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DOE OSTI2025

Bounds on Heavy Axions with an X-Ray Free Electron Laser

We present new exclusion bounds obtained at the European X-Ray Free Electron Laser facility (EuXFEL) on axionlike particles in the mass range 10 -3 eV ≲ m a ≲ 10 4 eV. Our experiment exploits the Primakoff effect via which photons can, in the presence of a strong external electric field, decay into axions, which then convert back into photons after passing through an opaque wall. While similar searches have been performed previously at a third-generation synchrotron [Yamaji et al., Phys. Lett. B 782, 523 (2018)], our work demonstrates improved sensitivity, exploiting the higher brightness of x-rays at EuXFEL.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗

DOE OSTI2024

The protein structurome of Orthornavirae and its dark matter

Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile-based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships. We constructed an Orthornavirae “structurome” consisting of already annotated as well as unannotated (“dark matter”) proteins and domains encoded in viral genomes. We used protein structure modeling and similarity searches to illuminate the remaining dark matter in hundreds of thousands of orthornavirus genomes. The vast majority of the dark matter domains showed either “generic” folds, such as single α-helices, or no high confidence structure predictions. Nevertheless, a variety of lineage-specific globular domains that were new either to orthornaviruses in general or to particular virus families were identified within the proteomic dark matter of orthornaviruses, including several predicted nucleic acid-binding domains and nucleases. In addition, we identified a case of exaptation of a cellular nucleoside monophosphate kinase as an RNA-binding protein in several virus families. Notwithstanding the continuing discovery of numerous orthornaviruses, it appears that all the protein domains conserved in large groups of viruses have already been identified. The rest of the viral proteome seems to be dominated by poorly structured domains including intrinsically disordered ones that likely mediate specific virus-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

CACTUS

CACTUS is an innovative LLM‐based agent that combines the cognitive capabilities of large language models with domain‐specific tools. By integrating cheminformatics tools, CACTUS assists researchers in tasks such as molecular property prediction, similarity searching, and drug‐likeness assessment.

Kumar, Neeraj↗

DOE OSTI2024

LTAU-FF: Loss Trajectory Analysis for Uncertainty in atomistic Force Fields

LTAU (Loss Trajectory Analysis for Uncertainty) is a technique for estimating the uncertainty in a model's predictions for any regression task by approximating the cumulative distribution function (CDF) of the model's errors over the course of training. The approximated CDF, combined with a similarity search algorithm in the model's descriptor space, can then be used to estimate the likelihood that the model's predictions on any given test point will fall below a chosen threshold. LTAU-FF (LTAU in atomistic Force Fields) is the application of LTAU specifically for use with atomistic force fields.

Vita, JoshuaA↗

DOE OSTI2024

TensorSearch v1

TensorSearch is a novel parallel similarity search paradigm designed to identify known patterns in high-dimensional tensors.

Dong, Bin↗

NASA NTRS1994

Upper limits on metals in quasar Lyman-alpha forest clouds: Absence of C 5 lines in echelle spectra

Recently Lu presented tentative evidence for C IV lines in Quasi-Stellar Object (QSO) Ly-alpha forest systems with strong lines. We have performed a similar search for C IV in our 10 km/s resolution echelle spectra of the bright QSO HS 1946+7658. We shifted the spectra to align the expected positions of the C IV lines in 65 Ly-alpha systems and then added them. The resulting composite spectrum, equivalent to 390 hr of exposure time on the Lick 3 m telescope, has a signal-to-noise ratio of 80 per 0.025 A in the rest frame of the absorbers. We do not see any C IV lines down to a 2 sigma limit of W(1548) less than or equal to 1.4 mA, about one fifth of the strength of the lines seen by Lu. The C IV lines that Lu saw must be restricted to rare Ly-alpha systems with large H I column densities greater than or equal to 10(exp 14)/sq cm, which are too rare to show C IV in our sample. More common Ly-alpha systems with H I column densities of 10(exp 13)-10(exp 14)/sq cm do not show C IV lines. If their ionization is H/H I = 10(exp 4) then they have (C/H) less than or equal to -2.0.

