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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Cuspy dark matter density profiles in massive dwarf galaxies

ABSTRACT Rotation curves of galaxies probe their total mass distributions, including dark matter. Dwarf galaxies are excellent systems to investigate the dark matter density distribution, as they tend to have larger fractions of dark matter compared to higher mass systems. The core-cusp problem describes the discrepancy found in the slope of the dark matter density profile in the centres of galaxies (β*) between observations of dwarf galaxies (shallower cores) and dark matter-only simulations (steeper cusps). We investigate β* in six nearby spiral dwarf galaxies for which high-resolution CO J = 1–0 data were obtained with ALMA (Atacama Large Millimeter/submillimeter Array). We derive rotation curves and decompose the mass profile of the dark matter using our CO rotation curves as a tracer of the total potential and 4.5 $\mu$m photometry to define the stellar mass distribution. We find 〈β*〉 = 0.6 with a standard deviation of ±0.1 among the galaxies in this sample, in agreement with previous measurements in this mass range. The galaxies studied are on the high stellar mass end of dwarf galaxies and have cuspier profiles than lower mass dwarfs, in agreement with other observations. When the same definition of the slope is used, we observe steeper slopes than predicted by the FIRE and NIHAO simulations. This may signal that these relatively massive dwarfs underwent stronger gas inflows towards their centres than predicted by these simulations, that these simulations overpredict the frequency of accretion or feedback events, or that a combination of these or other effects are at work.

Cooke, Lauren H. (ORCID:0000000284337553)↗
DOE OSTI2023

On the impact of the galaxy window function on cosmological parameter estimation

One important source of systematics in galaxy redshift surveys comes from the estimation of the galaxy window function. Up until now, the impact of the uncertainty in estimating the galaxy window function on parameter inference has not been properly studied. In this paper, we show that the uncertainty and the bias in estimating the galaxy window function will be salient for ongoing and next-generation galaxy surveys using a simulation-based approach. With a specific case study of cross-correlating emission-line galaxies from the DESI Legacy Imaging Surveys and the Planck cosmic microwave background lensing map, we show that neural network-based regression approaches to modelling the window function are superior in comparison to linear regression-based models. Here, we additionally show that the definition of the galaxy overdensity estimator can impact the overall signal-to-noise of observed power spectra. Finally, we show that the additive biases coming from the window functions can significantly bias the modes of the inferred parameters and also degrade their precision. Thus, a careful understanding of the window functions will be essential to conduct cosmological experiments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Can we observe the ion-neutral drift velocity in prestellar cores?

Given the low-ionization fraction of molecular clouds, ambipolar diffusion is thought to be an integral process in star formation. However, chemical and radiative-transfer effects, observational challenges, and the fact that the ion-neutral drift velocity is inherently very small render a definite detection of ambipolar diffusion extremely non-trivial. Here, we study the ion-neutral drift velocity in a suite of chemodynamical, non-ideal magnetohydrodynamic (MHD), two-dimensional axisymmetric simulations of prestellar cores where we alter the temperature, cosmic-ray ionization rate, visual extinction, mass-to-flux ratio, and chemical evolution. Subsequently, we perform a number of non-local thermodynamic equilibrium (non-LTE) radiative-transfer calculations considering various idealized and non-idealized scenarios in order to assess which factor (chemistry, radiative transfer, and/or observational difficulties) is the most challenging to overcome in our efforts to detect the ion-neutral drift velocity. We find that temperature has a significant effect in the amplitude of the drift velocity with the coldest modelled cores (T = 6 K) exhibiting drift velocities comparable to the sound speed. Against expectations, we find that in idealized scenarios (where two species are perfectly chemically co-evolving) the drift velocity ‘survives’ radiative-transfer effects and can in principle be observed. However, we find that observational challenges and chemical effects can significantly hinder our view of the ion-neutral drift velocity. Finally, we propose that HCN and HCNH + ⁠, being chemically co-evolving, could be used in future observational studies aiming to measure the ion-neutral drift velocity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Milky Way and M31 orbital history: did the Local Group evolve in isolation?

