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At least 55 records · Page 3

Repository scale classification and decomposition of tandem mass spectral data

Various studies have shown associations between molecular features and phenotypes of biological samples. These studies, however, focus on a single phenotype per study and are not applicable to repository scale metabolomics data. Here we report MetSummarizer, a method for predicting (i) the biological phenotypes of environmental and host-oriented samples, and (ii) the raw ingredient composition of complex mixtures. We show that the aggregation of various metabolomic datasets can improve the accuracy of predictions. Since these datasets have been collected using different standards at various laboratories, in order to get unbiased results it is crucial to detect and discard standard-specific features during the classification step. We further report high accuracy in prediction of the raw ingredient composition of complex foods from the Global Foodomics Project.

59 BASIC BIOLOGICAL SCIENCES↗

Tailoring the Electronic Structures and Spectral Properties of ZnO with Irradiation Defects Generated Under Intense Electronic Excitation: A Combined Experimental and DFT Approach

Here, the relationship between the composition of the internal defect states, spectral properties, and correlated electronic structures of wurtzite zinc oxide (ZnO) crystals under 645 MeV Xe 35+ irradiation is systematically investigated, employing experimental characterizations combined with first-principle calculations. Based on the ion irradiation-induced thermal expansion and relaxation processes, the high concentration of vacancy/interstitial defects produced from the transient disordered phase in molten track states trigger photoelectric changes, as follows: i) the generation of internal defect states effectively reduces the intrinsic bandgap (3.25 eV → 2.66 eV); ii) a large number of defective active sites inhibits the recombination between electron–hole pairs, causing dark conductance and photoconductance to increase with increasing damage levels until optimal fluence is achieved. Based on the density functional theory (DFT) with the GGA + U (GGA = generalized gradient approximation) method, the defective models associated with the different electronic structures, density of states, formation energy, and the nature of the chemical bonding are established. The narrowing of the bandgap observed experimentally and the enhancement of carrier concentration originating from the internal electron defect states are qualitatively verified, therefore laying the foundation for designing future nanoscale photoelectronic devices and microelectronics applications.

36 MATERIALS SCIENCE↗

Unraveling the Atomic Mechanism of the Crystalline Phase‐Dependent Structural Features and Special Spectral Design of α‐, β‐, and Ɛ‐Ga₂O₃

Atomic‐scale phase transformations profoundly influence the functional properties of Ga₂O₃ polymorphs. By combining irradiation experiments with microstructure characterization and theoretical approaches, phase‐specific energy‐dissipation pathways in α‐, β‐, and ε‐Ga₂O₃ are uncovered and strategies for targeted property design are outlined. Competing antiphase boundaries (APBs) and twin domain boundaries (TDBs) promote irreversible α→ε interconversion through domain fragmentation. In β‐Ga₂O₃, defect‐induced stress gradients drive two distinct local transformations: surface Ga‐aggregated β→δ that stabilizes transient states, and latent‐track‐confined β→κ phase transition with recoverable distortions via cation reordering. Under electronic excitation, β‐Ga₂O₃ forms nanohillocks via robust GaO₆ octahedra (high density/strong Ga─O bonds), while α/ε‐Ga₂O₃ generates nanopores from tetrahedral Ga looseness (low bonding energy), highlighting phase‐dependent surface dynamics shaped by atomic packing and bonding anisotropy. Defect‐regulated recombination suppresses visible photoluminescence in α/β‐Ga₂O₃, whereas in ε‐Ga₂O₃ bandgap narrowing of ΔE: 0.30 eV is observed, enhancing emission. Linking phase‐dependent defect‐carrier interactions and metastable‐phase engineering in Ga₂O₃ enables property optimization for power‐electronics and optoelectronics devices.

electronic state configuration↗

Unmixing Symmetries

The low-lying spectra of atomic nuclei display diverse behaviors, for example, rotational bands, which can be described phenomenologically by simple symmetry groups such as spatial SU(3). This leads to the idea of dynamical symmetry, where the Hamiltonian commutes with the Casimir operator(s) of a group, and is block diagonal in subspaces defined by the group’s irreducible representations or irreps. Detailed microscopic calculations, however, show these symmetries are in fact often strongly mixed and the wave function fragmented across many irreps. More commonly, the fragmentation across members of a band are similar, which is called a quasidynamical symmetry. In this Letter I explicitly, albeit numerically, construct unitary transformations from a quasidynamical symmetry to a dynamical symmetry, adapting the similarity renormalization group (SRG) in order to transform away the symmetry-mixing parts of the Hamiltonian. In this work, the standard SRG produces unsatisfactory results, forcing the induced dynamical symmetry to be dominated by high-weight irreps irrespective of the original decomposition. Using spectral distribution theory to rederive and diagnose standard SRG, I introduce a new form of SRG. The new SRG transforms a quasidynamical symmetry to a dynamical symmetry, that is, unmixes the mixed symmetries, with intuitively more appealing results.