Tytler, David↗

NASA NTRS2018

Exoplanet Biosignatures: Understanding Oxygen as a Biosignature in the Context of Its Environment

Here we review how environmental context can be used to interpret whether O 2 is a biosignature in extrasolar planetary observations. This paper builds on the overview of current biosignature research discussed in Schwieterman et al. (2017), and provides an in-depth, interdisciplinary example of biosignature identification and observation that serves as a basis for the development of the general framework for biosignature assessment described in Catling et al., (2017). O 2 is a potentially strong biosignature that was originally thought to be an unambiguous indicator for life at high-abundance. In exploring O 2 as a biosignature, we describe the coevolution of life with the early Earth's environment, and how the interplay of sources and sinks in the planetary environment may have resulted in suppression of O 2 release into the atmosphere for several billion years, a false negative for biologically generated O 2 . False positives may also be possible, with recent research showing potential mechanisms in exoplanet environments that may generate relatively high abundances of atmospheric O 2 without a biosphere being present. These studies suggest that planetary characteristics that may enhance false negatives should be considered when selecting targets for biosignature searches. Similarly our ability to interpret O 2 observed in an exoplanetary atmosphere is also crucially dependent on environmental context to rule out false positive mechanisms. We describe future photometric, spectroscopic and time-dependent observations of O 2 and the planetary environment that could increase our confidence that any observed O 2 is a biosignature, and help discriminate it from potential false positives. The rich, interdisciplinary study of O 2 illustrates how a synthesis of our understanding of life's evolution and the early Earth, scientific computer modeling of star-planet interactions and predictive observations can enhance our understanding of biosignatures and guide and inform the development of next-generation planet detection and characterization missions. By observing and understanding O 2 in its planetary context we can increase our confidence in the remote detection of life, and provide a model for biosignature development for other proposed biosignatures.

Victoria S Meadows↗

NASA NTRSDate not supplied

Identifying Indicators of Harmful Algal Blooms in Coastal Atacama Using Satellite Image Processing Techniques to Improve Industry and Authority Response

Over the past decade, Chile has experienced a significant rise in both the frequency and intensity of coastal Harmful Algal Blooms (HABs). These bloom events are a growing concern for the Atacama Region especially, with potential impacts on human health, aquaculture, and the environment. HABs are caused by an excess proliferation of microalgae, with certain algae species commonly found in Chilean HABs capable of producing toxins which can poison fish, toxify shellfish, and cause illness or death when ingested by humans. Collaborating with the Ministry of Health of Chile, Centro de Información de Recursos Naturales, the University of Atacama, and the Embassy of Chile’s Agricultural Office, this study identifies potential indicators of HABs in the Coastal Atacama Region using NASA Earth observations. Satellite imagery from the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument onboard NASA’s Aqua satellite was used for the identification of chlorophyll-a which provides direct estimates of the algae pigment’s concentration in water bodies. In addition, the spatiotemporal patterns of several other parameters were examined to identify correlations with occurrences of HABs, including sea surface temperature and normalized fluorescence line height using Aqua MODIS, Normalized Difference Turbidity Index (NDTI) using Landsat 8, and ocean wind speed measurements from the NOAA Joint Polar Satellite System. Analysis of these patterns revealed hotspots of high chlorophyll-a concentrations from the years 2014 to 2022, the most major of which occurring in the coastal zones of Chañaral, Bahía Inglesa, and Huasco. Also, through the use of a similarity search conducted, the seasonal variation of these indicators was mapped to highlight areas with great likelihood of experiencing HABs in the future. The results can guide future efforts for in-situ water sampling, toxin analysis and assessment, and HAB monitoring and prevention.

Cody O'Ferrall↗

NASA NTRS1992

Detection of the Earth with the SETI microwave observing system assumed to be operating out in the galaxy

This paper estimates the maximum range at which radar signals from the Earth could be detected by a search system similar to the NASA Search for Extraterrestrial Intelligence Microwave Observing Project (SETI MOP) assumed to be operating out in the galaxy. Figures are calculated for the Targeted Search, and for the Sky Survey parts of the MOP, both operating, as currently planned, in the second half of the decade of the 1990s. Only the most powerful terrestrial transmitters are considered, namely, the planetary radar at Arecibo in Puerto Rico, and the ballistic missile early warning systems (BMEWS). In each case the probabilities of detection over the life of the MOP are also calculated. The calculation assumes that we are only in the eavesdropping mode. Transmissions intended to be detected by SETI systems are likely to be much stronger and would of course be found with higher probability to a greater range. Also, it is assumed that the transmitting civilization is at the same level of technological evolution as ours on Earth. This is very improbable. If we were to detect another technological civilization, it would, on statistical grounds, be much older than we are and might well have much more powerful transmitters. Both factors would make detection by the NASA MOP a much more likely outcome.

