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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Benchmark Dose Analysis of DNA Damage Biomarker Responses Provides Compound Potency and Adverse Outcome Pathway Information for the Topoisomerase II Inhibitor Class of Compounds

Genetic toxicology data have traditionally been utilized for hazard identification to provide a binary call for a compound's risk. Recent advances in the scientific field, especially with the development of high‐throughput methods to quantify DNA damage, have influenced a change of approach in genotoxicity assessment. The in vitro MultiFlow® DNA Damage Assay is one such method which multiplexes γH2AX, p53, phospho‐histone H3 biomarkers into a single‐flow cytometric analysis (Bryce et al., [2016]: Environ Mol Mutagen 57:546–558). This assay was used to study human TK6 cells exposed to each of eight topoisomerase II poisons for 4 and 24 hr. Using PROAST v65.5, the Benchmark Dose approach was applied to the resulting flow cytometric datasets. With “compound” serving as covariate, all eight compounds were combined into a single analysis, per time point and endpoint. The resulting 90% confidence intervals, plotted in Log scale, were considered as the potency rank for the eight compounds. The in vitro MultiFlow data showed a maximum confidence interval span of 1Log, which indicates data of good quality. Patterns observed in the compound potency rank were scrutinized by using the expert rule‐based software program Derek Nexus, developed by Lhasa Limited. Compound sub‐classification and structural alerts were considered contributory to the potencies observed for the topoisomerase II poisons studied herein. The Topo II poison Adverse Outcome Pathway was evaluated with MultiFlow endpoints serving as Key Events. The step‐wise approach described herein can be considered as a foundation for risk assessment of compounds within a specific mode of action of interest. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.

Wheeldon, Ryan P.↗
DOE OSTI2024

RandONets: Shallow networks with random projections for learning linear and nonlinear operators

Deep neural networks have been extensively used for the solution of both the forward and the inverse problem for dynamical systems. However, their implementation necessitates optimizing a high-dimensional space of parameters and hyperparameters. This fact, along with the requirement of substantial computational resources, pose a barrier to achieving high numerical accuracy, but also interpretability. Here, to address the above challenges, we present Random Projection-based Operator Networks (RandONets): shallow networks with random projections and tailor-made numerical analysis methods that learn accurately and fast linear and nonlinear operators. Building on previous works, we prove that RandOnets are universal approximators of linear and nonlinear operators. Due to their simplicity, RandONets provide a one-step transformation of the input space, facilitating interpretability. For the evaluation of their performance, we focus on operators of PDEs. We show, that RandONets outperform by several orders of magnitude, both in terms of numerical approximation accuracy and computational cost, the “vanilla” DeepONets. Hence, we believe that our method will trigger further developments in the field of scientific machine learning, for the development of new ‘’light”schemes that will provide high accuracy while reducing dramatically the computational cost. A MATLAB toolbox for RandONets, including demos, is available on GitHub at https://github.com/GianlucaFabiani/RandONets.

Interpretable machine learning↗
DOE OSTI2023

Investigation of local distortion effects on X-ray absorption of ferroelectric perovskites from first principles simulations

Understanding the role of ferroelectric polarization in modulating the electronic and structural properties of crystals is critical for advancing these materials for overcoming various technological and scientific challenges. However, due to difficulties in performing experimental methods with the required resolution, or in interpreting the results of methods therein, the nanoscale morphology and response of these surfaces to external electric fields has not been properly elaborated. Here, in this work, we investigate the effect of ferroelectric polarization and local distortions in a BaTiO 3 perovskite, using two widely used computational approaches which treat the many-body nature of X-ray excitations using different philosophies, namely the many-body, delta-self-consistent-field determinant (mb-ΔSCF) and the Bethe–Salpeter equation (BSE) approaches. We show that in agreement with our experiments, both approaches consistently predict higher excitations of the main peak in the O–K edge for the surface with upward polarization. However, the mb-ΔSCF approach mostly fails to capture the L 2,3 separations at the Ti–L edge, due to the absence of spin–orbit coupling in Kohn–Sham density functional theory (KS-DFT) at the generalized gradient approximation level. On the other hand, and most promising, we show that application of the GW/BSE approach successfully reproduces the experimental XAS, both the relative peak intensities as well as the L 2,3 separations at the Ti–L edges upon ferroelectric switching. Thus simulated XAS is shown to be a powerful method for capturing the nanoscale structure of complex materials, and we underscore the need for many-body perturbation approaches, with explicit consideration of core-hole and multiplet effects, for capturing the essential physics in these systems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Comparative Analysis of Standard and Advanced USL Methodologies for Nuclear Criticality Safety

