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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson–Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Dissociation dynamics of the diamondoid adamantane upon photoionization by XUV femtosecond pulses

This work presents a photodissociation study of the diamondoid adamantane using extreme ultraviolet femtosecond pulses. The fragmentation dynamics of the dication is unraveled by the use of advanced ion and electron spectroscopy giving access to the dissociation channels as well as their energetics. To get insight into the fragmentation dynamics, we use a theoretical approach combining potential energy surface determination, statistical fragmentation methods and molecular dynamics simulations. We demonstrate that the dissociation dynamics of adamantane dications takes place in a two-step process: barrierless cage opening followed by Coulomb repulsion-driven fragmentation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

DDxNet: a deep learning model for automatic interpretation of electronic health records, electrocardiograms and electroencephalograms

Effective patient care mandates rapid, yet accurate, diagnosis. With the abundance of non-invasive diagnostic measurements and electronic health records (EHR), manual interpretation for differential diagnosis has become time-consuming and challenging. This has led to wide-spread adoption of AI-powered tools, in pursuit of improving accuracy and efficiency of this process. While the unique challenges presented by each modality and clinical task demand customized tools, the cumbersome process of making problem-specific choices has triggered the critical need for a generic solution to enable rapid development of models in practice. In this spirit, we develop DDxNet, a deep architecture for time-varying clinical data, which we demonstrate to be well-suited for diagnostic tasks involving different modalities (ECG/EEG/EHR), required level of characterization (abnormality detection/phenotyping) and data fidelity (single-lead ECG/22-channel EEG). Using multiple benchmark problems, we show that DDxNet produces high-fidelity predictive models, and sometimes even provides significant performance gains over problem-specific solutions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Revisiting trends in the exchange current for hydrogen evolution

Nørskov and collaborators proposed a simple kinetic model to explain the volcano relation for the hydrogen evolution reaction on transition metal surfaces such that j 0 = k 0 f(ΔG H ) where j 0 is the exchange current density, f(ΔG H ) is a function of the hydrogen adsorption free energy ΔG H as computed from density functional theory, and k 0 is a universal rate constant. Herein, focusing on the hydrogen evolution reaction in acidic medium, we revisit the original experimental data and find that the fidelity of this kinetic model can be significantly improved by invoking metal-dependence on k 0 such that the logarithm of k 0 linearly depends on the absolute value of ΔG H . Here, we further confirm this relationship using additional experimental data points obtained from a critical review of the available literature. Our analyses show that the new model decreases the discrepancy between calculated and experimental exchange current density values by up to four orders of magnitude. Furthermore, we show the model can be further improved using machine learning and statistical inference methods that integrate additional material properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Planck 2015 results: XVIII. Background geometry and topology of the Universe

We report that maps of cosmic microwave background (CMB) temperature and polarization from the 2015 release of Planck data provide the highestquality full-sky view of the surface of last scattering available to date. This enables us to detect possible departures from a globally isotropic cosmology. We present the first searches using CMB polarization for correlations induced by a possible non-trivial topology with a fundamental domain that intersects, or nearly intersects, the last-scattering surface (at comoving distance χ rec ), both via a direct scan for matched circular patterns at the intersections and by an optimal likelihood calculation for specific topologies. We specialize to flat spaces with cubic toroidal (T3) and slab (T1) topologies, finding that explicit searches for the latter are sensitive to other topologies with antipodal symmetry. These searches yield no detection of a compact topology with a scale below the diameter of the last-scattering surface. The limits on the radius R i of the largest sphere inscribed in the fundamental domain (at log-likelihood ratio ΔlnL > -5 relative to a simply-connected flat Planck best-fit model) are: R i > 0.97 χ rec for the T3 cubic torus; and R i > 0.56 χ rec for the T1 slab. The limit for the T3 cubic torus from the matched-circles search is numerically equivalent, R i > 0.97 χ rec at 99% confidence level from polarization data alone. We also perform a Bayesian search for an anisotropic global Bianchi VII h geometry. In the non-physical setting, where the Bianchi cosmology is decoupled from the standard cosmology, Planck temperature data favour the inclusion of a Bianchi component with a Bayes factor of at least 2.3 units of log-evidence. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. Fitting the induced polarization pattern for this model to the Planck data requires an amplitude of -0.10 ± 0.04 compared to the value of + 1 if the model were to be correct. In the physically motivated setting, where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VII h cosmology and constrain the vorticity of such models to (ω/H) 0 < 7.6 × 10 -10 (95% CL).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Unexpected topology of the temperature fluctuations in the cosmic microwave background

