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DOE OSTI2015

SPECTROSCOPIC SIGNATURES RELATED TO A SUNQUAKE

The presence of flare-related acoustic emission (sunquakes (SQs)) in some flares, and only in specific locations within the flaring environment, represents a severe challenge to our current understanding of flare energy transport processes. In an attempt to contribute to understanding the origins of SQs we present a comparison of new spectral observations from Hinode’s EUV imaging Spectrometer (EIS) and the Interface Region Imaging Spectrograph (IRIS) of the chromosphere, transition region, and corona above an SQ, and compare them to the spectra observed in a part of the flaring region with no acoustic signature. Evidence for the SQ is determined using both time–distance and acoustic holography methods, and we find that unlike many previous SQ detections, the signal is rather dispersed, but that the time–distance and 6 and 7 mHz sources converge at the same spatial location. We also see some evidence for different evolution at different frequencies, with an earlier peak at 7 mHz than at 6 mHz. Using EIS and IRIS spectroscopic measurements we find that in this location, at the time of the 7 mHz peak the spectral emission is significantly more intense, shows larger velocity shifts and substantially broader profiles than in the location with no SQ, and there is a good correlation between blueshifted, hot coronal, hard X-ray (HXR), and redshifted chromospheric emission, consistent with the idea of a strong downward motion driven by rapid heating by nonthermal electrons and the formation of chromospheric shocks. Exploiting the diagnostic potential of the Mg ii triplet lines, we also find evidence for a single large temperature increase deep in the atmosphere, which is consistent with this scenario. The time of the 6 mHz and time–distance peak signal coincides with a secondary peak in the energy release process, but in this case we find no evidence of HXR emission in the quake location, instead finding very broad spectral lines, strongly shifted to the red, indicating the possible presence of a significant flux of downward propagating Alfvén waves.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

DOE OSTI2014

Determination of electron-nucleus collisions geometry with forward neutrons

There are a large number of physics programs one can explore in electron-nucleus collisions at a future electron-ion collider. Collision geometry is very important in these studies, while the measurement for an event-by-event geometric control is rarely discussed in the prior deep-inelastic scattering experiments off a nucleus. This paper seeks to provide some detailed studies on the potential of tagging collision geometries through forward neutron multiplicity measurements with a zero degree calorimeter. As a result, this type of geometry handle, if achieved, can be extremely beneficial in constraining nuclear effects for the electron-nucleus program at an electron-ion collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

FEHM V3.0 - V3.X

The numerical background of the FEHM computer code can be traced to the early 1970s when it was used to simulate geothermal and hot dry rock reservoirs. The primary use over a number of years was to assist in the understanding of flow fields and mass transport in the saturated and unsaturated zones below the potential Yucca Mountain repository. Today FEHM is used to simulate groundwater and contaminant flow and transport in deep and shallow, fractured and un-fractured porous media throughout the US DOE complex. FEHM has proved to be a valuable asset on a variety of projects of national interest including Environmental Remediation of the Nevada Test Site, the LANL Groundwater Protection Program, geologic CO2 sequestration, Enhanced Geothermal Energy (EGS) programs, Oil and Gas production, Nuclear Waste Isolation, and Arctic Permafrost. Subsurface physics has ranged from single fluid/single phase fluid flow when simulating basin scale groundwater aquifers to complex multifluid/ multi-phase fluid flow that includes phase change with boiling and condensing in applications such as unsaturated zone surrounding nuclear waste storage facility or leakage of CO2/brine through faults or wellbores. The numerical method used in FEHM is the control volume method (CV) for fluid flow and heat transfer equations which allows FEHM to exactly enforce energy/mass conservation; while an option is available to use the finite element (FE) method for displacement equations to obtain more accurate stress calculations. In addition to these standard methods, an option to use FE for flow is available, as well as a simple Finite Difference scheme.

Pawar, Rajesh↗

DOE OSTI2021

HangulFonts v1.0.0

The software creates the Hangul Fonts data set.The Hangul Fonts Datasets consists of all possible blocks for each font along with a set of labels and features for each block which are common across all fonts. We provide scripts to render each block and font into an image and store them together in an HDF5 file for each font and fontsize specified. Each font has 11,172 possible blocks and we have curated 35 fonts for a total of 391,020 possible images. The spoken consonants and vowel correspond to a set of "initial", "medial", and "final" labels for each block with 19, 21, and 28 classes respectively. In addition, each block can also be assigned a hierarchy label based on the block geometry. Finally, the individual glyphs (atoms) are composed across the initial, medial, and final locations along with potential scalings, translations, or rotations. These features of the data set make it uniquely positioned in the deep representation learning field because of its compositionally and hierarchical organization, while retaining diverse types of variation in the realizations.

