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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies

A major goal of research in evolution and genetics is linking genotype to phenotype. This work could be direct, such as determining the genetic basis of a phenotype by leveraging genetic variation or divergence in a developmental, physiological, or behavioral trait. The work could also involve studying the evolutionary phenomena (e.g., reproductive isolation, adaptation, sexual dimorphism, behavior) that reveal an indirect link between genotype and a trait of interest. When the phenotype diverges across evolutionarily distinct lineages, this genotype-to-phenotype problem can be addressed using phylogenetic genotype-to-phenotype (PhyloG2P) mapping, which uses genetic signatures and convergent phenotypes on a phylogeny to infer the genetic bases of traits. The PhyloG2P approach has proven powerful in revealing key genetic changes associated with diverse traits, including the mammalian transition to marine environments and transitions between major mechanisms of photosynthesis. However, there are several intermediate traits layered in between genotype and the phenotype of interest, including but not limited to transcriptional profiles, chromatin states, protein abundances, structures, modifications, metabolites, and physiological parameters. Each intermediate trait is interesting and informative in its own right, but synthesis across data types has great promise for providing a deep, integrated, and predictive understanding of how genotypes drive phenotypic differences and convergence. We argue that an expanded PhyloG2P framework (the PhyloG2P matrix) that explicitly considers intermediate traits, and imputes those that are prohibitive to obtain, will allow a better mechanistic understanding of any trait of interest. Furthermore, this approach provides a proxy for functional validation and mechanistic understanding in organisms where laboratory manipulation is impractical.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Constraining primordial non-Gaussianity from the large scale structure two-point and three-point correlation functions

Surveys of cosmological large-scale structure (LSS) are sensitive to the presence of local primordial non-Gaussianity (PNG), and may be used to constrain models of inflation. Local PNG, characterized by f NL ⁠, the amplitude of the quadratic correction to the potential of a Gaussian random field, is traditionally measured from LSS two-point and three-point clustering via the power spectrum and bi-spectrum. We propose a framework to measure f NL using the configuration space two-point correlation function (2pcf) monopole and three-point correlation function (3pcf) monopole of survey tracers. Our model estimates the effect of the scale-dependent bias induced by the presence of PNG on the 2pcf and 3pcf from the clustering of simulated dark matter haloes. We describe how this effect may be scaled to an arbitrary tracer of the cosmological matter density. The 2pcf and 3pcf of this tracer are measured to constrain the value of f NL ⁠. In LSS surveys, the effect of imaging systematics on two-point statistics is often degenerate with the PNG signal. Our proposed model employs three-point statistics primarily to break this degeneracy. Using simulations of luminous red galaxies observed by the Dark Energy Spectroscopic Instrument (DESI), we demonstrate the accuracy and constraining power of our method. Our forecast indicates the ability to constrain f NL to a precision of σf NL ≈ 22 with one year of DESI survey data, as well as the ability to constrain the imaging systematic weights in situ.

early Universe↗
DOE OSTI2025

Unraveling emission line galaxy conformity at z ∼ 1 with DESI early data

Emission line galaxies (ELGs) are now the preeminent tracers of large-scale structure at z > 0.8 due to their high density and strong emission lines, which enable accurate redshift measurements. However, relatively little is known about ELG evolution and the ELG–halo connection, exposing us to potential modelling systematics in cosmology inference using these sources. In this paper, we use a variety of observations and simulated galaxy models to propose a physical picture of ELGs and improve ELG–halo connection modelling in a halo occupation distribution framework. We investigate Dark Energy Spectroscopic Instrument (DESI)-selected ELGs in COSMOS data, and infer that ELGs are rapidly star-forming galaxies with a large fraction exhibiting disturbed morphology, implying that many of them are likely to be merger-driven starbursts. We further postulate that the tidal interactions from mergers lead to correlated star formation in central–satellite ELG pairs, a phenomenon dubbed ‘conformity’. We argue for the need to include conformity in the ELG–halo connection using galaxy models such as IllustrisTNG, and by combining observations such as the DESI ELG autocorrelation, ELG cross-correlation with luminous red galaxies, and ELG–cluster cross-correlation. We also explore the origin of conformity using the UniverseMachine model and elucidate the difference between conformity and the well-known galaxy assembly bias effect.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

PAC in DESI. II. Galaxy-halo connection into the $10^{6}{\rm M}_{\odot}$ frontier

