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DOE OSTI2024

In-situ relative calibration of Bragg crystals with Monte Carlo line ratio analysis

X-ray line emission spectra can thoroughly characterize hot plasmas, especially when line shapes and ratios convey distinct aspects of plasma conditions. However, the high spectral resolution required for observing line shapes is often at odds with the large bandwidth required to observe many line ratios across a wide spectral range. One strategy to obtain high spectral resolution over a wide bandwidth is to use multiple crystals with calibrated reflectivity so that line intensities across different crystals can be compared. Here, we explore the use of a low-resolution, wide-bandwidth mica survey spectrometer to infer relative reflectivity of two high-resolution, narrow-bandwidth quartz crystals. Finally, a Monte Carlo error analysis determines comparable x-ray line ratios measured from both spectrometers, resulting in an in situ calibration factor and associated uncertainty for the relative reflectivity of the high-resolution crystals.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Micro-segregation phenomena and related spectroscopic signals in melt-grown β-Ga2O3 single crystals

One of the primary advantages of β-Ga2O3 over incumbent wide bandgap semiconductors is the ability to grow directly from the melt. Melt growth, using Czochralski or similar methods, results in impurities in the crystal which originate from the crucible, such as iridium and other transition metals like chromium. These impurities exhibit optoelectronic signatures useful for their identification and sensitive to the Fermi energy of a given crystal (i.e., signatures vary with the electrical conductivity of the matrix). In this work, we describe how laser Raman systems can be used to map and spatially correlate Cr3+ photoluminescence, electronic-coupled Raman scattering from Ir4+d–d internal transitions, and the Raman line attributed to hydrogenic shallow donors. Laser ablation inductively coupled plasma mass spectrometry directly measured spatially dependent relative metal concentrations and confirmed spectroscopic signals resulting from heterogeneities in impurity concentrations in β-Ga2O3 boules. Mapping of photoluminescence and Raman-related signatures is, thus, demonstrated as an effective and facile method for spatial measurement of chemical heterogeneities in both insulating and conductive melt-grown β-Ga2O3 crystals.

Dutton, Benjamin L. (ORCID:000000031272130X)↗

DOE OSTI2020

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Oscillon preheating in full general relativity

Abstract Oscillons are dense nonperturbative objects that may be copiously produced in the preheating period after inflation. Oscillon preheatings are usually simulated with nonlinear matter interactions but in a rigid FLRW background, without taking into account the gravitational backreactions. We investigate the oscillon preheating scenario in full general relativity with a full numerical relativity scheme, and compare the general-relativistic simulations with the traditional ones done in an FLRW background. We find that in certain parameter regions the general-relativistic corrections are significant, producing more and denser oscillons, and can be strong enough to collapse the oscillons to black holes.

Astronomy & Astrophysics↗

DOE OSTI2025

Generalized fractional approach to solving partial differential equations with arbitrary dispersion relations

The dynamics of physical systems are typically modeled by partial differential equations (PDEs). Because of the complexity in physical systems, PDE models rely on approximations or limiting cases. To model the full complexity of physical systems, it is necessary to use multiscale approaches where appropriate models are used at each level. Alternatively, complexity can be directly tackled by fractional integrodifferential equations that must be derived for each system. Here, we argue that complexity can be restored in PDEs by describing them from a fractional calculus perspective. Rather than deriving a fractional integrodifferential equation, we reinterpret the dispersion relation of the system by use of the Riesz definition, which contains the required information relating the energy and momentum space of the system and thus fully describes their dynamics. The approach is demonstrated by two examples: the Landau–Lifshitz equation in a 1D ferromagnetic chain and a modified KdV equation supporting surface gravity waves or Euler dispersion. The presented approach is applicable to fluids, soft matter, and solid-state matter and can be readily generalized to higher dimensions and more complex systems. While numerical calculations are needed to determine the fractional operator, the approach is analytical and can be utilized to determine analytical solutions and investigate nonlinear problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Multimodal representation learning for predicting molecule–disease relations

