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DOE OSTI2024

Bayesian Neural Network Variational Autoencoder Inverse Mapper (BNN-VAIM) and its application in Compton Form Factors extraction

Abstract We extend the Variational Autoencoder Inverse Mapper (VAIM) framework for the inverse problem of extracting Compton Form Factors (CFFs) from deeply virtual exclusive reactions, such as the unpolarized Deeply virtual exclusive scattering (DVCS) cross section. VAIM is an end-to-end deep learning framework to address the solution ambiguity issue in ill-posed inverse problems, which comprises of a forward mapper and a backward mapper to simulate the forward and inverse processes, respectively. In particular, we incorporate Bayesian Neural Network (BNN) into the VAIM architecture (BNN-VAIM) for uncertainty quantification. By sampling the weights and biases distributions of the BNN in the backward mapper of the VAIM, BNN-VAIM is able to estimate prediction uncertainty associated with each individual solution obtained for an ill-posed inverse problem. We first demonstrate the uncertainty quantification capability of BNN-VAIM in a toy inverse problem. Then, we apply BNN-VAIM to the inverse problem of extracting 8 CFFs from the unpolarized DVCS cross section.

Instruments & Instrumentation↗

DOE OSTI2025

Monte Carlo method for constructing confidence intervals with unconstrained and constrained nuisance parameters in the NOvA experiment

Measuring observables to constrain models using maximum-likelihood estimation is fundamental to many physics experiments. Wilks' theorem provides a simple way to construct confidence intervals on model parameters, but it only applies under certain conditions. These conditions, such as nested hypotheses and unbounded parameters, are often violated in neutrino oscillation measurements and other experimental scenarios. Monte Carlo methods can address these issues, albeit at increased computational cost. In the presence of nuisance parameters, however, the best way to implement a Monte Carlo method is ambiguous. Furthermore, this paper documents the method selected by the NOvA experiment, the profile construction. It presents the toy studies that informed the choice of method, details of its implementation, and tests performed to validate it. It also includes some practical considerations which may be of use to others choosing to use the profile construction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Daytime cooling efficiencies of urban trees derived from land surface temperature are much higher than those for air temperature

Accurately capturing the impact of urban trees on temperature can help optimize urban heat mitigation strategies. Recently, there has been widespread use of remotely sensed land surface temperature (T s ) to quantify the cooling efficiency (CE) of urban trees. However, remotely sensed T s reflects emitted radiation from the surface of an object seen from the point of view of the thermal sensor, which is not a good proxy for the air temperature (T a ) perceived by humans. The extent to which the CEs derived from T s reflect the true experiences of urban residents is debatable. Therefore, this study systematically compared the T s -based CE (CE T s ) with the T a -based CE (CE T a ) in 392 European urban clusters. CE T s and CE T a were defined as the reductions in T s and T a , respectively, for every 1% increase in fractional tree cover (FTC). The results show that the increase in FTC has a substantial impact on reducing T s and T a in most cities during daytime. However, at night, the response of T s and T a to increased FTC appears to be much weaker and ambiguous. On average, for European cities, daytime CE T s reaches 0.075 °C % -1 , which is significantly higher (by an order of magnitude) than the corresponding CE T a of 0.006 °C % -1 . In contrast, the average nighttime CE T s and CE T a for European cities are similar, both approximating zero. Overall, urban trees can lower daytime temperatures, but the magnitude of their cooling effect is notably amplified when using remotely sensed T s estimates compared to in situ T a measurements, which is important to consider for accurately constraining public health benefits. Our findings provide critical insights into the realistic efficiencies of alleviating urban heat through tree planting.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

The birth of a field through a marriage of scales: urban meteorological modeling meets regional climate modeling

Urban meteorological modeling and regional climate modeling developed largely independently, with each discipline addressing different aspects of atmospheric processes across space and time. In this review, I show that urban climate modeling did not arise as a simple scaling extension of urban meteorological modeling or an add-on to regional climate modeling, but instead emerged through the selective inheritance of complementary strengths from its parents after both disciplines reached sufficient methodological maturity. By tracing the parallel evolution of these disciplines, I demonstrate that urban climate modeling inherited the physically explicit treatment of the built environment developed within urban meteorological modeling, and the hierarchical scale translation and climatological framing that matured within regional climate modeling, allowing urban effects to influence climate-relevant outcomes. Building on this synthesis, I propose an objective, and methodologically-grounded definition of urban climate modeling that distinguishes it from urban meteorological modeling. This distinction is increasingly important as urban climate data informs decisions with long-lived societal consequences, and as ambiguity in terminology risks conflating fundamentally different modeling frameworks with distinct physical meaning and decision relevance. In addition to a clarifying definition, this review outlines a research framework for advancing urban climate modeling through scale-aware coupling strategies that preserve physically consistent urban-atmosphere interactions.

