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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The impact of curation errors in the PDBBind Database on machine learning predictions of protein–protein binding affinity

The PDBBind database has been widely utilized for the computational prediction of protein–protein binding affinities. While the accuracy of the PDBBind-curated equilibrium dissociation constants (K D ) has been reported for the protein–ligand subset of the PDBBind database, the curation accuracy has not been reported for the protein–protein subset. Here, we present a detailed manual analysis for the subset of PDBBind records with PubMed Central Open Access primary publications and find that ~19% of these records had K D values that were not supported by their primary publications. The impact of these putative curation errors on the machine learning-based prediction of K D from experimental protein–protein 3D structures was evaluated and correcting the curation errors improved the Pearson correlation coefficient between measured and random forest-predicted log 10 (K D ) values by ~8 percentage points. This finding underscores the importance of dataset accuracy for computational modelling and highlights the need for more stringent curation processes when extracting information from the scientific literature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

PM4Stell: A prototype permanent magnet stellarator structure

Permanent magnets provide a possible solution to simplify complicated stellarator coils. Here, a prototype permanent magnet stellarator structure, PM4Stell, has been funded to demonstrate the technical feasibility of using permanent magnets to create the shaping field of a stellarator. Permanent magnets in uniform cubes with three polarization directions will be carefully placed to generate the required magnetic field for a National Compact Stellarator eXperiment-like equilibrium together with planar toroidal field coils. Discrete magnets will be glued together and inserted into a “post-office-box-like” supporting structure. Electromagnetic and structural analyses have been done to validate the design. Error field correction magnets will be used to shim possible error fields. The design efforts of the prototype permanent magnet stellarator structure are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Properties of the new $ \mathcal{N} $ = 1 AdS 4 vacuum of maximal supergravity

The recent comprehensive numerical study of critical points of the scalar potential of four-dimensional N = 8, SO(8) gauged supergravity using Machine Learning software in [1] has led to a discovery of a new N = 1 vacuum with a triality-invariant SO(3) symmetry. Guided by the numerical data for that point, we obtain a consistent SO(3) × Z 2 -invariant truncation of the N = 8 theory to an N = 1 supergravity with three chiral multiplets. Critical points of the truncated scalar potential include both the N = 1 point as well as two new non-supersymmetric and perturbatively unstable points not found by previous searches. Studying the structure of the submanifold of SO(3) × Z 2 -invariant supergravity scalars, we find that it has a simple interpretation as a submanifold of the 14-dimensional Z $3\atop{2}$ -invariant scalar manifold (SU(1, 1)/U(1)) 7 , for which we find a rather remarkable superpotential whose structure matches the single bit error correcting (7, 4) Hamming code. This 14-dimensional scalar manifold contains approximately one quarter of the known critical points. We also show that there exists a smooth supersymmetric domain wall which interpolates between the new N = 1 AdS4 solution and the maximally supersymmetric AdS4 vacuum. Using holography, this result indicates the existence of an N = 1 RG flow from the ABJM SCFT to a new strongly interacting conformal fixed point in the IR.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Parametric Sensitivity and Uncertainty Quantification in the Version 1 of E3SM Atmosphere Model Based on Short Perturbed Parameter Ensemble Simulations

Abstract The atmospheric component of Energy Exascale Earth System Model version 1 has included many new features in the physics parameterizations compared to its predecessors. Potential complex nonlinear interactions among the new features create a significant challenge for understanding the model behaviors and parameter tuning. Using the one‐at‐a‐time method, the benefit of tuning one parameter may offset the benefit of tuning another parameter, or improvement in one target variable may lead to degradation in another target variable. To better understand the Energy Exascale Earth System Model version 1 model behaviors and physics, we conducted a large number of short simulations (three days) in which 18 parameters carefully selected from parameterizations of deep convection, shallow convection, and cloud macrophysics and microphysics were perturbed simultaneously using the Latin hypercube sampling method. From the perturbed parameter ensemble simulations and use of different skill score functions, we identified the most sensitive parameters, quantified how the model responds to changes of the parameters for both global mean and spatial distribution, and estimated the maximum likelihood of model parameter space for a number of important fidelity metrics. Comparison of the parametric sensitivity using simulations of two different lengths suggests that perturbed parameter ensemble using short simulations has some bearing on understanding parametric sensitivity of longer simulations. Results from this analysis provide a more comprehensive picture of the Energy Exascale Earth System Model version 1 behavior. The difficulty in reducing biases in multiple variables simultaneously highlights the need of characterizing model structural uncertainty (so‐called embedded errors) to inform future development efforts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Airborne Lidar Measurements of XCO 2 in Synoptically Active Environment and Associated Comparisons With Numerical Simulations

