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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Cosmological preference for a negative neutrino mass

The most precise determination of the sum of neutrino masses from cosmological data, derived from analysis of the cosmic microwave background (CMB) and baryon acoustic acoustic oscillations (BAO) from the Dark Energy Spectroscopic Instrument (DESI), favors a value below the minimum inferred from neutrino flavor oscillation experiments. We explore which data is most responsible of this puzzling aspect of the current constraints on neutrino mass and whether it is related to other anomalies in cosmology. We demonstrate conclusively that the preference for negative neutrino masses is a consequence of larger than expected lensing of the CMB in both the two- and four-point lensing statistics. Furthermore, we show that this preference is robust to changes in likelihoods of the BAO and CMB optical depth analyses given the available data. We then show that this excess clustering is not easily explained by changes to the expansion history and is likely distinct from the preference for for dynamical dark energy in DESI BAO data. Finally, we discuss how future data may impact these results, including an analysis of Planck CMB with mock DESI 5-year data. Here, we conclude that the negative neutrino mass preference is likely to persist even as more cosmological data is collected in the near future.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2021

Observation of Undulator Radiation Generated by a Single Electron Circulating in a Storage Ring and Possible Applications

An experimental study into the undulator radiation, generated by a single electron was carried out at the Integrable Optics Test Accelerator (IOTA) storage ring at Fermilab. The individual photons were detected by a Single Photon Avalanche Diode (SPAD) at an average rate of 1 detection per 300 revolutions in the ring. The detection events were continuously recorded by a picosecond event timer for as long as 1 minute at a time. The collected data were used to test if there is any deviation from the classically predicted Poissonian photostatistics. It was motivated by the observation * of sub-Poissonian statistics in a similar experiment. The observation * could be an instrumentation effect related to low detection efficiency and long detector dead time. In our experiment, the detector (SPAD) has a much higher efficiency (65%) and a much lower dead time. In addition, we show that the collected data (recorded detection times) can be used to study the synchrotron motion of a single electron and infer some parameters of the ring. For example, by comparing the results of simulation and measurement for the synchrotron motion we were able to estimate the magnitude of the RF phase jitter.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSCquartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study.

Bjorner, Marianne B.↗
DOE OSTI2025

Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data

Abstract Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007–2008 Swedish HIV-1 outbreak and the broader 1998–2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available at https://github.com/MolEvolEpid/SEEPS.

Virology↗
DOE OSTI2023

Constructing a Simulation Surrogate with Partially Observed Output

Gaussian process surrogates are a popular alternative to directly using computationally expensive simulation models. When the simulation output consists of many responses, dimension-reduction techniques are often employed to construct these surrogates. However, surrogate methods with dimension reduction generally rely on complete output training data. This article proposes a new Gaussian process surrogate method that permits the use of partially observed output while remaining computationally efficient. The new method involves the imputation of missing values and the adjustment of the covariance matrix used for Gaussian process inference. The resulting surrogate represents the available responses, disregards the missing responses, and provides meaningful uncertainty quantification. In conclusion, the proposed approach is shown to offer sharper inference than alternatives in a simulation study and a case study where an energy density functional model that frequently returns incomplete output is calibrated.

42 ENGINEERING↗
DOE OSTI2025

Correlations between the Neutron Star Mass–Radius Relation and the Equation of State of Dense Matter

We develop an analytic method of inverting the Tolman–Oppenheimer–Volkoff relations to high accuracy. In principle, a specified energy density–pressure relation gives a unique mass–radius (M–R) relation and vice versa. Our method is developed from the strong correlations that are shown to exist between the neutron star mass–radius curve and the equation of state (EOS) or pressure–energy density relation. Selecting points that have masses equal to fixed fractions of the maximum mass, we find a semi-universal power-law relation between the central energy densities, pressures, sound speeds, chemical potentials, and number densities of those stars, with the maximum mass and the radii of one or more fractional maximum mass points. Rms fitting accuracies, for EOSs without large first-order phase transitions, are typically 0.5% for all quantities at all mass points. The method also works well, although less accurately, in reconstructing the EOS of hybrid stars with first-order phase transitions. These results permit, in effect, an analytic method of inverting an arbitrary M–R curve to yield its underlying EOS. We discuss applications of this inversion technique to the inference of the dense matter EOS from measurements of neutron star masses and radii as a possible alternative to traditional Bayesian approaches.

