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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 181 records · Page 10

Predicting rare events using neural networks and short-trajectory data

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental dynamics, accurate prediction from direct observations becomes challenging. In such cases a more effective approach is to cast statistics of interest as solutions to Feynman-Kac equations (partial differential equations). Here, we develop an approach to solve Feynman-Kac equations by training neural networks on short-trajectory data. Our approach is based on a Markov approximation but otherwise avoids assumptions about the underlying model and dynamics. This makes it applicable to treating complex computational models and observational data. Additionally, we illustrate the advantages of our method using a low-dimensional model that facilitates visualization, and this analysis motivates an adaptive sampling strategy that allows on-the-fly identification of and addition of data to regions important for predicting the statistics of interest. Finally, we demonstrate that we can compute accurate statistics for a 75-dimensional model of sudden stratospheric warming. This system provides a stringent test bed for our method.

97 MATHEMATICS AND COMPUTING↗

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↗

The exit-wave power-cepstrum transform for scanning nanobeam electron diffraction: robust strain mapping at subnanometer resolution and subpicometer precision

Scanning nanobeam electron diffraction (NBED) with fast pixelated detectors is a valuable technique for rapid, spatially resolved mapping of lattice structure over a wide range of length scales. However, intensity variations caused by dynamical diffraction and sample mistilts can hinder the measurement of diffracted disk centers as necessary for quantification. Robust data processing techniques are needed to provide accurate and precise measurements for complex samples and non-ideal conditions. Here we present an approach to address these challenges using a transform, called the exit wave power cepstrum (EWPC), inspired by cepstral analysis in audio signal processing. The EWPC transforms NBED patterns into real-space patterns with sharp peaks corresponding to inter-atomic spacings. We describe a simple analytical model for interpretation of these patterns that cleanly decouples lattice information from the intensity variations in NBED patterns caused by tilt and thickness. With tracking the inter-atomic spacing peaks in EWPC patterns, strain mapping is demonstrated for two practical applications: mapping of ferroelectric domains in epitaxially strained PbTiO 3 films and mapping of strain profiles in arbitrarily oriented core-shell Pt-Co nanoparticle fuel-cell catalysts. The EWPC transform enables lattice structure measurement at sub-pm precision and sub-nm resolution that is robust to small sample mistilts and random orientations.

42 ENGINEERING↗

Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems

Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.

59 BASIC BIOLOGICAL SCIENCES↗

Function Preserving Projection (FPP): A Linear Projection Technique for Visual Interpretation of High-Dimensional Functions

In this work, we propose function preserving projection (FPP), a new class of scalable linear projection techniques for finding interpretable structure in highdimensional datasets. Instead of focusing on preserving the structure of highdimensional points as traditional dimensionality reduction methods, we aim to find a 2D view of the data, in which human interpretable patterns of meaningful properties (that defined on the high-dimensional points, i.e., functions in a highdimensional domain) are revealed. Such a visual-centric approach introduces new avenues for exploratory data analysis and allows efficient implementation that provides a scalable tool for exploring potentially unknown or unexpected relationships in complex and large high-dimensional data (e.g., beyond millions of samples and tens of thousands of dimensions).

97 MATHEMATICS AND COMPUTING↗

Indigenous Organic Molecular Biosignatures are Detectable via ToF-SIMS of a Kerogen-rich Jurassic Clay

Time of Flight - Secondary Ion Mass Spectrometry (ToF-SIMS) is a Mass Spectrometry (MS) imaging technique that can be used in conjunction with traditional organic geochemical analysis (organics extracted from a crushed sample) in order to determine how molecules observed in the organic extracts were incorporated into a particular rock sample. This type of analysis may be used on samples collected as part of Mars Sample Return (MSR) in order to determine if potential organic compounds were indigenous to Mars or whether they are contaminants.Here we show that Organic Molecular Biosignatures (OMBs including steranes and derivatives of a carotenoid) are detectable via ToF-SIMS within a Jurassic mudstone. The OMBs are only detectable in areas with high organic carbon, likely kerogen, indicating that they are indigenous to the rock. We conclude that: I) Indigenous OMBs are detectable via ToF-SIMS in ancient, kerogen-rich samples; II) the presence of a molecular ion strengthens the interpretation of ToF-SIMS spectra of complex natural material, and III) the spatial co-occurrence of kerogen and potentially indigenous OMBs in ancient sediments is a valid test of their character. These conclusions are directly relevant to MSR sample selection as well as the analysis of MSR samples upon return.