Frontal boundaries have been shown to cause large changes in CO 2 mole-fractions, but clouds and the complex vertical structure of fronts make these gradients difficult to observe. It remains unclear how the column average CO 2 dry air mole-fraction (XCO 2 ) changes spatially across fronts, and how well airborne lidar observations, data assimilation systems, and numerical models without assimilation capture XCO 2 frontal contrasts (ΔXCO 2 , i.e., warm minus cold sector average of XCO 2 ). We demonstrated the potential of airborne Multifunctional Fiber Laser Lidar (MFLL) measurements in heterogeneous weather conditions (i.e., frontal environment) to investigate the ΔXCO 2 during four seasonal field campaigns of the Atmospheric Carbon and Transport-America (ACT-America) mission. Most frontal cases in summer (winter) reveal higher (lower) XCO 2 in the warm (cold) sector than in the cold (warm) sector. During the transitional seasons (spring and fall), no clear signal in ΔXCO 2 was observed. Intercomparison among the MFLL, assimilated fields from NASA's Global Modeling and Assimilation Office (GMAO), and simulations from the Weather Research and Forecasting-—Chemistry (WRF-Chem) showed that (a) all products had a similar sign of ΔXCO 2 though with different levels of agreement in ΔXCO 2 magnitudes among seasons; (b) ΔXCO 2 in summer decreases with altitude; and (c) significant challenges remain in observing and simulating XCO 2 frontal contrasts. A linear regression analyses between ΔXCO 2 for MFLL versus GMAO, and MFLL versus WRF-Chem for summer-2016 cases yielded a correlation coefficient of 0.95 and 0.88, respectively. The reported ΔXCO 2 variability among four seasons provide guidance to the spatial structures of XCO 2 transport errors in models and satellite measurements of XCO 2 in synoptically-active weather systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Machine learning inversion from small-angle scattering for charged polymers

We develop Monte Carlo simulations for uniformly charged polymers and a machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments. The polymer is modeled as a chain of fixed-length bonds, where the connected bonds are subject to bending energy, and there is also a screened Coulomb potential for charge interaction between all joints. The bending energy is determined by the intrinsic bending stiffness, and the charge interaction depends on the interaction strength and screening length. All three contribute to the stiffness of the polymer chain and lead to longer and larger polymer conformations. The screening length also introduces a second length scale for the polymer besides the bending persistence length. To obtain the inverse mapping from the structure factor to these polymer conformation and energy-related parameters, we generate a large data set of structure factors by running simulations for a wide range of polymer energy parameters. We use principal component analysis to investigate the intra-polymer structure factors and determine the feasibility of the inversion using the nearest neighbor distance. We employ Gaussian process regression to achieve the inverse mapping and extract the characteristic parameters of polymers from the structure factor with low relative error.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Cosmological Constraints from Combining Photometric Galaxy Surveys and Gravitational Wave Observatories

Spatial variations in survey properties due to selection effects generate substantial systematic errors in large-scale structure measurements in optical galaxy surveys on very large scales. On such scales, the statistical sensitivity of optical surveys is also limited by their finite sky coverage. By contrast, gravitational wave (GW) sources appear to be relatively free of these issues, provided the angular sensitivity of GW experiments can be accurately characterized. We quantify the expected cosmological information gain from combining the forecast LSST 3$\times$2pt analysis (combination of three 2-point correlations of galaxy density and weak lensing shear fields) with the large-scale auto-correlation of GW sources from proposed next-generation GW experiments. We find that in $\Lambda$CDM and $w$CDM models, there is no significant improvement in cosmological constraints from combining GW with LSST 3$\times$2pt over LSST alone, due to the large shot noise for the former; however, this combination does enable a $\sim6\%$ constraint on the linear galaxy bias of GW sources. More interestingly, the optical-GW data combination provides tight constraints on models with primordial non-Gaussianity (PNG), due to the predicted scale-dependent bias in PNG models on large scales. Assuming that the largest angular scales that LSST will probe are comparable to those in Stage III surveys ($\ell_{\rm min}\sim50$), the inclusion of next-generation GW measurements could improve constraints on the PNG parameter $f_{\rm NL}$ by up to a factor of $\simeq6.6$ compared to LSST alone, yielding $\sigma(f_{\rm NL})=8.5$. These results assume the expected capability of a network of Einstein Telescope-like GW observatories, with a detection rate of $10^6$ events/year. We investigate the sensitivity of our results to different assumptions about future GW detectors as well as different LSST analysis choices.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Unified analysis of finite-size error for periodic Hartree-Fock and second order Møller-Plesset perturbation theory