NASA Center ARC↗

NASA NTRSDate not supplied

Search Enhancements using Natural Language Processing Techniques

NASA Goddard Earth Sciences Data and Information Services Center (GESDISC) is one of the 12 NASA Science Mission Directorate Data Centers. The main goal of GESDISC is to provide earth science data, information, and services to the earth science data community. Consequently, data discovery is at the center of our mission and our search engine is the primary tool for our users to interact, find, and access our data. Existing search approaches are largely focused on hard-matching of keywords in the search query with dataset metadata. Here we propose to expand the search by introducing a complementary natural language processing (NLP) search. At the heart of our proposed NLP search, we trained a joint embedding using scientific text corpus and a curated set of dataset metadata. The embedding learns the association between words in our dataset metadata and those of the scientific text corpus. This enables us to go beyond simple hard-matching of a query and data set metadata and have a notion of “similarity” between the search query and the datasets. We further integrated our NLP search into the Elastic Search (ES) framework leveraging similarity search capabilities offered through the “dense_vector” field type. Our preliminary evaluations show that our proposed NLP search has the potential to be utilized to complement the existing search engine and serve as a base for a dataset recommendation system.

Armin Mehrabian↗

NASA NTRS2011

Stratway: A Modular Approach to Strategic Conflict Resolution

In this paper we introduce Stratway, a modular approach to finding long-term strategic resolutions to conflicts between aircraft. The modular approach provides both advantages and disadvantages. Our primary concern is to investigate the implications on the verification of safety-critical properties of a strategic resolution algorithm. By partitioning the problem into verifiable modules much stronger verification claims can be established. Since strategic resolution involves searching for solutions over an enormous state space, Stratway, like most similar algorithms, searches these spaces by applying heuristics, which present especially difficult verification challenges. An advantage of a modular approach is that it makes a clear distinction between the resolution function and the trajectory generation function. This allows the resolution computation to be independent of any particular vehicle. The Stratway algorithm was developed in both Java and C++ and is available through a open source license. Additionally there is a visualization application that is helpful when analyzing and quickly creating conflict scenarios.

Hagen, George E.↗

NASA NTRS2016

A Full-Text-Based Search Engine for Finding Highly Matched Documents Across Multiple Categories

This report demonstrates the full-text-based search engine that works on any Web-based mobile application. The engine has the capability to search databases across multiple categories based on a user's queries and identify the most relevant or similar. The search results presented here were found using an Android (Google Co.) mobile device; however, it is also compatible with other mobile phones.

Web-based mobile application↗

NASA NTRS1989

Detection of the earth with the SETI microwave observing system assumed to be operating out in the Galaxy

The maximum range is calculated at which radar signals from the earth could be detected by a search system similar to the NASA SETI Microwave Observing Project (SETI MOP) assumed to be operating out in the Galaxy. Figures are calculated for the Targeted Search and for the Sky Survey parts of the MOP, both planned to be operating in the 1990s. The probability of detection is calculated for the two most powerful transmitters, the planetary radar at Arecibo (Puerto Rico) and the ballistic missile early warning systems (BMEWSs), assuming that the terrestrial radars are only in the eavesdropping mode. It was found that, for the case of a single transmitter within the maximum range, the highest probability is for the sky survey detecting BMEWSs; this is directly proportional to BMEWS sky coverage and is therefore 0.25.

