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DOE OSTI2023

Distributed out-of-memory NMF on CPU/GPU architectures

We propose an efficient distributed out-of-memory implementation of the non-negative matrix factorization (NMF) algorithm for heterogeneous high-performance-computing systems. The proposed implementation is based on prior work on NMFk, which can perform automatic model selection and extract latent variables and patterns from data. In this work, we extend NMFk by adding support for dense and sparse matrix operation on multi-node, multi-GPU systems. The resulting algorithm is optimized for out-of-memory problems where the memory required to factorize a given matrix is greater than the available GPU memory. Memory complexity is reduced by batching/tiling strategies, and sparse and dense matrix operations are significantly accelerated with GPU cores (or tensor cores when available). Input/output latency associated with batch copies between host and device is hidden using CUDA streams to overlap data transfers and compute asynchronously, and latency associated with collective communications (both intra-node and inter-node) is reduced using optimized NVIDIA Collective Communication Library (NCCL) based communicators. Benchmark results show significant improvement, from 32X to 76x speedup, with the new implementation using GPUs over the CPU-based NMFk. Good weak scaling was demonstrated on up to 4096 multi-GPU cluster nodes with approximately 25,000 GPUs when decomposing a dense 340 Terabyte-size matrix and an 11 Exabyte-size sparse matrix of density 10 -6 .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

WIYN Open Cluster Study. LXXXV. Li in NGC 2243: Implications for Stellar and Galactic Evolution

High-dispersion spectra in the Li λ6708 region have been obtained and analyzed in the old, metal-deficient cluster NGC 2243. From Hydra spectra for 29 astrometric and radial velocity members, we derive rotational velocities, as well as [Fe/H], [Ca/H], [Si/H], and [Ni/H] based on 17, 1, 1, and 3 lines, respectively. Using ROBOSPECT, an automatic equivalent width measurement program, we derive [Fe/H] = −0.54 ± 0.11 (MAD), for an internal precision for the cluster [Fe/H] below 0.03 dex. Given the more restricted line set, comparable values for [Ca/H], [Si/H], and [Ni/H] are −0.48 ± 0.19, −0.44 ± 0.11, and −0.61 ± 0.06, respectively. With E(B − V) = 0.055, appropriate isochrones imply (m − M) = 13.2 ± 0.1 and an age of 3.6 ± 0.2 Gyr. Using available VLT spectra and published Li abundances, we construct an Li sample of over 100 stars extending from the tip of the giant branch to 0.5 mag below the Li dip. The Li dip is well populated and, when combined with results for NGC 6819 and Hyades/Praesepe, implies a mass/metallicity slope of 0.4 M {sub ⊙}/dex for the high-mass edge of the Li dip. The A(Li) distribution among giants reflects the degree of Li variation among the turnoff stars above the Li dip, itself a function of stellar mass and metallicity and strongly anticorrelated with a v {sub rot} distribution that dramatically narrows with age. Potential implications of these patterns for the interpretation of Li among dwarf and giant field populations, especially selection biases tied to age and metallicity, are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

The R -process Alliance: Fifth Data Release from the Search for R -process-enhanced Metal-poor Stars in the Galactic Halo with the GTC

Understanding the abundance pattern of metal-poor stars and the production of heavy elements through various nucleosynthesis processes offers crucial insights into the chemical evolution of the Milky Way, revealing primary sites and major sources of rapid neutron-capture process (r-process) material in the Universe. In this fifth data release from the R-Process Alliance (RPA), we present the detailed chemical abundances of 41 faint (down to V = 15.8) and extremely metal-poor (down to [Fe/H] = -3.3) halo stars selected from the RPA. We obtained high-resolution spectra for these objects with the HORuS spectrograph on the Gran Telescopio Canarias. We measure the abundances of light, α, Fe-peak, and neutron-capture elements. We report the discovery of five carbon-enhanced metal-poor, one limited-r, three r-I, and four r-II stars, and six Mg-poor stars. We also identify one star of a possible globular cluster origin at an extremely low metallicity at [Fe/H] = -3.0. This adds to the growing evidence of a lower-limit metallicity floor for globular cluster abundances. We use the abundances of Fe-peak elements and the α-elements to investigate the contributions from different nucleosynthesis channels in the progenitor supernovae. We find the distribution of [Mg/Eu] as a function of [Fe/H] to have different enrichment levels, indicating different possible pathways and sites of their production. We also reveal differences in the trends of the neutron-capture element abundances of Sr, Ba, and Eu of various r-I and r-II stars from the RPA data releases, which provide constraints on their nucleosynthesis sites and subsequent evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp

