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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Race conditions and data partitioning: risks posed by common errors to reproducible parallel simulations

When parallel algorithms for simulation were introduced in the 1970s, their development and use interested only experts in parallel computation. This circumstance changed as multi-core processors became commonplace, putting a parallel computer into the hands of every modeler. A natural outcome is growing interest in parallel simulation among persons not intimately familiar with parallel computing. At the same time, parallel simulation tools continue to be developed with the implicit assumption that the modeler is knowledgeable about parallel programming. The unintended consequence is a rapidly growing number of users of parallel simulation tools that are unlikely to recognize when the interaction of race conditions, partitioning strategies, and simultaneous action in their simulation models make results non-reproducible, thereby calling into question the validity of conclusions drawn from the simulation data. Here, we illustrate the potential dangers of exposing parallel algorithms to users who are not experts in parallel computation with example models constructed using existing parallel simulation tools. By doing so, we hope to refocus tool developers on usability, even if this new focus incurs loss of some performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Semi-Automatic Geographic Information System Framework for Creating Photo-Realistic Digital Twin Cities to Support Autonomous Driving Research

Digital twin cities are frequently used in vehicle and traffic simulations to render realistic on-road driving scenarios under various traffic and environmental conditions. These digital twins provide a high-fidelity replica of the physical world (e.g., buildings, roads, infrastructures, traffic) to create three-dimensional (3D) virtual-physical environments to support various emerging vehicle and transportation technologies such as connected and automated vehicles. These virtual environments provide a cost-effective digital proving ground to evaluate, validate, and test emerging technologies that include control algorithms, localization, perception, and sensors. Replicating a real-world traffic scenario in a digital twin using a traditional 3D modeling approach is a time-consuming and labor-intensive effort. Here this paper presents a semi-automated spatial framework to construct realistic 3D digital twin cities to support autonomous driving research using readily available geographic information system (GIS) data and 3D prefabricated (prefab) models. We start with a comprehensive review of geospatial data sources of essential digital entities required in a 3D digital twin city and present an integrated GIS-3D modeling pipeline using customized QGIS/GDAL and Blender scripting in Python. The pipeline outputs are realistic 3D digital twin cities compatible with common vehicle simulation software, such as CARLA and IPG CarMaker. The paper closes with a showcase to demonstrate the quality and usability of a digital twin city created to replicate the Shallowford Road corridor in Chattanooga in both Unity and Unreal engine-based virtual environment. The generated digital twin city can be applied to a hardware-in-the-loop simulation environment with an actual testing vehicle to facilitate autonomous driving research.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Human Factors Evaluation of Energy Visualization Dashboards

Energy visualization systems provide information about use in real-time to assist users with energy efficiency. In this study, three energy visualization dashboards for small businesses were developed and tested. Performance measurement, NASA Task Load Index (TLX) workload assessment, and posttest survey were used to conduct the usability testing. Compared with the dashboards that were designed using line charts and tables, a dashboard designed using visuals (e.g., gauges, pie charts, and flashing lights) produced quicker response time, lower mental and temporal demand and effort ratings, and higher ratings of engagement, interest, and trustworthiness.

Nimbarte, Ashish D. (ORCID:0000000210599112)↗
DOE OSTI2024

Assessment of Electric Grid Transmission System Simulator for Human Factors Research

Over the past decades, various technologies have been developed for electric grid operations to support clean energy, meet rising electricity demands, and address infrastructure concerns. However, the human factors aspect is often overlooked during rapid integration. Questions persist about how these technologies impact human performance. Simulators play a critical role in supporting investigation of human factors design concepts and conducting comprehensive usability testing to evaluate human performance and assess human reliability. This paper aims to address human factors research simulator requirements and conduct a comparative study of six different simulators. A detailed evaluation reveals that the evaluated simulators lack the ability to customize user interfaces. Additionally, their user interface designs do not fulfill the basic human factors design principles, potentially leading to increased response variability and reduced statistical power when conducting controlled experimental research. In the future, it is essential to develop scripting tools to integrate customizable user interfaces and simulation models, ensuring meeting research requirements.

