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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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We present MLstructureMining, a machine learning tool that identifies a structural model from an experimental pair distribution function. We show how the method can be used for structure analysis of both crystalline and nanocrystalline materials.
Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding applications in both crystallography and cryo-EM. Indeed, previous crystallographic work on the errors in structural models is directly applicable to likelihood targets in cryo-EM. Likelihood targets in Fourier space are derived here to characterize, based on the comparison of half-maps, the direction- and resolution-dependent variation in the strength of both signal and noise in the data. Because the signal depends on local features, the signal and noise are analysed in local regions of the cryo-EM reconstruction. The likelihood analysis extends to prediction of the signal that will be achieved in any docking calculation for a model of specified quality and completeness. A related calculation generalizes a previous measure of the information gained by making the cryo-EM reconstruction.
Visual analytics supported by high performance computing (HPC) accelerates and enhances the discovery, exploration, and analysis of causal patterns in complex system dynamics (SD) models. We present a suite of visualization-assisted ensemble-based techniques for hypothesis generation and testing, and for sensitivity analysis. By employing HPC to provide parallel, on-demand simulation of SD models, one can “steer” an ensemble of simulated scenarios in real time as one first formulates and then informally tests those hypotheses: this provides rapid feedback for analysts to refine their understanding of the causal relationships emergent from a model. Such understandings can be followed and augmented by rigorous application of statistical methods, namely global variance-based sensitivity analysis, Monte-Carlo filtering, adaptive regional sensitivity analysis, and self-organized maps: here timely computation relies on HPC, while effective presentation emphasizes high-dimensional multivariate data visualization. Immersive visualization in virtual 3D environments provides an excellent adjunct to the traditional 2D graphics typically used for SD models, as it generates an embodied understanding of model behavior and facilitates an active, collaborative critique of model structure and output. Finally, we summarize prospects for HPC-enabled visual analytics applied to SD modeling.
Advances in nuclear power reactors include the use of mixed oxide fuel, containing uranium and plutonium oxides. The high-temperature behaviour and structure of PuO 2-x above 1,800 K remain largely unexplored, and these conditions must be considered for reactor design and planning for the mitigation of severe accidents. Here, in this study, we measure the atomic structure of PuO 2-x through the melting transition up to 3,000 +/- 50 K using X-ray scattering of aerodynamically levitated and laser-beam-heated samples, with O/Pu ranging from 1.57 to 1.76. Liquid structural models consistent with the X-ray data are developed using machine-learned interatomic potentials and density functional theory. Molten PuO 1.76 contains some degree of covalent Pu-O bonding, signalled by the degeneracy of Pu 5f and O 2p orbitals. The liquid is isomorphous with molten CeO 1.75 , demonstrating the latter as a non-radioactive, non-toxic, structural surrogate when differences in the oxidation potentials of Pu and Ce are accounted for. These characterizations provide essential constraints for modelling pertinent to reactor safety design. The molten structure of plutonium oxide-a component of mixed oxide nuclear fuels-is measured, showing some degree of covalent bonding. Its atomic structure is similar to that of cerium oxide, which could be a non-radioactive structural surrogate.
Mixed ionic-electronic conductors offer chemical and electrical means for active tuning of their optical constants, e.g. with variations in oxygen non-stoichiometry in Pr 0.1 Ce 0.9 O 2-δ , enabling implementation of adaptive thin film optical devices. Here, we demonstrate in-situ chemo-tuning of the extinction coefficient in Pr 0.1 Ce 0.9 O 2-δ at elevated temperatures and provide a tuning model that treats the interdependence of mobile oxygen vacancies and small polarons coupled to variations in optically active praseodymium ions. Further, a new means for electro-tuning of the optical constants of mixed ionic-electronic conductors was demonstrated experimentally and modeled for Pr 0.1 Ce 0.9 O 2-δ thin films deposited on grid-like electrode structures. Modeling of non-steady state optical transmittance modulations in the latter allows for estimation of oxygen vacancy mobility that determines the switching speed of the device. Quenched-in values of nr and k to room temperature become nonvolatile, providing a modulation range in the extinction coefficient of Δk ~0.1 (change of ~800%) and in the refractive index of Δn r ~0.1 (relative to initial n r of ~2.35). Key figures of merit including, transmission optical modulation of ~0.04 per 1 mV nm -1 , switching energy per area of 670 pJ μm -2 and switching times of seconds, were demonstrated, with further improvements possible.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.