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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

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ray-tracing image simulations of transparent objects with complex shape and inhomogeneous refractive index

Optical images of transparent three-dimensional objects can be different from a replica of the object’s cross section in the image plane, due to refraction at the surface or in the body of the object. Simulations of the object’s image are thus needed for the visualization and validation of physical models. We report ray tracing image simulations that achieved high physical fidelity, reproducing optical behaviors and image features not rendered in previous studies. We replicated brightfield microscopy images of drops with complex shapes, and images of pressure and shock waves traveling inside them. For high physical fidelity, the simulations must replicate the spatial and angular distribution of illumination rays, and both the experiment and the simulation must be designed for accurate optical modeling. The simulations are highly sensitive to the properties of the drops and can be used to diagnose and refine fluid dynamics models. The simulated images can also be optimized to extract multiple 3D properties from experimental images. Compared to specialized single-shot 3D imaging methods, this approach has the advantage that it preserves the experimental simplicity, the high resolution, and the visual interpretability characteristic to basic optical imaging. The techniques introduced here are directly applicable to optical microscopy, so they can be used in other fields, such as microfluidics and biology, to expand the type and the accuracy of three-dimensional information that can be extracted from basic optical images.

Cavitation↗

Femtoscopic study of the proton-proton and proton-deuteron systems in heavy-ion collisions at the LHC

This work reports femtoscopic correlations of p – – p ($\overline{p}$ – – $\overline{p}$) and p – – d ($\overline{p}$ – – $\overline{d}$) pairs measured in Pb–Pb collisions at center-of-mass energy per nucleon $\sqrt{s_{NN}}$ = 5.02 TeV in the ALICE Collaboration. A fit to the measured proton-proton correlation functions allows one to extract the dependence of the nucleon femtoscopic radius of the particle-emitting source on the pair transverse mass (m T ) and on the average charge particle multiplicity $\langle$dN ch /dη$\rangle$ 1/3 for three centrality intervals (0–10%, 10 – – 30 %, 30 – – 50 %). In both cases, the expected power-law and linear scalings are observed, respectively. The measured p–d correlations can be described by both two- and three-body calculations, indicating that the femtoscopy observable is not sensitive to the short-distance features of the dynamics of the p-(p-n) system, due to the large inter-particle distances in Pb–Pb collisions at the LHC. Indeed, in this study, the minimum measured femtoscopic source sizes for protons and deuterons have a minimum value at 2.73$^{+0.05}_{–0.05}$ and 3.10$^{+1.04}_{–0.86}$ fm, respectively, for the 30–50% centrality collisions. Moreover, the m T -scaling obtained for the p–p and p–d systems is compatible within 1σ of the uncertainties. These findings provide new input for fundamental studies on the production of light (anti)nuclei under extreme conditions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Development of message passing-based graph convolutional networks for classifying cancer pathology reports

Abstract Background Applying graph convolutional networks (GCN) to the classification of free-form natural language texts leveraged by graph-of-words features (TextGCN) was studied and confirmed to be an effective means of describing complex natural language texts. However, the text classification models based on the TextGCN possess weaknesses in terms of memory consumption and model dissemination and distribution. In this paper, we present a fast message passing network (FastMPN), implementing a GCN with message passing architecture that provides versatility and flexibility by allowing trainable node embedding and edge weights, helping the GCN model find the better solution. We applied the FastMPN model to the task of clinical information extraction from cancer pathology reports, extracting the following six properties: main site, subsite, laterality, histology, behavior, and grade. Results We evaluated the clinical task performance of the FastMPN models in terms of micro- and macro-averaged F1 scores. A comparison was performed with the multi-task convolutional neural network (MT-CNN) model. Results show that the FastMPN model is equivalent to or better than the MT-CNN. Conclusions Our implementation revealed that our FastMPN model, which is based on the PyTorch platform, can train a large corpus (667,290 training samples) with 202,373 unique words in less than 3 minutes per epoch using one NVIDIA V100 hardware accelerator. Our experiments demonstrated that using this implementation, the clinical task performance scores of information extraction related to tumors from cancer pathology reports were highly competitive.

