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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Abstract Motivation Cryogenic electron microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational heterogeneity. Although various global and local map-sharpening techniques are widely employed to improve cryo-EM density maps, it is still challenging to efficiently improve their quality for building better protein structures from them. Results In this study, we introduce CryoTEN—a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their corresponding simulated maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, automatic de novo protein structure modeling shows that protein structures built from the density maps processed by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing state-of-the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality of density maps, while running >10 times faster and requiring much less GPU memory than them. Availability and implementation The source code and data are freely available at https://github.com/jianlin-cheng/cryoten.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Clifford Circuit-Based Heuristic Optimization of Fermion-To-Qubit Mappings

Simulation of interacting Fermionic Hamiltonians is one of the most promising applications of quantum computers. However, the feasibility of analyzing Fermionic systems with a quantum computer hinges on the efficiency of Fermion-to-qubit mappings that encode nonlocal Fermionic degrees of freedom in local qubit degrees of freedom. While recent studies have highlighted the importance of designing Fermion-to-qubit mappings that are tailored to specific problem Hamiltonians, the methods proposed so far either are restricted to a narrow class of mappings or they use computationally expensive and unscalable brute-force search algorithms. Here, in this work, we address this challenge by designing a heuristic numerical optimization framework for Fermion-to-qubit mappings. To this end, we first translate the Fermion-to-qubit mapping problem to a Clifford circuit optimization problem and then use simulated annealing to optimize the average Pauli weight of the problem Hamiltonian. For all Fermionic Hamiltonians we have considered, the numerically optimized mappings outperform their conventional counterparts, including ternary-tree-based mappings that are known to be optimal for single creation and annihilation operators. We find that our optimized mappings yield between 15% and 40% improvements on the average Pauli weight when the simulation Hamiltonian has an intermediate level of complexity. Most remarkably, the optimized mappings improve the average Pauli weight for 6 × 6 nearest-neighbor hopping and Hubbard models by more than 40% and 20%, respectively. Surprisingly, we also find specific interaction Hamiltonians for which the optimized mapping outperforms any ternary-tree-based mapping. Our results establish heuristic numerical optimization as an effective method for obtaining mappings tailored for specific Fermionic Hamiltonian.

Hamiltonians↗
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Joint analysis of Dark Energy Survey Year 3 data and CMB lensing from SPT and Planck . I. Construction of CMB lensing maps and modeling choices

Joint analyses of cross-correlations between measurements of galaxy positions, galaxy lensing, and lensing of the cosmic microwave background (CMB) offer powerful constraints on the large-scale structure of the Universe. In a forthcoming analysis, we will present cosmological constraints from the analysis of such cross-correlations measured using Year 3 data from the Dark Energy Survey (DES), and CMB data from the South Pole Telescope (SPT) and Planck. Here we present two key ingredients of this analysis: (1) an improved CMB lensing map in the SPT-SZ survey footprint and (2) the analysis methodology that will be used to extract cosmological information from the cross-correlation measurements. Relative to previous lensing maps made from the same CMB observations, we have implemented techniques to remove contamination from the thermal Sunyaev Zel’dovich effect, enabling the extraction of cosmological information from smaller angular scales of the cross-correlation measurements than in previous analyses with DES Year 1 data. We describe our model for the cross-correlations between these maps and DES data, and validate our modeling choices to demonstrate the robustness of our analysis. We then forecast the expected cosmological constraints from the galaxy survey-CMB lensing auto and cross-correlations. We find that the galaxy-CMB lensing and galaxy shear-CMB lensing correlations will on their own provide a constraint on S 8 =σ 8 $\sqrt{Ωm/0.3}$ at the few percent level, providing a powerful consistency check for the DES-only constraints. Finally, we explore scenarios where external priors on shear calibration are removed, finding that the joint analysis of CMB lensing cross-correlations can provide constraints on the shear calibration amplitude at the 5% to 10% level.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Map-based cosmology inference with lognormal cosmic shear maps