Pasterski, Michael↗

Rancor-HUNTER: A Virtual Plant and Operator Environment for Predicting Human Performance

Advances in simulation capabilities to model physical systems have outpaced the development of simulations for humans using those physical systems. There is an argument that the infinite span of potential human behaviors inherently render human modeling more challenging than physical systems. Despite this challenge, the need for modeling humans interacting with these complex systems is paramount. As technologies have improved, many of the failure modes originating from the physical systems have been solved. This means the overall proportion of human errors has increased, such that it is not uncommon to be the primary driver of system failure in modern complex systems. Moreover, technologies such as automated systems may introduce emerging contexts that can cause new, unanticipated modes of human error. Therefore, it is now more important than ever to develop models of human behavior to realize overall system error reductions and achieve established safety margins. To support new and novel concepts of operations for the anticipated wave of advanced nuclear reactor deployments, human factors and human reliability analysis researchers need to develop advanced simulation-based approaches. This talk presents a simulation environment suitable to both collect data and then perform Monte Carlo simulations to evaluate human performance and develop better models of human behavior. Specifically, the Rancor Microworld Simulator models a complex energy production system in a simplified manner. Rancor includes computer-based procedures, which serve as a framework to automatically classify human behaviors without manual, subjective experimenter coding during scenarios. This method supports a detailed level of analysis at the task level. It is feasible for collecting large sample sizes required to develop quantitative modelling elements that have historically challenged traditional full-scope simulator study approaches. Additionally, the other portion of this experimental platform, the Human Unimodel for Nuclear Technology to Enhance Reliability (HUNTER), is presented to show how the collected data can be used to evaluate novel scenarios based on the contextual factors, or performance shaping factors, derived from Rancor simulations. Rancor-HUNTER is being used to predict operator performance with new procedures, such as results from control room modernization or new-build situations. Rancor-HUNTER is also proving a useful surrogate platform to model human performance for other complex systems.

99 GENERAL AND MISCELLANEOUS↗

Evaluating Retention Index Score Assumptions to Refine GC–MS Metabolite Identification

As metabolomics grows into a high-throughput and high demand research field, current metrics for the identification of small molecules in gas chromatography–mass spectrometry (GC–MS) still require manual verification. Though steps have been taken to improve scoring metrics by combining spectral similarity (SS) and retention index (RI), the problem persists. A large body of literature has analyzed and refined SS scores, but few studies have explicitly studied improvements to RI scores. Here, in this study, we examined whether uninvestigated assumptions of the RI score are valid and propose ways to improve them. Query RIs were matched to library RI with a generous window of ±35 to avoid unintentional removal of valid compound identifications. Each match was manually verified as a true positive (TP), true negative, or unknown. Metabolites with at least 30 TP identifications were included in downstream analyses, resulting in a total of 87 metabolites from samples of varying complexity and type (e.g., amino acid mixtures, human urine, fungal species, and so on.). Our results showed that the RI score assumptions of normality, consistent variance across metabolites, and a mean error centered at 0 are often violated. We demonstrated through a cross-validation analysis that modifying these underlying assumptions according to empirical metabolite-specific distributions improved the TP and negative rankings. Further, we statistically determined the minimum number of samples required to estimate distributional parameters for scoring metrics. Overall, this work proposes a robust statistical pipeline to reduce the time bottleneck of metabolite identification by improving RI scores and thus minimize the effort to complete manual verification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring 2D X-ray diffraction phase fraction analysis with convolutional neural networks: Insights from kinematic-diffraction simulations