Li, Ruixuan↗
DOE OSTI2023

HUMAN-ARTIFICIAL INTELLIGENCE TEAMING FOR THE U.S. NAVY: DEVELOPING A HOLISTIC RESEARCH ROADMAP

With the ever-increasing deluge of data and demand for warfighters to make decisions upon its analysis, U.S. defense strategy has prioritized the development of artificial intelligence (AI)/machine learning (ML) systems that can analyze multi-source data streams and suggest courses of action. However, there is a history of systems that have failed to be adopted by the warfighter due not only to unsolved technical challenges, but also a lack of usability or contributions to mission effectiveness, perceived or otherwise. To avoid this, research into human-AI teaming shows promise for developing AI systems that work with frontline operators. A recent National Academies of Sciences, Engineering, and Medicine report (NASEM, 2022) presented 57 research objectives in this area; however, the U.S. Navy requires a more-focused set of priorities, as it is impossible to tackle every priority. A workshop involving 23 human factors scientists, computer scientists, and active-duty sailors was organized at the Naval Information Warfare Center Pacific, resulting in a set of five research priorities spanning near-, mid-, and far-term time frames. This panel will summarize the results of this workshop, with a focus on the big questions both going into this workshop and coming out of it. The panel participants come from government, academia, and industry, providing perspective from the different kinds of organizations required to accomplish these research goals.

Wong, Jason↗
DOE OSTI2016

Programmer-guided reliability for extreme-scale applications

We present “programmer-guided reliability” (PGR) as a systematic conceptual approach to address the expected rise in soft errors in coming extreme-scale systems at the application level. The approach involves instrumentation of the application with code to detect data corruption errors. The location and nature of these error detectors are at the discretion of the programmer, who uses their knowledge and experience with the problem domain, the application, the solution algorithms, etc., to determine the most vulnerable areas of the code and the most appropriate ways to detect data corruption. To illustrate the approach, we provide examples of error detectors from four different benchmark-scale applications. We also describe a simple control framework that allows for runtime configuration of the error detectors without recompilation of the application, as well as dynamic reconfiguration during the execution of the application. Lastly, we discuss a number of future directions building on the basic PGR approach, including the incorporation of some general error detectors into the programming environment in order to make them more easily usable by the programmer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Human factors design, verification, and validation for two types of control room upgrades at a nuclear power plant

This paper describes the NUREG-0711 based human factors engineering (HFE) phases and associated elements required to support design, verification and validation (V&V), and implementation of a new plant process computer (PPC) and turbine control system (TCS) at a representative nuclear power plant. This paper reviews ways to take a human-system interface (HSI) specification and use it when migrating legacy PPC displays or designing displays with new functionality. These displays undergo iterative usability testing during the design phase and then undergo an integrated system validation (ISV) in a full scope control room training simulator. Following the successful demonstration of operator performance with the systems during the ISV, the new system is implemented at the plant, first in the training simulator and then in the main control room.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2014

Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro . The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. We used a combination of comparative genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7 . A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro . Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon. Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.

09 BIOMASS FUELS↗
DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

WTFgenes: What's The Function of these genes? Static sites for model-based gene set analysis

A common technique for interpreting experimentally-identified lists of genes is to look for enrichment of genes associated with particular ontology terms. The most common test uses the hypergeometric distribution; more recently, a model-based test was proposed. These approaches must typically be run using downloaded software, or on a server. We develop a collapsed likelihood for model-based gene set analysis and present WTFgenes, an implementation of both hypergeometric and model-based approaches, that can be published as a static site with computation run in JavaScript on the user's web browser client. Apart from hosting files, zero server resources are required: the site can (for example) be served directly from Amazon S3 or GitHub Pages. A C++11 implementation yielding identical results runs roughly twice as fast as the JavaScript version. WTFgenes is available from https://github.com/evoldoers/wtfgenes under the BSD3 license. A demonstration for the Gene Ontology is usable at https://evoldoers.github.io/wtfgo.