Motivation: Predicting molecule–disease indications and side effects is important for drug development and pharmacovigilance. Comprehensively mining molecule–molecule, molecule–disease and disease–disease semantic dependencies can potentially improve prediction performance. Methods: We introduce a Multi-Modal REpresentation Mapping Approach to Predicting molecular-disease relations (M2REMAP) by incorporating clinical semantics learned from electronic health records (EHR) of 12.6 million patients. Specifically, M2REMAP first learns a multimodal molecule representation that synthesizes chemical property and clinical semantic information by mapping molecule chemicals via a deep neural network onto the clinical semantic embedding space shared by drugs, diseases and other common clinical concepts. To infer molecule–disease relations, M2REMAP combines multimodal molecule representation and disease semantic embedding to jointly infer indications and side effects. Results: We extensively evaluate M2REMAP on molecule indications, side effects and interactions. Results show that incorporating EHR embeddings improves performance significantly, for example, attaining an improvement over the baseline models by 23.6% in PRC-AUC on indications and 23.9% on side effects. Further, M2REMAP overcomes the limitation of existing methods and effectively predicts drugs for novel diseases and emerging pathogens. Availability and implementation: The code is available at https://github.com/celehs/M2REMAP, and prediction results are provided at https://shiny.parse-health.org/drugs-diseases-dev/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Diabetes and hypertension are related to amyloid-beta burden in the population-based Rotterdam Study

Abstract Higher vascular disease burden increases the likelihood of developing dementia, including Alzheimer’s disease. Better understanding the association between vascular risk factors and Alzheimer’s disease pathology at the predementia stage is critical for developing effective strategies to delay cognitive decline. In this work, we estimated the impact of six vascular risk factors on the presence and severity of in vivo measured brain amyloid-beta (Aβ) plaques in participants from the population-based Rotterdam Study. Vascular risk factors (hypertension, hypercholesterolaemia, diabetes, obesity, physical inactivity and smoking) were assessed 13 (2004–2008) and 7 years (2009–2014) prior to 18F-florbetaben PET (2018–2021) in 635 dementia-free participants. Vascular risk factors were associated with binary amyloid PET status or continuous PET readouts (standard uptake value ratios, SUVrs) using logistic and linear regression models, respectively, adjusted for age, sex, education, APOE4 risk allele count and time between vascular risk and PET assessment. Participants’ mean age at time of amyloid PET was 69 years (range: 60–90), 325 (51.2%) were women and 190 (29.9%) carried at least one APOE4 risk allele. The adjusted prevalence estimates of an amyloid-positive PET status markedly increased with age [12.8% (95% CI 11.6; 14) in 60–69 years versus 35% (36; 40.8) in 80–89 years age groups] and APOE4 allele count [9.7% (8.8; 10.6) in non-carriers versus 38.4% (36; 40.8) to 60.4% (54; 66.8) in carriers of one or two risk allele(s)]. Diabetes 7 years prior to PET assessment was associated with a higher risk of a positive amyloid status [odds ratio (95% CI) = 3.68 (1.76; 7.61), P < 0.001] and higher standard uptake value ratios, indicating more severe Aβ pathology [standardized beta = 0.40 (0.17; 0.64), P = 0.001]. Hypertension was associated with higher SUVr values in APOE4 carriers (mean SUVr difference of 0.09), but not in non-carriers (mean SUVr difference 0.02; P = 0.005). In contrast, hypercholesterolaemia was related to lower SUVr values in APOE4 carriers (mean SUVr difference −0.06), but not in non-carriers (mean SUVr difference 0.02). Obesity, physical inactivity and smoking were not related to amyloid PET measures. The current findings suggest a contribution of diabetes, hypertension and hypercholesterolaemia to the pathophysiology of Alzheimer’s disease in a general population of older non-demented adults. As these conditions respond well to lifestyle modification and drug treatment, further research should focus on the preventative effect of early risk management on the development of Alzheimer’s disease neuropathology.

van Arendonk, Joyce (ORCID:0000000172941633)↗

DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

The biogeography of soil and airborne fungi in the Southwestern USA in relation to climate and vegetation