regional climate↗

DOE OSTI2021

The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Bezerra, Ana Rita (ORCID:0000000346131711)↗

DOE OSTI2022

Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis

Members of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch’s postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Probabilistic inversion of circular phase spectra: application to two-station phase-velocity dispersion estimation in western Canada

SUMMARY Periodic directional and temporal measurements are common in seismology, and necessitate specific statistical analyses that are appropriate for circular quantities. In this work, we explore the use of a von Mises distribution as a representation of errors on circular seismological observations. Specifically, we automate the estimation of surface-wave phase-velocity dispersion for the teleseismic two-station method, which generally suffers from a 2π phase ambiguity. The use of Bayesian inverse techniques, which aim to rigorously quantify model parameter uncertainty, have become widespread throughout seismology over the last decade. Here, we apply Bayesian inversion to measurements of surface-wave phase spectra in order to estimate 1-D, path-averaged Earth structure between station pairs. The dispersion curve and associated uncertainties are additional results of the inversion, which can then be used as input for subsequent analyses (e.g. tomography). We demonstrate this technique through application to surface-wave recordings from long-running seismic stations throughout western Canada. Our results for over 10 000 station pairs reveal first-order tectonic features consistent with previous studies, which provides confidence in our approach as well as an initial step towards resolving a full 3-D seismic velocity model for the region. This work also presents a foundation for the inversion of surface-wave phase spectra to estimate 3-D Earth structure directly. Finally, the ideas presented in this work are not limited to the inversion of surface-wave phase spectra, but can also be considered for Bayesian geophysical inversion of any circular quantities.

Gosselin, Jeremy M. (ORCID:0000000203754102)↗

DOE OSTI2022

Automatic information extraction from childhood cancer pathology reports

The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

The chemical compositions of accreted and in situ galactic globular clusters according to SDSS/APOGEE

ABSTRACT Studies of the kinematics and chemical compositions of Galactic globular clusters (GCs) enable the reconstruction of the history of star formation, chemical evolution, and mass assembly of the Galaxy. Using the latest data release (DR16) of the SDSS/APOGEE survey, we identify 3090 stars associated with 46 GCs. Using a previously defined kinematic association, we break the sample down into eight separate groups and examine how the kinematics-based classification maps into chemical composition space, considering only α (mostly Si and Mg) elements and Fe. Our results show that (i) the loci of both in situ and accreted subgroups in chemical space match those of their field counterparts; (ii) GCs from different individual accreted subgroups occupy the same locus in chemical space. This could either mean that they share a similar origin or that they are associated with distinct satellites which underwent similar chemical enrichment histories; (iii) the chemical compositions of the GCs associated with the low orbital energy subgroup defined by Massari and collaborators is broadly consistent with an in situ origin. However, at the low-metallicity end, the distinction between accreted and in situ populations is blurred; (iv) regarding the status of GCs whose origin is ambiguous, we conclude the following: the position in Si–Fe plane suggests an in situ origin for Liller 1 and a likely accreted origin for NGC 5904 and NGC 6388. The case of NGC 288 is unclear, as its orbital properties suggest an accretion origin, its chemical composition suggests it may have formed in situ.

Horta, Danny↗

DOE OSTI2021

General relativistic MHD simulations of non-thermal flaring in Sagittarius A*

Sgr A* exhibits regular variability in its multiwavelength emission, including daily X-ray flares and roughly continuous near-infrared (NIR) flickering. The origin of this variability is still ambiguous since both inverse Compton and synchrotron emission are possible radiative mechanisms. The underlying particle distributions are also not well constrained, particularly the non-thermal contribution. In this work, we employ the GPU-accelerated general relativistic magnetohydrodynamics code H-AMR to perform a study of flare flux distributions, including the effect of particle acceleration for the first time in high-resolution 3D simulations of Sgr A*. For the particle acceleration, we use the general relativistic ray-tracing code bhoss to perform the radiative transfer, assuming a hybrid thermal+non-thermal electron energy distribution. We extract ~60 h light curves in the sub-millimetre, NIR and X-ray wavebands, and compare the power spectra and the cumulative flux distributions of the light curves to statistical descriptions for Sgr A* flares. Our results indicate that non-thermal populations of electrons arising from turbulence-driven reconnection in weakly magnetized accretion flows lead to moderate NIR and X-ray flares and reasonably describe the X-ray flux distribution while fulfilling multiwavelength flux constraints. These models exhibit high rms per cent amplitudes, $\gtrsim 150{{\ \rm per\ cent}}$ both in the NIR and the X-rays, with changes in the accretion rate driving the 230 GHz flux variability, in agreement with Sgr A* observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