ABSTRACT We use new measurements of the M31 proper motion to examine the Milky Way (MW) – M31 orbit and angular momentum. For Local Group (LG) mass consistent with measured values, and assuming the system evolves in isolation, we show a wide range of orbits is possible. We compare to a sample of LG-like systems in the Illustris simulation, and find that ∼13 per cent of these pairs have undergone a pericentric passage. Using the simulated sample, we examine how accurately an isolated, two-body model describes the MW–M31 orbit, and show that ∼10 per cent of the analogues in the simulation are well-modelled by such an orbit. Systems that evolve in isolation by this definition are found to have a lower rate of major mergers, and in particular have no major mergers since $z \approx 0.3$. For all systems, we find an increase in the orbital angular momentum which is fairly independent of the merger rate, and is possibly explained by the influence of tidal torques on the LG. Given the likely quiet recent major merger history of the MW, it is plausible that the isolated two-body model appropriately describes the orbit, though recent evidence for a major merger in M31 may complicate this interpretation.

Hartl, Odelia V. (ORCID:0000000202379726)↗
DOE OSTI2025

Structural decomposition of merger-free galaxies hosting luminous AGNs

ABSTRACT Active galactic nucleus (AGN) growth in disc-dominated, merger-free galaxies is poorly understood, largely due to the difficulty in disentangling the AGN emission from that of the host galaxy. By carefully separating this emission, we examine the differences between AGNs in galaxies hosting a (possibly) merger-grown, classical bulge, and AGNs in secularly grown, truly bulgeless disc galaxies. We use galfit to obtain robust, accurate morphologies of 100 disc-dominated galaxies imaged with the Hubble Space Telescope. Adopting an inclusive definition of classical bulges, we detect a classical bulge component in $53.3 \pm 0.5$ per cent of the galaxies. These bulges were not visible in Sloan Digital Sky Survey photometry, however these galaxies are still unambiguously disc-dominated, with an average bulge-to-total luminosity ratio of $0.1 \pm 0.1$. We find some correlation between bulge mass and black hole mass for disc-dominated galaxies, though this correlation is significantly weaker in comparison to the relation for bulge-dominated or elliptical galaxies. Furthermore, a significant fraction ($\gtrsim 90$ per cent) of our black holes are overly massive when compared to the relationship for elliptical galaxies. We find a weak correlation between total stellar mass and black hole mass for the disc-dominated galaxies, hinting that the stochasticity of black hole–galaxy co-evolution may be higher in disc-dominated than bulge-dominated systems.

Fahey, Matthew J.↗
DOE OSTI2026

Uncertainties in the production of iron-group nuclides in core-collapse supernovae from Monte Carlo variations of reaction rates

Core-collapse supernovae, occurring at the end of massive star evolution, produce heavy elements, including those in the iron peak. Although the explosion mechanism is not yet fully understood, theoretical models can reproduce optical observations and observed elemental abundances. However, many nuclear reaction rates involved in explosive nucleosynthesis have large uncertainties, impacting the reliability of abundance predictions. To address this, we have previously developed a Monte Carlo-based nucleosynthesis code that accounts for reaction rate uncertainties and has been applied to nucleosynthesis processes beyond iron. Our framework is also well suited for studying explosive nucleosynthesis in supernovae. In this paper, we investigate 1D explosion models using the ‘PUSH method’ , focusing on progenitors with varying metallicities and initial masses around $M_{\rm ZAMS} = 16\, {\rm M}_{\odot }$. Detailed post-process nucleosynthesis calculations and Monte Carlo analyses are used to explore the effects of reaction rate uncertainties and to identify key reaction rates in explosive nucleosynthesis. We find that many reactions have little impact on the production of iron-group nuclei, as these elements are primarily synthesized in the nuclear statistical equilibrium. However, we identify a few ‘key reactions’ that significantly influence the production of radioactive nuclei, which may affect astrophysical observables. In particular, for the production of ${}^{44}{\rm Ti}$, we confirm that several traditionally studied nuclear reactions have a strong impact. However, determining a single reaction rate is insufficient to draw a definitive conclusion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Predictive Models of Genetic Redundancy in Arabidopsis thaliana

