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DOE OSTI2023

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Compound-Nucleus and Doorway-State Decays of β -Delayed Neutron Emitters K 51 , 52 , 53

We investigated decays of K 51 , 52 , 53 at the ISOLDE Decay Station at CERN in order to understand the mechanism of the β -delayed neutron-emission ( β n ) process. The experiment quantified neutron and γ -ray emission paths for each precursor. We used this information to test the hypothesis, first formulated by Bohr in 1939, that neutrons in the β n process originate from the structureless “compound nucleus.” The data are consistent with this postulate for most of the observed decay paths. The agreement, however, is surprising because the compound-nucleus stage should not be achieved in the studied β decay due to insufficient excitation energy and level densities in the neutron emitter. In the K 53 β n decay, we found a preferential population of the first excited state in Ca 52 that contradicted Bohr’s hypothesis. The latter was interpreted as evidence for direct neutron emission sensitive to the structure of the neutron-unbound state. We propose that the observed nonstatistical neutron emission proceeds through the coupling with nearby doorway states that have large neutron-emission probabilities. The appearance of “compound-nucleus” decay is caused by the aggregated small contributions of multiple doorway states at higher excitation energy. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Discrete-Direct Model Calibration and Uncertainty Propagation Method Confirmed on Multi-Parameter Plasticity Model Calibrated to Sparse Random Field Data

A discrete direct (DD) model calibration and uncertainty propagation approach is explained and demonstrated on a 4-parameter Johnson-Cook (J-C) strain-rate dependent material strength model for an aluminum alloy. The methodology's performance is characterized in many trials involving four random realizations of strain-rate dependent material-test data curves per trial, drawn from a large synthetic population. The J-C model is calibrated to particular combinations of the data curves to obtain calibration parameter sets which are then propagated to “Can Crush” structural model predictions to produce samples of predicted response variability. These are processed with appropriate sparse-sample uncertainty quantification (UQ) methods to estimate various statistics of response with an appropriate level of conservatism. This is tested on 16 output quantities (von Mises stresses and equivalent plastic strains) and it is shown that important statistics of the true variabilities of the 16 quantities are bounded with a high success rate that is reasonably predictable and controllable. The DD approach has several advantages over other calibration-UQ approaches like Bayesian inference for capturing and utilizing the information obtained from typically small numbers of replicate experiments in model calibration situations—especially when sparse replicate functional data are involved like force–displacement curves from material tests. The DD methodology is straightforward and efficient for calibration and propagation problems involving aleatory and epistemic uncertainties in calibration experiments, models, and procedures.

42 ENGINEERING↗

DOE OSTI2022

Microstructure Changes Observed in the Near-Surface Region of SRF Nb Cavities Cutouts upon Cooling/Heating Cycles Using GI-Synchrotron XRD

We have mapped microstructural changes in the near-surface region of Nb from SRF cavity-cutouts upon thermal cycles in the range from 300 to 30 K using grazing incidence synchrotron X-Ray diffraction (GIXRD). Segregation of secondary phases was observed after the thermal cycle, and their nature has been clarified and discussed in view of previous studies on hydrides formation in SRF bulk Nb cavities. The temperature dependence of the relative population of these formed phases was obtained from GIXRD patterns profile fitting. Both, Nb bulk matrix and the new phases formed after cool-down show specific structural features as thermal contraction/expansion, structural transitions, and Nb lattice variation due to the induced strain by precipitates formation. The information derived from this structural study can explain some phenomena as the dissipation at high accelerating field (i.e. High Field Q Slope, HFQS) in the Nb SRF performance as well as new mechanisms never addressed in previous studies.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Municipal Adaptation to Changing Curbside Demands: Findings from Semi-Structured Interviews with Ten U.S. Cities