Mungall, Christopher J.↗
DOE OSTI2026

Data for Mitochondrial ATP Generation is More Proteome Efficient than Glycolysis

Metabolic efficiency profoundly influences organismal fitness. Heterotrophs, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. While respiration is more energy-efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (i.e. faster). Through quantitative flux analysis and proteomics, we find however that mitochondrial respiration is actually more proteome-efficient than aerobic glycolysis. This is shown across yeasts, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which is valuable for hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth, but outgrow respiratory cells in oxygen limitation. Thus, aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.

Metabolomics↗
DOE OSTI2022

Tissue-mimicking phantoms for performance evaluation of photoacoustic microscopy systems

Phantom-based performance test methods are critically needed to support development and clinical translation of emerging photoacoustic microscopy (PAM) devices. While phantoms have been recently developed for macroscopic photoacoustic imaging systems, there is an unmet need for well-characterized tissue-mimicking materials (TMMs) and phantoms suitable for evaluating PAM systems. Our objective was to develop and characterize a suitable dermis-mimicking TMM based on polyacrylamide hydrogels and demonstrate its utility for constructing image quality phantoms. TMM formulations were optically characterized over 400–1100 nm using integrating sphere spectrophotometry and acoustically characterized using a pulse through-transmission method over 8–24 MHz with highly confident extrapolation throughout the usable band of the PAM system. This TMM was used to construct a spatial resolution phantom containing gold nanoparticle point targets and a penetration depth phantom containing slanted tungsten filaments and blood-filled tubes. These phantoms were used to characterize performance of a custom-built PAM system. The TMM was found to be broadly tunable and specific formulations were identified to mimic human dermis at an optical wavelength of 570 nm and acoustic frequencies of 10–50 MHz. Imaging results showed that tungsten filaments yielded 1.1–4.2 times greater apparent maximum imaging depth than blood-filled tubes, which may overestimate real-world performance for vascular imaging applications. Nanoparticles were detectable only to depths of 120–200 µm, which may be due to the relatively weaker absorption of single nanoparticles vs. larger targets containing high concentration of hemoglobin. The developed TMMs and phantoms are useful tools to support PAM device characterization and optimization, streamline regulatory decision-making, and accelerate clinical translation.

Hsu, Hsun-Chia↗
DOE OSTI2016

Concerning the Spatial Heterodyne Spectrometer

A modified Spatial Heterodyne Spectrometer (SHS) is used for measuring atomic emission spectra with high resolution. This device is basically a Fourier Transform Spectrometer, but the Fourier transform is taken in the directions perpendicular to the optical propagation and heterodyned around one preset wavelength. In recent descriptions of this device, one specific phenomenon - the tilt of the energy front of wave packets when diffracted from a grating - was neglected. This led to an overestimate of the resolving power of this spectrograph, especially in situations when the coherence length of the radiation under test is in the order of the effective aperture of the device. In conclusion, the limits of usability are shown here together with some measurements of known spectral lines.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Deterministic stabilization of eight-way 2D diffractive beam combining using pattern recognition

We demonstrate a new method for controlling diffractive, high-power beam combination, sensing phase errors by analyzing the intensity pattern of uncombined side beams at the output. A square array of eight beams is combined with <0.3% stability and 84.6% efficiency. As the channel count is increased, so does the usable information, enabling scaling to large channel counts without significant slowing of control loop response time, an advantage over single-input algorithms.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Offset lock with a 440-GHz range using electro-optic modulation

Offset locking is crucial to many physics experiments. Wide range offset locks are desirable, as they increase the span of usable frequencies in an experiment. Here, we experimentally realize a wide-range offset lock using a beat-note setup combined with electro-optic phase modulation. By using frequency down-conversion of the beat note and locking to sidebands generated by electro-optic modulation, we achieve an offset range of ± 220.1 GHz with offset frequency fluctuations under 0.1 Hz and a phase error variance of 0.017 rad 2 over a 100 kHz bandwidth, greatly widening the range compared to past setups using this method. The relative simplicity of our setup provides a compelling method for locking at offsets in the hundreds of GHz range.

