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DOE OSTI2023

Primordial non-Gaussianity with angular correlation function: integral constraint and validation for DES

ABSTRACT Local primordial non-Gaussianity (PNG) is a promising observable of the underlying physics of inflation, characterized by $f_{\rm NL}^{\rm loc}$. We present the methodology to measure $f_{\rm NL}^{\rm loc}$ from the Dark Energy Survey (DES) data using the two-point angular correlation function (ACF) with scale-dependent bias. One of the focuses of the work is the integral constraint (IC). This condition appears when estimating the mean number density of galaxies from the data and is key in obtaining unbiased $f_{\rm NL}^{\rm loc}$ constraints. The methods are analysed for two types of simulations: ∼246 goliat-png N-body small area simulations with fNL equal to −100 and 100, and 1952 Gaussian ice-cola mocks with fNL = 0 that follow the DES angular and redshift distribution. We use the ensemble of goliat-png mocks to show the importance of the IC when measuring PNG, where we recover the fiducial values of fNL within the 1σ when including the IC. In contrast, we found a bias of ΔfNL ∼ 100 when not including it. For a DES-like scenario, we forecast a bias of ΔfNL ∼ 23, equivalent to 1.8σ, when not using the IC for a fiducial value of fNL = 100. We use the ice-cola mocks to validate our analysis in a realistic DES-like set-up finding it robust to different analysis choices: best-fitting estimator, the effect of IC, BAO damping, covariance, and scale choices. We forecast a measurement of fNL within σ(fNL) = 31 when using the DES-Y3 BAO sample, with the ACF in the 1 deg < θ < 20 deg range.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

IGM damping wing constraints on the tail end of reionization from the enlarged XQR-30 sample

ABSTRACT The attenuation of Lyα photons by neutral hydrogen in the intergalactic medium (IGM) at z ≳ 5 continues to be a powerful probe for studying the epoch of reionization. Given a framework to estimate the intrinsic (true) Lyα emission of high-z sources, one can infer the ionization state of the IGM during reionization. In this work, we use the enlarged XQR-30 sample of 42 high-resolution and high signal-to-noise quasar spectra between $5.8\lesssim \, z\lesssim \, 6.6$ obtained with VLT/X-shooter to place constraints on the IGM neutral fraction. This is achieved using our existing Bayesian QSO reconstruction framework which accounts for uncertainties such as the: (i) posterior distribution of predicted intrinsic Lyα emission profiles (obtained via covariance matrix reconstruction of the Lyα and N v emission lines from unattenuated high-ionization emission line profiles; C iv, Si iv + O iv], and C iii]) and (ii) distribution of ionized regions within the IGM using synthetic damping wing profiles drawn from a 1.63 Gpc3 reionization simulation. Following careful quality control, we used 23 of the 42 available QSOs to obtain constraints/limits on the IGM neutral fraction during the tail-end of reionization. Our median and 68th percentile constraints on the IGM neutral fraction are: $0.20\substack{+0.14 -0.12}$ and $0.29\substack{+0.14 -0.13}$ at z = 6.15 and 6.35. Further, we also report 68th percentile upper limits of $\bar{x}_{\mathrm{H\, {\small I}}{}} \lt 0.21$, 0.20, 0.21, and 0.18 at z = 5.8, 5.95, 6.05, and 6.55. These results imply reionization is still ongoing at $5.8\lesssim \, z\lesssim \, 6.55$, consistent with previous results from XQR-30 (dark fraction and Lyα forest) along with other observational probes considered in the literature.

Greig, B. (ORCID:0000000240852094)↗
DOE OSTI2024

Measurements of the z > 5 Lyman-α forest flux autocorrelation functions from the extended XQR-30 data set

We present the first observational measurements of the Lyman-α (Ly α) forest flux autocorrelation functions in ten redshift bins from 5.1 ≤ z ≤ 6.0. We use a sample of 35 quasar sightlines at z > 5.7 from the extended XQR-30 data set; these data have signal-to-noise ratios of >20 per spectral pixel. We carefully account for systematic errors in continuum reconstruction, instrumentation, and contamination by damped Ly α systems. With these measurements, we introduce software tools to generate autocorrelation function measurements from any simulation. Our measurements of the smallest bin of the autocorrelation function increase with redshift when normalizing by the mean flux, $\langle{F}\rangle$. This increase may come from decreasing $\langle{F}\rangle$ or increasing mean free path of hydrogen-ionizing photons, λmfp. Recent work has shown that the autocorrelation function from simulations at z > 5 is sensitive to λmfp, a quantity that contains vital information on the ending of reionization. For an initial comparison, we show our autocorrelation measurements with simulation models for recently measured λmfp values and find good agreements. Further work in modelling and understanding the covariance matrices of the data is necessary to get robust measurements of λmfp from this data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A strong blend in the morning: studying the circumgalactic medium before cosmic noon with strong, blended Ly α forest systems