Understanding dwarf galaxy formation is crucial for testing dark matter models and reionization physics. However, constructing stellar-mass complete spectroscopic samples at low masses is increasingly difficult, and the potential existence of a local void complicates studies in an average environment. The Photometric object Around Cosmic webs (PAC) method, which combines deep photometric and spectroscopic data to measure the excess surface density $\bar{n}_2w_{\rm{p}}(r_{\rm{p}})$ of photometric objects around spectroscopic tracers, offers a promising path forward. We model 349 $\bar{n}_2w_{\rm{p}}(r_{\rm{p}})$ measurements from DESI Y1 BGS and DECaLS, reaching $M_*=10^{6.4}\,{\rm M}_{\odot}$, using a stellar mass-halo mass relation (SHMR)-based subhalo abundance matching framework applied to two high-resolution $N$-body simulations from the Jiutian suite. The resulting SHMR is constrained down to $M_{\rm h}\simeq10^{8.0}\,h^{-1}{\rm M}_{\odot}$, revealing a clear upturn at $\sim10^{10.0}\,h^{-1}{\rm M}_{\odot}$ toward lower masses, indicating rising star-formation efficiency (SFE) in small haloes. This feature persists under extensions of the model that allow mass-dependent scatter, reionization-induced suppression of the halo occupation fraction, galaxy assembly bias, and alternative cosmologies. Combining with the results from Paper I, we find that central red galaxies dominate the low-mass regime. Our results motivate a hypothesis in which SFE is significantly higher than previously thought prior to reionization, enabling relatively massive galaxies to form in small haloes. These systems are subsequently quenched by the UV background, producing the central red dwarf galaxies observed. Finally, we obtain $3σ$ and $5σ$ upper mass bounds of $10^{8.80}\,h^{-1}{\rm M}_{\odot}$ and $10^{10.24}\,h^{-1}{\rm M}_{\odot}$ on the smallest haloes required to exist.

Xu, Kun [Pennsylvania U.; Durham U., ICC; Tsung-Da↗
DOE OSTI2026

Nonadiabatic strong-field photoionization revisited: Detailed analysis

We develop a theoretical framework to interpret “bump-like” enhancements in the energy distribution of electrons emitted from cesium atoms subjected to intense infrared laser fields, as observed in a recent experiment. These emissions, detected at energies approaching twice the ponderomotive energy (2⁢𝑈 p ), indicate a mechanism where electrons are nonadiabatically ejected with substantial inward velocity following ionization. The bump-like features arise from returning trajectories that scatter off the residual ion. We interpret these experimental results classically using a periodically driven version of the Bohr model and quantum mechanically through Keldysh's adiabaticity parameter (𝛾 K ) and Reiss's continuum-state intensity parameter 𝒵 in a Coulomb-corrected version of the strong-field approximation (SFA) that incorporates “complex” electronic trajectories. Notably, our theoretical analysis shows that these emissions are independent of the specific short-range form of the atomic potential.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Probing the PeV region in the astrophysical neutrino spectrum using 𝜈 𝜇 from the Southern sky

IceCube has observed a diffuse astrophysical neutrino flux over the energy region from a few TeV to a few PeV. At PeV energies, the spectral shape is not yet well measured due to the low statistics of the data. This analysis probes the gap between 1 and 10 PeV by using high-energy downgoing muon neutrinos. Here, to reject the large atmospheric muon background, two complementary techniques are combined. The first technique selects events with high stochasticity to reject atmospheric muon bundles whose stochastic energy losses are smoothed due to high muon multiplicity. The second technique vetoes atmospheric muons with the IceTop surface array. Using 9 yrs of data, we found two neutrino candidate events in the signal region, consistent with expectation from background, each with relatively high signal probabilities. A joint maximum likelihood estimation is performed using this sample and an independent 9.5-yr sample of tracks to measure the neutrino spectrum. A likelihood ratio test is done to compare the single power-law (SPL) vs SPL+cutoff hypothesis; the SPL+cutoff model is not significantly better than the SPL. High-energy astrophysical objects from four source catalogs are also checked around the direction of the two events. No significant coincidence was found.

