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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Broken-Symmetry Density Functional Theory Analysis of the Ω Intermediate in Radical S -Adenosyl- l -methionine Enzymes: Evidence for a Near-Attack Conformer over an Organometallic Species

Radical S-adenosyl-L-methionine (SAM) enzymes are found in all domains of life and catalyze a wide range of biochemical reactions. Recently, an organometallic intermediate, Ω, has been experimentally implicated in the 5'-deoxyadenosyl radical generation mechanism of the radical SAM superfamily. In this work, we employ broken-symmetry density functional theory to evaluate several structural models of Ω. The results show that the calculated hyperfine coupling constants (HFCCs) for the proposed organometallic structure of Ω are inconsistent with the experiment. In contrast, a near-attack conformer of SAM bound to the catalytic [4Fe–4S] cluster, in which the distance between the unique iron and SAM sulfur is ~3 Å, yields HFCCs that are all within 1 MHz of the experimental values. Furthermore, these results clarify the structure of the ubiquitous Ω intermediate and suggest a paradigm shift reversal regarding the mechanism of SAM cleavage by members of the radical SAM superfamily.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Using PyBioNetFit to leverage qualitative and quantitative data in biological model parameterization and uncertainty quantification

Data generated in studies of cellular regulatory systems are often qualitative. For example, measurements of signaling readouts in the presence and absence of mutations may reveal a rank ordering of responses across conditions but not the precise extents of mutation-induced differences. Qualitative data are often ignored by mathematical modelers or are considered in an ad hoc manner, as in the study of Kocieniewski and Lipniacki (2013) [Phys Biol 10: 035006], which was focused on the roles of MEK isoforms in ERK activation. In this earlier study, model parameter values were tuned manually to obtain consistency with a combination of qualitative and quantitative data. This approach is not reproducible, nor does it provide insights into parametric or prediction uncertainties. Here, starting from the same data and the same ordinary differential equation (ODE) model structure, we generate formalized statements of qualitative observations, making these observations more reusable, and we improve the model parameterization procedure by applying a systematic and automated approach enabled by the software package PyBioNetFit. We also demonstrate uncertainty quantification (UQ), which was absent in the original study. Our results show that PyBioNetFit enables qualitative data to be leveraged, together with quantitative data, in parameterization of systems biology models and facilitates UQ. These capabilities are important for reliable estimation of model parameters and model analyses in studies of cellular regulatory systems and reproducibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Leiomodin creates a leaky cap at the pointed end of actin-thin filaments

Improper lengths of actin-thin filaments are associated with altered contractile activity and lethal myopathies. Leiomodin, a member of the tropomodulin family of proteins, is critical in thin filament assembly and maintenance; however, its role is under dispute. Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first atomic structural model of the binding interface between the tropomyosin-binding site of cardiac leiomodin and the N-terminus of striated muscle tropomyosin. Our structural data indicate that the leiomodin/tropomyosin complex only forms at the pointed end of thin filaments, where the tropomyosin N-terminus is not blocked by an adjacent tropomyosin protomer. This discovery provides evidence supporting the debated mechanism where leiomodin and tropomodulin regulate thin filament lengths by competing for thin filament binding. Data from experiments performed in cardiomyocytes provide additional support for the competition model; specifically, expression of a leiomodin mutant that is unable to interact with tropomyosin fails to displace tropomodulin at thin filament pointed ends and fails to elongate thin filaments. Together with previous structural and biochemical data, we now propose a molecular mechanism of actin polymerization at the pointed end in the presence of bound leiomodin. In the proposed model, the N-terminal actin-binding site of leiomodin can act as a “swinging gate” allowing limited actin polymerization, thus making leiomodin a leaky pointed-end cap. Results presented in this work answer long-standing questions about the role of leiomodin in thin filament length regulation and maintenance.