Bayesian statistics↗
DOE OSTI2026

Data Summarization and Inference at Scale

This is the final report for the DOE ASCR grant SC-0022260, Data Summarization and Inference at Scale, PI: Alex Pothen, Purdue University. The goal of the project was to solve data-intensive and compute-intensive problems in the physical sciences, engineering, information science, data science, etc. by designing and implementing new algorithms that could work with a subset of the data. The four subgoals were: (a) The solution of problems where the data is too large to be stored in the memory of a computer. In this streaming model of computation, the data arrives as a stream of elements to the computer, each element is processed as it arrives, and a decision is made to discard the data or to store it; only a small subset of the data proportional to the size of the output solution is stored, and when all the data has been streamed, a solution to the problem is computed from the stored subset. (b) The use of machine learning methods to compute solutions to data-intensive problems. The use of GPUs is critical to obtain high performance on machine learning tasks, but their memory sizes are smaller relative to that of CPUs. For large-scale problems, the data is sampled many times, and small samples are used with repetition, for robustness, to compute solutions to inference tasks. This sampling reduces the memory required to solve the problem, but attention is needed to avoid slow convergence to the solutions, and reduced accuracy of inference. We propose submodular optimization, Large Language Models, and physics-informed neural networks to enable GPU computations here. (c) Modeling and visualization of high-dimensional data using interpretable features. Clinical proteomic data sets from immunology for the detection of cancer and other diseases are temporal and high-dimensional, and algorithms for visualizing these data sets using clinically interpretable features are lacking. We propose methods that compute distances based on the optimal transportation problem and graph edit distances to address this problem. We also propose the use of optimal transport-based distances, spatial statistics, and network structure to classify image data sets, We apply these algorithms to electron micrographs of the peripheral nervous system in the digestive tract. (d) The design of data-intensive algorithms on emerging architectures, specifically, noisy, intermediate-scale quantum (NISQ) devices. Quantum computers offer the possibility of exploring large solution spaces due to the principle of superposition, but current quantum computers are limited by few qubits, short coherence times due to noise, poor interconections among the qubits, etc. We propose the use of the divide and conquer paradigm to solve large-scale problems, wherein collections of small subproblems are solved on the quantum devices, and the solutions to the subproblems are integrated into a solution for the original problem on a classical computer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Statistical Uncertainty in Paleoclimate Proxy Reconstructions

A quantitative analysis of any environment older than the instrumental record relies on proxies. Uncertainties associated with proxy reconstructions are often underestimated, which can lead to artificial conflict between different proxies, and between data and models. In this paper, using ordinary least squares linear regression as a common example, we describe a simple, robust and generalizable method for quantifying uncertainty in proxy reconstructions. We highlight the primary controls on the magnitude of uncertainty, and compare this simple estimate to equivalent estimates from Bayesian, nonparametric and fiducial statistical frameworks. We discuss when it may be possible to reduce uncertainties, and conclude that the unexplained variance in the calibration must always feature in the uncertainty in the reconstruction. This directs future research toward explaining as much of the variance in the calibration data as possible. We also advocate for a “data-forward” approach, that clearly decouples the presentation of proxy data from plausible environmental inferences.

58 GEOSCIENCES↗
DOE OSTI2023

Pulse profile modelling of thermonuclear burst oscillations – II. Handling variability

ABSTRACT Pulse profile modelling is a relativistic ray-tracing technique that can be used to infer masses, radii, and geometric parameters of neutron stars. In a previous study, we looked at the performance of this technique when applied to thermonuclear burst oscillations from accreting neutron stars. That study showed that ignoring the variability associated with burst oscillation sources resulted in significant biases in the inferred mass and radius, particularly for the high count rates that are nominally required to obtain meaningful constraints. In this follow-on study, we show that the bias can be mitigated by slicing the bursts into shorter segments where variability can be neglected, and jointly fitting the segments. Using this approach, the systematic uncertainties on the mass and radius are brought within the range of the statistical uncertainty. With about 106 source counts, this yields uncertainties of approximately 10 per cent for both the mass and radius. However, this modelling strategy requires substantial computational resources. We also confirm that the posterior distributions of the mass and radius obtained from multiple bursts of the same source can be merged to produce outcomes comparable to that of a single burst with an equivalent total number of counts.

