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At least 1,297 records · Page 72

High-Performance Design Patterns for Modern Fortran

This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed to become a language well-suited for state-of-the-art software development. Fortran’s new coarray distributed data structure, the language’s class mechanism, and its side-effect-free, pure procedure capability provide the scaffolding on which we implement HPC software. These features empower compilers to organize parallel computations with efficient communication. We present some programming patterns that support asynchronous evaluation of expressions comprised of parallel operations on distributed data. We implemented these patterns using coarrays and the message passing interface (MPI). We compared the codes’ complexity and performance. The MPI code is much more complex and depends on external libraries. The MPI code on Cray hardware using the Cray compiler is 1.5–2 times faster than the coarray code on the same hardware. The Intel compiler implements coarrays atop Intel’s MPI library with the result apparently being 2–2.5 times slower than manually coded MPI despite exhibiting nearly linear scaling efficiency. As compilers mature and further improvements to coarrays comes in Fortran 2015, we expect this performance gap to narrow.

Haveraaen, Magne↗

Surface-to-Interior Transport Timescales and Ventilation Patterns in a Time-Dependent Circulation Driven by Sustained Climate Warming

Abstract The effect of climate warming in response to rising atmospheric CO 2 on the ventilation of the ocean remains uncertain. Here we make theoretical advances in elucidating the relationship between ideal age and transit time distribution (TTD) in a time-dependent flow. Subsequently, we develop an offline tracer-transport model to characterize the ventilation patterns and time scales in the time-evolving circulation for the 1850–2300 period as simulated with the Community Earth System Model version 1 (CESMv1) under a business-as-usual warming scenario. We found that by 2300 2.1% less water originates from the high-latitude deep water formation regions (both hemispheres) compared to 1850. In compensation, there is an increase in the water originating from the subantarctic. We also found that slowing meridional overturning circulation causes a gradual increase in mean age during the 1850–2300 period, with a globally averaged mean-age increase of ∼110 years in 2300. Where and when the water will be re-exposed to the atmosphere depends on the post-2300 circulation. For example, if we assume that the circulation persists in its year-2300 state (scenario 1), the mean interior-to-surface transit time in year 1850 is ∼1140 years. In contrast, if we assume that the circulation abruptly recovers to its year-1850 state (scenario 2), the mean interior-to-surface transit time in 1850 is only ∼740 years. By 2300, these differences become even larger; in scenario 1, the mean interior-to-surface transit time increases by ∼200 years, whereas scenario 2 decreases by ∼80 years. The dependence of interior-to-surface transit time on the future ocean circulation produces an additional unavoidable uncertainty in the long-term durability of marine carbon dioxide removal strategies. Significance Statement The ocean’s circulation, when altered by climate warming, can affect its capacity to absorb heat and CO 2 , which are crucial for the global climate. In our study, we investigated how global warming, caused by rising CO 2 levels, might impact the ocean circulation—the way water moves from deep ocean to the surface and vice versa. We discovered that by 2300, if we continue on our current warming trajectory, the origins of water within the ocean will shift, with less coming from deep, cold zones near the poles and more from subantarctic regions. As a result, deep water will take longer time before it resurfaces than shallow water. How quickly this water travels from deep regions to the surface could change, depending on the state of future ocean circulation. If the circulation remains as predicted in 2300, this journey will take longer. Conversely, if it reverts to the pattern in 1850, the process will be quicker. This variability introduces added uncertainty to strategies aimed at mitigating climate change by storing CO 2 in the ocean. Our work highlights the intricate ways in which climate change can influence our oceans, potentially affecting our plans to mitigate global warming.

54 ENVIRONMENTAL SCIENCES↗

Climate mediates continental scale patterns of stream microbial functional diversity

Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively. We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change.

59 BASIC BIOLOGICAL SCIENCES↗

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics

Background: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life. Results: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark. Conclusions: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles. Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic “handoffs” in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.

59 BASIC BIOLOGICAL SCIENCES↗

Intrahepatic Recurrence Patterns Predict Survival After Resection of Colorectal Liver Metastases