Bouchard, Kristofer↗

DOE OSTI2019

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Background: Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c-type cytochromes, which are crucial for their respiratory versatility. In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, are investigated in S. oneidensis MR-1. Result: In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1ΔhemH1ΔhemH2, which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1ΔhemH1 mutant to compensate for the loss of hemH1. The periplasmic glutathione peroxidase gene pgpD, located in the same operon with hemH2, and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion: Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Geological Disposal of Nuclear Waste in Tuff: Yucca Mountain (USA) [Geological Disposal in Tuff: Yucca Mountain]

For more than three decades, the US Department of Energy has investigated the potential for permanent disposal of high-level radioactive waste and spent nuclear fuel in a deep-mined repository at Yucca Mountain, Nevada (USA). A detailed license application submitted to the US Nuclear Regulatory Commission in 2008 provides full documentation of the case for permanent disposal of nuclear waste in tuff. Furthermore, the aridity of the site and great depth to the water table provide a disposal environment and a design concept unique among deep-mined repositories currently or previously proposed worldwide.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2014

Morphology of Gas Release in Physical Simulants

This report documents testing activities conducted as part of the Deep Sludge Gas Release Event Project (DSGREP). The testing described in this report focused on evaluating the potential retention and release mechanisms of hydrogen bubbles in underground radioactive waste storage tanks at Hanford. The goal of the testing was to evaluate the rate, extent, and morphology of gas release events in simulant materials. Previous, undocumented scoping tests have evidenced dramatically different gas release behavior from simulants with similar physical properties. Specifically, previous gas release tests have evaluated the extent of release of 30 Pa kaolin and 30 Pa bentonite clay slurries. While both materials are clays and both have equivalent material shear strength using a shear vane, it was found that upon stirring, gas was released immediately and completely from bentonite clay slurry while little if any gas was released from the kaolin slurry. The motivation for the current work is to replicate these tests in a controlled quality test environment and to evaluate the release behavior for another simulant used in DSGREP testing. Three simulant materials were evaluated: 1) a 30 Pa kaolin clay slurry, 2) a 30 Pa bentonite clay slurry, and 3) Rayleigh-Taylor (RT) Simulant (a simulant designed to support DSGREP RT instability testing. Entrained gas was generated in these simulant materials using two methods: 1) application of vacuum over about a 1-minute period to nucleate dissolved gas within the simulant and 2) addition of hydrogen peroxide to generate gas by peroxide decomposition in the simulants over about a 16-hour period. Bubble release was effected by vibrating the test material using an external vibrating table. When testing with hydrogen peroxide, gas release was also accomplished by stirring of the simulant.

Gas release↗

DOE OSTI2022

Understanding the Physics Representation of Deep Learning Models in Environmental Applications

Deep learning (DL) models have been popular in earth and environmental modeling and analysis, which exhibit huge potential in capturing and reconstructing the non-linearity of relevant environmental processes. They are extensively used as analytical tools or emulators for multiple domains (atmosphere, land surface, ocean, and biogeochemistry). Despite their success, their internal working mechanism remains largely unknown. Such a lack of knowledge hinders the identification of physically consistent models that are fully adaptive to non-stationary climate, as well as the development of physics-informed machine learning such as physics-informed neural network (PINN). To establish preliminary knowledge and framework of such physics representation evaluation, this project focuses on an improved understanding of DL models in the environmental applications. DL models are increasingly applied to environmental modeling and prediction. However, they have been evaluated mostly from a performance perspective, and there is a gap in understanding how they represent the known physics internally. Such knowledge is especially critical when applying DL models under climate change conditions, where new inputs are likely outside the ranges of the training datasets. In this project, we reveal how the known physical processes are represented within DL models from both statistical and mechanistic perspectives. Leveraging the traditional model evaluations that focus more on the accuracies of predictions, we establish a framework that examines both the accuracy and physics representation of DL models. This analysis framework can identify DL models that make the correct predictions based on correct physics, thus enhancing the existing explainable artificial intelligence (explainable-AI) portfolio. It lays a foundation for developing novel metrics to evaluate the emerging DL models in environmental applications. This knowledge also informs the development of physics-informed DL models by revealing the direct connections between the known physical processes and specific model components or structures.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Exploring Meson and Nucleon Structure with Tagged Structure Functions