Abstract Deep-learning models are effective for analyzing the complex information in 2D X-ray diffraction (XRD) patterns. Accurately collecting parameters of the material sample is crucial during model training, significantly impacting model performance. In this study, we employ a kinematic-diffraction simulator to generate simulated 2D XRD patterns for Ti–6Al–4V alloy, allowing precise control of sample parameters. These simulated patterns are used to train convolutional neural networks, predicting $$\upbeta$$ β -phase volume fractions. The training data set consists exclusively of 2D XRD patterns with pure $$\upalpha$$ α - or pure $$\upbeta$$ β -phase, while the testing set incorporates patterns with intermediate phase volume fraction. In particular, we investigate how the architectures of the model influence prediction reliability and computational performance. Experimental results reveal that, with appropriate training, the convolutional neural network accurately detects intermediate phase volume fractions even trained with only pure-phase patterns, achieving a mean square error accuracy of $$9.4 \times 10^{-4}$$ 9.4 × 10 - 4 . Graphical abstract

Yue, Weiqi↗

Altersbestimmung an thermalen Tiefenwässern im Oberjura des Molassebeckens mittels Krypton-Isotopen

81 Kr (half-life 229,000 years) is an ideal tracer for old groundwater. The Upper Jurassic rock in the deep Molasse Basin is an outstanding geothermal groundwater reservoir (with temperatures up to 140 °C). However, due to the complex groundwater evolution (ion and isotope exchange, gas flux, etc.), comprehensive hydrogeological studies completed to date, including 14 C–DIC and He isotopes, could not resolve the recharge dynamics and residence times. Nine geothermal wells were therefore sampled for 81 Kr/ 85 Kr employing the laser-based atom trap tracer analysis technique (ATTA). In the western and central basin, the results reveal predominant groundwater recharge during the last glacial period with one sample influenced by infiltration during the earlier glacial period. Recharge signatures and 81 Kr-model-ages fit very well to subglacial recharge with cross-formational flow through the sedimentary cover (600 to >3000 m deep). In the eastern basin, the results point to the Cromerian complex, indicating a slower flow system with less influence from recharge during glacial periods.

54 ENVIRONMENTAL SCIENCES↗

Local atomic structure and Ni nanophase segregation in Zn 1-x Ni x S thin films

Here, the local atomic structure of Zn 1-x Ni x S thin films was investigated using X-ray absorption spectroscopy. The films were grown using RF-sputtering at atomic concentrations x = 0.00, x = 0.04, x = 0.08 and x = 0.14. X-ray diffraction shows that the lattice parameter contracts with increasing Ni concentration, consistent with the smaller atomic radii of Ni compared to that one of Zn. Optical absorption reveals a reduction of the bandgap as Ni concentration increases, except for sample x = 0.14 where a complex behavior is observed. Results from X-ray absorption near edge structure (XANES) spectroscopy indicate a shift in the valence state of Ni for the x = 0.14 sample. The analysis of the extended X-ray absorption fine structure (EXAFS) spectra indicate a contraction of ~0.7 Å in the Ni–S bond distance when compared to the Zn–S bond length, which generates local lattice distortions and an increment of the static disorder as the Ni concentration increases. The EXAFS results for sample x = 0.14 show the presence of a Zn 1-x Ni x S phase and a nanoscopic metallic Ni phase with domain sizes below the diffraction limit. These results reveal that the local atomic structure differs in a significant manner from the average crystalline structure, implying its importance for the determination of the electronic properties of this material.

36 MATERIALS SCIENCE↗

Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques

The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H 2 O/D 2 O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.