Emerging mobility services (e.g. ride-hailing, e-commerce, micro-mobility, etc.), are generating novel and rapidly growing demands to use curbside space, with potentially large impacts on mobility, energy consumption, and related outcomes. This presents both opportunities and challenges to municipal agencies responsible for managing this interface between the road network and adjacent land uses, as legacy practices require updating. In this study, we employ a semi-structured interviewing approach to establish how municipalities are adapting to these new pressures on their curbside. We interviewed senior staff responsible for curbside policy of ten large U.S. municipalities, with populations ranging from ~250,000 to ~5,000,000 (and the majority of which are the central city of their metropolitan region). We document a trend of organizational restructuring to more formally include curbside management teams, with the majority of interviewees also reporting increased staffing. Respondents reported that operational failures at their curbside (e.g. demand in excess of capacity) have impacts on safety, capacity, and emergency vehicle mobility, with impacts highly concentrated spatially and temporally (e.g. late evenings in nightlife districts). We document a diversity of data flows between ride-hailing operators (e.g. Uber, Lyft) and municipalities, with some cities reporting obtaining types of data that other cities report not receiving, despite requesting such data. Finally, respondents consistently expressed a desire for new data streams and methodologies to help manage the curbside of the future. It is hoped that establishing the state of practice in this rapidly changing context will be of use to practitioners facing similar pressures as those of our interviewees.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Sorted-cell proteomics reveals an AT1-associated epithelial cornification phenotype and suggests endothelial redox imbalance in human bronchopulmonary dysplasia

Bronchopulmonary dysplasia (BPD) is a neonatal lung disease characterized by inflammation and scarring leading to long-term tissue damage. Previous whole tissue proteomics identified BPD-specific proteome changes and cell type shifts. Little is known about the proteome-level changes within specific cell populations in disease. Here, we sorted epithelial (EPI) and endothelial (ENDO) cell populations based on their differential surface markers from normal and BPD human lungs. Using a low-input compatible sample preparation method (MicroPOT), proteins were extracted and digested into peptides and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteome analysis. Of the 4,970 proteins detected, 293 were modulated in abundance or detection in the EPI population and 422 were modulated in ENDO cells. Modulation of proteins associated with actin-cytoskeletal function, such as SCEL, LMO7, and TBA1B was observed in the BPD EPIs. Using confocal imaging and analysis, we validated the presence of aberrant multilayer-like structures comprising SCEL and LMO7, known to be associated with epidermal cornification, in the human BPD lung. This is the first report of the accumulation of cornification-associated proteins in BPD. Their localization in the alveolar parenchyma, primarily associated with alveolar type 1 (AT1) cells, suggests a role in the BPD postinjury response. In the ENDOs, redox balance and mitochondrial function pathways were modulated. Alternative mRNA splicing and cell proliferative functions were elevated in both populations, suggesting potential dysregulation of cell progenitor fate. This study characterized the proteome of epithelial and endothelial cells from the BPD lung for the first time, identifying population-specific changes in BPD pathogenesis.

BPD↗

DOE OSTI2022

Evolution of Bonding and Magnetism via Changes in Valence Electron Count in CuFe 2– x Co x Ge 2

A series of solid solutions, CuFe 2–x Co x Ge 2 (x = 0, 0.2, 0.4, 0.8, and 1.0), have been synthesized by arc-melting and characterized by powder X-ray and neutron diffraction, magnetic measurements, Mössbauer spectroscopy, and electronic band structure calculations. All compounds crystallize in the CuFe 2 Ge 2 structure type, which can be considered as a three-dimensional framework built of fused MGe6 octahedra and MGe 5 trigonal bipyramids (M = Fe and Co), with channels filled by rows of Cu atoms. As the Co content (x) increases, the unit cell volume decreases in an anisotropic fashion: the b and c lattice parameters decrease while the a parameter increases. The changes in all the parameters are nearly linear, thus following Vegard’s law. CuFe 2 Ge 2 exhibits two successive antiferromagnetic (AFM) orderings, corresponding to the formation of a commensurate AFM structure, followed by an incommensurate AFM structure observed at lower temperatures. Additionally, as the Co content increases, the AFM ordering temperature (TN) gradually decreases, and only one AFM transition is observed for x ≥ 0.2. The magnetic behavior of unsubstituted CuFe 2 Ge 2 was found to be sensitive to the preparation method. The temperature-dependent zero-field 57 Fe Mössbauer spectra reveal two hyperfine split components that evolve in agreement with the two consecutive AFM orderings observed in magnetic measurements. In contrast, the field-dependent spectra obtained for fields ≥ 2 T reveal a parallel arrangement of the moments associated with the two crystallographically unique metal sites. Electronic band structure calculations and chemical bonding analysis reveal a mix of strong M–M antibonding and non-bonding states at the Fermi level, in support of the overall AFM ordering observed in zero field. The substitution of Co for Fe reduces the population of the M–M antibonding states and the overall density of states at the Fermi level, thus suppressing the T N value.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Quantum dot polarisation converter in an optomechanical cavity