Billingham, John↗

NASA NTRS1996

Detectability of the Reflection Signal from Inner Planets

Mayor and Queloz (1996) and Marcy and Butler (1996) have found massive planets with orbital periods Tp=approx.4 days around two solar-like stars (51 Pegasi and v Andromeda). These planets are most likely similar in size and composition to the gas giants in our solar system (Burrows et al 1996). Based on this expectation and assuming the same albedo as Jupiter, we examined the feasibility of searching for similar planets with a dedicated space-based 1-m telescope. The Kepler mission will survey approximately 70,000 main-sequence dwarf stars from 9 to 14 mag continuously for four years to detect transiting Earthlike planets. Based on the detection statistics of Marcy and Butler, we expect to detect 1400 inner-orbit giant planets. Such planets in a much wider range of orbital inclinations (i) will produce nearly sinusoidal modulations of the star light flux due to the varying planetary phases. The relative signal amplitudes are of order 2x10(exp -5) and decrease as Tp(exp 4/3) for i >> 0deg. We estimated the expected signal to noise ratio (SNR) using the solar irradiance measurements from the ACRIM 1 experiment along with expected shot and detector noises. The figure shows SNR as a function of Tp for a 12 mag star, and indicates the planet radius required for detection. The survey will be sensitive to planets with periods from 12 hr to approx.8 days at the 6 sigma level.

Borucki, W. J.↗

DOE OSTI2022

Low-threshold sapphire detector for rare event searches

Low mass nuclear recoil dark matter and coherent-elastic-neutrino-nucleus-scattering (CE$v$NS) searches confront similar challenges in choosing ultra-low threshold and large-mass detectors. Here, we report experimental results from a 100 g single-crystal sapphire detector design with a diameter of 76 mm and thickness of 4 mm instrumented with transition edge sensors (TES). Sapphire is a crystal of aluminum oxide (Al 2 O) and has been found to be a good candidate for light mass dark matter search experiments due to its lower atomic mass compared to other detector materials such as germanium and silicon. This new phonon-assisted sapphire detector was characterized to yield a baseline recoil energy resolution of 28.4 ± 0.4 eV. The detector is designed to be sensitive to low-energy rare interactions with an intention to investigate the low-mass region of dark matter phase-space and search for CE$v$NS at the reactor site.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1980

Light flash phenomena induced by HzE particles

Astronauts and Apollo and Skylab missions have reported observing a variety of visual phenomena when their eyes are closed and adapted to darkness. These phenomena have been collectively labelled as light flashes. Visual phenomena which are similar in appearance to those observed in space have been demonstrated at the number of accelerator facilities by expressing the eyes of human subjects to beams of various types of radiation. In some laboratory experiments Cerenkov radiation was found to be the basis for the flashes observed while in other experiments Cerenkov radiation could apparently be ruled out. Experiments that differentiate between Cerenkov radiation and other possible mechanisms for inducing visual phenomena was then compared. The phenomena obtained in the presence and absence of Cerenkov radiation were designed and conducted. A new mechanism proposed to explain the visual phenomena observed by Skylab astronauts as they passed through the South Atlantic Anomaly, namely nuclear interactions in and near the sensitive layer of the retina, is covered. Also some studies to search for similar transient effects of space radiation on sensors and microcomputer memories are described.

Mcnulty, P. J.↗

DOE OSTI2020

The First Habitable-zone Earth-sized Planet from TESS. III. Climate States and Characterization Prospects for TOI-700 d

We present self-consistent three-dimensional climate simulations of possible habitable states for the newly discovered habitable-zone Earth-sized planet TOI-700 d. We explore a variety of atmospheric compositions, pressures, and rotation states for both ocean-covered and completely desiccated planets in order to assess the planet’s potential for habitability. For all 20 of our simulated cases, we use our climate model outputs to synthesize transmission spectra, combined-light spectra, and integrated broadband phase curves. These climatologically informed observables will help the community assess the technological capabilities necessary for future characterization of this planet—as well as similar transiting planets discovered in the future—and will provide a guide for distinguishing possible climate states if one day we do obtain sensitive spectral observations of a habitable planet around an M star. We find that TOI-700 d is a strong candidate for a habitable world and can potentially maintain temperate surface conditions under a wide variety of atmospheric compositions. Unfortunately, the spectral feature depths from the resulting transmission spectra and the peak flux and variations from our synthesized phase curves for TOI-700 d do not exceed 10 ppm. This will likely prohibit the James Webb Space Telescope from characterizing its atmosphere; however, this motivates the community to invest in future instrumentation that perhaps can one day reveal the true nature of TOI-700 d and to continue to search for similar planets around less distant stars.

79 ASTRONOMY AND ASTROPHYSICS↗