2D-NMR↗
DOE OSTI2025

A critical verification of beam and shell models of wind turbine blades

Ever-increasing wind turbine size has challenged predictive capabilities on several fronts. Here, to address part of the blade structural modeling uncertainty, a systematic model fidelity comparison study was conducted on commonly used finite elements. pyNuMAD was utilized to create beam, shell, and solid models of a 100 m long blade undergoing large static deflections. The solid model avoided the use of layered-solid elements by resolving core and facesheet layers. An unprecedented model with 73.7 million elements revealed insights that have never been possible from prior experimental and numerical studies. As compared to the solid element model, the tip deflection from the shell and beam model was found to be about 2% and 4.3% too low, respectively. The twist from the beam model was found to be about 5.6% too high, while the twist from shell model was 24% too low, though improvement was demonstrated with mesh refinement. The beam model adhesive stresses were more accurate than the shell model. Out-of-plane stresses were of great significance near geometric and material discontinuities, and neither the shell nor beam model captured these effects well. Failure predictions from beam, shell, or layered-solid models are unlikely to be reliable at trailing edges, adhesives, ply-drops, spar-cap boundaries.

17 WIND ENERGY↗
DOE OSTI2020

Measurement of the central exclusive production of charged particle pairs in proton-proton collisions at $\sqrt{s}$ = 200 GeV with the STAR detector at RHIC

We report on the measurement of the Central Exclusive Production of charged particle pairs h+h- (h = π, K, p) with the STAR detector at RHIC in proton-proton collisions at $\sqrt{s}$ = 200 GeV. The charged particle pairs produced in the reaction pp → p' + h + h - + p' are reconstructed from the tracks in the central detector and identified using the specific energy loss and the time of flight method, while the forward-scattered protons are measured in the Roman Pot system. Exclusivity of the event is guaranteed by requiring the transverse momentum balance of all four final-state particles. Differential cross sections are measured as functions of observables related to the central hadronic final state and to the forward-scattered protons. They are measured in a fiducial region corresponding to the acceptance of the STAR detector and determined by the central particles’ transverse momenta and pseudorapidities as well as by the forward-scattered protons’ momenta. This fiducial region roughly corresponds to the square of the four-momentum transfers at the proton vertices in the range 0.04 GeV 2 < -t 1 , -t 2 < 0.2 GeV 2 , invariant masses of the charged particle pairs up to a few GeV and pseudorapidities of the centrally-produced hadrons in the range |η| < 0.7. The measured cross sections are compared to phenomenological predictions based on the Double Pomeron Exchange (DPE) model. Structures observed in the mass spectra of π + π - and K + K - pairs are consistent with the DPE model, while angular distributions of pions suggest a dominant spin-0 contribution to π + π - production. For π + π - production, the fiducial cross section is extrapolated to the Lorentz-invariant region, which allows decomposition of the invariant mass spectrum into continuum and resonant contributions. The extrapolated cross section is well described by the continuum production and at least three resonances, the f 0 (980), f 2 (1270) and f 0 (1500), with a possible small contribution from the f 0 (1370). Fits to the extrapolated differential cross section as a function of t 1 and t 2 enable extraction of the exponential slope parameters in several bins of the invariant mass of π + π - pairs. These parameters are sensitive to the size of the interaction region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Out-of-Distribution Detection and Radiological Data Monitoring Using Statistical Process Control

Abstract Machine learning (ML) models often fail with data that deviates from their training distribution. This is a significant concern for ML-enabled devices as data drift may lead to unexpected performance. This work introduces a new framework for out of distribution (OOD) detection and data drift monitoring that combines ML and geometric methods with statistical process control (SPC). We investigated different design choices, including methods for extracting feature representations and drift quantification for OOD detection in individual images and as an approach for input data monitoring. We evaluated the framework for both identifying OOD images and demonstrating the ability to detect shifts in data streams over time. We demonstrated a proof-of-concept via the following tasks: 1) differentiating axial vs. non-axial CT images, 2) differentiating CXR vs. other radiographic imaging modalities, and 3) differentiating adult CXR vs. pediatric CXR. For the identification of individual OOD images, our framework achieved high sensitivity in detecting OOD inputs: 0.980 in CT, 0.984 in CXR, and 0.854 in pediatric CXR. Our framework is also adept at monitoring data streams and identifying the time a drift occurred. In our simulations tracking drift over time, it effectively detected a shift from CXR to non-CXR instantly, a transition from axial to non-axial CT within few days, and a drift from adult to pediatric CXRs within a day—all while maintaining a low false positive rate. Through additional experiments, we demonstrate the framework is modality-agnostic and independent from the underlying model structure, making it highly customizable for specific applications and broadly applicable across different imaging modalities and deployed ML models.