59 BASIC BIOLOGICAL SCIENCES↗

ATR-SEIRAS Reveals Potential Inversion and Associated Electron Transfer Kinetics in the Reduction of Surface-Confined Anthraquinone

The detection of stable semiquinone radicals on an anthraquinone (AQ) layer chemically grafted to an electrode surface in aqueous electrolytes has been elucidated by using attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS). In very alkaline conditions (pH 13), the reduction of the AQ involves no proton transfer, but surface sensitive infrared spectroscopy reveals that the anthraquinone dianion forms a strong hydrogen bonding network with coadsorbed water, leading to irreversible features in the voltammetry. The potential dependence of the IR band assigned to the AQ radical is consistent with the enhanced hydrogen bonding network causing increased stabilization of the quinone radical and supports the predicted response of a system under mild potential inversion, whereby the formal potential for the reduction of the anthraquinone radical is positive of the reduction potential of the neutral AQ molecule. Time-resolved ATR-SEIRAS is used to measure the transient formation of the AQ •– radical, from which rate constant information can be extracted using the Butler–Volmer model involving two one-electron transfers without a direct disproportionation reaction. The potential dependence of the rate constants is consistent with the potential inversion and can be used to qualitatively simulate the measured cyclic voltammograms. In conclusion, the thermodynamic and kinetic analyses re-emphasize long established deficiencies associated with using one-electron reaction formalisms to characterize multi-electron systems.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗

Role of slip in hydrogen-assisted crack initiation in Ni-based alloy 725

We conduct in situ tensile straining experiments to investigate the role of hydrogen and slip in crack initiation in nickel-based alloy 725. Our experiments reveal no tendency for hydrogen to enhance localized slip and no necessity of slip for crack initiation. We use electrochemical charging to introduce hydrogen into samples, melt extraction to measure hydrogen content, and digital image correlation to analyze localized plastic strains during in situ tensile tests in a scanning electron microscope. Cracks initiate both in regions with and without nearby localized slip. Moreover, the fraction of cracks initiating with no nearby slip is greater at higher hydrogen content. Slip-assisted crack initiation generally occurs at locations where intergranular slip is arrested, especially at intersections of slipping coherent twin boundaries with thin twin lamellae. Cracks that initiate without nearby slip occur at a wider variety of microstructural features, including inclusions, triple junctions, and surface flaws.

36 MATERIALS SCIENCE↗

Tropical Cyclone Super Resolution using conditional diffusion denoising probabilistic model from mesoscale simulation to LES

Accurate modeling of tropical cyclone wind fields is essential for the design, risk assessment, and operational planning of offshore energy infrastructure. While mesoscale simulations are widely used thanks to their computational efficiency, they lack the necessary resolution to capture key features such as wind shear and veer profiles as well as the distribution turbulent kinetic energy (TKE). High-fidelity large-eddy simulation (LES) models on the other hand, can resolve turbulent structures and provide a more accurate representation of the complex wind field, albeit at a higher computational cost. To address this modeling gap, we introduce a two-part generative framework to enhance the resolution and physics-capturing ability of mesoscale simulations. First, a reduced-order model based on Karhunen–Loève (KL) decomposition is used to extract dominant spatial modes from one-dimensional mean wind profiles. A multilayer perceptron (MLP) is trained to map mesoscale mode weights to their LES counterparts, enabling accurate reconstruction of vertical velocity profiles. Second, a conditional Diffusion Denoising Probabilistic Model (DDPM) is developed to super-resolve coarse and low-fidelity mesoscale velocity fields, recovering fine-scale turbulence structures and stress distributions. The framework is evaluated across different tropical cyclone intensity categories defined by the Saffir–Simpson scale and demonstrates strong performance in both interpolation and extrapolation tasks. The generated fields accurately reproduce spatial coherence, stress distributions, and spectral energy characteristics observed in LES data. By bridging the fidelity gap between mesoscale and LES outputs, this approach offers a scalable, data-driven solution for enhancing the representation of tropical cyclone wind fields, enabling more robust offshore energy infrastructure systems design in tropical-cyclone-prone areas.