Background: Pisolithus microcarpus (Cooke & Massee) G. Cunn is a gasteromycete that produces closed basidiocarps in symbiosis with eucalypts and acacias. The fungus produces a complex basidiocarp composed of peridioles at different developmental stages and an upper layer of basidiospores free of the hyphae and ready for wind dispersal upon the rupture of the basidiocarp pellis. During basidiosporogenesis, a process that takes place inside the basidiocarp peridioles, a conspicuous reserve of fatty acids is present throughout development. While several previous studies have described basidiosporogenesis inside peridioles, very little is known about gene expression changes that may occur during this part of the fungal life cycle. The objective of this work was to analyze gene transcription during peridiole and basidiospore development, while focusing specifically on cell cycle progression and lipid metabolism. Results: Throughout different developmental stages of the peridioles we analyzed, 737 genes were regulated between adjacent compartments (>5 fold, FDR-corrected p-value < 0.05) corresponding to 3.49% of the genes present in the P. microcarpus genome. We identified three clusters among the regulated genes which showed differential expression between the peridiole developmental stages and the basidiospores. During peridiole development, transcripts for proteins involved in cellular processes, signaling, and information storage were detected, notably those for coding transcription factors, DNA polymerase subunits, DNA repair proteins, and genes involved in chromatin structure. For both internal embedded basidiospores (hereto referred to as “Internal spores”, IS) and external free basidiospores (hereto referred to as “Free spores”, FS), upregulated transcripts were found to involve primary metabolism, particularly fatty acid metabolism (FA). High expression of transcripts related to β-oxidation and the glyoxylate shunt indicated that fatty acids served as a major carbon source for basidiosporogenesis. Conclusion: Our results show that basidiocarp formation in P. microcarpus involves a complex array of genes that are regulated throughout peridiole development. We identified waves of transcripts with coordinated regulation and identified transcription factors which may play a role in this regulation. This is the first work to describe gene expression patterns during basidiocarp formation in an ectomycorrhizal gasteromycete fungus and sheds light on genes that may play important roles in the developmental process.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

A study of the topology of dissipating motions in direct numerical simulations of time-developing compressible and incompressible mixing layers

A preliminary investigation of the geometry of flow patterns in numerically simulated compressible and incompressible mixing layers was carried out using 3-D critical point methodology. Motions characterized by high rates of kinetic energy dissipation and/or high enstrophy were of particular interest. In the approach the partial derivatives of the velocity field are determined at every point in the flow. These are used to construct the invariants of the velocity gradient tensor and the rate-of-strain tensor (P, Q, R, and P(sub s), Q(sub s), R(sub s) respectively). For incompressible flow the first invariant is zero. For the conditions of the compressible simulation, the first invariant is found to be everywhere small, relative to the second and third invariants, and so in both cases the local topology at a point is mainly determined by the second and third invariants. The data at every grid point is used to construct scatter plots of Q versus R and Q(sub s) versus R(sub s). Most points map to a cluster near the origin in Q-R space. However, fine scale motions, that is motions which are characterized by velocity derivatives which scale with the square root of R(sub delta), tend to map to regions which lie far from the origin. Definite trends are observed for motions characterized by high enstrophy and/or high dissipation. The observed trends suggest that, for these motions, the second and third invariants of the velocity gradient and rate-of-strain tensors are strongly correlated. The second and third invariants of the rate-of-strain tensor are related by K(-Q(sub s))(exp 3/2), which is consistent with the above scaling of velocity derivatives. The quantity K appears to depend on Reynolds number with an upper limit K = 2(the square root of 3)/9 corresponding to locally axisymmetric flow. For both the compressible and incompressible mixing layer, regions corresponding to high rates of dissipation are found to be characterized by comparable magnitudes of R(sub ij)R(sub ij) and S(sub ij)S(sub ij). For the incompressible mixing layer, regions characterized by the highest values of enstrophy are found to have relatively low strain rates.