We study the topology generated by the temperature fluctuations of the cosmic microwave background (CMB) radiation, as quantified by the number of components and holes, formally given by the Betti numbers, in the growing excursion sets. We compare CMB maps observed by the Planck satellite with a thousand simulated maps generated according to the $Λ$CDM paradigm with Gaussian distributed fluctuations. The comparison is multi-scale, being performed on a sequence of degraded maps with mean pixel separation ranging from 0.05 to 7.33°. The survey of the CMB over S 2 is incomplete due to obfuscation effects by bright point sources and other extended foreground objects like our own galaxy. To deal with such situations, where analysis in the presence of “masks” is of importance, we introduce the concept of relative homology. The parametric χ 2 -test shows differences between observations and simulations, yielding p -values at percent to less than permil levels roughly between 2 and 7°, with the difference in the number of components and holes peaking at more than 3 σ sporadically at these scales. The highest observed deviation between the observations and simulations for b 0 and b 1 is approximately between 3 σ and 4 σ at scales of 3–7°. There are reports of mildly unusual behaviour of the Euler characteristic at 3.66° in the literature, computed from independent measurements of the CMB temperature fluctuations by Planck ’s predecessor, the Wilkinson Microwave Anisotropy Probe (WMAP) satellite. The mildly anomalous behaviour of the Euler characteristic is phenomenologically related to the strongly anomalous behaviour of components and holes, or the zeroth and first Betti numbers, respectively. Further, since these topological descriptors show consistent anomalous behaviour over independent measurements of Planck and WMAP, instrumental and systematic errors may be an unlikely source. These are also the scales at which the observed maps exhibit low variance compared to the simulations, and approximately the range of scales at which the power spectrum exhibits a dip with respect to the theoretical model. Non-parametric tests show even stronger differences at almost all scales. Crucially, Gaussian simulations based on power-spectrum matching the characteristics of the observed dipped power spectrum are not able to resolve the anomaly. Understanding the origin of the anomalies in the CMB, whether cosmological in nature or arising due to late-time effects, is an extremely challenging task. Regardless, beyond the trivial possibility that this may still be a manifestation of an extreme Gaussian case, these observations, along with the super-horizon scales involved, may motivate the study of primordial non-Gaussianity. Alternative scenarios worth exploring may be models with non-trivial topology, including topological defect models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Correlated energy uncertainties in reaction rate calculations

Monte Carlo methods can be used to evaluate the uncertainty of a reaction rate that arises from many uncertain nuclear inputs. However, until now no attempt has been made to find the effect of correlated energy uncertainties in input resonance parameters. Our goal is to investigate the impact of correlated resonance energy uncertainties on reaction rates. Using a combination of numerical and Monte Carlo variation of resonance energies, the effect of correlations are investigated. Five reactions are considered: two fictional, illustrative cases and three reactions whose rates are of current interest. The effect of correlations in resonance energies depends on the specific reaction cross section and temperatures considered. When several resonances contribute equally to a reaction rate, and when they are located on either side of the Gamow peak, correlations between their energies dilute their effect on reaction rate uncertainties. If they are both located above or below the maximum of the Gamow peak, however, correlations between their resonance energies can increase the reaction rate uncertainties. This effect can be hard to predict for complex reactions with wide and narrow resonances contributing to the reaction rate.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Clustering of red sequence galaxies in the fourth data release of the Kilo-Degree Survey

