett. 2012, 108, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables.

Brown carbon: a significant atmospheric absorber of solar radiation?

Abstract: Several recent observational studies have shown organic carbon aerosols to be a significant source of absorption of solar radiation The absorbing part of organic aerosols is referred to as "brown" carbon (BrC) Using a global chemical transport model and a radiative transfer model, we estimate for the first time the enhanced absorption of solar radiation due to BrC in a global model The simulated wavelength dependence of aerosol absorption, as measured by the absorption Angstrom exponent (AAE), increases from 09 for non-absorbing organic carbon to 12 (10) for strongly (moderately) absorbing BrC The calculated AAE for the strongly absorbing BrC agrees with AERONET spectral observations at 440–870 nm over most regions but overpredicts for the biomass burning-dominated South America and southern Africa, in which the inclusion of moderately absorbing BrC has better agreement The resulting aerosol absorption optical depth increases by 18% (3%) at 550 nm and 56% (38%) at 380 nm for strongly (moderately) absorbing BrC The global simulations suggest that the strongly absorbing BrC contributes up to +025 W m−2 or 19% of the absorption by anthropogenic aerosols, while 72% is attributed to black carbon, and 9% is due to sulfate and non-absorbing organic aerosols coated on black carbon Like black carbon, the absorption of BrC (moderately to strongly) inserts a warming effect at the top of the atmosphere (TOA) (004 to 011 W m−2), while the effect at the surface is a reduction (−006 to −014 W m−2) Inclusion of the strongly absorption of BrC in our model causes the direct radiative forcing (global mean) of organic carbon aerosols at the TOA to change from cooling (−008 W m−2) to warming (+0025 W m−2) Over source regions and above clouds, the absorption of BrC is higher and thus can play an important role in photochemistry and the hydrologic cycle

The Atacama Cosmology Telescope: Sunyaev-Zel'dovich selected galaxy clusters at 148 GHz from three seasons of data

Abstract: We present a catalog of 68 galaxy clusters, of which 19 are new discoveries, detected via the Sunyaev-Zel'dovich effect (SZ) at 148 GHz in the Atacama Cosmology Telescope (ACT) survey on the celestial equator. With this addition, the ACT collaboration has reported a total of 91 optically confirmed, SZ detected clusters. The 504 square degree survey region includes 270 square degrees of overlap with SDSS Stripe 82, permitting the confirmation of SZ cluster candidates in deep archival optical data. The subsample of 48 clusters within Stripe 82 is estimated to be 90% complete for M{sub 500c} > 4.5 × 10{sup 14}M{sub s}un and redshifts 0.15 < z < 0.8. While a full suite of matched filters is used to detect the clusters, the sample is studied further through a ''Profile Based Amplitude Analysis'' using a statistic derived from a single filter at a fixed θ{sub 500} = 5.'9 angular scale. This new approach incorporates the cluster redshift along with prior information on the cluster pressure profile to fix the relationship between the cluster characteristic size (R{sub 500}) and the integrated Compton parameter (Y{sub 500}). We adopt a one-parameter family of ''Universal Pressure Profiles'' (UPP) with associated scaling laws, derived frommore » X-ray measurements of nearby clusters, as a baseline model. Three additional models of cluster physics are used to investigate a range of scaling relations beyond the UPP prescription. Assuming a concordance cosmology, the UPP scalings are found to be nearly identical to an adiabatic model, while a model incorporating non-thermal pressure better matches dynamical mass measurements and masses from the South Pole Telescope. A high signal to noise ratio subsample of 15 ACT clusters with complete optical follow-up is used to obtain cosmological constraints. We demonstrate, using fixed scaling relations, how the constraints depend on the assumed gas model if only SZ measurements are used, and show that constraints from SZ data are limited by uncertainty in the scaling relation parameters rather than sample size or measurement uncertainty. We next add in seven clusters from the ACT Southern survey, including their dynamical mass measurements, which are based on galaxy velocity dispersions and thus are independent of the gas physics. In combination with WMAP7 these data simultaneously constrain the scaling relation and cosmological parameters, yielding 68% confidence ranges described by σ{sub 8} = 0.829 ± 0.024 and Ω{sub m} = 0.292 ± 0.025.. We consider these results in the context of constraints from CMB and other cluster studies. The constraints arise mainly due to the inclusion of the dynamical mass information and do not require strong priors on the SZ scaling relation parameters. The results include marginalization over a 15% bias in dynamical masses relative to the true halo mass. In an extension to ΛCDM that incorporates non-zero neutrino mass density, we combine our data with WMAP7, Baryon Acoustic Oscillation data, and Hubble constant measurements to constrain the sum of the neutrino mass species to be Σ{sub ν}m{sub ν} < 0.29 eV (95% confidence limit)« less

Complex adaptive systems modeling with repast simphony

Abstract: This paper is to describe development of the features and functions of Repast Simphony, the widely used, free, and open source agent-based modeling environment that builds on the Repast 3 library. Repast Simphony was designed from the ground up with a focus on well-factored abstractions. The resulting code has a modular architecture that allows individual components such as networks, logging, and time scheduling to be replaced as needed. The Repast family of agent-based modeling software has collectively been under continuous development for more than 10 years. Includes reviewing other free and open-source modeling libraries and environments as well as describing the architecture of Repast Simphony. The architectural description includes a discussion of the Simphony application framework, the core module, ReLogo, data collection, the geographical information system, visualization, freeze drying, and third party application integration. Include a review of several Repast Simphony applications and brief tutorial on how to use Repast Simphony to model a simple complex adaptive system. We discuss opportunities for future work, including plans to provide support for increasingly large-scale modeling efforts.

Improved luminosity determination in pp collisions at root s=7 TeV using the ATLAS detector at the LHC

Abstract: The luminosity calibration for the ATLAS detector at the LHC during pp collisions at root s = 7 TeV in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at root s = 7 TeV. A luminosity uncertainty of delta L/L = +/- 3.5 % is obtained for the 47 pb(-1) of data delivered to ATLAS in 2010, and an uncertainty of delta L/L = +/- 1.8 % is obtained for the 5.5 fb(-1) delivered in 2011.

Improved Search for $\bar \nu_\mu \rightarrow \bar \nu_e$ Oscillations in the MiniBooNE Experiment

Abstract: The MiniBooNE experiment at Fermilab reports results from an analysis of ν¯e appearance data from 11.27×10²⁰ protons on target in the antineutrino mode, an increase of approximately a factor of 2 over the previously reported results. An event excess of 78.4±28.5 events (2.8σ) is observed in the energy range 200QEν<1250 MeV. If interpreted in a two-neutrino oscillation model, ν¯μ→ν¯e, the best oscillation fit to the excess has a probability of 66% while the background-only fit has a χ² probability of 0.5% relative to the best fit. The data are consistent with antineutrino oscillations in the 0.01<Δm²<1.0 eV² range and have some overlap with the evidence for antineutrino oscillations from the Liquid Scintillator Neutrino Detector. All of the major backgrounds are constrained by in situ event measurements so nonoscillation explanations would need to invoke new anomalous background processes. The neutrino mode running also shows an excess at low energy of 162.0±47.8 events (3.4σ) but the energy distribution of the excess is marginally compatible with a simple two neutrino oscillation formalism. Expanded models with several sterile neutrinos can reduce the incompatibility by allowing for CP violating effects between neutrino and antineutrino oscillations.

Advancing our understanding of the human microbiome using QIIME

Abstract: High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.