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At least 847 records · Page 47

Distributed Louvain Algorithm for Graph Community Detection

In most real-world networks, the nodes/vertices tend to be organized into tightly-knit modules known as communities or clusters, such that nodes within a community are more likely to be “related” to one another than they are to the rest of the network. The goodness of partitioning into communities is typically measured using a well known measure called modularity. However, modularity optimization is an NP-complete problem. In 2008, Blondel, et al. introduced a multi-phase, iterative heuristic for modularity optimization, called the Louvain method. Owing to its speed and ability to yield high quality communities, the Louvain method continues to be one of the most widely used tools for serial community detection. In this paper, we present the design of a distributed memory implementation of the Louvain algorithm for parallel community detection. Our approach begins with an arbitrarily partitioned distributed graph input, and employs several heuristics to speedup the computation of the different steps of the Louvain algorithm. We evaluate our implementation and its different variants using real-world networks from various application domains (including internet, biology, social networks). Our MPI+OpenMP implementation yields about 7x speedup (on 4K processes) for soc-friendster network (1.8B edges) over a state-of-the-art shared-memory multicore implementation (on 64 threads), without compromising output quality. Furthermore, our distributed implementation was able to process a larger graph (uk-2007; 3.3B edges) in 32 seconds on 1K cores (64 nodes) of NERSC Cori, when the state-of-the-art shared-memory implementation failed to run due to insufficient memory on a single Cori node containing 128 GB.

High performance computing, graph algorithms, Dist↗

Biomedical Integration of Metal–Organic Frameworks

Metal–organic frameworks (MOFs) have recently been demonstrated to be excellent platforms for biomedical applications. On account of their porous nature and modular structure, MOFs have served as bioactive-compound carriers, cell-imaging materials, and therapeutic agents. MOF cavities allow the encapsulation of a variety of guest molecules, facilitating controllable drug release and optical imaging. The metal components of MOFs make them suitable for magnetic resonance imaging (MRI) and computed tomography (CT). Further, MOF-embedded therapeutic agents have demonstrated promise in photodynamic and photothermal therapies. In this review, we describe several advanced examples that utilize MOFs in these cutting-edge applications. Investigation of the relationship between their structure and designated application will enable future, informed exploration of MOFs for biomedical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Edge-Enhanced Oxygen Evolution Reactivity at Ultrathin, Au-Supported Fe 2 O 3 Electrocatalysts

Transition metal oxides have gained attention as promising oxygen evolution reaction (OER) electrocatalysts in alkaline electrolytes, but heterogeneities in typical catalyst samples often obscure key structure–property relationships that are essential for developing higher performance materials. Here, we have combined ultrahigh vacuum surface science techniques, electrochemical measurements, and density functional theory (DFT) to quantify structure-dependent OER activity in a series of well-defined electrocatalysts. We describe a direct correlation between the population of Fe edge-site atoms and the OER activity of ultrathin Fe 2 O 3 nanostructures (~0.5 nm apparent height) grown on Au(111) substrates. Hydroxylated Fe atoms residing at edge-sites along the catalyst/support interface were spectroscopically identified as key reaction centers, and these Fe edge-site atoms were estimated to produce OER turnover frequencies approximately 150 times higher than that of Fe atoms on the catalyst surface at an applied potential of 1.8 V vs the reversible hydrogen electrode. Impressively, ultrathin Fe 2 O 3 /Au nanostructures with a high density of catalytically active Fe edge-site atoms outperformed an ultrathin IrOx/Au catalyst at moderate overpotentials. DFT calculations revealed more favorable OER at edge sites along the Fe 2 O 3 /Au interface, with lower predicted overpotentials due to beneficial modification of intermediate binding. Our results demonstrate how a combination of surface science, electrochemistry, and computational modeling can be used to identify key structure–property relationships in a well-defined electrocatalytic system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Explore Spatio‐Temporal Learning of Large Sample Hydrology Using Graph Neural Networks