We present a sample of luminous red sequence galaxies as the basis for a study of the large-scale structure in the fourth data release of the Kilo-Degree Survey. The selected galaxies are defined by a red sequence template, in the form of a data-driven model of the colour-magnitude relation conditioned on redshift. In this work, the red sequence template was built using the broad-band optical+near infrared photometry of KiDS-VIKING and the overlapping spectroscopic data sets. The selection process involved estimating the red sequence redshifts, assessing the purity of the sample and estimating the underlying redshift distributions of redshift bins. After performing the selection, we mitigated the impact of survey properties on the observed number density of galaxies by assigning photometric weights to the galaxies. We measured the angular two-point correlation function of the red galaxies in four redshift bins and constrain the large-scale bias of our red sequence sample assuming a fixed ΛCDM cosmology. We find consistent linear biases for two luminosity-threshold samples (‘dense’ and ‘luminous’). We find that our constraints are well characterised by the passive evolution model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

J-PLUS: Spectral evolution of white dwarfs by PDF analysis

We estimated the spectral evolution of white dwarfs with effective temperature using the Javalambre Photometric Local Universe Survey (J-PLUS) second data release (DR2), which provides 12 photometric optical passbands over 2176 deg 2 . We analyzed 5926 white dwarfs with r ≤ 19.5 mag in common between a white dwarf catalog defined from Gaia EDR3 and J-PLUS DR2. We performed a Bayesian analysis by comparing the observed J-PLUS photometry with theoretical models of hydrogen- and helium-dominated atmospheres. We estimated the probability distribution functions for effective temperature (T eff ), surface gravity, parallax, and composition; and the probability of having a H-dominated atmosphere (p H ) for each source. We applied a prior in parallax, using Gaia EDR3 measurements as a reference, and derived a self-consistent prior for the atmospheric composition as a function of T eff . We described the fraction of white dwarfs with a He-dominated atmosphere (f He ) with a linear function of the effective temperature at 5000 < T eff < 30 000 K. We find f He = 0.24 ± 0.01 at T eff = 10 000 K, a change rate along the cooling sequence of 0.14 ± 0.02 per 10 kK, and a minimum He-dominated fraction of 0.08 ± 0.02 at the high-temperature end. We tested the obtained p H by comparison with spectroscopic classifications, finding that it is reliable. We estimated the mass distribution for the 351 sources with distance d < 100 pc, mass M > 0.45 M ⊙ , and T eff > 6000 K. The result for H-dominated white dwarfs agrees with previous studies, with a dominant M = 0.59 M ⊙ peak and the presence of an excess at M ~ 0.8 M ⊙ . This high-mass excess is absent in the He-dominated distribution, which presents a single peak. The J-PLUS optical data provide a reliable statistical classification of white dwarfs into H- and He-dominated atmospheres. We find a 21 ± 3% increase in the fraction of He-dominated white dwarfs from T eff = 20 000 K to T eff = 5000 K.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

ConKer: An algorithm for evaluating correlations of arbitrary order

Context. High order correlations in the cosmic matter density have become increasingly valuable in cosmological analyses. However, computing these correlation functions is computationally expensive. Aims. We aim to circumvent these challenges by developing a new algorithm called ConKer for estimating correlation functions. Methods. This algorithm performs convolutions of matter distributions with spherical kernels using FFT. Since matter distributions and kernels are defined on a grid, it results in some loss of accuracy in the distance and angle definitions. We study the algorithm setting at which these limitations become critical and suggest ways to minimize them. Results. ConKer is applied to the CMASS sample of the SDSS DR12 galaxy survey and corresponding mock catalogs, and is used to compute the correlation functions up to correlation order n = 5. We compare the n = 2 and n = 3 cases to traditional algorithms to verify the accuracy of the new algorithm. We perform a timing study of the algorithm and find that three of the four distinct processes within the algorithm are nearly independent of the catalog size N , while one subdominant component scales as O ( N ). The dominant portion of the calculation has complexity of O ( N c 4/3 log N c ), where N c is the of cells in a three-dimensional grid corresponding to the matter density. Conclusions. We find ConKer to be a fast and accurate method of probing high order correlations in the cosmic matter density, then discuss its application to upcoming surveys of large-scale structure.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Detection of open cluster rotation fields from Gaia EDR3 proper motions