ABSTRACT We study of the properties of a new class of circumgalactic medium absorbers identified in the Ly α forest: ‘Strong, Blended Lyman-α’ (or SBLA) absorption systems. We study SBLAs at 2.4 < z < 3.1 in SDSS-IV/eBOSS spectra by their strong extended Ly α absorption complexes covering 138 $\, \, {\rm km}\, {\rm s}^{-1}$ with an integrated $\log (N_{\rm H\, {\small I}}/\mathrm{cm}^{-2}) =16.04$$\substack{+0.05 \\ -0.06}$ and Doppler parameter b = 18.1$\substack{+0.7 \\ -0.4}$$\, \, {\rm km}\, {\rm s}^{-1}$. Clustering with the Ly α forest provides a large-scale structure bias of b = 2.34 ± 0.06 and halo mass estimate of $M_h \approx 10^{12}\, h^{-1}\, {\rm M_{\odot }}$ for our SBLA sample. We measure the ensemble mean column densities of 22 metal features in the SBLA composite spectrum and find that no single-population multiphase model for them is viable. We therefore explore the underlying SBLA population by forward modelling the SBLA absorption distribution. Based on covariance measurements and favoured populations we find that ≈25 per cent of our SBLAs have stronger metals. Using silicon only we find that our strong metal SBLAs trace gas with a log (nH/cm−3) > −2.40 for T = 103.5 K and show gas clumping on <210 parsec scales. We fit multiphase models to this strong subpopulation and find a low ionization phase with nH = 1 cm−3, T = 103.5 K, and [X/H] = 0.8, an intermediate ionization phase with log (nH/cm−3) = −3.05, T = 103.5 K and [X/H] = −0.8, and a poorly constrained higher ionization phase. We find that the low ionization phase favours cold, dense super-solar metallicity gas with a clumping scale of just 0.009 parsecs.

Morrison, Sean (ORCID:0000000267702627)↗
DOE OSTI2024

The 3D Lyman- α forest power spectrum from eBOSS DR16

We measure the three-dimensional power spectrum (P3D) of the transmitted flux in the Lyman-α (Ly α) forest using the complete extended Baryon Oscillation Spectroscopic Survey data release 16 (eBOSS DR16). This sample consists of ~205 000 quasar spectra in the redshift range 2 ≤ z ≤ 4 at an effective redshift z = 2.334. We propose a pair-count spectral estimator in configuration space, weighting each pair by exp( i k ∙ r), for wave vector k and pixel pair separation r, effectively measuring the anisotropic power spectrum without the need for fast Fourier transforms. This accounts for the window matrix in a tractable way, avoiding artefacts found in Fourier-transform based power spectrum estimators due to the sparse sampling transverse to the line of sight of Ly α skewers. We extensively test our pipeline on two sets of mocks: (i) idealized Gaussian random fields with a sparse sampling of Ly α skewers, and (ii) log-normal LyaCoLoRe mocks including realistic noise levels, the eBOSS survey geometry and contaminants. On eBOSS DR16 data, the Kaiser formula with a non-linear correction term obtained from hydrodynamic simulations yields a good fit to the power spectrum data in the range $(0.02 ≤ k ≤ 0.35)$ h Mpc -1 at the 1–2σ level with a covariance matrix derived from LyaCoLoRe mocks. We demonstrate a promising new approach for full-shape cosmological analyses of Ly α forest data from cosmological surveys such as eBOSS, the currently observing Dark Energy Spectroscopic Instrument and future surveys such as the Prime Focus Spectrograph, WEAVE-QSO, and 4MOST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