Abstract Streamflow forecasting over gauged and ungauged basins play a vital role in water resources planning, especially under the changing climate. Increased availability of large sample hydrology data sets, together with recent advances in deep learning techniques, has presented new opportunities to explore temporal and spatial patterns in hydrological signatures for improving streamflow forecasting. The purpose of this study is to adapt and benchmark several state‐of‐the‐art graph neural network (GNN) architectures, including ChebNet, Graph Convolutional Network (GCN), and GraphWaveNet, for end‐to‐end graph learning. We explicitly represent river basins as nodes in a graph, learn the spatiotemporal nodal dependencies, and then use the learned relations to predict streamflow simultaneously across all nodes in the graph. The efficacy of the developed GNN models is investigated using the Catchment Attributes and MEteorology for Large‐sample Studies (CAMELS) data set under two settings, fixed graph topology (transductive learning), and variable graph topology (inductive learning), with the latter applicable to prediction in ungauged basins (PUB). Results indicate that GNNs are generally robust and computationally efficient, achieving similar or better performance than a baseline model trained using the long short‐term memory (LSTM) network. Further analyses are conducted to interpret the graph learning process at the edge and node levels and to investigate the effect of different model configurations. We conclude that graph learning constitutes a viable machine learning‐based method for aggregating spatiotemporal information from a multitude of sources for streamflow forecasting

Sun, Alexander Y.↗

Strength can be controlled by edge dislocations in refractory high-entropy alloys

Energy efficiency is motivating the search for new high-temperature (high-T) metals. Some new body-centered-cubic (BCC) random multicomponent “high-entropy alloys (HEAs)” based on refractory elements (Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr) possess exceptional strengths at high temperatures but the physical origins of this outstanding behavior are not known. Here we show, using integrated in-situ neutron-diffraction (ND), high-resolution transmission electron microscopy (HRTEM), and recent theory, that the high strength and strength retention of a NbTaTiV alloy and a high-strength/low-density CrMoNbV alloy are attributable to edge dislocations. This finding is surprising because plastic flows in BCC elemental metals and dilute alloys are generally controlled by screw dislocations. We use the insight and theory to perform a computationally-guided search over 10 7 BCC HEAs and identify over 10 6 possible ultra-strong high-T alloy compositions for future exploration.

36 MATERIALS SCIENCE↗

Absolute calibration of the Lyman-α measurement apparatus at DIII-D

The LLAMA (Lyman-Alpha Measurement Apparatus) diagnostic was recently installed on the DIII-D tokamak [Rosenthal et al., Rev. Sci. Instrum. (submitted) (2020)]. LLAMA is a pinhole camera system with a narrow band Bragg mirror, a bandpass interference filter, and an absolute extreme ultraviolet photodiode detector array, which measures the Ly-α brightness in the toroidal direction on the inboard, high field side (HFS) and outboard, low field side (LFS). This contribution presents a setup and a procedure for an absolute calibration near the Ly-α line at 121.6 nm. The LLAMA in-vacuum components are designed as a compact, transferable setup that can be mounted in an ex situ vacuum enclosure that is equipped with an absolutely calibrated Ly-α source. The spectral purity and stability of the Ly-α source are characterized using a vacuum ultraviolet spectrometer, while the Ly-α source brightness is measured by a NIST-calibrated photodiode. The non-uniform nature of the Ly-α source emission was overcome by performing a calibration procedure that scans the Ly-α source position and employs a numerical optimization to determine the emission pattern. Nominal and measured calibration factors are determined and compared, showing agreement within their uncertainties. A first conversion of the measured signal obtained from DIII-D indicates that the Ly-α brightness on the HFS and LFS is on the order of 1020 Ph sr-1 m-2 s-1. The established calibration setup and procedure will be regularly used to re-calibrate the LLAMA during DIII-D vents to monitor possible degradation of optical components and detectors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High-accuracy waveforms for black hole-neutron star systems with spinning black holes