Chen, J. H.↗
NASA NTRS2021

Geospatial Cluster Analysis of the State, Duration and Severity of Drought Over Paraíba State, Northeastern Brazil

Droughts threaten water resources, agriculture, socio-economic activities and the population at the global and regional level, so identifying areas with homogeneous drought behaviors is an important consideration in improving the management of water resources. The objective of this study is to identify homogenous zones over Paraíba State in relation to the state, duration and severity of droughts that have occurred over the last 20 years (1998–2017) using hierarchical cluster analysis based on both gauge-measured and Tropical Rainfall Measuring Mission (TRMM) estimated rainfall data (TMPA 3B42). The drought series were calculated using the Standardized Precipitation Index (SPI) based on eight time scales and were grouped according to drought state, duration and severity time series. The integrated results of state, duration and severity of droughts indicate that there is a basis for dividing Paraíba State into two major regions (a) Zone I, formed by Mata Paraibana and Agreste Paraibano, and (b) Zone II, composed by Borborema and Sertão Paraibano. This division is evident when assessing short-term droughts, but in the case of long-term droughts, Paraíba State has a high similarity in terms of drought state, duration, and severity. Factors such as proximity to the ocean, active climatic systems, and the local relief configuration were identified as influencing the drought regime. Finally, it is concluded that TMPA rainfall estimates represent a valuable source of data to regionalize and identify drought patterns over this part of Brazil and that other studies of this type should be carried out to monitor these phenomena based on other satellite-based rainfall data, including the Global Precipitation Mission (GPM).

SPI↗
DOE OSTI2015

Bayesian analysis of the dynamic cosmic web in the SDSS galaxy survey

Recent application of the Bayesian algorithm \textsc(borg) to the Sloan Digital Sky Survey (SDSS) main sample galaxies resulted in the physical inference of the formation history of the observed large-scale structure from its origin to the present epoch. In this work, we use these inferences as inputs for a detailed probabilistic cosmic web-type analysis. To do so, we generate a large set of data-constrained realizations of the large-scale structure using a fast, fully non-linear gravitational model. We then perform a dynamic classification of the cosmic web into four distinct components (voids, sheets, filaments, and clusters) on the basis of the tidal field. Our inference framework automatically and self-consistently propagates typical observational uncertainties to web-type classification. As a result, this study produces accurate cosmographic classification of large-scale structure elements in the SDSS volume. By also providing the history of these structure maps, the approach allows an analysis of the origin and growth of the early traces of the cosmic web present in the initial density field and of the evolution of global quantities such as the volume and mass filling fractions of different structures. For the problem of web-type classification, the results described in this work constitute the first connection between theory and observations at non-linear scales including a physical model of structure formation and the demonstrated capability of uncertainty quantification. A connection between cosmology and information theory using real data also naturally emerges from our probabilistic approach. Our results constitute quantitative chrono-cosmography of the complex web-like patterns underlying the observed galaxy distribution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Projecting Future Energy Production from Operating Wind Farms in North America. Part II: Statistical Downscaling

Abstract Capacity factors (CFs) derived from daily expected power at 22 operating wind farms in different regions of North America are used as predictands to train statistical downscaling algorithms using output from ERA5. The statistical downscaling models are then used to make CF projections for a suite of CMIP6 Earth System Models (ESMs). Downscaling is performed using a hybrid statistical approach that employs synoptic types derived using k -means clustering applied to sea level pressure fields with variance corrections applied as a function of the pressure gradient intensity. ESMs exhibit marked variability in terms of the skill with which the frequency of synoptic types and pressure gradients are reproduced relative to ERA5, and that differential skill is used to infer differential credibility in the associated CF projections. Projections of median annual mean CF [P50(CF)] in each 20-yr period from 1980 to 2099 show evidence of declines at most wind farms except in parts of the southern Great Plains, although the magnitude of the changes is strongly dependent on the ESM. For example, P50(CF) in 2080–99 deviate from those in 1980–99 by from −3.1 to +0.2 percentage points in the Northeast. The largest-magnitude declines in P50(CF) ranging from −3.9 to −2 percentage points are projected for the southern West Coast. CF trends exhibit marked seasonality and are strongly linked to changes in the relative intensity of future synoptic patterns, with much less impact from shifts in the occurrence of synoptic types over time. Internal climate modes continue to play a significant role in inducing interannual variability in wind power production, even under high radiative forcing scenarios. Significance Statement We describe how future climate changes may affect wind resources and wind power generation. Near-term changes in projected wind power electricity generation potential at operating wind farms over North America are small, but by the end of the current century electricity production is projected to decrease in many areas but may increase in parts of the southern Great Plains. The amount of change in projected wind power production is a strong function of the Earth system model that is downscaled and also depends on the continued presence of internally forced climate variability. An additional dependence on the amount of greenhouse gas–induced global warming indicates the transition of the energy sector to low-carbon sources may assist in maintaining the abundant U.S. wind resource.