17 WIND ENERGY↗

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

Stacked-mosaic amplifier and diode delivery concept for kJ-class inertial fusion energy laser driver

We report on a laser amplifier architecture designed as a modular element for scaling to multi-megajoule laser facilities intended for inertial fusion energy (IFE) power plants. This kilojoule-class module features a stacked mosaic of gain media integrated with a diode delivery system for efficient optical pumping of the mosaic-structured gain medium, enabling high-repetition-rate operation at high wall plug efficiencies, necessary for an IFE driver. Details of a diode delivery system capable of pumping the mosaic architecture are presented. Comprehensive numerical modeling demonstrates that the stacked-mosaic approach reduces transverse gain by five orders of magnitude compared to a conventional full-aperture Yb:YAG based amplifier, substantially suppressing transverse amplified spontaneous emission (TASE) and enabling enhanced longitudinal energy extraction. Detailed analysis of thermal management and wavefront distortion in a 4 × 4 mosaic array indicates that temperature gradients and thermally induced aberrations are effectively controlled using gas cooling and commercially available phase-plate and deformable mirror technologies. We further discuss the applicability of a stacked-mosaic architecture to direct-drive IFE schemes, where broad spectral bandwidth is critical, and its compatibility with frequency conversion modules for up-conversion to blue wavelengths. Finally, an example point design for a 10 kJ, 10 Hz Yb:YAG module operating at 175 K with wall-plug efficiency exceeding 10 % is presented, underscoring the feasibility of this approach for next-generation high-energy lasers for IFE drivers. The results establish the stacked-mosaic amplifier as a scalable, robust platform not only for IFE but also for a broad range of advanced scientific and industrial laser applications.

Lasers↗

Imaging nuclear shape through anisotropic and radial flow in high-energy heavy-ion collisions

Most atomic nuclei exhibit ellipsoidal shapes characterized by quadrupole deformation β 2 and triaxiality γ, and sometimes even a pear-like octupole deformation β 3 . The STAR experiment introduced a new ‘imaging-by-smashing’ technique to image the nuclear global shape by colliding nuclei at ultra-relativistic speeds and analyzing outgoing debris. Features of nuclear shape manifest in collective observables like anisotropic flow vn and radial flow via mean transverse momentum [p T ]. We present new measurements of the variances of v n (n = 2, 3, and 4) and [p T ], and the covariance of $v$$^{2}_{n}$ with [p T ], in collisions of highly deformed 238 U and nearly spherical 197 Au. Ratios of these observables between the two systems effectively suppress common final-state effects, isolating the strong impact of uranium’s deformation. By comparing results with state-of-the-art hydrodynamic model calculations, we extract β 2U and γ U values consistent with those deduced from low-energy nuclear structure measurements. Measurements of v 3 and its correlation with [p T ] also provide the first experimental suggestion of a possible octupole deformation for 238 U. These findings provide significant support for using high-energy collisions to explore nuclear shapes on femtosecond timescales, with implications for both nuclear structure and quark-gluon plasma studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Anisotropic electron damping and energy gap in Bi 2 ⁢Sr 2 ⁢CaCu 2 ⁢O 8+𝛿

The many-body electron-electron interaction in cuprates causes broadening of the electronic bands in 𝒌 space, leading to a deviation from the standard Fermi liquid. While a 𝒌-dependent anisotropic electronic scattering (𝒌-DAES) has been assessed by photoemission, its fingerprint in 𝑸 space has been scarcely considered. Here, we explore the 𝑸-dependent electron dynamics in optimally doped Bi 2⁢ Sr 2 ⁢CaCu 2 ⁢O 8+𝛿 through the evolution of low-energy charge excitations as measured by resonant inelastic x-ray scattering (RIXS). In the normal state, the RIXS spectra display a continuum of excitations down to 0 meV, while the superconducting state features a spectral weight suppression below 80 meV without any enhancement at higher energies. To interpret the energy and 𝑸 evolution of our data, we introduce a phenomenological expression of the charge susceptibility by including the 𝒌-DAES. We show that only the charge susceptibility with 𝒌-DAES captures the RIXS data, highlighting the importance of 𝒌-DAES when describing the 𝑸 dependence of charge excitations from 0 to a few eV scale. Furthermore, we also find that the inclusion of 𝒌-DAES is essential when quantitative parameters such as the electronic energy gap are extracted from RIXS data.