Context: Most stars from in groups which with time disperse, building the field population of their host galaxy. In the Milky Way, open clusters have been continuously forming in the disk up to the present time, providing it with stars spanning a broad range of ages and masses. Observations of the details of cluster dissolution are, however, scarce. One of the main difficulties is obtaining a detailed characterisation of the internal cluster kinematics, which requires very high-quality proper motions. For open clusters, which are typically loose groups with tens to hundreds of members, there is the additional difficulty of inferring kinematic structures from sparse and irregular distributions of stars. Aims: Here, we aim to analyse internal stellar kinematics of open clusters, and identify rotation, expansion, or contraction patterns. Methods: We use Gaia Early Data Release 3 (EDR3) astrometry and integrated nested Laplace approximations to perform vector-field inference and create spatio-kinematic maps of 1237 open clusters. The sample is composed of clusters for which individual stellar memberships were already known, thus minimising contamination from field stars in the velocity maps. Projection effects were corrected using EDR3 data complemented with radial velocities from Gaia Data Release 2 and other surveys. Results: We report the detection of rotation patterns in eight open clusters. Nine additional clusters display possible rotation signs. We also observe 14 expanding clusters, with 15 other objects showing possible expansion patterns. Contraction is evident in two clusters, with one additional cluster presenting a more uncertain detection. In total, 53 clusters are found to display kinematic structures. Within these, elongated spatial distributions suggesting tidal tails are found in five clusters. These results indicate that the approach developed here can recover kinematic patterns from noisy vector fields, as those from astrometric measurements of open clusters or other stellar or galactic populations, thus offering a powerful probe for exploring the internal kinematics and dynamics of these types of objects.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Massive star-forming galaxies have converted most of their halo gas into stars

In the local Universe, the efficiency for converting baryonic gas into stars is very low. In dark matter halos where galaxies form and evolve, the average efficiency varies with galaxy stellar mass and has a maximum of about 20% for Milky-Way-like galaxies. The low efficiency at higher mass is believed to be the result of some quenching processes, such as the feedback from active galactic nuclei. We perform an analysis of weak lensing and satellite kinematics for SDSS central galaxies. Our results reveal that the efficiency is much higher, more than 60%, for a large population of massive star-forming galaxies around 10 11 M ⊙ . This suggests that these galaxies acquired most of the gas in their halos and converted it into stars without being significantly affected by quenching processes. This population of galaxies is not reproduced in current galaxy formation models, indicating that our understanding of galaxy formation is incomplete. The implications of our results on circumgalactic media, star-formation quenching, and disk galaxy rotation curves are discussed. We also examine systematic uncertainties in halo-mass and stellar-mass measurements that might influence our results.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

BeyondPlanck: XV. Limits on large-scale polarized anomalous microwave emission from Planck LFI and WMAP

We constrained the level of polarized anomalous microwave emission (AME) on large angular scales using Planck Low-Frequency Instrument (LFI) and WMAP polarization data within a Bayesian cosmic microwave background (CMB) analysis framework. We modeled synchrotron emission with a power-law spectral energy distribution, as well as the sum of AME and thermal dust emission through linear regression with the Planck High-Frequency Instrument (HFI) 353 GHz data. This template-based dust emission model allowed us to constrain the level of polarized AME while making minimal assumptions on its frequency dependence. We neglected CMB fluctuations, but show through simulations that these fluctuations have a minor impact on the results. We find that the resulting AME polarization fraction confidence limit is sensitive to the polarized synchrotron spectral index prior. In addition, for prior means β s < -3.1 we find an upper limit of p AME max ≲ 0.6% (95% confidence). In contrast, for means β s = -3.0, we find a nominal detection of p AME = 2.5 ± 1.0% (95% confidence). These data are thus not strong enough to simultaneously and robustly constrain both polarized synchrotron emission and AME, and our main result is therefore a constraint on the AME polarization fraction explicitly as a function of β s . Combining the current Planck and WMAP observations with measurements from high-sensitivity low-frequency experiments such as C-BASS and QUIJOTE will be critical to improve these limits further.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Photometric redshift-aided classification using ensemble learning