Astronomy & Astrophysics↗
DOE OSTI2026

pop-cosmos : redshifts and physical properties of KiDS-1000 galaxies

ABSTRACT Principled Bayesian inference of galaxy properties has not previously been performed for wide-area weak-lensing surveys with millions of sources. We address this gap by applying the pop-cosmos generative model to perform spectral energy distribution (SED) fitting for 4 million KiDS (Kilo-Degree Survey)-1000 galaxies. Calibrated on deep COSMOS2020 photometric data, pop-cosmos specifies a physically motivated prior over the galaxy population up to $z \simeq 6$ in stellar population synthesis (SPS) parameter space. Using the Speculator SPS emulator with GPU (graphics processing unit)-accelerated Markov Chain Monte Carlo sampling, we perform full posterior inference at 8.2 GPU seconds per galaxy, obtaining joint constraints on galaxy redshifts and physical properties. We validate photometric redshifts against $\sim \!185\,\!000$ KiDS galaxies cross-matched to Dark Energy Spectroscopic Instrument Data Release 1 spectroscopic samples, achieving low bias ($2\times 10^{-3}$), scatter ($\sigma _{\mathrm{MAD}}=0.03$), and outlier fraction (3.2 per cent) for the Bright Galaxy Survey, with comparable performance (bias $3\times 10^{-2}$, $\sigma _{\mathrm{MAD}}=0.05$, 1.0 per cent outliers) for luminous red galaxies (LRGs). Within the LRG sample, we identify massive, dusty, star-forming contaminants at $z \simeq 0.4$ satisfying standard colour selections for quenched populations. We infer trends in stellar mass, star formation, metallicity, and dust across five tomographic redshift bins consistent with established scaling relations. Using specific star formation rate constraints, we identify $\sim$7 per cent of KiDS-1000 galaxies as quenched, versus 37 per cent implied by conservative colour cuts. This enables the construction of weak-lensing samples defined by physical properties while mitigating intrinsic alignment systematics and preserving statistical power. Our analysis validates pop-cosmos out of sample, establishing it as a scalable approach for galaxy evolution and cosmological analyses with photometric surveys.

Halder, Anik [Institute of Astronomy and Kavli Ins↗
DOE OSTI2025

Joint cosmic density reconstruction from photometric and spectroscopic samples

ABSTRACT We reconstruct the dark matter density field from spatially overlapping spectroscopic and photometric redshift catalogues through a field-level forward modelling approach. Instead of directly inferring the underlying density field, we find the best-fitting initial Gaussian fluctuations that will evolve into the observed cosmic volume. To account for the substantial uncertainty of photometric redshifts we employ a differentiable continuous Poisson process. As an initial test, we construct a mock based on the upcoming Prime Focus Spectrograph combined with photometric sample modelled on the Subaru Hyper Suprime-Cam. Depending on the statistic of interest, we find improvements in cosmic structure classification equivalent to 50–100 per cent more spectroscopic targets by combining relatively sparse spectroscopic with dense photometric samples.