The availability of accurate numerical waveforms is an important requirement for the creation and calibration of reliable waveform models for gravitational wave astrophysics. For black hole-neutron star binaries, very few accurate waveforms are however publicly available. Most recent models are calibrated to a large number of older simulations with good parameter space coverage for low-spin non-precessing binaries but limited accuracy, and a much smaller number of longer, more recent simulations limited to non-spinning black holes. In this paper, we present long, accurate numerical waveforms for three new systems that include rapidly spinning black holes, and one precessing configuration. Here, we study in detail the accuracy of the simulations, and in particular perform for the first time in the context of BHNS binaries a detailed comparison of waveform extrapolation methods to the results of Cauchy Characteristic Extraction. The new waveforms have <0.1rad phase errors during inspiral, rising to ~(0.2-0.4)rad errors at merger, and ≲1% error in their amplitude. We compute the faithfulness of recent analytical models to these numerical results, and find that models specifically designed for BHNS binaries perform well (F>0.99) for binaries seen face-on. For edge-on observations, particularly for precessing systems, disagreements between models and simulations increase, and models that include precession and/or higher-order modes start to perform better than BHNS models that currently lack these features.

79 ASTRONOMY AND ASTROPHYSICS↗

buhito

buhito is a Python library for graph analysis and machine learning. Graphs can represent networks with objects as nodes and their relationships as edges. buhito focuses on graphlet methods that study graphs through enumerating their component subgraphs to enable interpretable and fast models of complex systems. The package provides tools for different algorithmic designs for computing, analyzing, and applying graphlets to research problems such as machine learning, data compression, and anomaly detection in graph-structured data. A central feature is performing decomposition data analysis on graphs for machine learning models. Implemented in Python and built upon open-source scientific libraries such as NetworkX, NumPy, and SciPy, buhito provides high-performance methods for researchers exploring the mathematical and computational foundations of graphlet analysis applicable to systems of different sizes.

Pimonova, Yulia↗

Secondary sulfate is internally mixed with sea spray aerosol and organic aerosol in the winter Arctic

Abstract. Few measurements of aerosol chemical composition have been made during the winter–spring transition (following polar sunrise) to constrain Arctic aerosol–cloud–climate feedbacks. Herein, we report the first measurements of individual particle chemical composition near Utqiaġvik (Barrow), Alaska, in winter (seven sample days in January and February 2014). Individual particles were analyzed by computer-controlled scanning electron microscopy with energy dispersive X-ray spectroscopy (CCSEM-EDX, 24 847 particles), Raman microspectroscopy (300 particles), and scanning transmission X-ray microscopy with near-edge X-ray absorption fine structure spectroscopy (STXM-NEXAFS, 290 particles). Sea spray aerosol (SSA) was observed in all samples, with fresh and aged SSA comprising 99 %, by number, of 2.5–7.5 µm diameter particles, 65–95 % from 0.5–2.5 µm, and 50–60 % from 0.1–0.5 µm, indicating SSA is the dominant contributor to accumulation and coarse-mode aerosol during the winter. The aged SSA particles were characterized by reduced chlorine content with 94 %, by number, internally mixed with secondary sulfate (39 %, by number, internally mixed with both nitrate and sulfate), indicative of multiphase aging reactions during transport. There was a large number fraction (40 % of 1.0–4.0 µm diameter particles) of aged SSA during periods when particles were transported from near Prudhoe Bay, consistent with pollutant emissions from the oil fields participating in atmospheric processing of aerosol particles. Organic carbon and sulfate particles were observed in all samples and comprised 40–50 %, by number, of 0.1–0.4 µm diameter particles, indicative of Arctic haze influence. Soot was internally mixed with organic and sulfate components. All sulfate was mixed with organic carbon or SSA particles. Therefore, aerosol sources in the Alaskan Arctic and resulting aerosol chemical mixing states need to be considered when predicting aerosol climate effects, particularly cloud formation, in the winter Arctic.