Abstract Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Human Phenotype Ontology in 2021

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail. We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Human Phenotype Ontology in 2024: phenotypes around the world

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Survey of Gravitationally lensed objects in HSC Imaging (SuGOHI). VIII. New galaxy-scale lenses from the HSC SSP

Abstract We conduct a search for galaxy-scale strong gravitational lens systems in Data Release 4 of the Hyper Suprime-Cam Subaru Strategic Program (HSC SSP), consisting of data taken up to the S21A semester. We select 103191 luminous red galaxies from the Baryon Oscillation Spectroscopic Survey (BOSS) sample that have deep multiband imaging from the HSC SSP and use the YattaLens algorithm to identify lens candidates with blue arc-like features automatically. The candidates are visually inspected and graded based on their likelihood of being a lens. We find eight definite lenses, 28 probable lenses, and 138 possible lenses. The new lens candidates generally have lens redshifts in the range 0.3 ≲ zL ≲ 0.9, a key intermediate redshift range to study the evolution of galaxy structure. Follow-up spectroscopy will confirm these new lenses and measure source redshifts to enable detailed lens modeling.

Astronomy & Astrophysics↗
DOE OSTI2021

Flavonoids naringenin chalcone, naringenin, dihydrotricin, and tricin are lignin monomers in papyrus

Recent studies demonstrate that several polyphenolic compounds produced from beyond the canonical monolignol biosynthetic pathways can behave as lignin monomers, participating in radical coupling reactions and being incorporated into lignin polymers. Here, we show various classes of flavonoids, the chalconoid naringenin chalcone, the flavanones naringenin and dihydrotricin, and the flavone tricin, incorporated into the lignin polymer of papyrus (Cyperus papyrus L.) rind. These flavonoids were released from the rind lignin by Derivatization Followed by Reductive Cleavage (DFRC), a chemical degradative method that cleaves the β-ether linkages, indicating that at least a fraction of each was integrated into the lignin as β-ether-linked structures. Due to the particular structure of tricin and dihydrotricin, whose C-3' and C-5' positions at their B-rings are occupied by methoxy groups, these compounds can only be incorporated into the lignin through 4'–O–β bonds. However, naringenin chalcone and naringenin have no substituents at these positions and can therefore form additional carbon–carbon linkages, including 3'– or 5'–β linkages that form phenylcoumaran structures not susceptible to cleavage by DFRC. Furthermore, Nuclear Magnetic Resonance analysis indicated that naringenin chalcone can also form additional linkages through its conjugated double bond. The discovery expands the range of flavonoids incorporated into natural lignins, further broadens the traditional definition of lignin, and enhances the premise that any phenolic compound present at the cell wall during lignification could be oxidized and potentially integrated into the lignin structure, depending only on its chemical compatibility. This study indicates that papyrus lignin has a unique structure, as it is the only lignin known to date that integrates such a diversity of phenolic compounds from different classes of flavonoids. This discovery will open up new ways to engineer and design lignins with specific properties and for enhanced value.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Season of drought affects growth, but not nonstructural carbohydrates dynamics, in Pinus taeda saplings