59 BASIC BIOLOGICAL SCIENCES↗

Multimodal imaging of oil-in-water bilgewater emulsion and biofilms

Bilgewater emulsions, consisting of oil and surfactant mixtures in water, affect many aquatic species. Thus development of methods and techniques to treat or mitigate the formation and undesired consequences of shipboard emulsions are urgently needed. This work presents new results of the evolution of the bilgewaer chemical and physical properties using in situ imaging. A Navy O/W emulsion consisting of three oils and a detergent mixture was used as the synthetic bilgewater model [1, 2]. Synthetic oil-in-water (O/W) emulsion droplets were seled in a vacuum compatible microfluidic sample holder and imaged using a suite of tools including scanning electron microscopy (SEM), time-of-flight secondary ion mass spectrometry (ToF-SIMS), confocal laser scanning microscopy, and optical microscopy, highlighting the advantage of multiscale analysis and its applications in waste reduction and treatment in the environment. The transferrable and vacuum compatible microfluidic interface, System for Analysis at the Liquid Vacuum Interface (SALVI), was used in this study. SALVI enabled surface analysis of liquids and liquid-solid interactions using ToF-SIMS and SEM [3, 4]. Its detection window is an aperture of 2 ?m in diameter open to vacuum, permitting direct detection of the liquid surface. Liquid is withheld by surface tension within the aperture. The interface is composed of a silicon nitride membrane and polydimethylsiloxane microchannel [3, 4]. A variety of samples including complex liquid mixtures, ionic liquids, single mammalian cells, live biofilms, and solid-electrolyte interface have been analyzed using in situ imaging [5, 6]. The feasibility of using SALVI for in situ SEM imaging of nanoparticles and colloids in liquid was recently demonstrated [7]. This paper shows new findings of multimodal imaging and analysis of synthesized emulsion particles in water. Figure 1 depicts a schematic of multimodal in situ imaging of bilgewater emulsion using SEM and ToF-SIMS. Furthermore, we study the interactions of microbes and bilgewater emulsion. Microbes play an important role in the ocean. We hypothesize that microbes release organics that can act as surfactants that affect bilgewater formation or weakening. We present the first systematic study of emulsions and biofilms and investigate the effects of biofilms on bilgewater emulsions. Pseudomonas was selected as a model strain. Biofilms were cultured in a microchannel to allow culture [8]. Once a thick layer of biofilms was formed, the medium solution was changed to a mixture consisting of 50 % bilgewater emulsion. Dispersed biofilms were collected at 24 hrs. and 48 hrs. after emulsions were introduced into the channel. Bilgewater emulsions, biofilms, and mixtures of bilgewater emulsions and biofilms were analyzed using multiple in situ and ex situ techniques as described earlier. Our findings indicate that biofilms change the chemical makeup of the emulsion surface compositions and emulsion droplet size distribution, confirming the hypothesis that extracellular polymeric substance (EPS) related components released from biofilms can function as surfactants and change the oil-in-water interfaces.

bilgewater, multimodal imaging, biofilms↗

Extension of Complex Refractive Index Measurements to the Near-Infrared for Liquids: Methodology and Uncertainty Analysis

Optical identification of liquid droplets, aerosols, or thin films is important for many applications. While reference spectra are sometimes available for such measurements, they are not always applicable to the observed spectrum or the given sample morphology. Reference spectra for many forms can be modeled, however, if the n/k vectors (real and imaginary refractive indices) are available. In previous work we have reported protocols to determine the n/k vectors for dozens of liquids, primarily in the mid-infrared (MIR) spectral range from 7500 to 400 cm –1 . In this work we extend the spectral range into the near-infrared (NIR) region, demonstrating a method to measure and merge the data sets to create composite n/k data ranging from 10 000 to 400 cm –1 (1.0 to 25 µm) with absorbance fidelity spanning over four orders of magnitude, and vastly improved signal-to-noise in the NIR. The precision of the composite data is evaluated for three different liquids, focusing primarily on the steps for converting the raw absorbance spectra to k values. The variability in both MIR and NIR data as well as in the final n/k vectors is also investigated for several liquids. For typical liquids, the overall variability (reported as 2σ) in the final n and k-vectors is determined to be ∼0.4% and 3%, respectively. Finally, the derived n/k data are used to calculate absorbance spectra for aerosol droplets, showing marginal variability due to the typical measurement errors in the final n/k vectors.