54 ENVIRONMENTAL SCIENCES↗

Chemical Imaging of Atmospheric Organic Particles in the Eastern North Atlantic Field Campaign Report

The ability to reliably predict future climate is hindered, in major part, by an insufficient understanding of atmospheric aerosol-radiation interactions and aerosol-cloud interactions. (IPCC 2013; Bony and Dufresne 2005) Factors affecting marine stratocumulus clouds are particularly important given that they are the dominant cloud type globally. Global climate models frequently misrepresent ubiquitous marine stratocumulus clouds for a variety of reasons, including a lack of understanding of how these cloud properties change with aerosol cloud condensation nuclei (CCN) concentration and composition.(Nam et al. 2012) Limited information is available regarding the sources of CCN in remote regions where marine stratocumulus clouds dominate. Measurements in these marine locations, which are periodically influenced by anthropogenic emissions, provide additional opportunity to study the impact of humans on cloud characteristics. The U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility Eastern North Atlantic (ENA) observatory on Graciosa Island in the Azores is well suited to study these problems. The ENA site is exposed to a multitude of air masses as well as a variety of cloud regimes, as documented by passive and active satellite cloud retrieval. (Tselioudis et al. 2013) Thus, placing detailed aerosol and cloud measurements at the ARM ENA site may help gain a better understanding of the CCN budget and cloud interactions in remote environments. To provide detailed information on aerosol morphology, composition, and microphysical properties, size- segregated sampling was carried out at the ENA observatory on Graciosa Island during two intensive operating periods (IOPs). IOP1 occurred from June 17 to July 18, 2017, and IOP2 occurred from January 9 to February 21, 2018. Daytime and nighttime sampling were carried out separately to investigate any diurnal differences of aerosol composition due to differing meteorology. For both IOPs, a micro-orifice uniform deposit impactor (MOUDI) was used to collect particles for microscopic and microphysical analysis. A variety of microscopic substrates (formvar coated copper grids, silicon chips, silicon nitride windows, or molybdenum substrates) were used. Microscopic chemical characterization was carried out using computer-controlled scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (CCSEM-EDX) and the synchrotron-based scanning transmission X-ray microscopy coupled with near-edge X-ray absorption spectroscopy (STXM-NEXAFS). (Laskin et al. 2006; Kilcoyne et al. 2003; Moffet et al. 2010) Two light sources were used for this analysis: 1) the Advanced Light Source at Lawrence Berkeley National Laboratory, and 2) The Canadian Light Source.

Eastern North Atlantic, ACE-ENA field campaign, Gr↗

Method and apparatus for shape-based energy analysis of solids

A computer-readable medium stores instructions including storing a model of a physical structure and defining a mesh for the model. The mesh includes finite elements, each defined by a respective set of edges. The instructions include, for each finite element, identifying a governing differential equation and a set of complementary functions that exactly satisfy the governing differential equation. The instructions include determining an applied physical stimulus for the physical structure. The instructions include generating an energy optimization model that minimizes a difference between internal energy and external energy of the finite elements in response to the applied physical stimulus. The model includes a matrix of respective scalar multipliers for the complementary functions for each finite element. The instructions include transforming the matrix and calculating a physical parameter of interest. The instructions include, in response to the physical parameter not satisfying a design parameter, updating the model of the physical structure.

Spears, Robert E.↗

Cosmic Reionization On Computers. Mean and fluctuating redshifted 21 cm signal

We explore the mean and fluctuating redshifted 21 cm signal in numerical simulations from the Cosmic Reionization On Computers project. We find that the mean signal varies between about ±25 mK. Most significantly, we find that the negative pre-reionization dip at z ∼ 10–15 only extends to 〈ΔT{sub B}〉∼−25 mK, requiring substantially higher sensitivity from global signal experiments that operate in this redshift range (EDGES-II, LEDA, SCI-HI, and DARE) than has often been assumed previously. We also explore the role of dense substructure (filaments and embedded galaxies) in the formation of the 21 cm power spectrum. We find that by neglecting the semi-neutral substructure inside ionized bubbles, the power spectrum can be misestimated by 25%–50% at scales k ∼ 0.1–1h Mpc{sup −1}. This scale range is of particular interest, because the upcoming 21 cm experiments (Murchison Widefield Array, Precision Array for Probing the Epoch of Reionization, Hydrogen Epoch of Reionization Array) are expected to be most sensitive within it.