Abbasi, R. [Loyola University Chicago] (ORCID:0000↗
DOE OSTI2026

Nonadiabatic Strong-Field Photoionization Revisited

We measure strong field ionization of cesium atoms, observing a robust feature near 2⁢𝑈p in the photoelectron spectrum, which we call the intermediate energy structure (IES). Using a Coulomb-corrected strong-field approximation, we show it arises from electrons born with large inward velocities that rapidly undergo forward scattering off the Coulomb potential. The IES is similar to the previously identified low energy structure in that they are both due to forward scattering. However, it is different in that IES requires both nonadiabatic ionization conditions (as defined by the Keldysh parameter) and a more weakly bound initial state. Furthermore, our joint experimental and theoretical study supports the need for an additional parameter in characterization of strong field ionization, which depends both on nonadiabaticity of the process and the principal quantum number of the target. Together with Reiss and Keldysh parameters, this dimensionless parameter expands the description of strong field ionization across a broad range of atomic targets and incorporates ionization from excited states.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

DESI DR2 results. I. Baryon acoustic oscillations from the Lyman alpha forest

We present the baryon acoustic oscillation (BAO) measurements with the Lyman-𝛼 (Ly⁢𝛼) forest from the second data release (DR2) of the Dark Energy Spectroscopic Instrument (DESI) survey. Our BAO measurements include both the autocorrelation of the Ly⁢𝛼 forest absorption observed in the spectra of high-redshift quasars and the cross-correlation of the absorption with the quasar positions. The total sample size is approximately a factor of 2 larger than the DR1 dataset, with forest measurements in over 820,000 quasar spectra and the positions of over 1.2 million quasars. We describe several significant improvements to our analysis in this paper, and two supporting papers describe improvements to the synthetic datasets that we use for validation and how we identify damped Ly⁢𝛼 absorbers. Our main result is that we have measured the BAO scale with a statistical precision of 1.1% along and 1.3% transverse to the line of sight, for a combined precision of 0.65% on the isotropic BAO scale at 𝑧 eff =2.33. This excellent precision, combined with recent theoretical studies of the BAO shift due to nonlinear growth, motivated us to include a systematic error term in Ly⁢𝛼 BAO analysis for the first time. We measure the ratios 𝐷 𝐻 ⁡(𝑧 eff )/𝑟 𝑑 = 8.632 ± 0.098 ± 0.026 and 𝐷 𝑀 ⁡(𝑧 eff )/𝑟 𝑑 = 38.99 ± 0.52 ± 0.12, where 𝐷 𝐻 = 𝑐/𝐻⁡(𝑧) is the Hubble distance, 𝐷 𝑀 is the transverse comoving distance, 𝑟 𝑑 is the sound horizon at the drag epoch, and we quote both the statistical and the theoretical systematic uncertainty. The companion paper presents the BAO measurements at lower redshifts from the same dataset and the cosmological interpretation.

baryon acoustic oscillations↗
DOE OSTI2026

Probing neutrino emission at GeV energies from compact binary mergers with the IceCube Neutrino Observatory

The advent of multimessenger astronomy has allowed for new types of source searches by neutrino detectors. Here, we present the results of the search for 0.5–100 GeV astrophysical neutrinos detected with IceCube and emitted from compact binary mergers detected by the LIGO, Virgo, and KAGRA interferometers from their first run of observation (O1) to the end of the first part of the fourth (O4a). An innovative approach is used to lower the energy threshold to 0.5 GeV and to search for an excess of GeV neutrinos in time coincidence with astrophysical transient events. Furthermore, we use a statistical combination of all observations, a binomial test, to search for a subpopulation of neutrino emitters. No significant excess was found from the studied mergers, with a best post-trial 𝑝-value of 40%, and there is currently no hint of a population of GeV neutrino emitters found in the IceCube data (post-trial 𝑝−value=81%).

Abbasi, R. [Loyola University Chicago]↗
DOE OSTI2025

Attosecond X-Ray Core-Level Chronoscopy of Aromatic Molecules

Attosecond photoemission or photoionization delays are a unique probe of the structure and the electronic dynamics of matter. However, the spectral congestion of valence photoelectron spectra sets fundamental limits to the complexity of systems that can be studied, and the delocalization of valence electron wave functions blurs the spatial origin of the photoelectron wave packet. Using attosecond x-ray pulses from LCLS, we demonstrate the key advantages of measuring core-level delays: The photoelectron spectra remain atomlike, the measurements become element specific, and the observed scattering dynamics originate from a pointlike source when multicenter interference effects are negligible. We exploit these unique features to reveal the effects of changing functional groups (C-H vs N) and symmetry on attosecond scattering dynamics by measuring and calculating the photoionization delays between N−1⁢𝑠 and C−1⁢𝑠 core shells of a series of aromatic azabenzene molecules. Remarkably, the delays increase with the number of nitrogen atoms in the molecule and reveal multiple resonances. We identify two previously unknown mechanisms regulating the associated attosecond dynamics, namely the enhanced confinement of the trapped wave function with the replacement of C-H groups by N atoms and the decrease of the coupling strength among the photoemitted partial waves with increasing symmetry. This study demonstrates the unique opportunities opened by measurements of core-level photoionization delays for unraveling attosecond electron dynamics in complex matter.