To assess how fungal dispersal might respond to climate change, we examined how climate and geography influence the regional distribution of fungi in soil and air. Specifically, we hypothesized that neighboring fungal communities should be more similar than distant communities (i.e. spatially autocorrelated) and that fungal dispersal should be more limited in soil than in air. We collected soil and air samples from 60 sites across five states in the Southwestern USA. Then, we sequenced the ITS2 region to identify fungal taxa in each sample. Next, we used distance-based redundancy analysis to partition variation in fungal community composition between climate variables and spatial structure. Fungi were indeed spatially autocorrelated. Moreover, precipitation, maximum vapor pressure deficit, and soil moisture were significantly related to fungal community composition in soils. In comparison, only precipitation was significantly related to community composition in the air. After accounting for climate, the strength of spatial autocorrelation did not differ significantly in soilborne versus airborne fungi. Dispersal limitation was evident in soilborne fungi at short distances (<100 km) and was not observed at any distance in airborne fungi. Altogether, climate may influence which fungal taxa are present in soil and air, and fungi could feasibly wind disperse over regional scales.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Mass calibration of the CODEX cluster sample using SPIDERS spectroscopy – II. The X-ray luminosity–mass relation

ABSTRACT We perform the calibration of the X-ray luminosity–mass scaling relation on a sample of 344 CODEX clusters with z < 0.66 using the dynamics of their member galaxies. Spectroscopic follow-up measurements have been obtained from the SPIDERS survey, leading to a sample of 6658 red member galaxies. We use the Jeans equation to calculate halo masses, assuming an NFW mass profile and analysing a broad range of anisotropy profiles. With a scaling relation of the form $L_{\rm {X}} \propto \text{A}_{\rm {X}}M_{\text{200c}}^{\text{B}_{\rm {X}}} E(z)^2 (1+z)^{\gamma _{\rm {X}}}$, we find best-fitting parameters $\text{A}_{\rm {X}}=0.62^{+0.05}_{-0.06} (\pm 0.06)\times 10^{44}\, \mathrm{erg\, s^{-1}}$, $\text{B}_{\rm {X}}=2.35^{+0.21}_{-0.18}(\pm 0.09)$, $\gamma _{\rm {X}}=-2.77^{+1.06}_{-1.05}(\pm 0.79)$, where we include systematic uncertainties in parentheses and for a pivot mass and redshift of $3\times 10^{14}\, \mathrm{M}_\odot$ and 0.16, respectively. We compare our constraints with previous results, and we combine our sample with the SPT SZE-selected cluster subsample observed with XMM–Newton extending the validity of our results to a wider range of redshifts and cluster masses.

Capasso, R.↗

DOE OSTI2021

On the relation between active-region lifetimes and the autocorrelation function of light curves

ABSTRACT Rotational modulation of stellar light curves due to dark spots encloses information on spot properties and, thus, on magnetic activity. In particular, the decay of the autocorrelation function (ACF) of light curves is presumed to be linked to spot/active-region lifetimes, given that some coherence of the signal is expected throughout their lifetime. In the literature, an exponential decay has been adopted to describe the ACF. Here, we investigate the relation between the ACF and the active-region lifetimes. For this purpose, we produce artificial light curves of rotating spotted stars with different observation, stellar, and spot properties. We find that a linear decay and respective time-scale better represent the ACF than the exponential decay. We therefore adopt a linear decay. The spot/active-region time-scale inferred from the ACF is strongly restricted by the observation length of the light curves. For 1-yr light curves our results are consistent with no correlation between the inferred and the input time-scales. The ACF decay is also significantly affected by differential rotation and spot evolution: strong differential rotation and fast spot evolution contribute to a more severe underestimation of the active-region lifetimes. Nevertheless, in both circumstances the observed time-scale is still correlated with the input lifetimes. Therefore, our analysis suggests that the ACF decay can be used to obtain a lower limit of the active-region lifetimes for relatively long-term observations. However, strategies to avoid or flag targets with fast active-region evolution or displaying stable beating patterns associated with differential rotation should be employed.

Santos, A. R. G. (ORCID:0000000171956542)↗

DOE OSTI2022

Numerical relativity simulations of the neutron star merger GW190425: microphysics and mass ratio effects