Meteorology & Atmospheric Sciences↗
DOE OSTI2017

Evolution of Mass and Velocity Field in the Cosmic Web: Comparison Between Baryonic and Dark Matter

We investigate the evolution of the cosmic web since z = 5 in grid-based cosmological hydrodynamical simulations, focusing on the mass and velocity fields of both baryonic and cold dark matter. The tidal tensor of density is used as the main method for web identification, with λ {sub th} = 0.2–1.2. The evolution trends in baryonic and dark matter are similar, although moderate differences are observed. Sheets appear early, and their large-scale pattern may have been set up by z = 3. In terms of mass, filaments supersede sheets as the primary collapsing structures from z ∼ 2–3. Tenuous filaments assembled with each other to form prominent ones at z < 2. In accordance with the construction of the frame of the sheets, the cosmic divergence velocity, v {sub div}, was already well-developed above 2–3 Mpc by z = 3. Afterwards, the curl velocity, v {sub curl}, grew dramatically along with the rising of filaments, becoming comparable to v {sub div}, for <2–3 Mpc at z = 0. The scaling of v {sub curl} can be described by the hierarchical turbulence model. The alignment between the vorticity and the eigenvectors of the shear tensor in the baryonic matter field resembles that in the dark matter field, and is even moderately stronger between ω and e{sub 1}, and ω and e{sub 3}. Compared with dark matter, there is slightly less baryonic matter found residing in filaments and clusters, and its vorticity developed more significantly below 2–3 Mpc. These differences may be underestimated because of the limited resolution and lack of star formation in our simulation. The impact of the change of dominant structures in overdense regions at z ∼ 2–3 on galaxy formation and evolution is shortly discussed.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2007

Impact of Ring Current Ions on Electromagnetic Ion Cyclotron Wave Dispersion Relation

Effect of the ring current ions in the real part of electromagnetic ion Cyclotron wave dispersion relation is studied on global scale. Recent Cluster observations by Engebretson et al. showed that although the temperature anisotropy of is energetic (> 10 keV) ring current protons was high during the entire 22 November 2003 perigee pass, electromagnetic ion cyclotron waves were observed only in conjunction with intensification of the ion fluxes below 1 keV by over an order of magnitude. To study the effect of the ring current ions on the wave dispersive properties and the corresponding global wave redistribution, we use a self-consistent model of interacting ring current and electromagnetic ion cyclotron waves, and simulate the May 1998 storm. The main findings of our simulation can be summarized as follows: First, the plasma density enhancement in the night MLT sector during the main and recovery storm phases is mostly caused by injection of suprathermal plasma sheet H + (approximately < 1 keV), which dominate the thermal plasma density. Second, during the recovery storm phases, the ring current modification of the wave dispersion relation leads to a qualitative change of the wave patterns in the postmidnight-dawn sector for L > 4.75. This "new" wave activity is well organized by outward edges of dense suprathermal ring current spots, and the waves are not observed if the ring current ions are not included in the real part of dispersion relation. Third, the most intense wave-induced ring current precipitation is located in the night MLT sector and caused by modification of the wave dispersion relation. The strongest precipitating fluxes of about 8 X 10(exp 6)/ (cm(exp 2) - s X st) are found near L=5.75, MLT=2 during the early recovery phase on 4 May. Finally, the nightside precipitation is more intense than the dayside fluxes, even if there are less intense waves, because the convection field moves ring current ions into the loss cone on the nightside, but drives them out of the loss cone on the dayside. So convection and wave scattering reinforce each other in the nightside, but interfere in the dayside sector.