Zamzmi, Ghada↗
DOE OSTI2025

Microstructurally Strained Pyrochlore–Perovskite Biphasic Electrocatalysts for the Oxygen Evolution Reaction

Efficiency of water splitting for hydrogen production is often limited by the sluggish kinetics of multiple electronic transfers required in the heterogeneous oxygen evolution reaction (OER). Catalyst design for reducing the high OER overpotential remains a major scientific challenge. Lattice-strain engineering, a method for tuning the electronic structure and surface geometric configuration of active sites, may greatly affect the interaction between adsorbates and catalytic surfaces for high activity and stability. Here, in this study, we present the synthesis of biphasic oxides of YPrSrRuMnO x , which consists of distinct phases of Y 2 Ru 2 O 7 pyrochlore and (Pr 0.7 Sr 0.3 )MnO 3 perovskite, and the development of a suitable analytical approach to study the strain–catalytic property relationship. Linear sweep voltammetry results reveal that the biphasic oxide exhibits approximately 3.1 times greater mass activity and 2.4 times larger turnover frequency (TOF) than single-phase Y 2 Ru 2 O 7 in the 0.1 M HClO 4 electrolyte. The biphasic catalyst is also about 3 times more stable than the single-phase oxide under acidic conditions. X-ray photoelectron spectroscopy, nitrogen isotherm, and electrochemical surface area analyses indicate that the oxidation state, specific surface area, and electrochemical surface area do not cause enough difference in the observed enhancement of OER performance. We examined the effects of microstrain on electrocatalysis, originating from lattice mismatch between different phases, using three different structural models. Specifically, we compared the Williamson–Hall method, standard stress–strain analysis, and Rietveld refinement in analyzing the structure–property relationship. Strain mapping using geometric phase analysis (GPA) further revealed significant microstrain and lattice dislocations localized near phase boundaries in the biphasic oxide, in contrast to the uniform strain in single-phase materials. The results reveal that the increased microstrain correlates well with the improved OER performance, as the biphasic oxide catalyst exhibits 2–3 times greater microstrain than Y 2 Ru 2 O 7 pyrochlore.

electrocatalysts↗
DOE OSTI2023

Impacts of climate change on subannual hydropower generation: a multi-model assessment of the United States federal hydropower plant

Abstract Hydropower is a low-carbon emission renewable energy source that provides competitive and flexible electricity generation and is essential to the evolving power grid in the context of decarbonization. Assessing hydropower availability in a changing climate is technically challenging because there is a lack of consensus in the modeling representation of key dynamics across scales and processes. Focusing on 132 US federal hydropower plants, in this study we evaluate the compounded impact of climate and reservoir-hydropower models’ structural uncertainties on monthly hydropower projections. In particular, instead of relying on one single regression-based hydropower model, we introduce another conceptual reservoir operations-hydropower model in the assessment framework. This multi-model assessment approach allows us to partition uncertainties associated with both climate and hydropower models for better clarity. Results suggest that while at least 70% of the uncertainties at the annual scale and 50% at the seasonal scale can be attributed to the choice of climate models, up to 50% of seasonal variability can be attributed to the choice of hydropower models, particularly in regions over the western US where the reservoir storage is substantial. The analysis identifies regions where multi-model assessments are needed and presents a novel approach to partition uncertainties in hydropower projections. Another outcome includes an updated evaluation of Coupled Model Intercomparison Project Phase 5 (CMIP5)-based federal hydropower projection, at the monthly scale and with a larger ensemble, which can provide a baseline for understanding future assessments based on CMIP6 and beyond.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Closing the loop: model-predictive control for a closed-circuit reverse osmosis system