The American National Standards Institute/American Nuclear Society national standards 8.1 and 8.24 provide guidance on the requirements and recommendations for establishing confidence in the results of the computerized models used to support operation with fissionable materials. By design, the guidance is not prescriptive, leaving freedom to the analysts to determine how the various sources of uncertainties are to be statistically aggregated. Due to the involved use of statistics entangled with heuristic recipes, the resulting safety margins are often difficult to interpret. Also, these technical margins are augmented by additional administrative margins, which are required to ensure compliance with safety standards or regulations, eliminating the incentive to understand their differences. With the new resurgent wave of advanced nuclear systems, e.g., advanced reactors, fuel cycles, and fuel concepts, focused on economizing operation, there is a strong need to develop a clear understanding of the uncertainties and their consolidation methods to reduce them in manners that can be scientifically defended. In response, the current studies compare the analyses behind four notable methodologies for upper subcriticality limit estimation that have been documented in the nuclear criticality safety literature: the parametric, nonparametric, Whisper, and TSURFER methodologies. Specifically, the work offers a deep dive into the various assumptions of the noted methodologies, their adequacies, and their limitations to provide guidance on developing confidence for the emergent nuclear systems that are expected to be challenged by the scarcity of experimental data. Here, to limit the scope, the current work focuses on the application of these methodologies to criticality safety experiments, where the goal is to calculate a bias, a bias uncertainty, and a tolerance limit for k eff in support of determining an upper subcriticality limit for nuclear criticality safety.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2024

Roadmap on methods and software for electronic structure based simulations in chemistry and materials

This Roadmap article provides a succinct, comprehensive overview of the state of electronic structure methods and software for molecular and materials simulations. Seventeen distinct sections collect insights by 51 leading scientists in the field. Each contribution addresses the status of a particular area, as well as current challenges and anticipated future advances, with a particular eye towards software related aspects and providing key references for further reading. Foundational sections cover density functional theory and its implementation in real-world simulation frameworks, Green's function based many-body perturbation theory, wave-function based and stochastic electronic structure approaches, relativistic effects and semiempirical electronic structure theory approaches. Subsequent sections cover nuclear quantum effects, real-time propagation of the electronic structure, challenges for computational spectroscopy simulations, and exploration of complex potential energy surfaces. The final sections summarize practical aspects, including computational workflows for complex simulation tasks, the impact of current and future high-performance computing architectures, software engineering practices, education and training to maintain and broaden the community, as well as the status of and needs for electronic structure based modeling from the vantage point of industry environments. Overall, the field of electronic structure software and method development continues to unlock immense opportunities for future scientific discovery, based on the growing ability of computations to reveal complex phenomena, processes and properties that are determined by the make-up of matter at the atomic scale, with high precision.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

Summary As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

NCCS High Performance GMRES Mixed Precision

HPG-MxP is a software package that performs a fixed number of multigrid preconditioned (using a Gauss-Seidel smoother) Generalized minimal residual (PGMRES) iterations in order to solve a possibly nonsymmetric large sparse linear system of equations. It is designed to be a benchmark to measure a computer's performance for sparse linear algebra workloads typical in scientific computing while allowing the use of mixed precision methods. The solution is required to have convergence characteristics and accuracy similar to double precision GMRES. It is based on the High Performance Conjugate Gradient Benchmark (HPCG) which restricts all implementations to use only the IEEE double precision format (FP64). The original implementation (https://github.com/hpg-mxp/hpg-mxp) was written by Ichitaro Yamazaki, Jennifer Loe, Christian Glusa, Sivasankaran Rajamanickam, Piotr Luszczek, and Jack Dongarra. Please refer to that repository for documentation on the original implementation. This version is maintained by the National Center for Computational Sciences at Oak Ridge National Laboratory. It is highly scalable and optimized for Oak Ridge Leadership Computing Facility (OLCF) systems, particularly Frontier.