Khazanov, G. V.↗
DOE OSTI2021

Thermal effects mediating the flow induced by laser-induced optical breakdown

Here, a short focused laser pulse can generate a hot plasma, which expands then contracts and can eject a hot jet, the speed and direction of which is sensitive to the details of the plasma kernel. The coupling of thermal and chemical nonequilibrium plasma mechanisms with this hydrodynamic development is assessed with detailed simulations of a two-temperature, three-species plasma model. Time scales for electron recombination, thermal relaxation, and diffusion are compared to that of the plasma expansion to anticipate conditions in which these mechanisms might affect the vorticity generation that leads to the ultimate flow pattern. The effect of these mechanisms are analyzed through comparison with corresponding inert-gas and equilibrium models. Thermal-nonequilibrium effects are found to be weak due to rapid relaxation of the heavy-particle and electronic temperatures. In contrast, chemical equilibration occurs at a rate comparable to the expansion and thereby enhance both it and subsequent hydrodynamic mechanisms as the energy stored in ion formation during the preceding breakdown is released by electron recombination. Thermal conduction, enhanced by high-temperature free electrons, weakens the ejection.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

WIYN Open Cluster Study. LXXVI. Li Evolution Among Stars of Low/Intermediate Mass: The Metal-deficient Open Cluster NGC 2506

HYDRA spectra of 287 stars in the field of NGC 2506 from the turnoff through the giant branch are analyzed. With previous data, 22 are identified as probable binaries; 90 more are classified as potential non-members. Spectroscopic analyses of ∼60 red giants and slowly rotating turnoff stars using line equivalent widths and a neural network approach lead to [Fe/H] = −0.27 ± 0.07 (s.d.) and [Fe/H] = −0.27 ± 0.06 (s.d.), respectively. Li abundances are derived for 145 probable single-star members, 44 being upper limits. Among turnoff stars outside the Li-dip, A(Li) = 3.04 ± 0.16 (s.d.), with no trend with color, luminosity, or rotation speed. Evolving from the turnoff across the subgiant branch, there is a well-delineated decline to A(Li) ∼1.25 at the giant branch base, coupled with the rotational spindown from between ∼20 and 70 km s{sup −1} to less than 20 km s{sup −1} for stars entering the subgiant branch and beyond. A(Li) remains effectively constant from the giant branch base to the red giant clump level. A new member above the clump redefines the path of the first-ascent red giant branch; its Li is 0.6 dex below the first-ascent red giants. With one exception, all post-He-flash stars have upper limits to A(Li), at or below the level of the brightest first-ascent red giant. The patterns are in excellent qualitative agreement with the model predictions for low/intermediate-mass stars which undergo rotation-induced mixing at the turnoff and subgiant branch, first dredge-up, and thermohaline mixing beyond the red giant bump.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Automated Classification of Vehicle Movements at Signalized Intersections Using Vehicle Trajectories

Accurate vehicle movement classification through signalized intersections is of paramount importance to the analysis of intersection performance and the optimization of traffic control strategies. Conventional techniques for tracking vehicle turning movements depend on infrastructure-based strategies like human counts, loop detectors, and video analytics, all of which are costly, prone to errors, and spatially constrained. High-frequency trajectory data can be utilized to determine vehicle movement patterns in a scalable and infrastructure-independent method due to the adoption of connected vehicles (CVs). In recent years, several studies have utilized connected vehicle data to generate performance measures. Most of the trajectory-based performance measures approaches, however, require map matching-i.e., extracting geospatial references from maps to identify the movements that individual vehicles make at a signalized intersection. These approaches are often time-consuming and hinder scalability since geographic features need to be provided for an analysis to be conducted. Map matching methods are prone to errors as different map versions change these geographic features. This research presents a novel automatic classification pipeline that uses CV trajectory data to classify vehicle movements at signalized crossings, specifically pass-through left-turn and right-turn maneuvers. The process starts by filtering trips that cross a spatial bounding box that has been defined at the target intersection. Approach and departure headings for each trajectory crossing the boundary are computed and are clustered together to identify dominant movements. The proposed algorithm is used to classify the movement of vehicles at 10 intersections in the state of California, and the results indicate that the algorithm can classify movements at these intersections with varying traffic volumes and road network configurations, all in a map-less framework with no need for conflation of vehicle trajectories to a digital base map.