CMB low multipole alignments across WMAP and Planck data releases

ABSTRACT The first observations of the cosmic microwave background (CMB) from NASA's Wilkinson Microwave Anisotropy Probe (WMAP) led to finding ‘alignment’ anomalies not expected from fluctuations in the isotropic cosmological model. We study the data of all 8 full-sky public releases since then to test for anomalous alignments and shapes of the first 60 multipoles, i.e. over the range $2\le l \le 61$. We use rotationally invariant and covariant statistics to test isotropy of all subsequent WMAP data releases, along with those from the ESA’s Planck mission. Anomalous alignments among the multipoles $l=1, 2, 3$ are very consistent and robust. More alignments are detected, some of them new, while significance is diluted by the large range of the search. Power entropy, a measure of the randomness of the multipoles, is consistently anomalous at about $2\sigma$ level or better across all data releases. It appears that the CMB is not as random as the cosmological principle predicts on large angular scales.

Patel, Sanjeet Kumar↗
DOE OSTI2019

Modelling baryonic physics in future weak lensing surveys

Modifications of the matter power spectrum due to baryonic physics are one of the major theoretical uncertainties in cosmological weak lensing measurements. Developing robust mitigation schemes for this source of systematic uncertainty increases the robustness of cosmological constraints, and may increase their precision if they enable the use of information from smaller scales. Here we explore the performance of two mitigation schemes for baryonic effects in weak lensing cosmic shear: the principal component analysis (PCA) method and the halo-model approach in hmcode. We construct mock tomographic shear power spectra from four hydrodynamical simulations, and run simulated likelihood analyses with cosmolike assuming LSST-like survey statistics. With an angular scale cut of ℓmax < 2000, both methods successfully remove the biases in cosmological parameters due to the various baryonic physics scenarios, with the PCA method causing less degradation in the parameter constraints than hmcode. For a more aggressive ℓmax = 5000, the PCA method performs well for all but one baryonic physics scenario, requiring additional training simulations to account for the extreme baryonic physics scenario of Illustris; hmcode exhibits tensions in the 2D posterior distributions of cosmological parameters due to lack of freedom in describing the power spectrum for $k \gt 10\ h^{-1}\, \mathrm{Mpc}$. We investigate variants of the PCA method and improve the bias mitigation through PCA by accounting for the noise properties in the data via Cholesky decomposition of the covariance matrix. Our improved PCA method allows us to retain more statistical constraining power while effectively mitigating baryonic uncertainties even for a broad range of baryonic physics scenarios.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Cosmological constraints from galaxy–lensing cross-correlations using BOSS galaxies with SDSS and CMB lensing

ABSTRACT We present cosmological parameter constraints based on a joint modelling of galaxy–lensing cross-correlations and galaxy clustering measurements in the SDSS, marginalizing over small-scale modelling uncertainties using mock galaxy catalogues, without explicit modelling of galaxy bias. We show that our modelling method is robust to the impact of different choices for how galaxies occupy dark matter haloes and to the impact of baryonic physics (at the $\sim 2{{\ \rm per\ cent}}$ level in cosmological parameters) and test for the impact of covariance on the likelihood analysis and of the survey window function on the theory computations. Applying our results to the measurements using galaxy samples from BOSS and lensing measurements using shear from SDSS galaxies and CMB lensing from Planck, with conservative scale cuts, we obtain $S_8\equiv \left(\frac{\sigma _8}{0.8228}\right)^{0.8}\left(\frac{\Omega _\mathrm{ m}}{0.307}\right)^{0.6}=0.85\pm 0.05$ (stat.) using LOWZ × SDSS galaxy lensing, and S8 = 0.91 ± 0.1 (stat.) using combination of LOWZ and CMASS × Planck CMB lensing. We estimate the systematic uncertainty in the galaxy–galaxy lensing measurements to be $\sim 6{{\ \rm per\ cent}}$ (dominated by photometric redshift uncertainties) and in the galaxy–CMB lensing measurements to be $\sim 3{{\ \rm per\ cent}}$, from small-scale modelling uncertainties including baryonic physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Cosmology with stacked cluster weak lensing and cluster–galaxy cross-correlations