79 ASTRONOMY AND ASTROPHYSICS↗

A discrete dislocation dynamics study of precipitate bypass mechanisms in nickel-based superalloys

Order strengthening in nickel-based superalloys is associated with the extra stress required for dislocations to bypass the $\gamma'$ precipitates distributed in the $\gamma$ matrix. Depending on the operating conditions and microstructure, a rich variety of bypass mechanism has been identified, with various shearing and Orowan looping processes gradually giving way to climb bypass as the operating conditions change from the low/intermediate temperatures and high stress regime, to the high temperature and low stress regime. When anti phase boundary (APB) shearing and Orowan looping mechanisms operate, the classical picture is that, at for a given volume fraction, the bypass mechanism changes from shearing to looping with increased particle size and within a broad coexistence size window. Another possibility, which is supported by indirect experimental evidence, is that a third “hybrid” transition mechanism may operate. Here, in this paper we use discrete dislocation dynamics (DDD) simulations to study dislocation bypass mechanisms in Ni-based superalloys. We develop a new method to compute generalized stacking fault forces in DDD simulations, based on a concept borrowed from complex analysis and known as the winding number of a closed curve about a point. We use this method to study the mechanisms of bypass of a square lattice of spherical $\gamma'$ precipitates by $a/2\langle110\rangle$ {111} edge dislocations, as a function of the precipitates volume fraction and size. We show that not only the hybrid mechanism is possible, but also that it operates as the transition mechanism between the shearing and looping regimes over a wide range of precipitates volume fraction and radii. Based on our simulation results, we propose a simple model for the strength of this mechanism. We also consider the effects of a $\gamma$/$\gamma'$ lattice misfit on the bypass mechanisms, which we approximate by an additional precipitate stress computed according to Eshelby’s inclusion theory. We show that in the shearing and hybrid looping-shearing regimes, a lattice misfit generally results in an increased bypass stress. For sufficiently high lattice misfit, the critical bypass configuration in attractive dislocation-precipitates interactions changes dramatically, and the bypass stress is controlled by the pinning of the trailing dislocation on the exit side of the precipitates, similar to what has been reported in the high-temperature creep literature.

36 MATERIALS SCIENCE↗

Second Target Station Computer Science and Math Workshop Report

Discovery science drives innovation and underpins the technological advances that will solve some of society’s most challenging issues, including clean energy technologies, better medicines, safe potable water, and addressing aging infrastructures, including transportation. Many of these advances will result from basic research into new materials and new ways to optimize our use of existing materials. Oak Ridge National Laboratory’s neutron sources provide cutting-edge scientific tools to probe the structure and dynamics of matter in unique ways. This insight is fundamental to advancing our ability to discover, design, control, and use new materials to address society’s most pressing needs.

97 MATHEMATICS AND COMPUTING↗

Resolving local structural motifs across the phase evolution of zinc titanates with computational x-ray absorption spectroscopy