Despite decades of practice, finite-size errors in many widely used electronic structure theories for periodic systems remain poorly understood. For periodic systems using a general Monkhorst-Pack grid, there has been no comprehensive and rigorous analysis of the finite-size error in the Hartree-Fock theory (HF) and the second order Møller-Plesset perturbation theory (MP2), which are the simplest wavefunction based method, and the simplest post-Hartree-Fock method, respectively. Such calculations can be viewed as a multi-dimensional integral discretized with certain trapezoidal rules. Due to the Coulomb singularity, the integrand has many points of discontinuity in general, and standard error analysis based on the Euler-Maclaurin formula gives overly pessimistic results. The lack of analytic understanding of finite-size errors also impedes the development of effective finite-size correction schemes. We propose a unified analysis to obtain sharp convergence rates of finite-size errors for the periodic HF and MP2 theories. Our main technical advancement is a generalization of the result of Lyness [Math. Comp. 30 (1976), pp. 1–23] for obtaining sharp convergence rates of the trapezoidal rule for a class of non-smooth integrands. Our result is applicable to three-dimensional bulk systems as well as low dimensional systems (such as nanowires and 2D materials). Our unified analysis also allows us to prove the effectiveness of the Madelung-constant correction to the Fock exchange energy, and the effectiveness of a recently proposed staggered mesh method for periodic MP2 calculations (see X. Xing, X. Li, and L. Lin [J. Chem. Theory Comput. 17 (2021), pp. 4733–4745]). In conclusion, our analysis connects the effectiveness of the staggered mesh method with integrands with removable singularities, and suggests a new staggered mesh method for reducing finite-size errors of periodic HF calculations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Influence of sun zenith angle on canopy clumping and the resulting impacts on photosynthesis

Addressing the impact of vegetation architecture on shortwave radiation transfer in land surface models is important for accurate weather forecasting, carbon budget estimates, and climate predictions. This paper investigates to what extent it is possible to retrieve structural parameters of two different parameterization schemes from direct transmittance derived from digital hemispherical photography and 3D radiative transfer modeling for two study sites with different vegetation canopy architectures. Neglecting the representation of 3D canopy structure in radiative transfer schemes leads to significant errors in shortwave radiation partitioning (up to 3.5 times more direct transmittance in the 3D model). Structural parameters, referred to as whole canopy ‘clumping indices’, were obtained in order to evaluate the impact of angular variation in clumping on shortwave radiation transfer. Impacts on photosynthesis were evaluated at site level with the UKESM land surface model, JULES. A comparison between flux tower derived and modeled photosynthesis indicates that considering zenith angular variations of structural parameters in the radiative transfer scheme of the UKESM land surface model significantly improves photosynthesis prediction in light limited ecosystems (from RMSE = 2.91 μmol CO 2 .m -2 .s -1 to RMSE = 1.51 μmol CO 2 .m -2 .s -1 , 48% smaller), typically with enhanced photosynthesis from bottom layers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

INTERFACES. A Program for Determining the 3D Structures of Surfaces Sites Using NMR Data

Dynamic nuclear polarization surface enhanced NMR spectroscopy has enabled the determination of high-resolution structures from surface-supported molecules, including singlesite heterogeneous catalysts. Structure determinations have largely mimicked the approaches used in biomolecular NMR spectroscopy, namely, using distance measurements to constrain a conformational search. These early demonstrations made use of purpose-built software, which has limited the adoption of the technique. Herein, we describe the open-source program INTERFACES (Interpret NMR to Elucidate or Reconstruct the Full Atomistic Configurations of External Surfaces) which automates the analysis of RE(SP)DOR data as well as the structure determination for surface sites. Distances, angles, dihedral angles, complex orientation, and distance from the support can all be sampled to find all structures that agree with the experimental data. A χ 2 metric is used to define the error ranges of the REDOR fits and produce structures with an arbitrary level of confidence. Structural solutions are then provided as both overlays and ORTEP-like probability ellipsoids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Does jackknife scale really matter for accurate large-scale structure covariances?