36 MATERIALS SCIENCE↗

Leveraging Open-Source Satellite-Derived Building Footprints for Height Inference

At a global scale, cities are growing and characterizing the built environment is essential for deeper understanding of human population patterns, urban development, energy usage, climate change impacts, among others. Buildings are a key component of the built environment and significant progress has been made in recent years to scale building footprint extractions from satellite datum and other remotely sensed products. Billions of building footprints have recently been released by companies such as Microsoft and Google at a global scale. However, research has shown that depending on the methods leveraged to produce a footprint dataset, discrepancies can arise in both the number and shape of footprints produced. Therefore, each footprint dataset should be examined and used on a case-by-case study. In this work, we find through two experiments on Oak Ridge National Laboratory and Microsoft footprints within the same geographic extent that our approach of inferring height from footprint morphology features is source agnostic. Regardless of the differences associated with the methods used to produce a building footprint dataset, our approach of inferring height was able to overcome these discrepancies between the products and generalize, as evidenced by 98% of our results being within 3m of the ground-truthed height. This signifies that our approach can be applied to the billions of open-source footprints which are freely available to infer height, a key building metric. This work impacts the broader domain of urban science in which building height is a key, and limiting factor.

Stipek, Clinton [ORNL] (ORCID:0000000280501096)↗

Simulation-trained machine learning models for Lorentz transmission electron microscopy

Understanding the collective behavior of complex spin textures, such as lattices of magnetic skyrmions, is of fundamental importance for exploring and controlling the emergent ordering of these spin textures and inducing phase transitions. It is also critical to understand the skyrmion–skyrmion interactions for applications such as magnetic skyrmion-enabled reservoir or neuromorphic computing. Magnetic skyrmion lattices can be studied using in situ Lorentz transmission electron microscopy (LTEM), but quantitative and statistically robust analysis of the skyrmion lattices from LTEM images can be difficult. In this work, we show that a convolutional neural network, trained on simulated data, can be applied to perform segmentation of spin textures and to extract quantitative data, such as spin texture size and location, from experimental LTEM images, which cannot be obtained manually. This includes quantitative information about skyrmion size, position, and shape, which can, in turn, be used to calculate skyrmion–skyrmion interactions and lattice ordering. We apply this approach to segmenting images of Néel skyrmion lattices so that we can accurately identify skyrmion size and deformation in both dense and sparse lattices. The model is trained using a large set of micromagnetic simulations as well as simulated LTEM images. This entirely open-source training pipeline can be applied to a wide variety of magnetic features and materials, enabling large-scale statistical studies of spin textures using LTEM.

McCray, Arthur R. C. (ORCID:0000000160774698)↗

Exploring diversion-pathway analysis of a generic molten-salt fast reactor using multiphysics informed signatures

Molten salt reactors are being explored by multiple commercial ventures due to their inherent safety features, flexibility in fuel sources, and high fuel utilization and thermal efficiency. The continual flow of fuel salt, large fissile quantities present, and ability to add or divert material due to the liquid nature introduces new challenges for international safeguards. To understand how international safeguards should be applied, it is important to capture the inherent multi-physics nature of a molten salt reactor. This work examines a generic molten salt fast reactor to understand how potential diversion scenarios would affect the concentration of radionuclides in the primary and auxiliary systems. Three types of diversion were examined: a slow drip of fuel salt, gaseous plutonium extraction, and uranium metal plating. The analysis determined that several key isotopes become statistically significant once diversion begins, indicating that detection of such diversion cases would be possible through measuring specific signatures such as gamma spectra.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Exploring Local Vibrational Structure in Protein-Bound Chlorophyll a: Isotope-Enrichment Experiments and Electrostatic Analysis