The kinematics, metallicities, and orbits of six recently discovered Galactic star clusters with Magellan/M2FS spectroscopy

ABSTRACT We present Magellan/M2FS spectroscopy of four recently discovered Milky Way star clusters (Gran 3/Patchick 125, Gran 4, Garro 01, and LP 866) and two newly discovered open clusters (Gaia 9 and Gaia 10) at low Galactic latitudes. We measure line-of-sight velocities and stellar parameters ([Fe/H], log g, Teff, and [Mg/Fe]) from high-resolution spectroscopy centred on the Mg triplet and identify 20–80 members per star cluster. We determine the kinematics and chemical properties of each cluster and measure the systemic proper motion and orbital properties by utilizing Gaia astrometry. We find Gran 3 to be an old, metal-poor (mean metallicity of [Fe/H] = −1.83) globular cluster located in the Galactic bulge on a retrograde orbit. Gran 4 is an old, metal-poor ([Fe/H] = −1.84) globular cluster with a halo-like orbit that happens to be passing through the Galactic plane. The orbital properties of Gran 4 are consistent with the proposed LMS-1/Wukong and/or Helmi streams merger events. Garro 01 is metal-rich ([Fe/H] = −0.30) and on a near-circular orbit in the outer disc but its classification as an open cluster or globular cluster is ambiguous. Gaia 9 and Gaia 10 are among the most distant known open clusters at $R_{\mathrm{GC}}\sim 18,~21.2~\mathrm{\, kpc}$ and most metal-poor with [Fe/H] ∼−0.50, −0.34 for Gaia 9 and Gaia 10, respectively. LP 866 is a nearby, metal-rich open cluster ([Fe/H] = +0.10). The discovery and confirmation of multiple star clusters in the Galactic plane shows the power of Gaia astrometry and the star cluster census remains incomplete.

Pace, Andrew B. (ORCID:0000000260218760)↗

DOE OSTI2022

Passive spiral galaxies deeply captured by Subaru Hyper Suprime-Cam

Abstract This paper presents a thousand passive spiral galaxy samples at z = 0.01–0.3 based on a combined analysis of the Third Public Data Release of the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP PDR3) and the GALEX–SDSS–WISE Legacy Catalog (GSWLC-2). Among 54871 gri galaxy cutouts taken from the HSC-SSP PDR3 over 1072 deg2, we conducted a search with deep-learning morphological classification for candidates of passive spirals below the star-forming main sequence derived by ultraviolet to mid-infrared spectral energy distribution fitting in the GSWLC-2. We then classified the candidates into 1100 passive spirals and 1141 secondary samples based on visual inspections. Most of the latter cases are considered to be passive ringed S0 or pseudo-ringed galaxies. The remaining secondary samples have ambiguous morphologies, including two peculiar objects with diamond-shaped stellar wings. The selected passive spirals have a similar distribution to the general quiescent galaxies on the EWHδ–Dn4000 diagram and concentration indices. Moreover, we detected an enhanced passive fraction of spiral galaxies in X-ray clusters. Passive spirals in galaxy clusters are preferentially located in the midterm or late infall phase on the phase–space diagram, supporting the ram pressure scenario, which has been widely advocated in previous studies. The source catalog and gri-composite images are available on the HSC-SSP PDR3 website 〈https://hsc.mtk.nao.ac.jp/ssp/data-release/〉. Future updates, including integration with a citizen science project dedicated to the HSC data, will achieve more effective and comprehensive classifications.

Shimakawa, Rhythm (ORCID:0000000344422750)↗

DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗

DOE OSTI2026

𝑁 = 8 Shell Breaking in 12 Be from a Single-Particle Perspective

Experimental observations of the low-lying states in 12 Be and their accurate modeling play an essential role in understanding the disappearance of the 𝑁 = 8 magic number. Long-standing experimental ambiguities have been clarified using an one-neutron adding (𝑑, 𝑝) reaction on 11 Be using the ISOLDE Solenoidal Spectrometer at CERN’s HIE-ISOLDE facility. The single-particle energies of 1⁢𝑠 1/2 , 0⁢𝑑 5/2 , and 0⁢𝑝 1/2 orbitals in 12 Be have been determined from the extracted spectroscopic factors. A significant reduction between the separation of 1⁢𝑠 1/2 and 0⁢𝑝 1/2 orbitals is found in comparison with the carbon isotones, highlighting the breakdown of the 𝑁 = 8 shell. These observations serve as an important test of different effects incorporated in theoretical models. It is found that two synergistic mechanisms, core deformation and weak binding, are responsible for the 𝑁 = 8 shell breaking and the exotic near-threshold phenomena observed in 12 Be, including the narrow unnatural-parity resonance $0^{-}_1$ and the possible halolike nature of the $0^+_2$ isomer.