ABSTRACT Most cosmic shear analyses to date have relied on summary statistics (e.g. ξ+ and ξ−). These types of analyses are necessarily suboptimal, as the use of summary statistics is lossy. In this paper, we forward-model the convergence field of the Universe as a lognormal random field conditioned on the observed shear data. This new map-based inference framework enables us to recover the joint posterior of the cosmological parameters and the convergence field of the Universe. Our analysis properly accounts for the covariance in the mass maps across tomographic bins, which significantly improves the fidelity of the maps relative to single-bin reconstructions. We verify that applying our inference pipeline to Gaussian random fields recovers posteriors that are in excellent agreement with their analytical counterparts. At the resolution of our maps – and to the extent that the convergence field can be described by the lognormal model – our map posteriors allow us to reconstruct all summary statistics (including non-Gaussian statistics). We forecast that a map-based inference analysis of LSST-Y10 data can improve cosmological constraints in the σ8–Ωm plane by $\approx\!{30}{{\ \rm per\ cent}}$ relative to the currently standard cosmic shear analysis. This improvement happens almost entirely along the $S_8=\sigma _8\Omega _{\rm m}^{1/2}$ directions, meaning map-based inference fails to significantly improve constraints on S8.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

AXI4MLIR: User-Driven Automatic Host Code Generation for Custom AXI-Based Accelerators

Tensor algebra operations represent an important class of algorithms used across many applications, including machine learning, scientific computing, and data analytics. As a result, the efficient generation of custom accelerators for tensor operations has received increased attention. Previous efforts have produced automated tools enabling users to prototype and explore optimized accelerators. However, little effort has been focused on the host-accelerator interaction in these tools. Efficient use of hardware accelerators requires knowledge about the accelerator's capabilities (operations, data formats, and opcode support), the host CPU microarchitecture (e.g., memory hierarchy), the host-accelerator interface, and the application's features (which code regions should be mapped onto an accelerator). Manually rewriting the original applications to facilitate improved custom accelerator mapping is an error-prone and time-consuming endeavor. To cope with this, we propose AXI4MLIR, a new framework to automatically generate and optimize the communication between the host CPU and arbitrary accelerators that implement linear algebra algorithms. AXI4MLIR extends the MLIR compiler framework to automatically generate efficient host-accelerator driver code for accelerators with AXI-based interfaces. Our compiler extensions enable automatic driver code generation while carefully considering the host's memory hierarchy and target accelerator features. To demonstrate the flexibility and utility of AXI4MLIR, we test it with diverse use cases that include different types of accelerators, tiling scenarios, and dataflow schemes. We compare our experimental results to manual implementations of host-accelerator driver code and find that our approach can reduce CPU cache references by 56% and deliver up to a 1.65x speedup.

Bohm Agostini, Nicolas↗
DOE OSTI2024

PV Soiling Losses: Measurements, Modeling, and Mitigation Strategies

An update will be provided on NREL's ongoing work to address the range of soiling challenges the PV community is facing. First, results will be shown on the efforts to develop a low-cost and low-maintenance soiling measurement sensor. Second, the latest NREL soiling map will be demonstrated as well as how the PVfleets database is enabling regular improvement to the map. Additionally, PVfleets is uncovering challenges with pollen and other bio-soiling in rainy regions in the southeast United States. Finally new results will be presented for improvement of automated algorithms to extract soiling losses from PV data.

ENGINEERING,SOLAR ENERGY↗
DOE OSTI2020

Planck 2018 results: III. High frequency instrument data processing and frequency maps

This paper presents the High Frequency Instrument (HFI) data processing procedures for the Planck 2018 release. Major improvements in mapmaking have been achieved since the previous Planck 2015 release, many of which were used and described already in an intermediate paper dedicated to the Planck polarized data at low multipoles. These improvements enabled the first significant measurement of the reionization optical depth parameter using Planck-HFI data. This paper presents an extensive analysis of systematic effects, including the use of end-to-end simulations to facilitate their removal and characterize the residuals. The polarized data, which presented a number of known problems in the 2015 Planck release, are very significantly improved, especially the leakage from intensity to polarization. Calibration, based on the cosmic microwave background (CMB) dipole, is now extremely accurate and in the frequency range 100-353 GHz reduces intensity-to-polarization leakage caused by calibration mismatch. The Solar dipole direction has been determined in the three lowest HFI frequency channels to within one arc minute, and its amplitude has an absolute uncertainty smaller than 0.35 μK, an accuracy of order 10 -4 . This is a major legacy from the Planck HFI for future CMB experiments. The removal of bandpass leakage has been improved for the main high-frequency foregrounds by extracting the bandpass-mismatch coefficients for each detector as part of the mapmaking process; these values in turn improve the intensity maps. This is a major change in the philosophy of "frequency maps", which are now computed from single detector data, all adjusted to the same average bandpass response for the main foregrounds. End-to-end simulations have been shown to reproduce very well the relative gain calibration of detectors, as well as drifts within a frequency induced by the residuals of the main systematic effect (analogue-to-digital convertor non-linearity residuals). Using these simulations, we have been able to measure and correct the small frequency calibration bias induced by this systematic effect at the 10 -4 level. There is no detectable sign of a residual calibration bias between the first and second acoustic peaks in the CMB channels, at the 10 -3 level.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