Horowitz, B.↗
DOE OSTI2020

STRIDES: a 3.9 per cent measurement of the Hubble constant from the strong lens system DES J0408−5354

We present a blind time-delay cosmographic analysis for the lens system DES J0408−5354. This system is extraordinary for the presence of two sets of multiple images at different redshifts, which provide the opportunity to obtain more information at the cost of increased modelling complexity with respect to previously analysed systems. We perform detailed modelling of the mass distribution for this lens system using three band Hubble Space Telescope imaging. We combine the measured time delays, line-of-sight central velocity dispersion of the deflector, and statistically constrained external convergence with our lens models to estimate two cosmological distances. We measure the ‘effective’ time-delay distance corresponding to the redshifts of the deflector and the lensed quasar |$D_{\Delta t}^{\rm eff}=$||$3382_{-115}^{+146}$| Mpc and the angular diameter distance to the deflector D_d = |$1711_{-280}^{+376}$| Mpc, with covariance between the two distances. From these constraints on the cosmological distances, we infer the Hubble constant H_0= |$74.2_{-3.0}^{+2.7}$| km s^−1 Mpc^−^1 assuming a flat ΛCDM cosmology and a uniform prior for Ω_m as |$\Omega _{\rm m} \sim \mathcal {U}(0.05, 0.5)$|⁠. This measurement gives the most precise constraint on H_0 to date from a single lens. Our measurement is consistent with that obtained from the previous sample of six lenses analysed by the H_0 Lenses in COSMOGRAIL’s Wellspring (H0LiCOW) collaboration. It is also consistent with measurements of H_0 based on the local distance ladder, reinforcing the tension with the inference from early Universe probes, for example, with 2.2σ discrepancy from the cosmic microwave background measurement.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Inference of the Mass Composition of Cosmic Rays with Energies from 10 18.5 to 10 20 eV Using the Pierre Auger Observatory and Deep Learning

We present measurements of the atmospheric depth of the shower maximum X max , inferred for the first time on an event-by-event level using the surface detector of the Pierre Auger Observatory. Using deep learning, we were able to extend measurements of the X max distributions up to energies of 100 EeV ( 10 20 eV ), not yet revealed by current measurements, providing new insights into the mass composition of cosmic rays at extreme energies. Gaining a 10-fold increase in statistics compared to the fluorescence detector data, we find evidence that the rate of change of the average X max with the logarithm of energy features three breaks at 6.5 ± 0.6 ( stat ) ± 1 ( syst ) EeV , 11 ± 2 ( stat ) ± 1 ( syst ) EeV , and 31 ± 5 ( stat ) ± 3 ( syst ) EeV , in the vicinity to the three prominent features (ankle, instep, suppression) of the cosmic-ray flux. The energy evolution of the mean and standard deviation of the measured X max distributions indicates that the mass composition becomes increasingly heavier and purer, thus being incompatible with a large fraction of light nuclei between 50 and 100 EeV. Published by the American Physical Society 2025

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Evidence for Suppression of Structure Growth in the Concordance Cosmological Model

We present evidence for a suppressed growth rate of large-scale structure during the dark-energy dominated era. Modeling the growth rate of perturbations with the ``growth index'' γ, we find that current cosmological data strongly prefer a higher growth index than the value γ=0.55 predicted by general relativity in a flat ΛCDM cosmology. Both the cosmic microwave background data from Planck and the large-scale structure data from weak lensing, galaxy clustering, and cosmic velocities separately favor growth suppression. When combined, they yield γ = 0.633$^{+0.025}_{–0.024}$, excluding γ = 0.55 at a statistical significance of 3.7σ. The combination of fσ8 and Planck measurements prefers an even higher growth index of γ = 0.639$^{+0.024}_{–0.025}$, corresponding to a 4.2σ-tension with the concordance model. In Planck data, the suppressed growth rate offsets the preference for nonzero curvature and fits the data equally well as the latter model. Furthermore, a higher γ leads to a higher matter fluctuation amplitude S 8 inferred from galaxy clustering and weak lensing measurements, and a lower S 8 from Planck data, effectively resolving the S 8 tension.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

State-to-State Molecular Reactions in the Ultracold Regime (Final Scientific Report)