Resolving the local structure motifs that characterize phase evolution as a function of composition is a key challenge in structure characterization of complex materials. Here, in this study, we combine first-principles simulations and x-ray absorption near-edge structures (XANES) analysis to gain insights into the structure evolution revealed by measurements across a combinatorial zinc titanate thin film, which was grown with smoothly varying composition over a wide range of the Ti:Zn ratio. Specifically, we propose a cluster blind-signal-separation (cBSS) method for XANES spectral analysis based on a library of the structures and spectra of representative local motifs. In addition to motifs from zinc titanate crystals, two types of Ti-defect models constructed in this study are key to the understanding of the structure characteristics in the Zn-rich region. The cBSS method makes use of both spectral clustering of the simulated site-XANES spectra library and the BSS procedure to construct high-fidelity spectral basis functions from an experimental spectral sequence. The method provides a rigorous measure of the spectral sensitivity and basis completeness. The results of the XANES analysis are corroborated with other experimental modalities, including x-ray diffraction and spectroscopic ellipsometry, to validate the cBSS method. The calculated motif weights resulting from fitting the XANES spectra with the cBSS basis probe the atomic structure characteristics of both crystalline and amorphous phases as a function of the Ti/Zn composition. The insights of the local structure motif evolution are pivotal to the understanding of the nonmonotonic trend in the optical gap, which may lead to potential applications through tuning the optical properties of zinc titanate. The workflow of the XANES spectral analysis developed in this work can be generalized to construct the structure-property relationship in a broad material space.

36 MATERIALS SCIENCE↗

Excited-State Dynamics of a CsPbBr 3 Nanocrystal Terminated with Binary Ligands: Sparse Density of States with Giant Spin–Orbit Coupling Suppresses Carrier Cooling

Fully inorganic lead halide perovskite nanocrystals (NCs) are of interest for photovoltaic and light-emitting devices due to optoelectronic properties that can be tuned/optimized via halide composition, surface passivation, doping, and confinement. Compared to bulk materials, certain excited-state properties in NCs can be adjusted by electronic confinement effects such as suppressed hot carrier cooling and enhanced radiative recombination. In this paper, we use spinor Kohn–Sham orbitals (SKSOs) with spin–orbit coupling (SOC) interaction as a basis to compute excited-state dissipative dynamics simulations on a fully passivated CsPbBr 3 NC atomistic model. Redfield theory in the density matrix formalism is used to describe electron–phonon interactions which drive hot carrier cooling and nonradiative recombination ( k nonrad ). Radiative recombination ( k rad ) is calculated through oscillator strengths using SKSO basis. From k rad and k rad + k nonrad , we compute a theoretical photoluminescence quantum yield (PLQY) of 53%. Computed rates of hot carrier cooling ( k cooling ≈ 10 –1 1/ps) compare favorably with what has been reported in the literature. Interestingly, we observe that hot electron cooling slows down near the band edge, which we attribute to large SOC in the conduction band combined with strong confinement, which creates subgaps above the band edge. This slow carrier cooling could potentially impact hot carrier extraction before complete thermalization in photovoltaics (PVs). Implications of this work suggest that strong/intermediate confined APbX 3 NCs are better suited to applications in PVs due to slower carrier cooling near the conduction band edge, while intermediate/weak confined NCs are more appropriate for light-emitting applications, such as LEDs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Increasing the applicability of density functional theory. V. X-ray absorption spectra with ionization potential corrected exchange and correlation potentials

Core excitation energies are computed with time-dependent density functional theory (TD-DFT) using the ionization energy corrected exchange and correlation potential QTP(0,0). QTP(0,0) provides C, N, and O K-edge spectra to about an electron volt. A mean absolute error (MAE) of 0.77 and a maximum error of 2.6 eV is observed for QTP(0,0) for many small molecules. TD-DFT based on QTP (0,0) is then used to describe the core-excitation spectra of the 22 amino acids. TD-DFT with conventional functionals greatly underestimates core excitation energies, largely due to the significant error in the Kohn-Sham occupied eigenvalues. To the contrary, the ionization energy corrected potential, QTP(0,0), provides excellent approximations (MAE of 0.53 eV) for core ionization energies as eigenvalues of the Kohn-Sham equations. As a consequence, core excitation energies are accurately described with QTP(0,0), as are the core ionization energies important in X-ray photoionization spectra or electron spectroscopy for chemical analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