A new flow pattern map for flow boiling of R410A in horizontal micro-fin tubes considering the effect of the helix angle

This paper presents an improved flow pattern map for flow boiling in horizontal micro-fin tubes considering the effect of helix angle. The proposed map is modified from the one developed for horizontal smooth tubes by Wojtan et al. (2005) and takes the early transition to annular flow due to micro-fin geometry into account. Visualization of R410A flow boiling is carried out through the transparent smooth and micro-fin tubes with 0°, 10° and 18° helix angle and plotted on the proposed map for comparison. The result shows that the flow pattern map for micro-fin tube with 0° helix angle is generally similar to that for the smooth tube. For the tube with 10° and 18° helix angle, the annular flow occurs at lower vapor quality and lower mass flux. The proposed map shows good agreements when compared with the visualization and reflects the downward shift (to lower mass flux and vapor quality conditions) of the SW-WA transition with the increase of the helix angle. In order to further validate the proposed model, the flow pattern transitions calculated from the equations are also compared with the experimental data of the micro-fin tube in literature. The results show that the modified map increase the prediction accuracy of the flow patterns in the micro-fin tube.

42 ENGINEERING↗
DOE OSTI2021

Chemical state mapping of simulant Chernobyl lava-like fuel containing material using micro-focused synchrotron X-ray spectroscopy

Uranium speciation and redox behaviour is of critical importance in the nuclear fuel cycle. X-ray absorption near-edge spectroscopy (XANES) is commonly used to probe the oxidation state and speciation of uranium, and other elements, at the macroscopic and microscopic scale, within nuclear materials. Two-dimensional (2D) speciation maps, derived from microfocus X-ray fluorescence and XANES data, provide essential information on the spatial variation and gradients of the oxidation state of redox active elements such as uranium. In the present work, we elaborate and evaluate approaches to the construction of 2D speciation maps, in an effort to maximize sensitivity to the U oxidation state at the U L 3 -edge, applied to a suite of synthetic Chernobyl lava specimens. Our analysis shows that calibration of speciation maps can be improved by determination of the normalized X-ray absorption at excitation energies selected to maximize oxidation state contrast. The maps are calibrated to the normalized absorption of U L 3 XANES spectra of relevant reference compounds, modelled using a combination of arctangent and pseudo-Voigt functions (to represent the photoelectric absorption and multiple-scattering contributions). We validate this approach by microfocus X-ray diffraction and XANES analysis of points of interest, which afford average U oxidation states in excellent agreement with those estimated from the chemical state maps. This simple and easy-to-implement approach is general and transferrable, and will assist in the future analysis of real lava-like fuel-containing materials to understand their environmental degradation, which is a source of radioactive dust production within the Chernobyl shelter.

36 MATERIALS SCIENCE↗
DOE OSTI2025

In situ Detection of Plasma Induced Surface Interaction based on Deep Learning based Visual Diagnostics (Technical Report)