ABSTRACT GW190425 was the second gravitational wave (GW) signal compatible with a binary neutron star (BNS) merger detected by the Advanced LIGO and Advanced Virgo detectors. Since no electromagnetic counterpart was identified, whether the associated kilonova was too dim or the localization area too broad is still an open question. We simulate 28 BNS mergers with the chirp mass of GW190425 and mass ratio 1 ≤ q ≤ 1.67, using numerical-relativity simulations with finite-temperature, composition dependent equations of state (EOS) and neutrino radiation. The energy emitted in GWs is $\lesssim 0.083\mathrm{\, M_\odot }c^2$ with peak luminosity of 1.1–$2.4\times ~10^{58}/(1+q)^2\, {\rm {erg \, s^{-1}}}$. Dynamical ejecta and disc mass range between 5 × 10−6–10−3 and 10−5–$0.1 \mathrm{\, M_\odot }$, respectively. Asymmetric mergers, especially with stiff EOSs, unbind more matter and form heavier discs compared to equal mass binaries. The angular momentum of the disc is 8–$10\mathrm{\, M_\odot }~GM_{\rm {disc}}/c$ over three orders of magnitude in Mdisc. While the nucleosynthesis shows no peculiarity, the simulated kilonovae are relatively dim compared with GW170817. For distances compatible with GW190425, AB magnitudes are always dimmer than ∼20 mag for the B, r, and K bands, with brighter kilonovae associated to more asymmetric binaries and stiffer EOSs. We suggest that, even assuming a good coverage of GW190425’s sky location, the kilonova could hardly have been detected by present wide-field surveys and no firm constraints on the binary parameters or EOS can be argued from the lack of the detection.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The relation between accretion rate and jet power in early-type galaxies with thermally unstable hot atmospheres

ABSTRACT We use Chandra X-ray data and Very Large Array radio observations for a sample of 20 nearby, massive, X-ray bright, early-type galaxies to investigate the relation between the Bondi accretion rates and the mechanical jet powers. We find a strong correlation ($\rho = 0.96^{+0.03}_{-0.09}$; BF10 > 100) between the Bondi accretion power, PBondi, and the mechanical jet power, Pjet, for a subsample of 14 galaxies, which also host cool H α+[N ii] line emitting gas and thus likely have thermally unstable atmospheres. The relation between the Bondi accretion power and the mechanical jet power for this subsample is well described by a power-law model $\log \frac{P_{\mathrm{Bondi}}}{{10^{43} \, \mathrm{erg \, s^{-1}}}} = \alpha + \beta \log \frac{P_{\mathrm{jet}}}{{10^{43} \, \mathrm{erg \, s^{-1}}}}$, where α = 1.10 ± 0.25 and β = 1.10 ± 0.24 with an intrinsic scatter $\sigma = 0.08^{+0.14}_{-0.06}$ dex. The results indicate that in all galaxies with thermally unstable atmospheres the cooling atmospheric gas feeds the central black holes at a similar jet-to-Bondi power ratio. For the full sample of 20 galaxies, the correlation is weaker and in a subset of galaxies with no signs of H α+[N ii] emission, we see a hint for a systematically lower jet-to-Bondi power ratio. We also investigate the dependence of jet power on individual quantities in the Bondi formula such as the supermassive black hole mass (M•) and the specific entropy of the gas (K) at the Bondi radius. For the subsample of H α+[N ii] emitting galaxies, we find a very tight correlation of Pjet with M• ($\rho = 0.91^{+0.06}_{-0.11}$; BF10 > 100) and, although poorly constrained, a hint of an anticorrelation for Pjet and K ($\rho = -0.47^{+0.60}_{-0.37}$; BF10 = 1.1).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Turning points in the age–metallicity relations – created by late satellite infall and enhanced by radial migration

ABSTRACT The present-day age–metallicity relation (AMR) is a record of the star formation history of galaxies, as this traces the chemical enrichment of the gas over time. We use a zoomed-in cosmological simulation that reproduces key signatures of the Milky Way (MW), g2.79e12 from the NIHAO-UHD project, to examine how stellar migration and satellite infall shape the AMR across the disc. We find in the simulation, similar to the MW, the AMR in small spatial regions (R, z) shows turning points that connect changes in the direction of the relations. The turning points in the AMR in the simulation are a signature of late satellite infall. This satellite infall has a mass radio similar as that of the Sagittarius dwarf to the MW (∼0.001). Stars in the apex of the turning points are young and have nearly not migrated. The late satellite infall creates the turning points via depositing metal-poor gas in the disc, triggering star formation of stars in a narrow metallicity range compared to the overall AMR. The main effect of radial migration on the AMR turning points is to widen the metallicity range of the apex. This can happen when radial migration brings stars born from the infallen gas in other spatial bins, with slightly different metallicities, into the spatial bin of interest. These results indicate that it is possible that the passage of the Sagittarius dwarf galaxy played a role in creating the turning points that we see in the AMR in the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

DESI complete calibration of the colour–redshift relation (DC3R2): results from early DESI data

