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At least 739 records · Page 41

ECLEIRS: Exact conservation law embedded identification of reduced states for parameterized nonlinear conservation laws from sparse and noisy data

Multi-query applications such as parameter estimation, uncertainty quantification and design optimization for parameterized partial differential equation (PDE) systems are expensive. While reduced/latent state dynamics approaches for parameterized PDEs offer a viable alternative, these approaches rely on high-quality data and struggle with highly sparse spatiotemporal noisy measurements typically obtained from experiments. Furthermore, there is no guarantee that these models satisfy governing physical conservation laws. In this article, we propose a reduced state dynamics approach, referred to as ECLEIRS, that embeds exact conservation in the solution and flux representation by utilizing a space-time divergence-free neural network formulation. We compare ECLEIRS with other reduced state dynamics approaches, those that do not enforce any physical constraints and those with physics-informed loss functions, for three shock-propagation problems: 1-D advection, 1-D Burgers and 2-D Euler equations. In conclusion, the numerical experiments conducted in this study demonstrate that ECLEIRS provides the most accurate prediction of dynamics for unseen parameters even in the presence of highly sparse and noisy data.

97 MATHEMATICS AND COMPUTING↗

A Study of the Terahertz Spectra of Crystalline Materials (Polyethylene, Poly(Vinylidene Fluoride) form II, and α-D-Glucose) Using NDDO Semiempirical Methods

Semiempirical quantum chemistry methods offer a very interesting compromise between accuracy and computational complexity. The low-frequency vibration modes of three crystalline materials, namely, polyethylene, poly(vinylidene fluoride) form II, and α-D-glucose, have been studied using the PM6 and PM7 Hamiltonians in order to assess the performance of NDDO methods in the interpretation of terahertz spectra. The results have been compared with the available experimental data and former calculations performed using alternative methods. NDDO calculations are in good qualitative or semiquantitative agreement with the experimentally observed terahertz spectra.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron Transfer Dissociation of All Ions at All Times, MS{sup ETD}, in a Quadrupole Time-of-Flight (Q-ToF) Mass Spectrometer

Data-independent mass spectral acquisition is particularly powerful when combined with ultra-performance liquid chromatography (LC) that provides excellent separation of most components present in a given sample. Data-independent analysis (DIA) consists of alternating full MS scans and scans with fragmentation of all ions within a selected m/z range, providing precursor masses and structure information, respectively. Fragmentation spectra are acquired either by sequential isolation and fragmentation of sliding m/z ranges or fragmenting all ions entering the MS instrument with no ion isolation, termed broadband DIA. Previously, broadband DIA has only been possible using collision induced dissociation (CID). Here, we report the use of electron transfer dissociation (ETD) as the fragmentation technique in broadband DIA instead of traditional collision induced dissociation (CID) during MS{sup E}. In this approach, which we refer to as MS{sup ETD}, we implement the inherent benefits provided by ETD, such as discrimination of leucine and isoleucine, in a DIA setup. The combination of DIA analysis and ETD fragmentation with supplemental CID energy provides a powerful platform to obtain information on all precursors and their sequence from a single experiment. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Quantification of silicon carbide grain structure in TRISO fuel by BSE image analysis

The grain structure of the silicon carbide (SiC) layer in tristructural-isotropic (TRISO) fuels has commonly been qualified in fuel specifications based on a qualitative comparison to visual standards to ensure undesirable microstructure are not produced. This approach is inherently dependent on subjective judgement and provides limited data for analysis or comparison. An alternative method to rapidly quantify (i.e., provide a numeric measure of) the grain structure of the SiC layer in TRISO fuels has been developed. This method relies on the identification of silicon carbide grain boundaries based on brightness variation in backscattered electron (BSE) images through the application of automated image processing algorithms. The speed with which the requisite BSE imaging and analysis may be completed enables the practical use of this method on an industrial scale as a part of qualifying TRISO fuel to meet a given specification on silicon carbide grain structure, which is an important parameter for TRISO fuel performance. The method is benchmarked by comparison to prior Electron-Backscattered Diffraction (EBSD) results for TRISO particles from the Advanced Gas Reactor (AGR) program.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Selective One-Dimensional 13 C– 13 C Spin-Diffusion Solid-State Nuclear Magnetic Resonance Methods to Probe Spatial Arrangements in Biopolymers Including Plant Cell Walls, Peptides, and Spider Silk