ABSTRACT Cluster weak lensing is a sensitive probe of cosmology, particularly the amplitude of matter clustering σ8 and matter density parameter Ωm. The main nuisance parameter in a cluster weak lensing cosmological analysis is the scatter between the true halo mass and the relevant cluster observable, denoted $\sigma _{\ln M_\mathrm{ c}}$. We show that combining the cluster weak lensing observable ΔΣ with the projected cluster–galaxy cross-correlation function wp,cg and galaxy autocorrelation function wp,gg can break the degeneracy between σ8 and $\sigma _{\ln M_\mathrm{ c}}$ to achieve tight, per cent-level constraints on σ8. Using a grid of cosmological N-body simulations, we compute derivatives of ΔΣ, wp,cg, and wp,gg with respect to σ8, Ωm, $\sigma _{\ln M_\mathrm{ c}}$, and halo occupation distribution (HOD) parameters describing the galaxy population. We also compute covariance matrices motivated by the properties of the Dark Energy Survey cluster and weak lensing survey and the BOSS CMASS galaxy redshift survey. For our fiducial scenario combining ΔΣ, wp,cg, and wp,gg measured over 0.3−30.0 h−1 Mpc, for clusters at z = 0.35−0.55 above a mass threshold Mc ≈ 2 × 1014 h−1 M⊙, we forecast a $1.4{{\ \rm per\ cent}}$ constraint on σ8 while marginalizing over $\sigma _{\ln M_\mathrm{ c}}$ and all HOD parameters. Reducing the mass threshold to 1 × 1014 h−1 M⊙ and adding a z = 0.15−0.35 redshift bin sharpens this constraint to $0.8{{\ \rm per\ cent}}$. The small-scale (rp < 3.0 h−1 Mpc) ‘mass function’ and large-scale (rp > 3.0 h−1 Mpc) ‘halo-mass cross-correlation’ regimes of ΔΣ have comparable constraining power, allowing internal consistency tests from such an analysis.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Evidence for C ii diffuse line emission at redshift z ∼ 2.6

ABSTRACT C ii is one of the brightest emission lines from star-forming galaxies and is an excellent tracer for star formation. Recent work measured the C ii emission line amplitude for redshifts 2 < z < 3.2 by cross-correlating Planck High Frequency Instrument emission maps with tracers of overdensity from the Baryon Oscillation Spectroscopic Sky Survey, finding ${I}_{{\text C}\,\rm {\small II}}=6.6^{+5.0}_{-4.8}\times {10}^{4}$ Jy sr−1 at $95\,{\text{per cent}}$ confidence level. In this paper, we present a refinement of this earlier work by improving the mask weighting in each of the Planck bands and the precision in the covariance matrix. We report a detection of excess emission in the 545 GHz Planck band separate from the cosmic infrared background (CIB) present in the 353–857 GHz Planck bands. This excess is consistent with redshifted C ii emission, in which case we report $b_{{\text C} \,\rm {\small II}}I_{{\text C} \,\rm {\small II}} =2.0^{+1.2}_{-1.1}\times 10^5$ Jy sr−1 at $95\ {\text {per cent}}$ confidence level, which strongly favours many collisional excitation models of C ii emission. Our detection shows strong evidence for a model with a non-zero C ii parameter, though line intensity mapping observations at high spectral resolution will be needed to confirm this result.

Yang, Shengqi↗
DOE OSTI2021

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases and it lacked a scalable Application Programming Interface (API) for integration into other tools developed by the systems biology community. Here, we report on the recent updates to the database as well as the addition of a new Python-based interface to eQuilibrator that adds many new features such as a 100-fold larger compound database, the ability to add novel compounds, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, the new interface can compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modelling. We foresee that these improvements will make thermodynamic modelling more accessible and facilitate the integration of eQuilibrator into other software platforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of a cap-independent translation enhancer RNA

In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV 2 ) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV 2 tertiary architecture is conserved among these homologs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Abstract New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness over both time and space. In this paper we extend the tools available for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to estimate selection effects at the global level while incorporating both measured and unmeasured heterogeneity among countries. Applying this model to the spread of Omicron in forty countries, we find evidence for very strong but very heterogeneous selection effects. To test whether this heterogeneity is explained by differences in the immune landscape, we considered several measures of vaccination rates and recent population-level infection as covariates, finding moderately strong, statistically significant effects. We also found a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that other region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard consumer-grade computing resources, and will be straightforward to apply to future variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Environmental and ecological signals predict food shortages for subtropical populations of Australian flying foxes, reservoirs of Hendra virus