Novel tagged beam and target techniques are being developed to create effective neutron, pion, and other targets from nucleon and nuclear targets and beams. The effective meson targets in particular open the opportunity to uniquely probe the structure and composition of mesons and the nucleon sea. This talk will discuss some results from the 6 GeV era at Jefferson Lab, approved and possible tagged deep inelastic scattering experiments at Jefferson Lab in the 12 GeV era, and look forward also to potential tagged experiments at the Electron Ion Collider.

Keppel, Cynthia↗

DOE OSTI2018

Influence of Microbial Membranes on Biofilm Formation, Scaling Reactions, and Production Chemistry in Engineered Energy Systems (Final Report)

Humans are engineering the deep subsurface for the purposes of energy-capture, energy-storage, and environmental mitigation. Despite the potential for microbial communities to significantly alter the effectiveness of these technologies, we have historically lacked a clear understanding of how microbial cells interact in a fractured shale system. Existing knowledge has been heavily based on genomic information, lacking studies on in situ physiologies, kinetic rates, and attachment mechanisms governing biogeochemical reactions in the system. The overarching goal of this research was to advance understanding of engineered hydrocarbon extraction systems as they evolve from newly developed environments to mature use. Plasma membranes protect microbial cells, mediate many critical functions, and respond to intracellular cues and ecological perturbations through physicochemical modifications. The project objectives were to 1) characterize variables influencing growth and membrane features of shale taxa, 2) characterize the interactions between shale matrices and microorganisms and 3) elucidate engineered and environmental processes driving biogeochemical signatures at the field scale. Objectives were realized through laboratory experiments involving growth of pure cultures and enrichments in continuous culture and biofilms; access to samples from two DOE-NETL funded energy-capture sites: Marcellus Shale Energy and Environmental Laboratory (MSEEL and MSEEL II); and through collaborations with scientists and engineers at the Environmental Molecular Science Laboratory (EMSL) and National Energy Technology Laboratory (NETL). Key findings showed (a) Halanaerobium congolense WG10 makes its membrane more fluid and thicker through increasing its polyunsaturated fatty acid (PUFA) composition under non-optimal salinities (7% and 20%) compared to the optimum (13% NaCl); (b) anionic phospholipids within the plasma membrane are important for high salinity tolerance in H. congolense WG10 while zwitterionic species modulate biofilm physiologies in both isolate and mixed cultures, and (c) tyrosine accumulation with overexpression of Na+/H+ antiporters are essential for osmoprotection in H. congolense WG10 under high salinity while upregulation of aromatic amino acid synthesis and cell envelope maintenance underpin biofilm formation. It is clear from these results that microbial persistence in fractured shale reservoirs under environmental and engineered perturbations requires strategic plasma membrane lipid chemistry adjustments and metabolic restructuring, with implications for improved shale microbiology management and more efficient hydrocarbon extraction approaches targeting microorganisms.

03 NATURAL GAS↗

DOE OSTI2026

Deep Learning Methods for Symbolic Calculations in HEP

This project develops machine learning methods to accelerate symbolic calculations in high-energy physics. Using sequence-to-sequence transformer models, we construct frameworks to predict squared amplitudes and related quantities for Standard Model processes, including quantum electrodynamics, quantum chromodynamics, and electroweak interactions. The results demonstrate that deep learning can successfully learn complex symbolic relationships and provide a scalable approach to symbolic computation with potential applications in precision calculations and collider phenomenology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1974

Probes for measuring noise current in an electronic cable

Electromagnetic interference in deep-space network receiver is often caused by stray coupling from power lines. These stray signals create potential differences between ground terminals, which leads to excessive noise in receiver circuits. Pair of probes detect and measure noise currents in conductors.