Two-dimensional (2D) and 3D through-space 13 C– 13 C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13 C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13 C– 13 C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13 C– 13 C spin-diffusion methods described here apply in select cases in which the 1D 13 C solid-state NMR spectrum displays chemical shift-resolved moieties. Furthermore, this is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13 C– 13 C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13 C– 13 C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13 C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ~0.45–0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs

The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F 6.52 . Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized -- but only from archaeal methanogens that are anaerobic, O 2 -sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O 2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O 2 -sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

59 BASIC BIOLOGICAL SCIENCES↗

Iterative random forests to discover predictive and stable high-order interactions

Significance We developed a predictive, stable, and interpretable tool: the iterative random forest algorithm (iRF). iRF discovers high-order interactions among biomolecules with the same order of computational cost as random forests. We demonstrate the efficacy of iRF by finding known and promising interactions among biomolecules, of up to fifth and sixth order, in two data examples in transcriptional regulation and alternative splicing.

Science & Technology - Other Topics↗

Cooperative Behavior in the Evolution of Alignment and Structure in Vertically Aligned Carbon-Nanotube Arrays Grown using Chemical Vapor Deposition

We discuss the origin and the influence of autocatalytic kinetics on the structure-property relationship in the evolution of macromolecular structure during self-organized growth of vertically aligned carbon-nanotube arrays by chemical vapor deposition of acetylene. Real-time thickness measurements consistent with postgrowth structural characterization show that the rate of carbon incorporation governs not just the length of individual nanotubes, but also cooperative properties such as packing density, alignment, and order in the arrays, which profoundly affect the mechanical strength and the thermal and electrical conductivity of the assembly. Our analysis shows that the autocatalytic kinetics points to radical chain polymerization of acetylene as the most likely mechanism capable of producing the large variations in carbon-addition rates revealed by real-time data. Furthermore this fresh insight provides alternative approaches for targeting specific array properties using the polymerization reaction framework for creating novel applications in high-density energy storage, advanced interconnects, and high-efficiency heat dissipation.

36 MATERIALS SCIENCE↗

Measurements of the Tm 169 ( n , 2 n ) Tm 168 cross section from threshold to 15 MeV

Measurements of the 169 Tm(n,2n) 168 Tm cross section have been performed via the activation technique at 13 energies between 8.5 and 15.0 MeV. The purpose of this comprehensive data set is to provide an alternative diagnostic tool for obtaining subtle information on the neutron energy distribution produced in inertial confinement deuterium-tritium fusion experiments at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory. In conclusion, the 169 Tm(n,2n) 168 Tm reaction not only provides the primary 14-MeV neutron fluence, but also the important down-scattered neutron fluence, the latter providing information on the density achieved in the deuterium-tritium plasma during a laser shot.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Machine Learning Benchmarks for the Classification of Equivalent Circuit Models from Electrochemical Impedance Spectra

Analysis of Electrochemical Impedance Spectroscopy (EIS) data for electrochemical systems often consists of defining an Equivalent Circuit Model (ECM) using expert knowledge and then optimizing the model parameters to deconvolute various resistance, capacitive, inductive, or diffusion responses. For small data sets, this procedure can be conducted manually; however, it is not feasible to manually define a proper ECM for extensive data sets with a wide range of EIS responses. Automatic identification of an ECM would substantially accelerate the analysis of large sets of EIS data. We showcase machine learning methods to classify the ECMs of 9,300 impedance spectra provided by QuantumScape for the BatteryDEV hackathon. The best-performing approach is a gradient-boosted tree model utilizing a library to automatically generate features, followed by a random forest model using the raw spectral data. A convolutional neural network using boolean images of Nyquist representations is presented as an alternative, although it achieves a lower accuracy. We publish the data and open source the associated code. The approaches described in this article can serve as benchmarks for further studies. A key remaining challenge is the identifiability of the labels, underlined by the model performances and the comparison of misclassified spectra.