Food availability determines where and how animals use space across a landscape and, therefore, affects the risk of encounters leading to zoonotic spillover. This relationship is evident in Australian flying foxes (Pteropus spp.; fruit bats), where acute food shortages precede clusters of Hendra virus spillovers. Using machine learning, we predicted months of food shortages from climatological and ecological covariates (1996–2022) in subtropical Australia. Overall accuracy in predicting months of low food availability on a test set from 2018 up to 2022 reached 93.33 and 92.59% based on climatological and bat-level features, respectively. Seasonality and the Oceanic El Niño Index were the most important environmental features, while the number of bats in rescue centres and their body weights were the most important bat-level features. These models support predictive signals up to nine months in advance, facilitating action to mitigate spillover risk.

Pteropus↗
DOE OSTI2025

Study of the connected four-point correlation function of galaxies from the DESI Data Release 1 luminous red galaxy sample

We present a measurement of the non-Gaussian four-point correlation function (4PCF) from the DESI DR1 luminous red galaxy (LRG) sample. For the gravitationally induced parity-even 4PCF, we detect a signal with a significance of 14.7⁢𝜎 using our fiducial setup. We assess the robustness of this detection through a series of validation tests, including auto and cross-correlation analyses, sky partitioning across multiple patch combinations, and variations in radial scale cuts. Due to the low completeness of the sample, we find that differences in fiber assignment implementation schemes can significantly impact estimation of the covariance and introduce biases in the data vector. After correcting for these effects, all tests yield consistent results. This is one of the first measurements of the connected 4PCF on the DESI LRG sample; the good agreement between the simulation and the data implies that the amplitude of the density fluctuation inferred from the connected 4PCF is consistent with the Planck Λ⁢ CDM cosmology. The methodology and diagnostic framework established in this work provide a foundation for interpreting parity-odd 4PCF.

Cosmology↗
DOE OSTI2025

Cosmology with second- and third-order shear statistics for the Dark Energy Survey: Methods and simulated analysis

We present a new pipeline designed for the robust inference of cosmological parameters using both second- and third-order shear statistics. We build a theoretical model for rapid evaluation of three-point correlations using our fastnc code and integrate it into the cosmosis framework. We measure the two-point functions 𝜉 ± and the full configuration-dependent three-point shear correlation functions across all auto- and cross-redshift bins. We compress the three-point functions into the mass aperture statistic ⟨ℳ$^{3}_{ap}$⟩ for a set of 796 simulated shear maps designed to model the Dark Energy Survey Year 3 data. We estimate from it the full covariance matrix and model the effects of intrinsic alignments, shear calibration biases and photometric redshift uncertainties. We apply scale cuts to minimize the contamination from the baryonic signal as modeled through hydrodynamical simulations. We find a significant improvement of 83% on the figure of merit in the Ω m − 𝑆 8 plane when we add the ⟨ℳ$^{3}_{ap}$⟩ data to 𝜉 ± . Here, we present our findings for all relevant cosmological and systematic uncertainty parameters and discuss the complementarity of third-order and second-order statistics.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Self-consistent microscopic calculations for electron captures on nuclei in core-collapse supernovae

Calculations for electron capture rates on nuclei with atomic numbers between 𝑍 = 20 and 𝑍 = 52 are performed in a self-consistent finite-temperature covariant energy density functional theory within the relativistic quasiparticle random-phase approximation. Electron captures on these nuclei contribute most to reducing the electron fraction during the collapse phase of core-collapse supernovae. The rates include contributions from allowed (Gamow-Teller) and first-forbidden (FF) transitions, and it is shown that the latter become dominant at high stellar densities and temperatures. Temperature-dependent effects such as Pauli unblocking and transitions from thermally excited states are also included. The new rates are implemented in a spherically symmetric one-dimensional simulation of the core-collapse phase. The results indicate that the increase in electron capture rates, due to inclusion of FF transitions, leads to reductions of the electron fraction at nuclear saturation density, the peak neutrino luminosity, and enclosed mass at core bounce. The new rates reaffirm that the most relevant nuclei for the deleptonization situate around the 𝑁 = 50 and 82 shell closures, but, compared to previous simulations, nuclei are less proton rich. Here, the new rates developed in this work are available, and will be of benefit to improve the accuracy of multidimensional supernova simulations.

Electron & muon capture↗