Background: After resection of colorectal liver metastases (CLM), up to 40% of patients will develop intrahepatic recurrence. This study aims to identify patterns of intrahepatic recurrence and their impact on survival after preoperative chemotherapy and CLM resection. Methods: A retrospective review was performed of patients developing intrahepatic recurrence after CLM resection following preoperative chemotherapy. Prechemotherapy, preoperative, and postoperative computed tomography scans were reviewed. Recurrences were classified as in situ, de novo, or both in situ and de novo. Median follow-up was 42 months (range 2–144 months). Results: Among 223 patients meeting study criteria, intrahepatic recurrence was identified a median of 9 months after hepatectomy. Isolated de novo or in situ recurrence developed in 105 (47%) and 86 (39%) patients, respectively. Thirty-two patients (14%) developed both in situ and de novo recurrence, which was associated with significantly lower median overall survival of 33 months compared with 49 and 45 months with isolated in situ or de novo recurrence, respectively (p = 0.048). Among 118 patients (53%) who developed in situ recurrence as a component of disease relapse, recurrences resulted from disappearing or missed liver metastases in 47 patients (40%). Conclusions: An intrahepatic recurrence pattern of both in situ and de novo metastases after CLM resection following preoperative chemotherapy predicts significantly worse overall survival compared with isolated in situ or de novo recurrence.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Data for "Event Horizon Telescope Pattern Speeds in the Visibility Domain”

Visibility Amplitude Pattern Speeds from the v3 Sgr A* Library. Data for "Event Horizon Telescope Pattern Speeds in the Visibility Domain” (Conroy et al.). Data are provided in 2 file formats: a TXT table which is a standard format for the Astrophysical Journal (ApJ) where the paper is submitted and the original NPY format.

Conroy, Nicholas S. [University of Illinois] (ORCI↗

Modeling photovoltaic performance in periodic patterned colloidal quantum dot solar cells

Colloidal quantum dot (CQD) solar cells have attracted tremendous attention mostly due to their wide absorption spectrum window and potentially low processability cost. The ultimate efficiency of CQD solar cells is highly limited by their high trap state density. Here in this paper we show that the overall device power conversion efficiency could be improved by employing photonic structures that enhance both charge generation and collection efficiencies. By employing a two-dimensional numerical model, we have calculated the characteristics of patterned CQD solar cells based of a simple grating structure. Our calculation predicts a power conversion efficiency as high as 11.2%, with a short circuit current density of 35.2 mA/cm 2 , a value nearly 1.5 times larger than the conventional flat design, showing the great potential value of patterned quantum dot solar cells.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants

Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4.2. A total of 1610 genes covering 13 virulence factors and 1903 genes belonging to 11 ARG families were detected respectively. The bacterial virulence genes exhibited significant spatial distribution patterns of a latitudinal biodiversity gradient and a distance-decay relationship across China. Moreover, virulence genes tended to coexist with ARGs as shown by their strongly positive associations. In addition, key environmental factors shaping the overall virulence gene structure were identified. This study profiles the occurrence, composition and distribution of virulence genes and ARGs in current WWTPs in China, and uncovers spatial patterns and important environmental variables shaping their structure, which may provide the basis for further studies of bacterial virulence factors and antibiotic resistance in WWTPs.

54 ENVIRONMENTAL SCIENCES↗

Development of a pattern recognition algorithm for reconstructing multi-particle events in the Mu2e detector

Mu2e is an upcoming experiment at Fermilab and its main goal is to search for the Charged Lepton Flavor Violation (CLFV) in the coherent transition of a muon into an electron on an Al target. In Mu2e, multi-particle events can occur simultaneously within the same time region and it is crucial to accurately identify each particle track, including signals, to improve the robustness of track finding methods and enhance reconstruction efficiency. ¯p annihilation is one of the background events and produces multiple particles that can mimic signal events. Additionally, photons from radiative pion captures can produce a γ → $e+e−$ pair, which can be used to calibrate the Mu2e momentum scale and the resolution. The Mu2e track reconstruction sequence begins by grouping hits produced in the tracker based on time and z coordinate information, called TimeCluster, and selected hits are processed to reconstruct helices and determine their momentum. The current pattern recognition algorithms identify a single helix per TimeCluster for single track events. A new pattern recognition algorithm is being developed to reconstruct multi-particle events and its features for finding multiple tracks and the current evaluation results are reported.

Kitagawa, H. [Pisa U.]↗

Quantifying irradiation defects in zirconium alloys: a comparison between transmission electron microscopy and whole-pattern diffraction line-profile analysis - 2016-0089

Irradiation-induced dislocations significantly affect the mechanical properties of zirconium alloys, altering slip and influencing creep and growth. Thus, the quantitative characterization of irradiation defects as a function of fluence, cold work, and/or thermal treatments is important for models that attempt to predict their impact on properties. Whole-pattern diffraction line-profile analysis (DLPA) is a well-established modern tool for microstructure characterization based on first-principle physical models for dislocation density measurements in plastically deformed materials. However, applying these DLPA methods directly to irradiated materials yields higher than expected dislocation density values compared with historical transmission electron microscopy (TEM) measurements and past line-broadening analysis studies calibrated to TEM observations. In an effort to understand these differences, a new microstructural model was developed for DLPA to specifically address dislocation structures consisting of elliptical - and -component loops. To compare the refined DLPA method with TEM measurements, high-resolution neutron diffraction patterns on nonirradiated and irradiated Zr-2.5Nb samples were collected with the Neutron Powder Diffractometer instrument at the Los Alamos Neutron Science Center and were evaluated. High-resolution TEM measurements were performed at the Reactor Materials Testing Laboratory, Queen's University, for comparison with the DLPA results. The capabilities and inherent uncertainties of both the refined DLPA and TEM methods are compared and discussed in detail. We show that the differences between the density values provided by DLPA and TEM are inherent to the methods and can be reconciled with the interpretation of the data. (authors)