It is characteristic for many plasma devices to undergo plasma-material interaction leading to surface erosion. These processes, often not easily detectable, lead to changes in device performance and lifespan. State-of-the-art lifetime tests and wear experiments require over 1000s hours. A self-consistent model for accurately predicting the erosion's effects is not available. In situ detection of these processes is not a trivial task since the surface variations at the early stages have a micron scale. Such limitations not only restrict testing and prediction capabilities but also slow the development of new thrusters and limit mission duration. To address these challenges, an in-situ diagnostic for real-time erosion assessment has been developed, aiming to expedite lifetime testing and broaden experimental campaigns. Several works were dedicated to real-time and in situ monitoring of material erosion during plasma exposure using laser holography, microscopy, and with telemicroscopes. However, the applicability of these approaches is limited due to complexity, cost and less flexibility as they often require placing diagnostic equipment inside the vacuum chamber. In collaboration with Princeton Collaborative Research Facility (PCRF), Princeton Plasma Physics Laboratory (PPPL), a new diagnostic approach is developed, where geometry modifications to the ceramic channel walls were introduced that would result in accelerated channel erosion. We employed Long-distance microscope (LDM) imagery, combined with Deep-Learning based Shape from focus or depth from focus (DFF or SFF) approach, that provides an accessible and cost-effective solution. LDM employs focus variation techniques to continuously capture multiple images of the target object at distinct focal planes. DFF, an optical focus variation method, generates a 3D topographical surface depth map from a sequence of variably focused images. Combined with the developed diagnostic, this approach offers a controllable means to study erosion under accelerated conditions. In this work, we develop Neural Network-based DFF algorithm applicable for LDM data to quantitatively evaluate plasma induced surface modification from LDM data. Next, we develop Deep Learning-based super-resolution depth map image reconstruction technique to increase the resolution of depth maps obtained from DFF algorithm to improve the accuracy of erosion measurements. Thirdly, we develop several image processing techniques to remove noise and improve the quality of depth map image. Here we report the results of initial tests for this approach. An experimental setup designed and built in PPPL was employed that consists of a 3-cm gridded ion source that produces a neutralized argon beam with energies up to 600 eV. A hexagonal boron nitride (h-BN) ceramic target, designed based on computational predictions, was used. Tests were conducted to reconstruct the complex geometry of the target under the lighting conditions of the operated ion source.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

AI-Driven Crack Detection for Remanufacturing Cylinder Heads Using Deep Learning and Engineering-Informed Data Augmentation

Detecting cracks in cylinder heads traditionally relies on manual inspection, which is time-consuming and susceptible to human error. As an alternative, automated object detection utilizing computer vision and machine learning models has been explored. However, these methods often face challenges due to a lack of sufficiently annotated training data, limited image diversity, and the inherently small size of cracks. Addressing these constraints, this paper introduces a novel automated crack-detection method that enhances data availability through a synthetic data generation technique. Unlike general data augmentation practices, our method involves copying cracks from one location to another, guided by both random and informed engineering decisions about likely crack formations due to cyclic thermomechanical loads. The innovative aspect of our approach lies in the integration of domain-specific engineering knowledge into the synthetic generation process, which substantially improves detection accuracy. We evaluate our method’s effectiveness using two metrics: the F2 score, which emphasizes recall to prioritize detecting all potential cracks, and mean average precision (MAP), a standard measure in object detection. Experimental results demonstrate that, without engineering insights, our method increases the F2 score from 0.40 to 0.65, while maintaining a stable MAP. Incorporating detailed engineering knowledge further enhances the F2 score to 0.70 and improves MAP to 0.57, representing increases of 63% and 43%, respectively. These results confirm that our approach not only mitigates the limitations of traditional data augmentation but also significantly advances the reliability and precision of crack detection in industrial settings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Analysis of Geothermal Resources in Three Texas Counties

This project updates the geothermal resources beneath our oil and gas fields, as part of the research for the Texas GEO project. This report "Analysis of Geothermal Resources in Three Texas Counties" (October 2020) improves on previous mapping of the Texas resources for the counties of Crockett (West Texas), Jackson (central Gulf Coast) and Webb (South Texas). Through additional bottom-hole temperatures (BHT), the number of well sites increased from 532 to 5,410 in total for these counties. The improved methodology to calculate formation temperatures from 3.5 km (11,500 ft) to 10 km (32,800 ft) includes thermal conductivity values more closely related to the actual county geological formations, incorporated radiogenic heat production of formations, and the related mapped depth to basement. The results show deep temperatures as hotter than previously calculated, with temperatures of 150 degrees Celcius possible for Webb County between depths of 2.6 - 5.1 km, Jackson County between depths 3.0 - 5.4 km, and Crockett County between depths of 2.7 - 8.0 km.