Local chlorophyll (Chl) vibrations play an essential role in biological photosynthesis by facilitating rapid energy transfer between pigments. In research studies, they also provide a useful spectroscopic probe of the local protein environment that surrounds each pigment. However, measuring the complete vibrational absorption spectrum of a protein-bound Chl molecule is much more difficult than, for example, Chl in neat solvent due to overlap with protein vibrations that typically drown out Chl vibrational features. Resonance Raman and fluorescence spectroscopies provide a way around this problem for Franck–Condon active vibrations, but these often rely on cryogenic measurement conditions and fail to capture vibrational signatures from, e.g., ester-group vibrations that lack coupling to a convenient electronic transition. In the present contribution, we use 13 C-enrichment of the protein backbone to shift protein background signals to lower frequency, providing a largely clean spectral window in which to study local Chl a C═O stretch modes. A room-temperature absorption spectrum for Chl a in the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum is thus extracted as a difference between protein-plus-pigment and protein-only vibrational spectra. Excellent agreement in the molecular fingerprint region with the vibrational spectrum of Chl a in organic solvents confirms that the resulting spectrum represents the response of the protein-bound Chl a molecule. Furthermore, the ester group resonance is observed to shift in response to the S53P mutation that eliminates a 17 3 ester group hydrogen bond from the protein environment. Finally, we analyze these experimental results using MD-based electrostatic analysis, finding that electric-field mapping at the C atom of the ester group provides a satisfactory explanation for the observed frequency shifts between organic solvent and protein environment. MD analysis further suggests that a red-shifted ester peak observed experimentally for the S53P mutant results from solvation of the 17 3 Chl ester group due increase water penetration into the Chl-binding pocket relative to wild-type WSCP. Here, we anticipate that these results will prove useful both for benchmarking future simulation work and as a reference for interpreting Chl vibrational spectra as a probe of pigment–protein interactions.

14 SOLAR ENERGY↗

Machine learning for slow-extraction uniformity at the Fermilab Delivery Ring

The Muon-to-Electron Conversion Experiment (Mu2e) requires uniform slow extraction from the Fermilab Delivery Ring during each 43 ms spill. This project analyzed 13,737 spills from seven parquet files collected during March and June 2026 commissioning. Each spill contained 430 samples at 0.1 ms resolution and was summarized by the Spill Duty Factor. Null Action and active proportional-integral-derivative conditions established operational baselines. Fixed-ramp sessions were segmented to evaluate reproducibility, drift, and spill-to-spill spread, while a deliberate quadrupole-ramp step identified the beam-response peak and trough. Median profiles were reproducible within fixed conditions but drifted over multi-hour periods. The resulting baselines and response features support future physics-based and machine-learning approaches to real-time spill regulation.

Prescott, Matthew J. [Purdue U., West Lafayette; F↗

Binary pseudo-random array standard for extreme ultraviolet lithography tool characterization

Extreme ultraviolet (EUV) imaging tools play a crucial role in EUV lithography. Achieving high accuracy in EUV metrology is essential for advanced semiconductor manufacturing. A thorough characterization of the instrumentation in use is required. Binary pseudo-random arrays (BPRAs) are an established standard for calibrating and characterizing optical instruments in the frequency domain. Here, we expand the BPRA standard to applications in EUV imaging. To extend the technology to the EUV spectral range, a high-resolution BPRA target with the smallest feature size of 40 nm is developed. The EUV BPRA target establishes an in situ and portable calibration and alignment standard for EUV imaging. The target is patterned by means of electron-beam lithography, using a nickel absorber with a thickness of 39 nm. The substrate is a 4″ silicon wafer with a molybdenum/silicon multilayer coating. To demonstrate the efficacy of the target and develop the instrument calibration protocol, the target is imaged on the Sharp Hyper-NA Actinic Reticle Review Project EUV mask microscope. Power spectral density (PSD) data are presented. The characteristics of the imaging system are imprinted on the PSD. The modulation transfer function is extracted from the PSD data. A partially coherent imaging model is used as a reference to the experimental results.

BPRA↗