We propose a scheme of a quantum photon polarisation converter, which is based on controlled electron – photon – phonon transitions in a hybrid semiconductor nanostructure. This structure consists of a GaAs/InAs quantum dot (QD) that has a parallelepiped shape and contains a single electron, and an optomechanical microcavity (MC) based on a photonic crystal (PC) that supports two orthogonally polarised photonic modes and one mechanical (phonon) mode. Within the framework of the microscopic theory, the QD and MC performance characteristics are found. Populations of states of the system as functions of time and its parameters are calculated. The principal possibility of photon polarisation conversion using transitions in a five-level resonance scheme for coherent (single-photon) and steady-state (subphoton) regimes is shown. The MC optical and mechanical spectra are simulated, and the PC structure parameters are selected to ensure the efficient operation of the converter. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Bulk and element-specific magnetism of medium-entropy and high-entropy Cantor-Wu alloys

Magnetic Compton scattering, x-ray magnetic circular dichroism spectroscopy, and bulk magnetometry measurements are performed on a set of medium- (NiFeCo and NiFeCoCr) and high-entropy (NiFeCoCrPd and NiFeCoCrMn) Cantor-Wu alloys. The bulk spin momentum densities determined by magnetic Compton scattering are remarkably isotropic, and this is a consequence of the smearing of the electronic structure by disorder scattering of the electron quasiparticles. Nonzero x-ray magnetic circular dichroism signals are observed for every element in every alloy indicating differences in the populations of the majority and minority spin states implying finite magnetic moments. When Cr is included in the solid solution, the Cr spin moment is unambiguously antiparallel to the total magnetic moment, while a vanishingly small magnetic moment is observed for Mn, despite calculations indicating a large moment. Some significant discrepancies are observed between the experimental bulk and surface magnetic moments. Furthermore, despite the lack of quantitative agreement, the element-specific surface magnetic moments seem to be qualitatively reasonable.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

APOGEE Net: Improving the Derived Spectral Parameters for Young Stars through Deep Learning

Machine learning allows for efficient extraction of physical properties from stellar spectra that have been obtained by large surveys. The viability of machine-learning approaches has been demonstrated for spectra covering a variety of wavelengths and spectral resolutions, but most often for main-sequence (MS) or evolved stars, where reliable synthetic spectra provide labels and data for training. Spectral models of young stellar objects (YSOs) and low-mass MS stars are less well-matched to their empirical counterparts, however, posing barriers to previous approaches to classify spectra of such stars. In this work, we generate labels for YSOs and low-mass MS stars through their photometry. We then use these labels to train a deep convolutional neural network to predict logg, T {sub eff}, and Fe/H for stars with Apache Point Observatory Galactic Evolution Experiment (APOGEE) spectra in the DR14 data set. This “APOGEE Net” has produced reliable predictions of logg for YSOs, with uncertainties of within 0.1 dex and a good agreement with the structure indicated by pre-MS evolutionary tracks, and it correlates well with independently derived stellar radii. These values will be useful for studying pre-MS stellar populations to accurately diagnose membership and ages.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