36 MATERIALS SCIENCE↗

Modeling spatial patterns in soil arsenic to estimate natural baseline concentrations

ABSTRACT Arsenic in soil is an important public health concern. Toxicity guidelines and models based on laboratory studies (i.e., U.S. EPA’s Integrated Risk Information System) should consider natural soil As concentrations to avoid unnecessary remediation burdens on society. We used soil and stream sediment samples from the USGS National Geochemical Survey database to assess the spatial distribution of natural As in a 1.16E+5 km2 area. Samples were collected at 348 soil and 144 stream locations, providing approximately one sample for every 290 km2. Sample sites were selected to minimize the potential influence of anthropogenic inputs. Samples were processed using acid digestion of whole samples (concentrated HCl and ascorbic acid) and concentrations were measured using hydride-generation atomic absorption spectrometry. Soil As ranged from 2.0 to 45.6 mg kg-1. Geostatistical techniques were used to model and map the spatial variability of As. The mean and variance at unsampled locations were estimated using sequential Gaussian simulation. Five areas of elevated concentration (> the median of 10 mg kg-1) were identified and the relationships to geologic parent materials, glacial sedimentation patterns, and soil conditions interpreted. Our results showed As concentrations >10 mg kg-1 were common, and >20 mg kg-1 were not unusual for the central and west central portions of Ohio (USA). In contrast, concentrations <4 mg kg-1 were rare. Measured concentrations typically exceeded the soil As human generic screening levels of 0.39 mg/kg (1); the calculated value that corresponds to a cancer risk level of 1 in 1,000,000 for soil ingestion. Because the As content of Ohio soils is similar to many world soils, the USEPA generic soil screening level of 0.39 mg/kg is of little utility. A more useful and practical approach would be the uses of natural background levels. Regional soil As patterns based on geology and biogeochemistry and not political boundaries should be used for soil screening and other risk assessment determinations.

arsenic, background, mapping, geostatistics, toxic↗

Pattern ANalytics To Support High-performance Exploitation and Reasoning (PANTHER)

Sandia researchers are developing analytic techniques that efficiently detect patterns in high-volume, noisy, remote sensing and other geospatial data, improving an analysts’ ability to detect possibly off-normal events in complex homeland security, nuclear weapons, and emerging threat environments. High-consequence, national security decisions rely on timely, comprehensive answers to complex questions, yet critical gaps in our approach to these questions remain. PANTHER addresses these gaps through fundamental research on: geospatial-temporal feature extraction via image segmentation and classification; geospatial-temporal graph algorithms and computational geometry; and domain-relevant models of human perception and cognition informing the design of analytic systems. PANTHER’s cross-disciplinary R&D approach uses fundamental science and mathematics to understand how to maximize decision systems through rethinking key aspects of geospatial data analysis. New methods in motion and trajectory analysis support both rapid search for known trajectories as well as rapid clustering and anomaly detection. Thus, the perceptual and visual load on users is reduced by providing pattern analytics with elegant visual cues to spatial and temporal characteristics.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Development and Industrialization of InGaN/GaN LEDs on Patterned Sapphire Substrates for Low Cost Emitter Architecture

Patterned sapphire substrate (PSS) technology has proven to be an effective approach to improve efficacy and reduce cost of light-emitting diodes (LEDs). The volume emission from the transparent substrate leads to high package efficiency, while the simple and robust architecture of PSS-based LEDs enables low cost. PSS substrates have gained wide use in mid-power LEDs over the past years. In this project, Lumileds has developed and industrialized PSS and epitaxy technology for high- power flip-chip LEDs to bring these benefits to a broader range of applications and accelerate the adoption of energy-efficient solid-state lighting (SSL). PSS geometries were designed for highly efficient light extraction in a flip-chip architecture and high-volume manufacturability, and corresponding sapphire patterning and epitaxy manufacturing processes were integrally developed. Concurrently, device and package architectures were developed to take advantage of the PSS flip-chip die in different types of products that meet application needs. The developed PSS and epitaxy technology has been fully implemented in manufacturing at Lumileds’ San Jose, CA location, and incorporated in illumination-grade LED products that have been successfully introduced to the market, including LUXEON Q and LUXEON FlipChip White.