This article presents a model-predictive controller (MPC) for the maximization of the energy efficiency of a closed-circuit desalination reverse osmosis (CCRO) system. CCRO is a process for producing drinking water that is based on a cyclic operation with the following two phases: (a) filtration and (b) drain. In this article, we test model predictive control for optimal control of this process. The most important features of our approach are as follows: (a) the selection of a model structure that enables reliable forecasts of the filtration phase (up to 3 h), (b) an on-line model calibration strategy that ensures model forecast reliability, and (c) the satisfaction of equipment safety and operational constraints on the selected setpoints. We challenge this through deliberate introduction of changes in the unmeasured feed concentration and the applied constraints. Our results indicate that frequent model parameter updates are critical to maintain model reliability for MPC purposes. In addition, we illustrate that parameter identifiability is not guaranteed and that deliberate variation in flow rates is necessary even though the process never operates in steady state. Finally, MPC can compute flow rate setpoints that maximize the energy efficiency of the CCRO process while satisfying the applicable equipment and safety constraints.

closed-circuit reverse osmosis↗
DOE OSTI2023

HLA-Clus: HLA class I clustering based on 3D structure

In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria. The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained and transformed into clouds of labeled points. Second, similarities between alleles are determined using a newly defined structure distance metric that accounts for spatial and physicochemical similarities. Finally, alleles are clustered via hierarchical or nearest-neighbor approaches. We also interfaced HLA-Clus with the peptide:HLA affinity predictor MHCnuggets. By using the nearest neighbor clustering method to select optimal allele-specific deep learning models in MHCnuggets, the average accuracy of peptide binding prediction of rare alleles was improved. The HLA-Clus package offers a solution for characterizing the peptide binding specificities of a large number of HLA alleles. This method can be applied in HLA functional studies, such as the development of peptide affinity predictors, disease association studies, and HLA matching for grafting. HLA-Clus is freely available at our GitHub repository (https://github.com/yshen25/HLA-Clus).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Synthesis and symmetry of perovskite oxynitride CaW(O,N) 3

Perovskite oxynitrides, in addition to being promising electrocatalysts and photoabsorbers, present an interesting case study in crystal symmetry. Full or partial ordering of the O and N anions affects global symmetry and influences material performance and functionality; however, anion ordering is challenging to detect experimentally. In this work, we synthesize a novel perovskite oxynitride CaW(O,N) 3 and characterize its crystal structure using both X-ray and neutron diffraction. Through co-refinement of the diffraction patterns with a range of literature and theory-derived model structures, we demonstrate that CaW(O,N) 3 adopts an orthorhombic Pnma average structure and exhibits octahedral distortion with evidence for preferred anion site occupancy. However, through comparison with a large, low-symmetry unit cell, we identify the presence of disorder that is not fully accounted for by the high-symmetry model. We compare CaW(O,N) 3 with SrW(O,N) 3 to demonstrate the broader presence of such disorder and identify contrasting features in the electronic structures. This work signifies an updated perspective on the inherent crystal symmetry present in perovskite oxynitrides.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Predicting RNA structure and dynamics with deep learning and solution scattering

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg 2+ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg 2+ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The energy budget and figure of Earth during recovery from the Moon-forming giant impact

Quantifying the energy budget of Earth in the first few million years following the Moon-forming giant impact is vital to understanding Earth's initial thermal state and the dynamics of lunar tidal evolution. After the impact, the body was substantially vaporized and rotating rapidly, very different from the planet we know today. The subsequent evolution of Earth's energy budget, as the body cooled and angular momentum was transferred during lunar tidal recession, has not been accurately calculated with all relevant energy components included. In this work, we use giant impact simulations and planetary structure models to calculate the energy budget at stages in Earth's evolution. We show that the figure and internal structure of Earth changed substantially during its post-impact evolution and that changes in kinetic, potential, and internal energy were all significant. These changes have important implications for the dynamics of tidal recession and the thermal structure of early Earth.