Kashi, Aditya [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2020

Information Content of JWST NIRSpec Transmission Spectra of Warm Neptunes

Warm Neptunes offer a rich opportunity for understanding exo-atmospheric chemistry. With the upcoming James Webb Space Telescope (JWST), there is a need to elucidate the balance between investments in telescope time versus scientific yield. We use the supervised machine-learning method of the random forest to perform an information content (IC) analysis on a 11-parameter model of transmission spectra from the various NIRSpec modes. The three bluest medium-resolution NIRSpec modes (0.7–1.27 μm, 0.97–1.84 μm, 1.66–3.07 μm) are insensitive to the presence of CO. The reddest medium-resolution mode (2.87–5.10 μm) is sensitive to all of the molecules assumed in our model: CO, CO{sub 2}, CH{sub 4}, C{sub 2}H{sub 2}, H{sub 2}O, HCN, and NH{sub 3}. It competes effectively with the three bluest modes on the information encoded on cloud abundance and particle size. It is also competitive with the low-resolution prism mode (0.6–5.3 μm) on the inference of every parameter except for the temperature and ammonia abundance. We recommend astronomers to use the reddest medium-resolution NIRSpec mode for studying the atmospheric chemistry of 800–1200 K warm Neptunes; its corresponding high-resolution counterpart offers diminishing returns. We compare our findings to previous JWST IC analyses that favor the blue orders and suggest that the reliance on chemical equilibrium could lead to biased outcomes if this assumption does not apply. A simple, pressure-independent diagnostic for identifying chemical disequilibrium is proposed based on measuring the abundances of H{sub 2}O, CO, and CO{sub 2}.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1973

The Space Shuttle System description, operations, and payload capabilities

General characteristics of the Space Shuttle System are presented with overall capabilities and operating characteristics detailed. Mission operations and performance baselines are presented. The relationships between orbital parameters and payload capabilities are highlighted. On-orbit scientific and applications operating modes are briefly reviewed and methods of achieving a versatile payloads program using standard payload carriers are discussed.

Heberlig, J. C.↗
NASA NTRS1985

An estimate of the outgassing of space payloads, their internal pressures, contaminations and gaseous influences on the environment

Experimentally measured outgassing as a function of time is presented for 14 space systems including several spacecraft instruments, spacecraft, the shuttle bay, and a spent solid fuel motor. The weights, volumes, and some of the scientific functions of the instruments involved are indicated. The methods used to obtain the data are briefly described. General indications on how to use the data to obtain the internal pressure versus time for a payload, its self-contamination, the gaseous flow in its vicinity, the column densities in its field of view, and other environmental parameters which are dependent on the outgassing of a payload are provided.

Scialdone, J. J.↗
NASA NTRS1992

Global magnetospheric imaging

The demonstrated and developing methods for global magnetospheric imaging are presented and the scientific expectations of having global observations in conjunction with local measurements are discussed. The global observations of the previously invisible magnetosphere will provide the first look at the overall magnetosphere, its dynamics, and the interactions between its component parts. The capability of imaging magnetospheric plasmas marks the first occasion where an astrophysical plasma system which has been well characterized by in situ measurements, i.e., the earth's magnetosphere, can also be characterized globally by remote sensing.

Williams, D. J.↗
NASA NTRS1989

Lunar deep drill apparatus

Proposed as a baseline configuration, this rotary drill apparatus is designed to produce 100-mm diameter holes in the lunar surface at depths up to 50 meters. The drill is intended to acquire samples for scientific analysis, mineral resource location, calibration of electronic exploration devices, and foundation analysis at construction sites. It is also intended to prepare holes for emplacement of scientific instruments, the setting of structural anchors, and explosive methods in excavation and mining activities. Defined as a deep drill because of the modular drill string, it incorporates an automatic rod changer. The apparatus is teleoperated from a remote location, such as earth, utilizing supervisory control techniques. It is thus suitable for unmanned and man-tended operation. Proven terrestrial drilling technology is used to the extent it is compatible with the lunar environment. Augers and drive tubes form holes in the regolith and may be used to acquire loose samples. An inertial cutting removal system operates intermittently while rock core drilling is in progress. The apparatus is carried to the work site by a three-legged mobile platform which also provides a 2-meter feed along the hole centerline, an off-hole movement of approximately .5 meters, an angular alignment of up to 20 deg. from gravity vertical, and other dexterity required in handling rods and samples. The technology can also be applied using other carriers which incorporate similar motion capabilities. The apparatus also includes storage racks for augers, rods, and ancillary devices such as the foot-plate that holds the down-hole tooling during rod changing operations.

Source record↗
NASA NTRS1994

A land-surface Testbed for EOSDIS

The main objective of the Testbed project was to deliver satellite images via the Internet to scientific and educational users free of charge. The main method of operations was to store satellite images on a low cost tape library system, visually browse the raw satellite data, access the raw data filed, navigate the imagery through 'C' programming and X-Windows interface software, and deliver the finished image to the end user over the Internet by means of file transfer protocol methods. The conclusion is that the distribution of satellite imagery by means of the Internet is feasible, and the archiving of large data sets can be accomplished with low cost storage systems allowing multiple users.