Lundy, C. C.↗

NASA NTRS1978

Oceanic Geoid and Tides Obtained from GEOS-3 Satellite Data in the Northwestern Atlantic Ocean

Two sets of GEO-3 altimeter data which fall within about a 2.5 degree width are analyzed for ocean geoid and tides. One set covers a linear path from Newfoundland to Cuba and the other from Puerto Rico to the North Carolina coast. Forty different analyses using various parameters are performed in order to investigate convergence. Profiles of the geoid and four tides, M sub 2 O sub 1, S sub 2, and K sub 1, are obtained along the two strips. The results demonstrate convergent solutions for all forty cases and show, within expectation, fair agreement with those obtained from the MODE deep-sea tide gauge. It is also shown that the oceanic geoid obtained through this analysis can potentially improve the short wavelength structure over existing geoid models.

Won, I. J.↗

NASA NTRS1979

Preliminary assessment of industrial needs for an advanced ocean technology

A quick-look review of selected ocean industries is presented for the purpose of providing NASA OSTA with an assessment of technology needs and market potential. The size and growth potential, needs and problem areas, technology presently used and its suppliers, are given for industries involved in deep ocean mining, petrochemicals ocean energy conversion. Supporting services such as ocean bottom surveying; underwater transportation, data collection, and work systems; and inspection and diving services are included. Examples of key problem areas that are amenable to advanced technology solutions are included. Major companies are listed.

Mourad, A. G.↗

NASA NTRS1982

The interactive role of subsynoptic scale jet sreak and planetary boundary layer adjustments in organizing an apparently isolated convective complex

A mesoscale atmospheric simulation system is described that is being developed in order to improve the simulation of subsynoptic and mesoscale adjustments associated with cyclogenesis, severe storm development, and significant atmospheric transport processes. Present emphasis in model development is in the parameterization of physical processes, time-dependent boundary conditions, sophisticated initialization and analysis procedures, nested grid solutions, and applications software development. Basic characteristics of the system as of March 1982 are listed. In a case study, the Grand Island tornado outbreak of 3 June 1980 is considered in substantial detail. Results of simulations with a mesoscale atmospheric simulation system indicate that over the high plains subtle interactions between existing jet streaks and deep well mixed boundary layers can lead to well organized patterns of mesoscale divergence and pressure falls. The amplitude and positioning of these mesoscale features is a function of the subtle nonlinear interaction between the pre-existing jet-streak and deep well mixed boundary layers. Model results for the case study indicate that the model has the potential for forecasting the precursor mesoscale convective environment.

Kaplan, M. L.↗

NASA NTRS1989

Determination of Earth orientation using the Global Positioning System

Modern spacecraft tracking and navigation require highly accurate Earth-orientation parameters. For near-real-time applications, errors in these quantities and their extrapolated values are a significant error source. A globally distributed network of high-precision receivers observing the full Global Positioning System (GPS) configuration of 18 or more satellites may be an efficient and economical method for the rapid determination of short-term variations in Earth orientation. A covariance analysis using the JPL Orbit Analysis and Simulation Software (OASIS) was performed to evaluate the errors associated with GPS measurements of Earth orientation. These GPS measurements appear to be highly competitive with those from other techniques and can potentially yield frequent and reliable centimeter-level Earth-orientation information while simultaneously allowing the oversubscribed Deep Space Network (DSN) antennas to be used more for direct project support.

Freedman, A. P.↗

NASA NTRS1994

Search for extraterrestrial intelligence/High Resolution Microwave Survey team member

This final report summarizes activities conducted during the three years of the NASA High Resolution Microwave Survey (HRMS). With primary interest in the Sky Survey activity, the principal investigator attended nine Working Group meetings and traveled independently to conduct experiments or present results at other meetings. The major activity involved evaluating the effects of spaceborne radio frequency interference (RFI) on both the SETI sky survey and targeted search. The development of a database of all unclassified earth or biting and deep space transmitters, along with accompanying search software, was a key accomplishment. The software provides information about potential sources of interference and gives complete information regarding the frequencies, positions and levels of interference generated by the spacecraft. A complete description of this search system (called HRS, or HRMS RFI Search) is provided. Other accomplishments include development of a 32,000 channel Fast-Fourier-Transform Spectrum analyzer for use in studies of interference from satellites and in a 1.4 mm SETI observational study. The latest revision of HRS has now been distributed to the extended radio astronomy and SETI community.

Steffes, Paul G.↗