47 OTHER INSTRUMENTATION↗

Quantum algorithm to simulate Lindblad master equations

We present a quantum algorithm for simulating a family of Markovian master equations that can be realized through a probabilistic application of unitary channels and state preparation. Our approach employs a second-order product formula for the Lindblad master equation, achieved by decomposing the dynamics into dissipative and Hamiltonian components and replacing the dissipative segments with randomly compiled, easily implementable elements. The sampling approach eliminates the need for ancillary qubits to simulate the dissipation process and reduces the gate complexity in terms of the number of jump operators. We provide a rigorous performance analysis of the algorithm. We also extend the algorithm to time-dependent Lindblad equations, generalize the family of Markovian master equations it can be applied to, and explore applications beyond the Markovian noise model. A new error bound, in terms of the diamond norm, for second-order product formulas for time-dependent Liouvillians is provided that might be of independent interest. Published by the American Physical Society 2025

Borras, Evan (ORCID:000900017709037X)↗

DOE JGI Metagenome Workflow

The DOE Joint Genome Institute (JGI) Metagenome Workflow performs metagenome data processing, including assembly; structural, functional, and taxonomic annotation; and binning of metagenomic data sets that are subsequently included into the Integrated Microbial Genomes and Microbiomes (IMG/M) (I.-M. A. Chen, K. Chu, K. Palaniappan, A. Ratner, et al., Nucleic Acids Res, 49:D751–D763, 2021, https://doi.org/10.1093/nar/gkaa939) comparative analysis system and provided for download via the JGI data portal (https://genome.jgi.doe.gov/portal/). This workflow scales to run on thousands of metagenome samples per year, which can vary by the complexity of microbial communities and sequencing depth. Here, we describe the different tools, databases, and parameters used at different steps of the workflow to help with the interpretation of metagenome data available in IMG and to enable researchers to apply this workflow to their own data. We use 20 publicly available sediment metagenomes to illustrate the computing requirements for the different steps and highlight the typical results of data processing. The workflow modules for read filtering and metagenome assembly are available as a workflow description language (WDL) file (https://code.jgi.doe.gov/BFoster/jgi_meta_wdl). The workflow modules for annotation and binning are provided as a service to the user community at https://img.jgi.doe.gov/submit and require filling out the project and associated metadata descriptions in the Genomes OnLine Database (GOLD) (S. Mukherjee, D. Stamatis, J. Bertsch, G. Ovchinnikova, et al., Nucleic Acids Res, 49:D723–D733, 2021, https://doi.org/10.1093/nar/gkaa983).

59 BASIC BIOLOGICAL SCIENCES↗

Nb3Sn Coating of Twin Axis Cavity for SRF Applications

The twin axis cavity with two identical accelerating beams has been proposed for Energy recovery linac (ERL) applications. Nb3Sn is a superconducting material with a higher critical temperature and a higher critical field as compared to Nb, which promises a lower operating cost due to higher quality factors. Two niobium twin axis cavities fabricated at JLab and were proposed to be coated with Nb3Sn. Due to their more complex geometry, the typical coating process used for basic elliptical cavities needs to be improved to coat these cavities. This devel-opment advances the current coating system at JLab for coating complex cavities. Two twin axis cavities were coated recently for the first time. This contribution dis-cusses initial results from coating of twin axis cavities, RF testing and witness sample analysis with an overview of the current challenges towards high performance Nb3Sn coated twin axis cavities.

Tiskumara, J.↗

Nb₃Sn Coating of Twin Axis Cavity for SRF Applications

The twin axis cavity with two identical accelerating beams has been proposed for energy recovery linac (ERL) applications. Nb₃Sn is a superconducting material with a higher critical temperature and a higher critical field as compared to Nb, which promises a lower operating cost due to higher quality factors. Two niobium twin axis cavities were fabricated at JLab and were proposed to be coated with Nb₃Sn. Due to their more complex geometry, the typical coating process used for basic elliptical cavi-ties needs to be improved to coat these cavities. This development advances the current coating system at JLab for coating complex cavities. Two twin axis cavities were coated recently for the first time. This contribution dis-cusses initial results from coating of twin axis cavities, RF testing and witness sample analysis with an overview of the current challenges towards high performance Nb₃Sn coated twin axis cavities.

43 PARTICLE ACCELERATORS↗