We present initial results from the Dark Energy Spectroscopic Instrument (DESI) complete calibration of the colour–redshift relation (DC3R2) secondary target survey. Our analysis uses 230 k galaxies that overlap with KiDS-VIKING ugriZYJHK s photometry to calibrate the colour–redshift relation and to inform photometric redshift (photo-z) inference methods of future weak lensing surveys. Together with emission line galaxies (ELGs), luminous red galaxies (LRGs), and the Bright Galaxy Survey (BGS) that provide samples of complementary colour, the DC3R2 targets help DESI to span 56 percent of the colour space visible to Euclid and LSST with high confidence spectroscopic redshifts. The effects of spectroscopic completeness and quality are explored, as well as systematic uncertainties introduced with the use of common Self-Organizing Maps trained on different photometry than the analysis sample. We further examine the dependence of redshift on magnitude at fixed colour, important for the use of bright galaxy spectra to calibrate redshifts in a fainter photometric galaxy sample. We find that noise in the KiDS-VIKING photometry introduces a dominant, apparent magnitude dependence of redshift at fixed colour, which indicates a need for carefully chosen deep drilling fields, and survey simulation to model this effect for future weak lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Experimental entropic uncertainty relations in dimensions three to five

We provide experimental validation of tight entropic uncertainty relations for the Shannon entropies of observables with mutually unbiased eigenstates in high dimensions. In particular, we address the cases of dimensions 𝑑 = 3, 4, and 5 and consider from 2 to 𝑑 + 1 mutually unbiased bases. The experiment is based on pulsed frequency bins measured with a multioutput quantum pulse gate, which can perform projective measurements on a complete high-dimensional basis in the time-frequency domain. Our results fit the theoretical predictions: the bound on the sum of the entropies is never violated and is saturated by the states that minimize the uncertainty relations.

Serino, Laura [Paderborn University (Germany)] (OR↗

DOE OSTI2022

Universal relation between doping content and normal-state resistance in gate voltage tuned ultrathin Bi 2 Sr 2 CaCu 2 O 8 + x flakes

We report gate voltage tunable ultra-thin high-T c cuprates supply a unique platform to investigate the electronic phase diagram and superconductor-insulator transition. One of the challenges in this field is the precise determination of the doping content in the underdoped non-superconducting region. Here we report the discovery of a universal relation between the doping content p and the normal-state resistance at a fixed temperature R(T f ), p = α + β ln[1/R(T f )], in the ultra-thin Bi 2 Sr 2 CaCu 2 O 8+x flakes. The in-depth analysis shows that the evolution of carrier scattering probability with doping content and the change of effective mass caused by superconductor-insulator transition are two key factors leading to this logarithmic relation. Based on our finding, the more precise electronic phase diagram can be established. In addition, the superconductor-insulator transition is verified to be a quantum phase transition using a finite size scaling analysis. The scaling exponent z v is found to have a close correlation with the disorder levels. The present result provides an important foundation to investigate the fascinating electronic states in the ultra-thin cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Back-to-back relative-excess observable to identify the chiral magnetic effect

Background: The chiral magnetic effect (CME) is extensively studied in heavy-ion collisions at RHIC and LHC. In the commonly used reaction-plane (RP)-dependent, charge-dependent azimuthal correlator ($Δ_γ$), both the close and back-to-back pairs are included. Many backgrounds contribute to the close pairs (e.g., resonance decays, jet correlations), whereas the back-to-back pairs are relatively free of those backgrounds. Purpose: In order to reduce those backgrounds, we propose a new observable, which only focuses on the back-to-back pairs, namely, the relative back-to-back opposite-sign over same-sign pair excess ($r_{BB}$) as a function of the pair azimuthal orientation with respect to the RP ($φ_{BB}$). Methods: We use analytical calculations and toy model simulations to demonstrate the sensitivity of $r_{BB}(φ_{BB})$ to the CME and its insensitivity to backgrounds. Results: With finite CME, the $φ_{BB}$ distribution of $r_{BB}$ shows a clear characteristic modulation. Its sensitivity to background is significantly reduced compared to the previous $Δ_γ$ observable. The simulation results are consistent with our analytical calculations. Conclusions: In this work, our studies demonstrate that the $r_{BB}(φ_{BB})$ observable is sensitive to the CME signal and rather insensitive to the resonance backgrounds.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