We have achieved the proposed goal to experimentally probe the AB + CD and AB + C types of reactions with state-to-state resolution, which we also compared to advanced theoretical calculations to help elucidate the role of quantum mechanics in the processes of bond breakage and formation. Our approach uses reactants that are prepared at ultracold temperatures (< 1µK) such that the quantum effects of translational motion are an important factor. Specific example reactions, including the potassium-rubidium metathesis reaction KRb + KRb → K 2 + Rb 2 as well as the atom exchange reaction Rb + KRb → Rb2 + K, are chosen because the technology of quantum internal and motional state control of these types of molecules is particularly advanced. The results for the entire funding period are fruitful. For the majority of this grant, we have constructed a one-of-the-kind quantum degenerate gas apparatus that integrates ion detection and velocity map imaging capabilities, allowing us to explore the KRb + KRb → K 2 + Rb 2 bimolecular reaction in detail. Specifically, we first verified such a reaction indeed proceed at ultracold temperatures by direct detection of reaction products. We then mapped out the complete product state distribution, which was compared to a state-counting model based on statistical theory. Our results show an overall agreement with the statistical state counting model, but also reveal several deviating state-pairs. An exact quantum calculation for molecule-molecule collisions, that is needed to understand these deviations, is however beyond the current state-of-the-art. Beside scrutinizing the reaction products, we also directly observe the reaction intermediate complex, which was quite a surprise to us. The intermediate complexes are long-lived and can interact with the inferred light that we use to trap the ultracold gas. After molecule-molecule collisions, we then explored the more theoretically tractable Rb + KRb reaction, which is endothermic. Surprisingly, we observed an exceedingly long-lived KRb$^*_2$ collisional complexes, with our experimentally measured complex lifetime deviating from conventional theoretical calculations by five orders of magnitude. This discrepancy has motivated many explorations of possible underlying causes, though no model yet captures this phenomenon completely. In the final year and the work that continues today, we extend upon these atom-molecule collision experiments to explore the origin of the long-lived KRb$^*_2$ complex lifetime and develop means to control the outcome of the reaction complex. The 5-year funded work advanced our understanding of chemical reactions at the lowest possible temperatures and at the same time opened up many new questions that are beyond our initial imaginations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Computing Nonlinear Power Spectra Across Dynamical Dark Energy Model Space with Neural ODEs

I show how to compute the nonlinear power spectrum across the entire $w(z)$ dynamical dark energy model space. Using synthetic ΛCDM data, I train a neural ordinary differential equation (ODE) to infer the evolution of the nonlinear matter power spectrum as a function of the background expansion and mean matter density across ∼9 Gyr of cosmic evolution. After training, the model generalises to any dynamical dark energy model parameterised by $w(z)$. With little optimisation, the neural ODE is accurate to within 4% up to $k = 5\, h\, {\mathrm Mpc}^{−1}$. Unlike simulation rescaling methods, neural ODEs naturally extend to summary statistics beyond the power spectrum that are sensitive to the growth history.

cosmology↗
DOE OSTI2023

A forward modeling approach to analyzing galaxy clustering with S IM BIG

We present cosmological constraints from a simulation-based inference (SBI) analysis of galaxy clustering from the SimBIG forward modeling framework. SimBIG leverages the predictive power of high-fidelity simulations and provides an inference framework that can extract cosmological information on small nonlinear scales. In this work, we apply SimBIG to the Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxy sample and analyze the power spectrum, P ℓ (k), to k max = 0.5 h/Mpc. We construct 20,000 simulated galaxy samples using our forward model, which is based on 2,000 high-resolution Quijote N -body simulations and includes detailed survey realism for a more complete treatment of observational systematics. We then conduct SBI by training normalizing flows using the simulated samples and infer the posterior distribution of ΛCDM cosmological parameters: Ω m , Ω b , h, n s , σ 8 . We derive significant constraints on Ω m and σ 8 , which are consistent with previous works. Our constraint on σ 8 is 27% more precise than standard P ℓ analyses because we exploit additional cosmological information on nonlinear scales beyond the limit of current analytic models, k > 0.25 h/Mpc. This improvement is equivalent to the statistical gain expected from a standard P ℓ analysis of galaxy sample ~ 60% larger than CMASS. While we focus on P ℓ in this work for validation and comparison to the literature, SimBIG provides a framework for analyzing galaxy clustering using any summary statistic. We expect further improvements on cosmological constraints from subsequent SimBIG analyses of summary statistics beyond P ℓ .

79 ASTRONOMY AND ASTROPHYSICS↗