36 MATERIALS SCIENCE↗

Characteristics and Travel Patterns of New York Residents: Subpopulations of Persons with a Disability in 2009

In this study, Oak Ridge National Laboratory (ORNL) was tasked by the NYS Department of Transportation (DOT) to conduct a detailed examination of travel behaviors, and identify patterns and trends, on several NYS subpopulations, including disabled persons. Unlike other studies that concentrated on national level statistics, this research is focused on examining issues associated with travelers among NYS residents only. For each special subpopulation group, ORNL will identify differences, if any, in travel patterns that are attributable to demographic characteristics, household characteristics, modal characteristics, geographic location, and other concepts. Focus will be given to trip frequency, trip chaining, as well as travel by time of day, trip purpose, and mode choice.

97 MATHEMATICS AND COMPUTING↗

Hotel Room Computational Fluid Dynamics to Investigate Airborne Pathogen Dispersal Patterns

A hotel room unit consisting of a bedroom and bathroom was modelled using computational fluid dynamics (CFD) to investigate airborne pathogen dispersal patterns. The full-scale model includes a ‘typical’ hotel room configuration, furniture, and vents. The air sources and sinks include a bathroom vent, a heating, ventilation, and cooling (HVAC) unit located in the bedroom, and a ½” gap at the bottom of the entry door. In addition, the entry door and window can be opened or closed, as desired. Three key configuration simulations were conducted: 1) both the bathroom vent and HVAC were on, 2) only the HVAC was on, and 3) only the bathroom vent was on. If the HVAC air is from a fresh, clean source, or passes through a high-efficiency filter/UV device, then the first configuration is the safest, as contaminated air is highly reduced. The second configuration is also safe, but does not benefit from the outsourcing of potentially-infected air, such as contaminated air flowing through an ineffective filter. The third configuration should be avoided, as the bathroom vent causes air to flow from the hallway, which can be of dubious origin. The CFD simulations also showed that recirculation and swirling regions tend to accumulate the largest concentrations of heavier airborne particles, pathogens, dust, etc. These regions are associated with the largest turbulence kinetic energy (TKE) , and tend to occur in areas with flow recirculation and corners. Therefore, TKE presents a reasonable metric to guide the strategic location of pathogen mitigation devices. The simulations show complex flow patterns with distinct upper and lower flow regions, swirling flow, and significant levels of turbulent mixing. These simulations provide intriguing insights that can be applied to help mitigate pathogen aerosol dispersal, generate building design guidelines, as well as provide insights for the strategic placement of mitigation devices, such as ultraviolet (UV) light, supplemental fans, and filters.

54 ENVIRONMENTAL SCIENCES↗

Novel In-situ Patterning Technique to Fabricate Single Quantum Dots for Quantum Photonics

Photon sources able to emit single or entangled photon pairs are key components in quantum information systems. Semiconductor quantum dots (QDs) are promising candidates due to their high efficiencies and ease of integration with other photonic or electronic components. State-of-the-art QDs, however, are limited to certain emission wavelengths and specific applications due to material choice constraints and their randomness in shape/size. This project is focused on developing a novel in-situ patterning technique to realize QDs with a broad emission range, shape/size control and the ability to emit single/entangled photons. Our approach has two key elements: (1) In-situ patterning via arsenic-induced nanovoid etching on antimonide surfaces and (2) In-filling of nanovoids to form QDs. By closely controlling the experimental conditions, it is shown that this technique can be used to realize III-V QDs in As 2 - etched nanovoids on a GaSb surface. The exposure to As 2 in terms of substrate temperature, time and flux is found to have a significant impact on the process variables such as nanovoid depth, QD dimensions etc. An in-depth analysis of the etch mechanism reveals that by controlling the As 2 exposure, uniform 3-dimensional nanostructures with varying areal densities can be obtained without an in-filling step. Preliminary optical characterization of these nanostructures shows that these QDs may be relevant for realizing emitters in the telecom wavelength range.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Travel Patterns and Characteristics of Population in Rural Areas of New York State

Travel activities in rural communities tend to be reliant on personal vehicles due to limited public transportation options and long distances to essential services, with demographic factors such as age and income level influencing travel patterns. Addressing transportation challenges in rural New York State (NYS) necessitates an understanding of demographic trends and travel behaviors. This study examines rural households and populations by studying their demographics, mobility patterns, perspectives on transportation services, and how COVID-19 has influenced their transportation-related behaviors.

99 GENERAL AND MISCELLANEOUS↗