Emery, William↗
NASA NTRS1994

CELSS Antarctic Analog Project (CAAP): A New Paradigm for Polar Life Support and CELSS Research

The CELSS Antarctic Analog Project (CAAP) is a joint National Science Foundation (NSF) and National Aeronautics and Space Administration (NASA) project for the development, deployment and operation of CELSS technologies at the Amundsen-Scott South Pole Station. CAAP is implemented through the joint NSF/NASA Antarctic Space Analog Program (ASAP), initiated to support the pursuit of future NASA missions and to promote the transfer of space technologies to the NSF. Under a Memorandum of Agreement, the CAAP represents an example of a working dual agency cooperative project. NASA goals are operational testing of CELSS technologies and the conduct of scientific study to facilitate . technology selection, system design and methods development, including human dynamics as required for the operation of a CELSS. Although not fully closed, food production, water purification, and waste recycle and reduction provided by CAAP will improve the quality of life for the South Pole inhabitants, reduce logistics dependence, and minimize environmental impacts associated with human presence on the polar plateau. The CAAP facility will be highly integrated with the new South Pole Station infrastructure and will be composed of a deployed hardware facility and a research activity. This paper will include a description of CAAP and its functionality, conceptual designs, component selection and sizing for the crop growth chamber, crop production expectations, and a brief report on an initial on-site visit. This paper will also provide a discussion of issues associated with power and energy use and the applicability of CAAP to direct technology transfer to society in general and remote communities in particular.

Bubenheim, David L.↗
NASA NTRS2005

Atmospheric Hydroperoxides in West Antarctica: Links to Stratospheric Ozone and Atmospheric Oxidation Capacity

The troposphere above the West Antarctic Ice Sheet (WAIS) was sampled for hydroperoxides at 21 locations during 2-month-long summer traverses from 2000 to 2002, as part of US ITASE (International Transantarctic Scientific Expedition). First time quantitative measurements using an HPLC method showed that methylhydroperoxide (MHP) is the only important organic hydroperoxide occurring in the Antarctic troposphere, and that it is found at levels ten times those previously predicted by photochemical models. During three field seasons, means and standard deviations for hydrogen peroxide (H2O2) were 321+/-158 pptv, 650+/-176 pptv and 330+/-147 pptv. While MHP was detected, but not quantified in December 2000, levels in summer 2001 and 2002 were 317+128 pptv and 304+/-172.2 pptv. Results from firn air experiments and diurnal variability of the two species showed that atmospheric H2O2 is significantly impacted by a physical snow pack source between 76 and 90degS, whereas MHP is not. We show strong evidence of a positive feedback between stratospheric ozone and H2O2 at the surface. Between November-27 and December-12 in 2001, when ozone column densities dropped below 220 DU (means in 2000 and 2001 were 318 DU and 334 DU, respectively), H2O2 was 1.7 times that observed in the same period in 2000 and 2002, while MHP was only 80% of the levels encountered in 2002. Photochemical box model runs suggest that NO and OH levels on WAIS are closer to coastal values, while Antarctic Plateau levels are higher, confirming that region to be a highly oxidizing environment. The modeled sensitivity of H2O2 and particularly MHP to NO offers the potential to use atmospheric hydroperoxides to constrain the NO background and thus estimate the past oxidation capacity of the remote atmosphere. Index Terms: 0365 Atmospheric Composition and Structure: Troposphere: composition and chemistry; 0322 Atmospheric Composition and Structure: Constituent sources and sinks; 1610 Global Change: Atmosphere (03 15,0325); 0736 Cryosphere: Snow (1827, 1863); 0724 Cryosphere: Ice Cores (4932) Keywords: hydrogen peroxide, methylhydroperoxide, Antarctica, air-snow exchange, stratospheric ozone, atmospheric oxidation capacity

Frey, Markus M.↗
NASA NTRS2013

Potassium Isotopic Compositions of NIST Potassium Standards and 40Ar/39Ar Mineral Standards