Ji, Jia-Bao [Eidgenoessische Technische Hochschule↗
DOE OSTI2026

Sampling off-axis neutrino fluxes with the short-baseline near detector

The short-baseline near detector (SBND), the near detector in the short-baseline neutrino program at Fermi National Accelerator Laboratory, is located just 110 m from the booster neutrino beam target. Thanks to this close proximity, relative to its 4 m × 4 m front face, neutrinos enter SBND over a range of angles from 0° to approximately 1.6°, enabling the detector to sample variations in the neutrino flux as a function of the angle—a technique known as precision reaction-independent spectrum measurement (PRISM), referred to here as SBND-PRISM. In this paper, we show how muon- and electron-neutrino fluxes vary as a function of the neutrino beam axis angle and how this can be exploited to expand the physics potential of SBND. We make use of a model that predicts an angle-dependent electron-neutrino excess signal to illustrate this effect, such as 𝜈 𝜇 → 𝜈 𝑒 oscillations. We present how SBND-PRISM provides a method to add robustness against uncertainties in cross-section modeling and, more generally, uncertainties that do not depend on the spatial position of neutrino interaction inside the detector. The fluxes, along with their associated covariance matrices, are made publicly available with this publication.

Abratenko, P. [Tufts University]↗
DOE OSTI2025

Validation of the DESI DR2 measurements of baryon acoustic oscillations from galaxies and quasars

The Dark Energy Spectroscopic Instrument (DESI) Data Release 2 (DR2) galaxy and quasar clustering data represents a significant expansion of data from Data Release 1 (DR1), providing improved statistical precision in baryon acoustic oscillation (BAO) constraints across multiple tracers, including bright galaxies, luminous red galaxies, emission line galaxies, and quasars. In this paper, we validate the BAO analysis of DR2. We present the results of robustness tests on the blinded DR2 data and, after unblinding, consistency checks on the unblinded DR2 data. All results are compared with those obtained from a suite of mock catalogs that replicate the selection and clustering properties of the DR2 sample. We confirm the consistency of DR2 BAO measurements with DR1 while achieving a reduction in statistical uncertainties due to the increased survey volume and completeness. The combined BAO precision, including both statistical and systematic errors, improves from ∼0.52% in DR1 to 0.30% in DR2—a factor of 1.7 gain. We assess the impact of analysis choices, including different data vectors (correlation function vs power spectrum), modeling approaches and systematics treatments, and an assumption of the Gaussian likelihood, finding that our BAO constraints are stable across these variations and assumptions with a few minor refinements to the baseline setup of the DR1 BAO analysis. We summarize a series of pre-unblinding tests that confirmed the readiness of our analysis pipeline, the final systematic errors, and the DR2 BAO analysis baseline. The successful completion of these tests led to the unblinding of the DR2 BAO measurements, ultimately leading to the DESI DR2 cosmological analysis, with their implications for the expansion history of the Universe and the nature of dark energy presented in the DESI key paper (companion paper).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Long-Range Transverse-Momentum Correlations and Radial Flow in Pb-Pb Collisions at the LHC

This Letter presents measurements of long-range transverse-momentum correlations using a new observable, 𝑣 0⁡ (𝑝 T ), serving as a probe of event-by-event radial-flow fluctuations, the underlying radial expansion, and the medium’s properties in heavy-ion collisions. Results are reported for inclusive charged particles, pions, kaons, and protons across various centrality intervals in Pb-Pb collisions at $\sqrt{𝑠_{\textrm{NN}}}$ = 5.02 TeV, recorded by the ALICE detector. A pseudorapidity-gap technique, similar to that used in anisotropic-flow studies, is employed to suppress short-range correlations. At low 𝑝 T , a characteristic mass ordering consistent with hydrodynamic collective flow is observed. At higher 𝑝 T (>3 GeV/𝑐), protons exhibit larger 𝑣 0 ⁡(𝑝 T ) than pions and kaons, in agreement with expectations from quark-recombination models. Comparisons to viscous hydrodynamic calculations with varying bulk viscosity and equation of state demonstrate the sensitivity of the 𝑣 0 ⁡(𝑝 T ) observable to these key medium properties. The findings establish 𝑣 0 ⁡(𝑝 T ) as a valuable addition to the set of observables used in Bayesian analyses for extracting the transport properties and constraining the equation of state of strongly interacting matter, while also helping to systematically explore its sensitivity and impact within such global studies.