ABSTRACT The jackknife method gives an internal covariance estimate for large-scale structure surveys and allows model-independent errors on cosmological parameters. Using the SDSS-III BOSS CMASS sample, we study how the jackknife size and number of resamplings impact the precision of the covariance estimate on the correlation function multipoles and the error on the inferred baryon acoustic scale. We compare the measurement with the MultiDark Patchy mock galaxy catalogues, and we also validate it against a set of lognormal mocks with the same survey geometry. We build several jackknife configurations that vary in size and number of resamplings. We introduce the Hartlap factor in the covariance estimate that depends on the number of jackknife resamplings. We also find that it is useful to apply the tapering scheme to estimate the precision matrix from a limited number of resamplings. The results from CMASS and mock catalogues show that the error estimate of the baryon acoustic scale does not depend on the jackknife scale. For the shift parameter α, we find an average error of 1.6 per cent, 2.2 per cent and 1.2 per cent, respectively, from CMASS, Patchy, and lognormal jackknife covariances. Despite these uncertainties fluctuate significantly due to some structural limitations of the jackknife method, our α estimates are in reasonable agreement with published pre-reconstruction analyses. Jackknife methods will provide valuable and complementary covariance estimates for future large-scale structure surveys.

Favole, Ginevra (ORCID:000000028218563X)↗
DOE OSTI2026

Z α 2 correction to superallowed beta decays in effective field theory and implications for | V u d |

Superallowed ( 0 + → 0 + ) beta decays currently provide the most precise extraction of quark mixing in the Standard Model. Their interpretation as a measurement of | V u d | relies on a reliable first-principles computation of QED radiative corrections expressed as a series in Z α and α . In this work, we provide the first model-independent result for two-loop, O ( Z α 2 ) , long-distance radiative corrections where the nuclei are treated as heavy pointlike particles. We use renormalization group analysis to obtain new results at O ( Z α 3 ) for the coefficient of double logarithms in the ratio of the maximal beta energy to the inverse nuclear size, E m / R - 1 . We use the Kinoshita-Lee-Nauenberg theorem to obtain new results at O ( Z 2 α 3 ) for the coefficient of logarithms in the ratio of maximal beta energy to the electron mass, log ( 2 E m / m ) . We identify a structure-dependent, and, therefore, short-distance, contribution to the traditional Z α 2 correction that should be revisited. We provide the first comprehensive update to the long-distance corrections in almost 40 years and comment on the impact of our findings for extractions of | V u d | . We find that shifts in the long-distance corrections are 2.5 × larger than past estimates of their uncertainty, 1.5 × larger than the statistical uncertainty from the combined fit of superallowed decays, and about 1 / 2 the size of estimated systematic error, which stems dominantly from nuclear structure effects.

Cao, Zehua [Kentucky U.] (ORCID:0009000354256423)↗
DOE OSTI2019

A spatially adaptive high-order meshless method for fluid–structure interactions

We present a scheme implementing an a posteriori refinement strategy in the context of a high-order meshless method for problems involving point singularities and fluid–solid interfaces. The generalized moving least squares (GMLS) discretization used in this work has been previously demonstrated to provide high-order compatible discretization of the Stokes and Darcy problems, offering a high-fidelity simulation tool for problems with moving boundaries. The meshless nature of the discretization is particularly attractive for adaptive h -refinement, especially when resolving the near-field aspects of variables and point singularities governing lubrication effects in fluid–structure interactions. We demonstrate that the resulting spatially adaptive GMLS method is able to achieve optimal convergence in the presence of singularities for both the div-grad and Stokes problems. Furthermore, we present a series of simulations for flows of colloid suspensions, in which the refinement strategy efficiently achieved highly accurate solutions, particularly for colloids with complex geometries.