Chen, Jie [Southern University of Science and Tech↗

DOE OSTI2026

Magnetism and magnetoelastic effect in the two-dimensional van der Waals multiferroic CuCrP 2 ⁢S 6

Here, we report a magnetic and neutron diffraction study on the ground state magnetism and field evolution of single-crystal van der Waals multiferroic CuCrP 2 ⁢S 6 . The ordered moments align along the 𝑏 axis in the "𝐴-type" antiferromagnetic configuration with a spin-flop transition along the same direction. Field application along 𝑎 introduces a smooth transition to a fully polarized ferromagnetic state via in-plane spin rotation. These findings resolve the ambiguity of the ground state magnetization direction in CuCrP 2 ⁢S 6 and uncover its field responses, providing a firm basis for future magnetoelectric study. A magnetoelastic coupling effect connecting the interlayer spacing and the magnetic order was further revealed, highlighting the out-of-plane strain as an effective control knob for tuning magnetism both in this system and in related van der Waals magnets.

Guo, Jiasen [Oak Ridge National Laboratory (ORNL),↗

DOE OSTI2023

Toward precision Fermi-liquid theory in two dimensions

The ultracold and weakly coupled Fermi gas in two spatial dimensions is studied in an effective field theory framework. It has long been observed that universal corrections to the energy density to two orders in the interaction strength do not agree with Monte Carlo simulations in the weak-coupling regime. Here, universal corrections to three orders in the interaction strength are obtained, and are shown to provide agreement between theory and simulation. Special consideration is given to the scale ambiguity associated with the nontrivial renormalization of the singular contact interactions. Further, the isotropic superfluid gap is obtained to next-to-leading order, and nonuniversal contributions to the energy density due to effective range effects, p -wave interactions, and three-body forces are computed. Results are compared with precise Monte Carlo simulations of the energy density and the contact in the weakly coupled attractive and repulsive Fermi-liquid regimes. In addition, the known all-orders sum of ladder and ring diagrams is compared with Monte Carlo simulations at weak coupling and beyond.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Precision Measurement of the Microwave Dielectric Loss of Sapphire in the Quantum Regime with Parts-per-Billion Sensitivity

Dielectric loss is known to limit state-of-the-art superconducting qubit lifetimes. Recent experiments imply upper bounds on bulk dielectric loss tangents on the order of 100 parts per billion but because these inferences are drawn from fully fabricated devices with many loss channels, these experiments do not definitely implicate or exonerate the dielectric. To resolve this ambiguity, we devise a measurement method capable of separating and resolving bulk dielectric loss with a sensitivity at the level of 5 ×10 –9 . The method, which we call the dielectric dipper, involves the in situ insertion of a dielectric sample into a high-quality microwave cavity mode. Smoothly varying the participation of the sample in the cavity mode enables a differential measurement of the dielectric loss tangent of the sample. The dielectric dipper can probe the low-power behavior of dielectrics at cryogenic temperatures and does so without the need for any lithographic process, enabling controlled comparisons of substrate materials and processing techniques. We demonstrate the method with measurements of sapphire grown by edge-defined film-fed growth (EFG) in comparison to high-grade sapphire grown by the heat-exchanger method (HEMEX). For EFG sapphire, we infer a bulk loss tangent of 63⁢(8) ×10 –9 and a substrate-air interface loss tangent of 15⁢(3) ×10 –4 (assuming a sample surface thickness of 3 nm). For a typical transmon, this bulk loss tangent would limit device quality factors to Q ≲20 ×10 6 , suggesting that bulk loss is likely the dominant loss mechanism in the longest-lived transmons on sapphire. We also demonstrate this method on HEMEX sapphire and bound its bulk loss tangent to be less than 19⁢(6) ×10 –9 . As this bound is about 3 times smaller than the bulk loss tangent of EFG sapphire, the use of HEMEX sapphire as a substrate would lift the bulk dielectric coherence limit of a typical transmon qubit to several milliseconds.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Thermal Hall conductance and a relative topological invariant of gapped two-dimensional systems

We derive a Kubo-like formula for the thermal Hall conductance of a 2d lattice systems which is free from ambiguities associated with the definition of energy magnetization. We use it to define a relative topological invariant of gapped 2d lattice systems at zero temperature. Up to a numerical factor, it can be identified with the difference of chiral central charges for the corresponding edge modes. This establishes the bulk-boundary correspondence for the chiral central charge. Here, we also show that for any local commuting projector Hamiltonian, the relative chiral central charge vanishes, while for free fermionic systems, it is related to the zero-temperature electric Hall conductance via the Wiedemann-Franz law.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