25 ENERGY STORAGE↗

Lightfall v0.0.1

Lightfall is a desktop application for synchrotron beamline instrument control, data acquisition, and live analysis at the Advanced Light Source (ALS). Built on Python and Qt, it provides a native graphical interface for operating beamline hardware, configuring and executing experimental scans, and visualizing results in real time. Key features include direct integration with EPICS control systems, a built-in electronic logbook, remote beamline access over secure tunnels, and an interprocess communication (IPC) architecture that coordinates with external analysis applications via ZMQ and EPICS process variables. This IPC approach allows Lightfall to orchestrate specialized analysis tools—including GPU-accelerated streaming correlators—without embedding them, avoiding the dependency conflicts common in monolithic scientific software platforms. Compared to prior approaches such as Xi-CAM's plugin-based architecture, Lightfall's design cleanly separates instrument control from domain-specific analysis, enabling feedback-driven acquisition where live analysis results can adjust scan parameters during an experiment. Its native Qt interface provides responsive performance for real-time data visualization that web-based alternatives struggle to match. Lightfall is designed for use by beamline scientists and staff operating synchrotron instruments at national user facilities.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

Surface Water Mass Transformation in the Southern Ocean: The Role of Eddies Revisited

The water mass transformation (WMT) framework describes how water of one class, such as a discrete interval of density, is converted into another class via air–sea fluxes or interior mixing processes. Here, this paper investigates how this process is modified at the surface when mesoscale ocean eddies are present, using a state-of-the-art high-resolution climate model with reasonable fidelity in the Southern Ocean. The method employed is to coarse-grain the high-resolution model fields to remove eddy signatures, and compare the results with those from the full model fields. This method shows that eddies reduced the WMT by 2–4 Sv (10%–20%; 1 Sv ≡ 10 6 m 3 s −1 ) over a wide range of densities, from typical values of 20 Sv in the smoothed case. The corresponding water mass formation was reduced by 40% at one particular density increment, namely, between 1026.4 and 1026.5 kg m −3 , which corresponds to the lighter end of the range of Indian Ocean Mode Water in the model. The effect of eddies on surface WMT is decomposed into three terms: direct modulation of the density outcrops, then indirectly, by modifying the air–sea density flux, and the combined effect of the two, akin to a covariance. It is found that the first and third terms dominate, i.e., smoothing the outcrops alone has a significant effect, as does the combination of smoothing both outcrops and density flux distributions, but smoothing density flux fields alone has little effect. Results from the coarse-graining method are compared to an alternative approach of temporally averaging the data. Implications for climate model resolution are also discussed.

54 ENVIRONMENTAL SCIENCES↗

Advancing the science of explosive fragmentation and afterburn fireballs though experiments and simulations at the benchtop scale

Detonation of explosive devices produces extremely hazardous fragments and hot, luminous fireballs. Prior experimental investigations of these post-detonation environments have primarily considered devices containing hundreds of grams of explosives. While relevant to many applications, such large- scale testing also significantly restricts experimental diagnostics and provides limited data for model validation. As an alternative, the current work proposes experiments and simulations of the fragmentation and fireballs from commercial detonators with less than a gram of high explosive. As demonstrated here, reduced experimental hazards and increased optical access significantly expand the viability of advanced imaging and laser diagnostics. Notable developments include the first known validation of MHz-rate optical fragment tracking and the first ever Coherent Anti-Stokes Raman Scattering (CARS) measures of post-detonation fireball temperatures. While certainly not replacing the need for full-scale verification testing, this work demonstrates new opportunities to accelerate developments of diagnostics and predictive models of post-detonation environments.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Seismic Monitoring at the Farnsworth CO2-EOR Field Using Time-Lapse Elastic-Waveform Inversion of 3D-3C VSP Data