In temperate evergreen conifers, growth occurs mostly in summer but photosynthesis proceeds year-round; thus, nonstructural carbohydrates (NSCs) increase in winter but decrease in summer. Given that mild drought reduces growth but not photosynthesis, a drought in summer should increase NSCs more than one in winter. However, the active regulation hypothesis suggests that to increase future drought resilience, plants might downregulate growth to increase NSCs after a winter drought even if NSCs do not increase during the drought. To test whether this is so, potted Pinus taeda saplings (age year) were subjected to 6-month droughts in a greenhouse with one treatment receiving drought during winter (September–March), and another during summer (March–September). Here, both treatments were compared with a control. To measure dry biomass and NSCs, we harvested plants monthly following each drought, while to assess changes in growth rates, we measured height and diameter monthly. While we observed seasonal variation and an overall increase during the study, we found no drought-related changes in NSC dynamics; however, drought did reduce growth. Furthermore, drought in winter did reduce growth during the following summer, but the reduction was less than for a drought in summer. We conclude that the effect of drought on NSCs was too small to detect in our plants. While better control of soil water would have reduced a major source of uncertainty, plants with larger NSC reserves or more intense stress would also yield easier-to-detect effects. Although not definitive, our results suggest that water stress does not lead to dramatic changes in seasonal NSC dynamics in its aftermath, despite what one might expect under the active regulation hypothesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Steroid responsiveness in alcohol-associated hepatitis is linked to glucocorticoid metabolism, mitochondrial repair, and heat shock proteins

Alcohol-associated hepatitis (AH) is one of the clinical presentations of alcohol-associated liver disease. AH has poor prognosis, and corticosteroids remain the mainstay of drug therapy. However, ~40% of patients do not respond to this treatment, and the mechanisms underlying the altered response to corticosteroids are not understood. The current study aimed to identify changes in hepatic protein expression associated with responsiveness to corticosteroids and prognosis in patients with AH. Patients with AH were enrolled based on the National Institute on Alcohol Abuse and Alcoholism inclusion criteria for acute AH and further confirmed by a diagnostic liver biopsy. Proteomic analysis was conducted on liver samples acquired from patients with AH grouped as nonresponders (AH-NR, n = 7) and responders (AH-R, n = 14) to corticosteroids, and nonalcohol-associated liver disease controls (n = 10). The definition of responders was based on the clinical prognostic model, the Lille Score, where a score < 0.45 classified patients as AH-R and a score > 0.45 as AH-NR. Primary outcomes used to assess steroid response were Lille Score (eg, improved liver function) and survival at 24 weeks. Reduced levels of the glucocorticoid receptor and its transcriptional co-activator, glucocorticoid modulatory element-binding protein 2, were observed in the hepatic proteome of AH-NR versus AH-R. The corticosteroid metabolizing enzyme, 11-beta-hydroxysteroid dehydrogenase 1, was increased in AH-NR versus AH-R along with elevated mitochondrial DNA repair enzymes, while several proteins of the heat shock pathway were reduced. Analysis of differentially expressed proteins in AH-NR who survived 24 weeks relative to AH-NR nonsurvivors revealed several protein expression changes, including increased levels of acute phase proteins, elevated coagulation factors, and reduced mast cell markers. This study identified hepatic proteomic changes that may predict responsiveness to corticosteroids and mortality in patients with AH.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dose Coefficients for Internal Dose Assessments for Exposure to Radioactive Fallout

This paper presents values as well as the bases for calculating internal dose coefficients suitable for estimating organ doses from the exposure to radioactive fallout that could result from the detonation of a nuclear fission device. The 34 radionuclides discussed are the same as those given in a priority list of radionuclides for fallout dose assessments presented in a companion overview paper. The radionuclides discussed are those that are believed to account for a preponderance of the organ doses that might be received by intake by persons of all ages (including in utero and via breast feeding for infants) following exposure to radioactive fallout. The presented dose coefficients for ingestion account for age and include modifications for variations in solubility with distance as discussed previously in the literature, and those for inhalation similarly account for age, solubility, and particle sizes that would be relevant at various distances of exposure as discussed in a companion paper on ingestion dose methods. The proposed modifications peculiar to radioactive fallout account for systematic changes in solubility and particle sizes with distance from the site of detonation, termed here as the region of “local fallout” and the region “beyond local fallout.” Brief definitions of these regions are provided here with more detailed discussion in a companion paper on estimating deposition of fallout radionuclides. This paper provides the dose coefficients for ingestion and inhalation (for particle sizes of 1 μm, 5 μm, 10 μm, and 20 μm) for the region “local fallout.” These dose coefficients for “local fallout” are specific for particles formed in a nuclear explosion that can be large and have radionuclides, particularly the more refractory ones, distributed throughout the volume where the radionuclide has reduced solubility. The dose coefficients for the region “beyond local fallout” are assumed to be the ones published by the International Commission on Radiological Protection (ICRP) in 1995. Comparisons of the presented dose coefficients are made with values published by the ICRP.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2022