Zhou, Ocean (ORCID:0000000279192636)↗
DOE OSTI2023

Scaling comb-driven resonator-based DWDM silicon photonic links to multi-Tb/s in the multi-FSR regime

The use of chip-based micro-resonator Kerr frequency combs in conjunction with dense wavelength-division multiplexing (DWDM) enables massively parallel intensity-modulated direct-detection data transmission with low energy consumption. Resonator-based modulators and filters used in such systems can limit the number of usable wavelength channels due to practical constraints on the maximum achievable free spectral range (FSR). In this work, we introduce the design of multi-Tb/s comb-driven resonator-based silicon photonic links by leveraging the multi-FSR regime. We demonstrate the viability of the link architecture with yield estimates that are supported by extensive wafer-scale measurements of 704 micro-resonators fabricated in a commercial complementary metal–oxide–semiconductor foundry. We show that a 2.80 Tb/s link is realizable with a ≥6 σ yield (∼99.999%), and that aggregate bandwidths of 3.76 Tb/s and 4.72 Tb/s are possible if yield targets are relaxed (3 σ and 1 σ , respectively). All designs represent a 1.94−3.28× boost to aggregate link bandwidth while maintaining BER≤10 −10 performance, with a theoretical bandwidth of 10.51 Tb/s being possible for sufficiently robust resonators. We use high-speed BER measurements to inform co-optimization of data rate and aggressor spacing ( λ ag ), limiting any additional loss-based power penalties to off-resonance insertion loss (IL) and routing loss. This work demonstrates that, through the multi-FSR regime, there is a clear path toward Kerr comb-driven ultra-broadband, high bandwidth silicon photonic links that can support next-generation data centers and high-performance computers.

James, Aneek (ORCID:0000000262527807)↗
DOE OSTI2014

Genetic Basis of Metabolome Variation in Yeast

Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Modeling magnetic fields from a DC power cable buried beneath San Francisco Bay based on empirical measurements

Here, the Trans Bay Cable (TBC) is a ±200-kilovolt (kV), 400 MW 85-km long High Voltage Direct Current (DC) buried transmission line linking Pittsburg, CA with San Francisco, CA (SF) beneath the San Francisco Estuary. The TBC runs parallel to the migratory route of various marine species, including green sturgeon, Chinook salmon, and steelhead trout. In July and August 2014, an extensive series of magnetic field measurements were taken using a pair of submerged Geometrics magnetometers towed behind a survey vessel in four locations in the San Francisco estuary along profiles that cross the cable’s path; these included the San Francisco-Oakland Bay Bridge (BB), the Richmond-San Rafael Bridge (RSR), the Benicia- Martinez Bridge (Ben) and an area in San Pablo Bay (SP) in which a bridge is not present. In this paper, we apply basic formulas that ideally describe the magnetic field from a DC cable summed vectorially with the background geomagnetic field (in the absence of other sources that would perturb the ambient field) to derive characteristics of the cable that are otherwise not immediately observable. Magnetic field profiles from measurements taken along 170 survey lines were inspected visually for evidence of a distinct pattern representing the presence of the cable. Many profiles were dominated by field distortions unrelated to the cable caused by bridge structures or other submerged objects, and the cable’s contribution to the field was not detectable. BB, with 40 of the survey lines, did not yield usable data for these reasons. The unrelated anomalies could be up to 100 times greater than those from the cable. In total, discernible magnetic field profiles measured from 76 survey lines were regressed against the equations, representing eight days of measurement. The modeled field anomalies due to the cable (the difference between the maximum and minimum field along the survey line at the cable crossing) were virtually identical to the measured values. The modeling yielded a pooled cable depth below the bay floor of 2.06 m (±1.46 std dev), and estimated the angle to the horizontal of the imaginary line connecting the crosssectional center of the cable’s two conductors (0.1143 m apart) as 178.9° ±61.9° (std dev) for Ben, 78.6°±37.0° (std dev) for RSR, and 139.9°±27.4° (std dev) for SP. The mean of the eight daily average currents derived from the regressions was 986 ±185 amperes (A) (std dev), as compared to 722 ±95 A (std dev) provided by Trans Bay Cable LLC. Overall, the regressions based on fundamental principles (Biot Savart law) and the vectorial summation of cable and geomagnetic fields provide estimates of cable characteristics consistent with plausible expectations.

54 ENVIRONMENTAL SCIENCES↗