Knowledge of the isotopic ratios of standards, spikes, and reference materials is fundamental to the accuracy of many geochronological methods. For example, the 238U/235U ratio relevant to U-Pb geochronology was recently re-determined [1] and shown to differ significantly from the previously accepted value employed during age determinations. These underlying values are fundamental to accurate age calculations in many isotopic systems, and uncertainty in these values can represent a significant (and often unrecognized) portion of the uncertainty budget for determined ages. The potassium isotopic composition of mineral standards, or neutron flux monitors, is a critical, but often overlooked component in the calculation of K-Ar and 40Ar/39Ar ages. It is currently assumed that all terrestrial materials have abundances indistinguishable from that of NIST SRM 985 [2]; this is apparently a reasonable assumption at the 0.25per mille level (1σ) [3]. The 40Ar/39Ar method further relies on the assumption that standards and samples (including primary and secondary standards) have indistinguishable 40K/39K values. We will present data establishing the potassium isotopic compositions of NIST isotopic K SRM 985, elemental K SRM 999b, and 40Ar/39Ar biotite mineral standard GA1550 (sample MD-2). Stable isotopic compositions (41K/39K) were measured by the peak shoulder method with high resolution MC-ICP-MS (Thermo Scientific NEPTUNE Plus), using the accepted value of NIST isotopic SRM 985 [2] for fractionation [4] corrections [5]. 40K abundances were measured by TIMS (Thermo Scientific TRITON), using 41K/39K values from ICP-MS measurements (or, for SRM 985, values from [2]) for internal fractionation corrections. Collectively these data represent an important step towards a metrologically traceable calibration of 40K concentrations in primary 40Ar/39Ar mineral standards and improve uncertainties by ca. an order of magnitude in the potassium isotopic compositions of standards.

Morgan, Leah↗
NASA NTRS2001

Strategies for Engaging NASA Earth Scientists in K-12 Education and Public Outreach

Engagement of the Earth Science research community in formal education at the kindergarten through high school level and in various aspects of informal education and in professional development of practitioners in related fields has been and continues to be a challenge. A range of approaches is being used and new ones are constantly being tried. Fundamental to our strategies is an understanding of the priorities, skills, academic experiences, motivation, rewards and work experiences of most scientists. It is within this context that efforts to engage a scientist in education efforts are attempted. A key strategy is to limit our requests to activities where the scientist's contribution of time and expertise can have the most impact. Don't waste the scientist's time! Time is one of their most prized resources, it is extremely valuable to you, and to them, we treat their time like a treasured resource. The clearer a scientist's role, their unique contribution and the finite nature of their effort, the more likely they are to participate. It is critical that commitments made to scientists are kept. If they want and can do more, great! Don't expect or assume more will be forthcoming. Another approach that we use is to create periodic venues that, among other things, serve to identify individuals who have an interest or inclination to con , tribute to education efforts. Once identified we strive to determine their interests so that we can make the best match between their interests and the needs of the education program or efforts. In this way, we try to make the best use of their time while engaging them in efforts which will be personally rewarding, and will further the overall education objectives. In addition, we try to make it easier for scientists to participate by providing focused training, such as development of their interviewing skills, and exposure to key concepts, knowledge and skills which are well known among educators but are not common knowledge among scientists. Another strategy with which we are still struggling is how to create and provide career meaningful rewards for individuals who demonstrate excellence in education equivalent to excellence in science. We do not yet have a yardstick to measure excellence in education nor is there a consensus among scientific peers that these two can be equivalent. None-the-less, methods to identify excellence in education, such as the peer review process, are being tried with some success. Use of solicitation and selection of educational efforts via a peer review process that is the same as for scientific research to identify unique, interesting and creative ideas has been somewhat effective. Furthermore, the application of the same peer review process to the output of an educational effort is used to validate and ensure the quality of this output. An example will be used to illustrate the application of some of these strategies to the development of a high school Earth and Space System Science curriculum created in partnership with a local county school system (Anne Arundel County, MD).

Meeson, Blanche W.↗
DOE OSTI2020

Threat Reduction Research Networks: Fostering Sustainable Collaborations Through Trainings for Genomics for Biosurveillance

Scientific research communities can be represented as heterogeneous or multidimensional networks encompassing multiple types of entities and relationships. These networks might include researchers, institutions, meetings, and publications, connected by relationships like authorship, employment, and attendance. We describe a method for efficiently and flexibly capturing, storing, and extracting information from multidimensional scientific networks using a graph database. The database structure is based on an ontology that captures allowable types of entities and relationships. This allows us to construct a variety of projections of the underlying multidimensional graph through database queries to answer specific research questions. We demonstrate this process through a study of the U.S. Biological Threat Reduction Program (BTRP), which seeks to develop Threat Reduction Networks to build and strengthen a sustainable international community of biosecurity, biosafety, and biosurveillance experts to address shared biological threat reduction challenges. Networks like these create connectional intelligence among researchers and institutions around the world, and are central to the concept of cooperative threat reduction. Our analysis focuses on a series of seven BTRP genome sequencing training workshops, showing how they created a growing network of participants and countries over time, which is also reflected in coauthorship relationships among attendees. By capturing concept and relationship hierarchies, our ontology-based approach allows us to pose general or specific questions about networks within the same framework. This approach can be applied to other research communities or multidimensional social networks to capture, analyze, and visualize different types of interactions and how they change over time.

59 BASIC BIOLOGICAL SCIENCES↗