Solving generalized eigenvalue problems by ordinary differential equations on a quantum computer

Many eigenvalue problems arising in practice are often of the generalized form A x = λ B x . One particularly important case is symmetric, namely A , B are Hermitian and B is positive definite. The standard algorithm for solving this class of eigenvalue problems is to reduce them to Hermitian eigenvalue problems. For a quantum computer, quantum phase estimation is a useful technique to solve Hermitian eigenvalue problems. In this work, we propose a new quantum algorithm for symmetric generalized eigenvalue problems using ordinary differential equations. The algorithm has lower complexity than the standard one based on quantum phase estimation. Moreover, it works for a wider case than symmetric: B is invertible, B - 1 A is diagonalizable and all the eigenvalues are real.

Science & Technology - Other Topics↗
DOE OSTI2024

Unified wavefront singularity characterization of three-dimensional elastodynamic time-domain half-space Green's function under impulsive boundary and internal loads

Founded on a novel analytical formulation that led to a rigorous yet compact path-integral representation of the time-domain elastodynamic half-space Green's function, a unified analysis of the possible occurrence of different singular wavefront behaviour in the response under arbitrary impulsive internal or surface point loads at arbitrary source-receiver locations is presented. With the decomposition of the general solution into distinct initiating and reflected wave group integrals that share a common factored format and simple contour definitions, the mathematical framework is shown to allow a straightforward identification of the specific conditions and the particular wave groups that are responsible for the singular wavefront phenomena without resorting to advanced analytic function theories or asymptotic methods. Analytic characterizations of the nature, strength and direction of all intrinsic singular wavefront behaviours of the three-dimensional Green's function in three canonical cases of source-receiver configurations are given in a dual integral-closed form format to facilitate their theoretical understanding as well as computational applications. Graphical illustrations of their variation with the source-receiver configuration and the medium's Poisson's ratio together with relevant comparison and clarifications of some classical treatments are included.

Green’s functions↗
DOE OSTI2023

Ecosystem and soil respiration radiocarbon detects old carbon release as a fingerprint of warming and permafrost destabilization with climate change

The permafrost region has accumulated organic carbon in cold and waterlogged soils over thousands of years and now contains three times as much carbon as the atmosphere. Global warming is degrading permafrost with the potential to accelerate climate change as increased microbial decomposition releases soil carbon as greenhouse gases. A 19-year time series of soil and ecosystem respiration radiocarbon from Alaska provides long-term insight into changing permafrost soil carbon dynamics in a warmer world. Nine per cent of ecosystem respiration and 23% of soil respiration observations had radiocarbon values more than 50‰ lower than the atmospheric value. Furthermore, the overall trend of ecosystem and soil respiration radiocarbon values through time decreased more than atmospheric radiocarbon values did, indicating that old carbon degradation was enhanced. Boosted regression tree analyses showed that temperature and moisture environmental variables had the largest relative influence on lower radiocarbon values. This suggested that old carbon degradation was controlled by warming/permafrost thaw and soil drying together, as waterlogged soil conditions could protect soil carbon from microbial decomposition even when thawed. Overall, changing conditions increasingly favoured the release of old carbon, which is a definitive fingerprint of an accelerating feedback to climate change as a consequence of warming and permafrost destabilization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Dynamic and transient processes in warm dense matter

In this paper, we discuss some of the key challenges in the study of time-dependent processes and non-equilibrium behaviour in warm dense matter. We outline some of the basic physics concepts that have underpinned the definition of warm dense matter as a subject area in its own right and then cover, in a selective, non-comprehensive manner, some of the current challenges, pointing along the way to topics covered by the papers presented in this volume.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