County Level Annual Population Projections for SSP3 and SSP5

This dataset consist of annual (2020-2100) county-level population projections for the United States (U.S.) for Shared Socioeconomic Pathways (SSPs) 3 and 5. The original decadal state-level data is used as an input to the gridded population data model to downscale the state-level projections for each SSP to a 1 km grid. The 1 km data is then aggregated to the county-level using the 2020 TIGER/Line county shapefiles from the U.S. Census Bureau. The two data files are shared as .csv files with the following structure: Rows = Data for individual counties which are identified using their Federal Information Processing Standard (FIPS) code. The FIPS code is stored in the first column. Columns = Each year from 2020-2100 is an individual column. For easier reference, the state name associated with each row is stored in the last column. Values in each cell are the downscaled estimated population for that county-year combination. Values are fractional due to the weighting scheme used in the downscaling. The paper and model source code cited in the "Related Works" section describes the initial source of the population projections.

FIPS↗

DOE OSTI2026

Pb-Apatite Framework as a Generator of Novel Flat-Band CuO-Based Physics

Based upon density functional theory (DFT) calculations, we present the basic electronic structure of CuPb 9 (PO 4 ) 6 O (Cu-doped lead apatite, aka LK-99), in two scenarios: (1) where the structure is constrained to the P3 symmetry and (2) where no symmetry is imposed. At the DFT level, the former is predicted to be metallic while the latter is found to be a charge-transfer insulator. In both cases the filling of these states is nominally d 9 , consistent with the standard Cu 2+ valence state, and Cu with a local magnetic moment of order 0.7 μ B . In the metallic case we find these states to be unusually flat (∼0.2 eV dispersion), giving a very high density of electronic states (DOS) at the Fermi level that we argue can be a host for novel electronic physics. The flatness of the bands is the likely origin of symmetry-lowering gapping possibilities that would remove the spectral weight from E F . Motivated by some initial experimental observations of metallic or semiconducting behavior, we propose that disorder (likely structural) is responsible for closing the gap. Here, we consider a variety of possibilities that could possibly close the charge-transfer gap but limit consideration to kinds of disorder that preserve electron count. Of the possible kinds we considered (spin disorder, O populating vacancy sites, and Cu on less energetically favorable Pb sites), the local Cu moment, and consequently the charge-transfer gap, remains robust. We conclude that disorder responsible for metallic behavior entails some kind of doping where the electron count changes. Further, we claim that the emergence of the flat bands should be due to weak wave function overlap between the orbitals on Cu and O sites, owing to the directional character of the constituent orbitals. Therefore, finding an appropriate host structure for minimizing hybridization between Cu and O while allowing them to still weakly interact should be a promising route for generating flat bands at E F which can lead to interesting electronic phenomena, regardless of whether LK-99 is a superconductor.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Observation of T = 3/2 isobaric analog states in 9 Be using p + 8 Li resonance scattering

Background: Resonance scattering has been extensively used to study the structure of exotic, neutron-deficient nuclei. Extension of the resonance scattering technique to neutron-rich nuclei was suggested more than 20 years ago. This development is based on the isospin conservation law. In spite of broad field of the application, it has never gained a wide-spread acceptance. Purpose: To benchmark the experimental approach to study the structure of exotic neutron-rich nuclei through resonance scattering on a proton target. Method: In this work, the excitation function for p + 8 Li resonance scattering is measured using a thick target by recording coincidence between light and heavy recoils, populating T = 3/2 isobaric analog states (IAS) in 9 Be. Results: A good fit of the 8 Li(p, p) 8 Li resonance elastic scattering excitation function was obtained using previously tentatively known 5/2 – T = 3/2 state at 18.65 MeV in 9 Be and a new broad T = 3/2 s-wave state—the 5/2 + at 18.5 MeV. These results fit the expected isomirror properties for the T = 3/2 A = 9 isoquartet. Conclusions: Our analysis confirmed isospin as a good quantum number for the investigated highly excited T = 3/2 states and demonstrated that studying the structure of neutron-rich exotic nuclei through IAS is a promising approach.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Modeling the Galactic Neutron Star Population for Use in Continuous Gravitational-wave Searches