42 ENGINEERING↗
DOE OSTI2026

Leveraging Qubit Loss Detection in Fault-Tolerant Quantum Algorithms

Qubit loss errors constitute a dominant source of noise in many quantum hardware systems, particularly in neutral-atom quantum computers. We develop a theoretical framework to effectively detect and correct loss errors in logical algorithms and leverage such loss information in decoding. Considering general quantum error correction codes and logical circuits, we introduce a delayed-erasure decoder for experimentally motivated error models which leverages information from delayed loss detection to accurately correct loss errors, even when the precise moment of the error is unknown. Using this decoder, we identify strategies for detecting and correcting loss errors based on the logical circuit structure. For deep circuits prior to logical measurement, we explore methods to integrate loss detection into syndrome extraction with minimal overhead, identifying optimal strategies depending on the qubit loss fraction in the noise and hardware capabilities. In contrast, we find that many key algorithmic subroutines involve frequent gate teleportation, shortening the circuit depth before logical measurement and naturally replacing qubits with no additional experimental overhead. We simulate this setting using a toy model algorithm for small-angle synthesis and find a significant performance improvement as the loss fraction increases. These results provide a path forward for advancing large-scale fault-tolerant quantum computation in systems with loss error detection.

atoms↗
DOE OSTI2021

Constrained Block Nonlinear Neural Dynamical Models

Neural network modules conditioned by known priors can be effectively trained and combined to represent systems with nonlinear dynamics. This work explores a novel formulation for data-efficient learning of deep control-oriented nonlinear dynamical models by embedding local model structure and constraints. The proposed method consists of neural network blocks that represent input, state, and output dynamics with constraints placed on the network weights and system variables. For handling partially observable dynamical systems, we utilize a state observer neural network to estimate the states of the system's latent dynamics. We evaluate the performance of the proposed architecture and training methods on system identification tasks for three nonlinear systems: a continuous stirred tank reactor, a two tank interacting system, and an aerodynamics body. Models optimized with a few thousand system state observations accurately represent system dynamics in open loop simulation over thousands of time steps from a single set of initial conditions. Experimental results demonstrate an order of magnitude reduction in open-loop simulation mean squared error for our constrained, block-structured neural models when compared to traditional unstructured and unconstrained neural network models.

Skomski, Elliott↗
DOE OSTI2019

SAD phasing of XFEL data depends critically on the error model

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Assessing Clouds Using Satellite Observations Through Three Generations of Global Atmosphere Models

Abstract Clouds are parameterized in climate models using quantities on the model grid‐scale to approximate the cloud cover and impact on radiation. Because of the complexity of processes involved with clouds, these parameterizations are one of the key challenges in climate modeling. Differences in parameterizations of clouds are among the main contributors to the spread in climate sensitivity across models. In this work, the clouds in three generations of an atmosphere model lineage are evaluated against satellite observations. Satellite simulators are used within the model to provide an appropriate comparison with individual satellite products. In some respects, especially the top‐of‐atmosphere cloud radiative effect, the models show generational improvements. The most recent generation, represented by two distinct branches of development, exhibits some regional regressions in the cloud representation; in particular the southern ocean shows a positive bias in cloud cover. The two branches of model development show how choices during model development, both structural and parametric, lead to different cloud climatologies. Several evaluation strategies are used to quantify the spatial errors in terms of the large‐scale circulation and the cloud structure. The Earth mover's distance is proposed as a useful error metric for the passive satellite data products that provide cloud‐top pressure‐optical depth histograms. The cloud errors identified here may contribute to the high climate sensitivity in the Community Earth System Model, version 2 and in the Energy Exascale Earth System Model, version 1.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition

3-β-hydroxysteroid-Δ 8 , Δ 7 -isomerase, known as Emopamil-Binding Protein (EBP), is an endoplasmic reticulum membrane protein involved in cholesterol biosynthesis, autophagy, oligodendrocyte formation. The mutation on EBP can cause Conradi-Hunermann syndrome, an inborn error. Interestingly, EBP binds an abundance of structurally diverse pharmacologically active compounds, causing drug resistance. Here, we report two crystal structures of human EBP, one in complex with the anti-breast cancer drug tamoxifen and the other in complex with the cholesterol biosynthesis inhibitor U18666A. EBP adopts an unreported fold involving five transmembrane-helices (TMs) that creates a membrane cavity presenting a pharmacological binding site that accommodates multiple different ligands. The compounds exploit their positively-charged amine group to mimic the carbocationic sterol intermediate. Mutagenesis studies on specific residues abolish the isomerase activity and decrease the multidrug binding capacity. Finally, this work reveals the catalytic mechanism of EBP-mediated isomerization in cholesterol biosynthesis and how this protein may act as a multi-drug binder.

59 BASIC BIOLOGICAL SCIENCES↗