10 km↗
DOE OSTI2020

Density modification of cryo-EM maps

Density modification uses expectations about features of a map such as a flat solvent and expected distributions of density in the region of the macromolecule to improve individual Fourier terms representing the map. This process transfers information from one part of a map to another and can improve the accuracy of a map. Here, the assumptions behind density modification for maps from electron cryomicroscopy are examined and a procedure is presented that allows the incorporation of model-based information. Density modification works best in cases where unfiltered, unmasked maps with clear boundaries between the macromolecule and solvent are visible, and where there is substantial noise in the map, both in the region of the macromolecule and the solvent. It also is most effective if the characteristics of the map are relatively constant within regions of the macromolecule and the solvent. Model-based information can be used to improve density modification, but model bias can in principle occur. Here, model bias is reduced by using ensemble models that allow an estimation of model uncertainty. A test of model bias is presented that suggests that even if the expected density in a region of a map is specified incorrectly by using an incorrect model, the incorrect expectations do not strongly affect the final map.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Time-sliced quantum circuit partitioning for modular architectures

Current quantum computer designs will not scale. To scale beyond small prototypes, quantum architectures will likely adopt a modular approach with clusters of tightly connected quantum bits and sparser connections between clusters. We exploit this clustering and the statically-known control flow of quantum programs to create tractable partitioning heuristics which map quantum circuits to modular physical machines one time slice at a time. Specifically, we create optimized mappings for each time slice, accounting for the cost to move data from the previous time slice and using a tunable lookahead scheme to reduce the cost to move to future time slices. We compare our approach to a traditional statically-mapped, owner-computes model. Our results show strict improvement over the static mapping baseline. Here, we reduce the non-local communication overhead by 89.8% in the best case and by 60.9% on average. Our techniques, unlike many exact solver methods, are computationally tractable.

Baker, Jonathan M.↗
DOE OSTI2025

Microstructural Characteristics, Mechanical Properties, and Corrosion Behavior of Field-Assisted Diffusion Welded Alloy 617

This study investigated the microstructural characteristics, mechanical response, and corrosion resistance of Alloy 617 diffusion welded by electric field-assisted sintering (EFAS). The microstructure exhibited good grain boundary (GB) migration across the interface and flat interface in the samples bonded at different conditions. Graded grain size was observed, with grain coarsening being more significant near sample surface due to EFAS-induced temperature gradient. Tensile testing revealed that the specimens fractured in the matrix away from the interface. The peak strength of 807 MPa was obtained in the samples welded at 1000°C. The materials obtained at 1100°C exhibited reduced tensile strength but improved ductility. Strain maps revealed by digital image correlation showed the flat interfaces were less ductile compared to the matrix. The hardness reduced near sample surfaces due to enlarged grains induced by temperature gradient. The interfaces with GB migration exhibited improved corrosion resistance in molten salt compared to the flat interfaces.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Electric field enhanced diffusion welding of alloy 617: Microstructural characteristics and mechanical properties

This study investigated the microstructural characteristics and mechanical behavior of diffusion welded nickel-based Alloy 617 obtained by electric field-assisted sintering (EFAS) using various parameters. The interfacial microstructure exhibited different characteristics including good grain boundary (GB) migration across the interface in the samples diffusion-welded at 1100 °C and a flat interface in the samples joined at 1000 °C and 1050 °C. The interface consisted of fine Al 2 O 3 oxides, while precipitation of interfacial M 23 C 6 carbides was not observed. Grain boundaries migrated across the Al 2 O 3 oxides, leaving these oxides within the grains. Graded grain size was observed, with grain coarsening being more significant near the sample surface due to the temperature gradient induced by EFAS. Tensile testing revealed that the specimens fractured in the matrix away from the interface, indicting strong diffusion-welded joints. Further, the peak tensile strength of 807 MPa was obtained in the samples welded at 1000 °C due to minimal grain growth. The materials obtained at 1100 °C exhibited reduced tensile strength but improved ductility. Strain maps revealed by digital image correlation showed alternating high and low strain segments in the samples produced at 1000 °C and 1050 °C, indicating that the flat interfaces with no GB migration were less ductile compared to the matrix. A greater strain uniformity was observed along the bond interfaces with improved GB migration. The hardness reduced near the sample surfaces due to enlarged grains induced by temperature gradient. This study demonstrates that GB migration and enhanced mechanical strength can be achieved in diffusion-welded Alloy 617.

36 MATERIALS SCIENCE↗