We present SHEEP, a new machine learning approach to the classic problem of astronomical source classification, which combines the outputs from the XGBoost, LightGBM, and CatBoost learning algorithms to create stronger classifiers. A novel step in our pipeline is that prior to performing the classification, SHEEP first estimates photometric redshifts, which are then placed into the data set as an additional feature for classification model training; this results in significant improvements in the subsequent classification performance. SHEEP contains two distinct classification methodologies: (i) Multi-class and (ii) one versus all with correction by a meta-learner. We demonstrate the performance of SHEEP for the classification of stars, galaxies, and quasars using a data set composed of SDSS and WISE photometry of 3.5 million astronomical sources. The resulting F1 -scores are as follows: 0.992 for galaxies; 0.967 for quasars; and 0.985 for stars. In terms of the F1-scores for the three classes, SHEEP is found to outperform a recent RandomForest-based classification approach using an essentially identical data set. Our methodology also facilitates model and data set explainability via feature importances; it also allows the selection of sources whose uncertain classifications may make them interesting sources for follow-up observations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The miniJPAS survey: White dwarf science with 56 optical filters

We analyze the white dwarf population in miniJPAS, the first square degree observed with 56 medium-band, 145 Å in width optical filters by the Javalambre Physics of the accelerating Universe Astrophysical Survey (J-PAS), to provide a data-based forecast for the white dwarf science with low-resolution ($R$ ~ 50) photo-spectra. We define the sample of the bluest point-like sources in miniJPAS with $r$ < 21.5 mag, a point-like probability larger than 0.5, ($u$ - $r$)< 0.80 mag, and ($g$ - $i$)< 0.25 mag. This sample comprises 33 sources with spectroscopic information: 11 white dwarfs and 22 quasi-stellar objects (QSOs). We estimate the effective temperature ($T$ eff ), the surface gravity, and the composition of the white dwarf population by a Bayesian fitting to the observed photo-spectra. The miniJPAS data are sensitive to the Balmer series and the presence of polluting metals. Our results, combined with those from the Javalambre Photometric Local Universe Survey (J-PLUS) which has a lower spectral resolution but has already observed thousands of white dwarfs, suggest that J-PAS photometry would permit – down to $r$ ~ 21.5 mag and at least for sources with 7000 < $T$ eff < 22 000 K – both the classification of the observed white dwarfs into H-dominated and He-dominated with 99% confidence and the detection of calcium absorption for equivalent widths larger than 15 Å. The effective temperature is estimated with a 2% uncertainty, which is close to the 1% from spectroscopy. A precise estimation of the surface gravity depends on the available parallax information. In addition, the white dwarf population at $T$ eff > 7000 K can be segregated from the bluest extragalactic QSOs, providing a clean sample based on optical photometry alone. The J-PAS low-resolution photo-spectra would produce precise effective temperatures and atmospheric compositions for white dwarfs, complementing the data from Gaia. J-PAS will also detect and characterize new white dwarfs beyond the Gaia magnitude limit, providing faint candidates for spectroscopic follow-up.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Spectral evidence of solar neighborhood analogs in CALIFA galaxies

We introduce a novel nonparametric method to find solar neighborhood analogs (SNAs) in extragalactic integral field spectroscopic surveys. The main ansatz is that the physical properties of the solar neighborhood (SN) should be encoded in its optical stellar spectrum. We assume that our best estimate of such a spectrum is the one extracted from the analysis performed by the Code for Stellar properties Heuristic Assignment (CoSHA) from the MaStar stellar library. It follows that finding SNAs in other galaxies consist in matching, in a χ 2 sense, the SN reference spectrum across the optical extent of the observed galaxies. We applied this procedure to a selection of CALIFA galaxies, by requiring a close to face-on projection, relative isolation, and non-active galactic nucleus. We explore how the local and global properties of the SNAs (stellar age, metallicity, dust extinction, mass-to-light ratio, stellar surface mass density, star-formation density, and galactocentric distance) and their corresponding host galaxies (morphological type, total stellar mass, star-formation rate, and effective radius) compared with those of the SN and the Milky Way (MW). We find that SNAs are located preferentially in S(B)a–S(B)c galaxies, in a ring-like structure, which radii seem to scale with the galaxy size. Despite the known sources of systematics and errors, most properties present a considerable agreement with the literature on the SN. We conclude that the solar neighborhood is relatively common in our sample of SNAs. Our results warrant a systematic exploration of correlations among the physical properties of the SNAs and their host galaxies. We reckon that our method should inform current models of the galactic habitable zone in our MW and other galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