During the Development Phase of the U.S. Southwest Regional Partnership on Carbon Sequestration, supercritical CO2 was continuously injected into the deep oil-bearing Morrow B formation of the Farnsworth Unit in Texas for Enhanced Oil Recovery (EOR). The project injected approximately 94 kilotons of CO2 to study geologic carbon storage during CO2-EOR. A three-dimensional (3D) surface seismic dataset was acquired in 2013 to characterize the subsurface structures of the Farnsworth site. Following this data acquisition, the baseline and three time-lapse three-dimensional three-component (3D-3C) vertical seismic profiling (VSP) data were acquired at a narrower surface area surrounding the CO2 injection and oil/gas production wells between 2014 and 2017 for monitoring CO2 injection and migration. With these VSP datasets, we inverted for subsurface velocity models to quantitatively monitor the CO2 plume within the Morrow B formation. We first built 1D initial P-wave (Vp) and S-wave (Vs) velocity models by upscaling the sonic logs. We improved the deep region of the Vp and Vs models by incorporating the deep part of a migration velocity model derived from the 3D surface seismic data. We improved the shallow region of 3D Vp and Vs models using 3D traveltime tomography of first arrivals of VSP downgoing waves. We further improved the 3D baseline velocity models using elastic-waveform inversion (EWI) of the 3D baseline VSP upgoing data. Our advanced EWI method employs alternative tomographic and conventional gradients and total-variation-based regularization to ensure the high-fidelity updates of the 3D baseline Vp and Vs models. We then sequentially applied our 3D EWI method to the three time-lapse datasets to invert for spatiotemporal changes of Vp and Vs in the reservoir. Our inversion results reveal the volumetric changes of the time-lapse Vp and Vs models and show the evolution of the CO2 plume from the CO2 injection well to the oil/gas production wells.

42 ENGINEERING↗

Technical note: Uncertainties in eddy covariance CO 2 fluxes in a semiarid sagebrush ecosystem caused by gap-filling approaches

Abstract. Gap-filling eddy covariance CO2 fluxes is challenging at dryland sites due to small CO2 fluxes. Here, four machine learning (ML) algorithms including artificial neural network (ANN), k-nearest neighbors (KNNs), random forest (RF), and support vector machine (SVM) are employed and evaluated for gap-filling CO2 fluxes over a semiarid sagebrush ecosystem with different lengths of artificial gaps. The ANN and RF algorithms outperform the KNN and SVM in filling gaps ranging from hours to days, with the RF being more time efficient than the ANN. Performances of the ANN and RF are largely degraded for extremely long gaps of 2 months. In addition, our results suggest that there is no need to fill the daytime and nighttime net ecosystem exchange (NEE) gaps separately when using the ANN and RF. With the ANN and RF, the gap-filling-induced uncertainties in the annual NEE at this site are estimated to be within 16 g C m−2, whereas the uncertainties by the KNN and SVM can be as large as 27 g C m−2. To better fill extremely long gaps of a few months, we test a two-layer gap-filling framework based on the RF. With this framework, the model performance is improved significantly, especially for the nighttime data. Therefore, this approach provides an alternative in filling extremely long gaps to characterize annual carbon budgets and interannual variability in dryland ecosystems.

Yao, Jingyu↗

The quiet solar wind

Data from nine spacecraft are combined to study the properties of solar wind protons and the interplanetary magnetic field under unusual conditions that proton speed, density, and temperature variations are small over periods comparable to the solar wind expansion time. From the 14 quiet intervals studied it is determined that (1) the square root of T versus velocity relation is less steep than was calculated from long-term-averaged or 3-hour quiet data; (2) the density varies approximately as the inverse square of the velocity; however, the data scatter is large, and an alternative interpretation is that mass flux is constant for velocities over about 400 km/s, in agreement with earlier studies; (3) the magnitude of the interplanetary magnetic field is independent of solar wind speed and density; and (4) the average field direction varies with the solar wind speed as predicted by Parker's spiral model. The intercalibration of solar wind measurements by different spacecraft is discussed in an appendix.

Neugebauer, M.↗