24 POWER TRANSMISSION AND DISTRIBUTION↗
NASA NTRS2016

Africa's Megafans and Their Tectonic Setting

Megafans are a really extensive continental sediment bodies, fluvially derived, and fan-shaped in planform. Only those >80 km long were included in this study. Africa's megafans were mapped for purposes of both comprehensive geomorphic description and as a method of mapping by remote sensing large probable fluvial sediment bodies (we exclude sediment bodies deposited in well defined, modern floodplains and coastal deltas). Our criteria included a length dimension of >80 km and maximum width >40 km, partial cone morphology, and a radial drainage pattern. Visible and especially IR imagery were used to identify the features, combined with topographic SRTM data. We identified 99 megafans most of which are unstudied thus far. Their feeder rivers responsible for depositing megafan sediments rise on, and are consequent drainages oriented down the slopes of the swells that have dominated African landscapes since approximately 34 Ma (the high points in Africa's so-called basin-and-swell topography [1]). Most megafans (66%) have developed along these consequent rivers relatively near the swell cores, oriented radially away from the swells. The vast basins between the swells provide accommodation for megafan sediment wedges. Although clearly visible remotely, most megafans are inactive as a result of incision by the feeder river (which then no longer operates on the fan surface). Two tectonic settings control the location of Africa's megafans, 66% on swell flanks, and 33% related to rifts. (i) Swell flanks Most megafans are apexed relatively near the core of the parent swell, and are often clustered in groups: e.g., six on the west and north flanks of the Hoggar Swell (Algeria), seven on the north and south flanks of the Tibesti Swell (Libya-Chad borderlands), twelve on the west flank of the Ethiopian Swell, four on the east flank of the East African Swell (Kenya), Africa's largest, and eight around Angola's Bié Swell (western Zambia, northern Namibia). A cluster of possible fans lies on the western margin of the Congo Basin (Mayombe Swell), and on the coastal slopes of the Namibia Swell. Sheer size may have militated aginst the recognition of many megafans: the largest in the Sahara are the Teghahart (378 km, Hoggar Swell, Algeria), and the Wadi Albalata (340 km, Uweinat Swell, Egypt). In southern Africa the largest are the Cubango (320 km, Bié Swell, Angola/ Namibia), and the Limpopo (230 km, Mozambique). (ii) Rift zones (a) Steer's horns basins-wide depressions centered on rifts. The largest contiguous group (n=14) developed in a steer's-horns basin occupies the wide Muglad depression (200-350 km, South Sudan). Four rift-related megafans lie SE of Lake Chad (Chad). Nine megafans occupy the complex Anza Rift in Kenya/South Somalia. The Salamat megafan (Chad), is unusual because it oriented parallel with the linked Salamat, Doseo and Doba rift axes, and is consequently one of the longest in Africa (465 km). (b) Rift depressions sensu stricto. Most rifts are too narrow to provide a transverse dimension large enough to accommodate megafans. Although well-known, the Okavango Rift (NW Botswana, NE Namibia) is unique in Africa in hosting three megafans within identifiable faulted margins. The Nile megafan is Africa's largest (476 km) and comprises the vast Sudd wetland (South Sudan). An explanation for its remarkable size may be its location in a depression at the junction of two conducive tectonic zones, the East African Swell margin and the Muglad steer's-horns depression. Discharge of the River Nile, the largest in the region, has allowed the Nile megafan to outcompete neighboring megafans for space.

Wilkinson, M. J.↗
DOE OSTI2020

Structure of chalcogen overlayers on Au(111): Density functional theory and lattice-gas modeling

Ordering of different chalcogens, S, Se, and Te, on Au(111) exhibit broad similarities but also some distinct features, which must reflect subtle differences in relative values of the long-range pair and many-body lateral interactions between adatoms. We develop lattice-gas (LG) models within a cluster expansion framework, which includes about 50 interaction parameters. These LG models are developed based on density functional theory (DFT) analysis of the energetics of key adlayer configurations in combination with the Monte Carlo (MC) simulation of the LG models to identify statistically relevant adlayer motifs, i.e., model development is based entirely on theoretical considerations. The MC simulation guides additional DFT analysis and iterative model refinement. Given their complexity, development of optimal models is also aided by strategies from supervised machine learning. The model for S successfully captures ordering motifs over a broader range of coverage than achieved by previous models, and models for Se and Te capture the features of ordering, which are distinct from those for S. More specifically, the modeling for all three chalcogens successfully explains the linear adatom rows (also subtle differences between them) observed at low coverages of ~0.1 monolayer. The model for S also leads to a new possible explanation for the experimentally observed phase with a (5 × 5)-type low energy electron diffraction (LEED) pattern at 0.28 ML and to predictions for LEED patterns that would be observed with Se and Te at this coverage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Bayesian Analysis of Congruence of Core Genes in Prochlorococcus and Synechococcus and Implications on Horizontal Gene Transfer