Searches for continuous gravitational waves (GW) from unknown Galactic neutron stars provide limits on the shapes of neutron stars. A rotating neutron star will produce GW if asymmetric deformations exist in its structure that are characterized by the star's ellipticity. Here, in this study, we use a simple model of the spatial and spin distribution of Galactic neutron stars to estimate the total number of neutron stars probed, using GW, to a given upper limit on the ellipticity. This may help optimize future searches with improved sensitivity. The improved sensitivity of third-generation GW detectors may increase the number of neutron stars probed, to a given ellipticity, by factors of 100 to 1000.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Apolipoprotein A-I modulates HDL particle size in the absence of apolipoprotein A-II

Human high-density lipoproteins (HDLs) are a complex mixture of structurally related nanoparticles that perform distinct physiological functions. We previously showed that human HDL containing apolipoprotein A-I (APOA1) but not apolipoprotein A-II (APOA2), designated LpA-I, is composed primarily of two discretely sized populations. Here, we isolated these particles directly from human plasma by antibody affinity chromatography, separated them by high-resolution size-exclusion chromatography and performed a deep molecular characterization of each species. The large and small LpA-I populations were spherical with mean diameters of 109 Å and 91 Å, respectively. Unexpectedly, isotope dilution MS/MS with [ 15 N]-APOA1 in concert with quantitation of particle concentration by calibrated ion mobility analysis demonstrated that the large particles contained fewer APOA1 molecules than the small particles; the stoichiometries were 3.0 and 3.7 molecules of APOA1 per particle, respectively. MS/MS experiments showed that the protein cargo of large LpA-I particles was more diverse. Human HDL and isolated particles containing both APOA1 and APOA2 exhibit a much wider range and variation of particle sizes than LpA-I, indicating that APOA2 is likely the major contributor to HDL size heterogeneity. We propose a ratchet model based on the trefoil structure of APOA1 whereby the helical cage maintaining particle structure has two “settings”—large and small—that accounts for these findings. This understanding of the determinants of HDL particle size and protein cargo distribution serves as a basis for determining the roles of HDL subpopulations in metabolism and disease states.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

Abstract Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Functional Data Analysis for Extracting the Intrinsic Dimensionality of Spectra: Application to Chemical Homogeneity in the Open Cluster M67

High-resolution spectroscopic surveys of the Milky Way have entered the Big Data regime and have opened avenues for solving outstanding questions in Galactic archeology. However, exploiting their full potential is limited by complex systematics, whose characterization has not received much attention in modern spectroscopic analyses. In this work, we present a novel method to disentangle the component of spectral data space intrinsic to the stars from that due to systematics. Using functional principal component analysis on a sample of 18,933 giant spectra from APOGEE, we find that the intrinsic structure above the level of observational uncertainties requires ≈10 functional principal components (FPCs). Our FPCs can reduce the dimensionality of spectra, remove systematics, and impute masked wavelengths, thereby enabling accurate studies of stellar populations. To demonstrate the applicability of our FPCs, we use them to infer stellar parameters and abundances of 28 giants in the open cluster M67. We employ Sequential Neural Likelihood, a simulation-based Bayesian inference method that learns likelihood functions using neural density estimators, to incorporate non-Gaussian effects in spectral likelihoods. By hierarchically combining the inferred abundances, we limit the spread of the following elements in M67: Fe ≲ 0.02 dex; C ≲ 0.03 dex; O, Mg, Si, Ni ≲ 0.04 dex; Ca ≲ 0.05 dex; N, Al ≲ 0.07 dex (at 68% confidence). Our constraints suggest a lack of self-pollution by core-collapse supernovae in M67, which has promising implications for the future of chemical tagging to understand the star formation history and dynamical evolution of the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