Acharya, S. [INFN] (ORCID:0000000292135329)↗
DOE OSTI2025

Measurement of the mean number of muons with energies above 500 GeV in air showers detected with the IceCube Neutrino Observatory

We present a measurement of the mean number of muons with energies larger than 500 GeV in near-vertical extensive air showers initiated by cosmic rays with primary energies between 2.5 and 100 PeV. The measurement is based on events detected in coincidence between the surface and in-ice detectors of the IceCube Neutrino Observatory. Air showers are recorded on the surface by IceTop, while a bundle of high-energy muons (TeV muons) from the shower can subsequently produce a tracklike event in the IceCube in-ice array. Results are obtained assuming the hadronic interaction models Sibyll 2.1, QGSJet-II.04, and EPOS-LHC. The measured number of TeV muons is found to be in agreement with predictions from air-shower simulations. The results have also been compared to a measurement of low-energy muons by IceTop, indicating an inconsistency between the predictions for low- and high-energy muons in simulations based on the EPOS-LHC model.

Abbasi, R. [Loyola University Chicago]↗
DOE OSTI2025

Measurement of 𝜔 meson production in 𝑝⁢𝑝 and 𝑝-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

We present the measurement of the 𝑝 T -differential production cross section of 𝜔 mesons in pp and 𝑝-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV at midrapidity by ALICE. In addition, the first measurement of the nuclear modification factor 𝑅 𝑝⁢Pb for 𝜔 mesons at LHC energies is presented, complementing the existing measurements of lighter neutral mesons such as the 𝜋 0 and 𝜂. Within the measured 𝑝 T range, the 𝑅 𝑝⁢Pb of 𝜔 mesons is compatible with no cold nuclear matter effects within the uncertainties, consistent with previous measurements at lower energies. The 𝜔/𝜋 0 ratio is presented for both collision systems, showing no collision system dependence within the uncertainties. The comparison to previously published 𝜔/𝜋 0 ratios at lower and higher collision energies in pp collisions suggests a decreasing trend of the ratio above 𝑝T = 4 GeV/𝑐 with increasing collision energy. The data in both collision systems are compared to predictions from PYTHIA 8, EPOS LHC, and DPMJET event generators, revealing significant shortcomings in these models’ ability to describe the production of 𝜔 mesons.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Accessing the deuteron source with pion-deuteron femtoscopy in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

Femtoscopy of nonidentical particle pairs has been instrumental for precision measurements of both two-particle sources and the final-state interactions in high-energy elementary and heavy-ion collisions. The majority of measurements assessing the source properties are based on identical particle pairs, providing direct access to the characteristics of the single-particle source. The work in this paper demonstrates, via femtoscopy measurements of charged pion-deuteron pairs in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV, the feasibility of accessing the characteristics of the single-particle femtoscopic source by using particle pairs with large mass differences such as pions and deuterons. The first experimental results of the measurement of deuteron source sizes in ultrarelativistic heavy-ion collisions are presented. The results show good agreement with the trend derived from other charged hadrons such as pions, kaons, and protons as a function of transverse mass, indicating similar source properties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Measurement of exclusive 𝜋 + -argon interactions using ProtoDUNE-SP

We present the measurement of 𝜋 + -argon inelastic cross sections using the ProtoDUNE single-phase liquid argon time projection chamber in the incident 𝜋 + kinetic energy range of 500–800 MeV in multiple exclusive channels (absorption, charge exchange, and the remaining inelastic interactions). The results of this analysis are important inputs to simulations of liquid argon neutrino experiments such as the Deep Underground Neutrino Experiment and the Short Baseline Neutrino program at Fermi National Accelerator Laboratory. They will be employed to improve the modeling of final state interactions within neutrino event generators used by these experiments, as well as the modeling of 𝜋 + -argon secondary interactions within the liquid argon. This is the first measurement of 𝜋 + -argon absorption at this kinetic energy range as well as the first ever measurement of 𝜋 + -argon charge exchange.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