It is often suggested that horizontal gene transfer is so ubiquitous in microbes that the concept of a phylogenetic tree representing the pattern of vertical inheritance is oversimplified or even positively misleading. “Universal proteins” have been used to infer the organismal phylogeny, but have been criticized as being only the “tree of one percent.” Currently, few options exist for those wishing to rigorously assess how well a universal protein phylogeny, based on a relative handful of well-conserved genes, represents the phylogenetic histories of hundreds of genes. Here, we address this problem by proposing a visualization method and a statistical test within a Bayesian framework. We use the genomes of marine cyanobacteria, a group thought to exhibit substantial amounts of HGT, as a test case. We take 379 orthologous gene families from 28 cyanobacteria genomes and estimate the Bayesian posterior distributions of trees – a “treecloud” – for each, as well as for a concatenated dataset based on putative “universal proteins.” We then calculate the average distance between trees within and between all treeclouds on various metrics and visualize this high-dimensional space with non-metric multidimensional scaling (NMMDS). We show that the tree space is strongly clustered and that the universal protein treecloud is statistically significantly closer to the center of this tree space than any individual gene treecloud. We apply several commonly-used tests for incongruence/HGT and show that they agree HGT is rare in this dataset, but make different choices about which genes were subject to HGT. Our results show that the question of the representativeness of the “tree of one percent” is a quantitative empirical question, and that the phylogenetic central tendency is a meaningful observation even if many individual genes disagree due to the various sources of incongruence.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

New ISTP Solar Max: A Multi-Spacecraft Study of the Flow of Ionospheric Plasma

The unique instrumentation on the Polar satellite combined with the simultaneous measurement of different parts of the magnetosphere with multiple satellites make possible the study of magnetospheric processes in a special way. In particular, the study of the ionospheric supply of plasma to the magnetosphere can by accomplished to give important results on the plasmas which drive the dynamics of the magnetosphere. This study concentrated on the period of September to December, 2001 in which the Polar orbit had precessed to the point that the line of apsides was near the equatorial plane. This unique orbital configuration enabled the TIDE instrument to measure outflowing ions across the polar cap and then transit the magnetotail lobes and observe the dramatic change in plasma characteristics as the satellite entered the plasma sheet. Contact was made with investigators on the Cluster and Geotail satellite missions and corresponding time frames were studied in the data. There were two approximate conjunctions between Polar and Geotail and data were compared to look for features which might be related. The higher energy concentration of the Geotail instrument made direct comparisons with TIDE difficult, and the Cluster measurements did not surface any cases that corresponded closely in space and time. There were, however, many interesting aspects of the Polar orbits which permitted the observation of the changing ionospheric outflowing plasma characteristics. As in earlier measurements, the ionospheric plasma could be seen flowing up the magnetic field lines out of the northern and southern polar caps. Its energy suggested a polar wind origin energized by the centrifugal acceleration of flow through the polar cusp. The roughly 10eV ions then moved out into the lobes of the magnetotail where they could be seen flowing toward the plasma sheet in both the northern and southern magnetotail lobes. There was also a double field-aligned region of warm ions observed just outside the plasmasphere, stretching toward the auroral zone and inner plasma sheet boundary. Upon entering the plasma sheet, the plasma energy jumped from 10 s of eV to greater than 1 keV. The single field aligned flows transitioned to highly variable spatially choppy energized ion distributions with a variety of pitch angle configurations. This pattern was quite repeatable in all of the Polar orbits that were examined and are compatible with the source of ions being the polar wind which is then energized to 10 s of eV by the centrifugal acceleration. These modestly energized polar wind ions are then carried to the magnetotail where they are substantially energized by the curvature drift-induced movement across the cross-tail potential of the magnetotail. This latter drift energizes the ions to the energies typically found in the plasma sheet. Subsequent drift and energization can cause the ions to become part of the ring current. The results of this study were presented at the Spring AGU meeting in 2002 and the GEM meeting in June 2003. They are the foundation for a paper that has been submitted by Matthew Huddleston to the Journal of Geophysical Research in December 2003. This work was part of the thesis that Matthew completed in finishing his Ph.D. in Physics at Vanderbilt University.

Chappell, Charles R.↗