58 GEOSCIENCES↗
DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Refining perovskite structures to pair distribution function data using collective Glazer modes as a basis

Structural modelling of octahedral tilts in perovskites is typically carried out using the symmetry constraints of the resulting space group. In most cases, this introduces more degrees of freedom than those strictly necessary to describe only the octahedral tilts. It can therefore be a challenge to disentangle the octahedral tilts from other structural distortions such as cation displacements and octahedral distortions. This paper reports the development of constraints for modelling pure octahedral tilts and implementation of the constraints in diffpy-CMI, a powerful package to analyse pair distribution function (PDF) data. The model in the program allows features in the PDF that come from rigid tilts to be separated from non-rigid relaxations, providing an intuitive picture of the tilting. The model has many fewer refinable variables than the unconstrained space group fits and provides robust and stable refinements of the tilt components. It further demonstrates the use of the model on the canonical tilted perovskite CaTiO 3 which has the known Glazer tilt system α + β – β – . The Glazer model fits comparably to the corresponding space-group model Pnma below r = 14 Å and becomes progressively worse than the space-group model at higher r due to non-rigid distortions in the real material.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Modeling inter‐reader variability in clinical target volume delineation for soft tissue sarcomas using diffusion model

Abstract Background Accurate delineation of the clinical target volume (CTV) is essential in the radiotherapy treatment of soft tissue sarcomas. However, this process is subject to inter‐reader variability due to the need for clinical assessment of risk and extent of potential microscopic spread. This can lead to inconsistencies in treatment planning, potentially impacting treatment outcomes. Most existing automatic CTV delineation methods do not account for this variability and can only generate a single CTV for each case. Purpose This study aims to develop a deep learning‐based technique to generate multiple CTV contours for each case, simulating the inter‐reader variability in the clinical practice. Methods We employed a publicly available dataset consisting of fluorodeoxyglucose positron emission tomography (FDG‐PET), x‐ray computed tomography (CT), and pre‐contrast T1‐weighted magnetic resonance imaging (MRI) scans from 51 patients with soft tissue sarcoma, along with an independent validation set containing five additional patients. An experienced reader drew a contour of the gross tumor volume (GTV) for each patient based on multi‐modality images. Subsequently, two additional readers, together with the first one, were responsible for contouring three CTVs in total based on the GTV. We developed a diffusion model‐based deep learning method that is capable of generating arbitrary number of different and plausible CTVs to mimic the inter‐reader variability in CTV delineation. The proposed model incorporates a separate encoder to extract features from the GTV masks, leveraging the critical role of GTV information in accurate CTV delineation. Results The proposed diffusion model demonstrated superior performance with the highest Dice Index (0.902 compared to values below 0.881 for state‐of‐the‐art models) and the best generalized energy distance (GED) (0.209 compared to values exceeding 0.221 for state‐of‐the‐art models). It also achieved the second‐highest recall and precision metrics among the compared ambiguous image segmentation models. Results from both datasets exhibited consistent trends, reinforcing the reliability of our findings. Additionally, ablation studies exploring different model structures and input configurations highlighted the significance of incorporating prior GTV information for accurate CTV delineation. Conclusions The proposed diffusion model successfully generates multiple plausible CTV contours for soft tissue sarcomas, effectively capturing inter‐reader variability in CTV delineation.

Dong, Yafei [Yale Biomedical Imaging Institute Yal↗
DOE OSTI2023

Synthesis, crystal and electronic structure of the Zintl phase Ba 16 Sb 11 . A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca 16 Sb 11 structure type

The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