74 ATOMIC AND MOLECULAR PHYSICS↗

Hierarchical model reduction driven by a proper orthogonal decomposition for parametrized advection-diffusion-reaction problems

This work combines the Hierarchical Model (HiMod) reduction technique with a standard Proper Orthogonal Decomposition (POD) to solve parametrized partial differential equations for the modeling of advection-diffusion-reaction phenomena in elongated domains (e.g., pipes). This combination leads to what we define as HiPOD model reduction, which merges the reliability of HiMod reduction with the computational efficiency of POD. Two HiPOD techniques are presented and assessed by an extensive numerical verification.

97 MATHEMATICS AND COMPUTING↗

Simulation of high-frequency dissolved oxygen dynamics in a shallow estuary, the Corsica River, Chesapeake Bay

Understanding shallow water biogeochemical dynamics is a challenge in coastal regions, due to the presence of highly variable land-water interface fluxes, tight coupling with sediment processes, tidal dynamics, and diurnal variability in biogeochemical processes. While the deployment of continuous monitoring devices has improved our understanding of high-frequency (12 - 24 hours) variability and spatial heterogeneity in shallow regions, mechanistic modeling of these dynamics has lagged behind conceptual and empirical models. The inherent complexity of shallow water systems is represented in the Corsica River estuary, a small basin within the Chesapeake Bay ecosystem, where abundant monitoring data have been collected from long-term monitoring stations, continuous monitoring sensors, synoptic sensor surveys, and measurements of sediment-water fluxes. A state-of-the-art modeling system, the Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM), was applied to the Corsica domain with a high-resolution grid and nutrient loads from the most recent version of the Chesapeake Bay watershed model. The Corsica SCHISM model reproduced observed high-frequency variability in dissolved oxygen, as well as seasonal variability in chlorophyll-a and sediment-water fluxes. Time-series signal analyses using Empirical Model Decomposition and spectral analysis revealed that the diurnal and M2 tide frequencies are the dominant high-frequency modes and physical transport contributes a larger share to dissolved oxygen budgets than biogeochemical processes on an hourly time scale. Heterogeneity and patchiness in dissolved oxygen resulting from phytoplankton distributions and geometry-driven eddies amplify the physical transport effect, and on longer time scales oxygen is controlled more by photosynthesis and respiration. Our simulation demonstrates that interactions among physical and biological dynamics generate complex high-frequency variability in water quality and non-linear reposes to nutrient loading and environmental forcing in shallow water systems.

54 ENVIRONMENTAL SCIENCES↗

Variable Active Galactic Nuclei in the Galaxy Evolution Explorer Time Domain Survey

We searched the northern hemisphere fields of the Galaxy Evolution Explorer Time Domain Survey for galaxies with UV variability indicative of active galactic nuclei (AGNs). We identified 48 high-probability candidate AGNs from a parent sample of 1819 galaxies in the NASA Sloan Atlas catalog. We further characterized these systems using optical spectroscopic diagnostics, Wide-field Infrared Survey Explorer IR color selection criteria, and spectral energy distribution modeling. Of the 48 candidates, eight were identified as AGNs from optical emission lines, two were identified by their IR colors, and 28 were identified through spectral energy decomposition. Observational biases of each selection method are discussed in connecting these AGN subsamples to another. By selecting AGNs based on UV variability, we also identified six low-mass AGN candidates, all of which would have been missed by spectroscopic selection.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling Aerial Gamma-Ray Backgrounds Using Non-negative Matrix Factorization

Airborne gamma-ray surveys are useful for many applications, ranging from geology and mining to public health and nuclear security. In all these contexts, the ability to decompose a measured spectrum into a linear combination of background source terms can provide useful insights into the data and lead to improvements in the techniques that use spectral energy windows. Multiple methods for the linear decomposition of spectra exist but are subject to various drawbacks, such as allowing negative photon fluxes or requiring detailed Monte Carlo modeling. In this work, we propose using non-negative matrix factorization (NMF) as a data-driven approach to spectral decomposition. Using aerial surveys that include flights over water, we demonstrate that the mathematical approach of NMF finds physically relevant structure in the aerial gamma-ray background, namely, that measured spectra can be expressed as the sum of nearby terrestrial emission, distant terrestrial emission, and radon and cosmic emission. Furthermore, these NMF background components are compared with the background components obtained by noise-adjusted singular value decomposition (NASVD), which contain negative photon fluxes and, thus, do not represent the emission spectra in as straightforward a way. Finally, we comment on the potential areas of research that are enabled by NMF decompositions, such as new approaches to spectral anomaly detection and data fusion.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

System-Independent X-Ray Characterization

We have developed a method for image reconstruction and analysis of dual-energy X-ray scans that has been demonstrated to yield a physically intuitive characterization of materials (by electron density and effective atomic number) in a system-independent way. Our methodology stands in contrast to common practice of reconstructing images to yield linear attenuation coefficients, which depend strongly on system spectral response. At the core of our method, a technique called dual-energy decomposition is used to generate spectral energy-independent characterizations of the attenuation properties of a material. Inputs to this decomposition include system spectral response estimates and dual-energy X-ray projection data. X-ray cross-section tables are used to convert decomposition results to physical feature estimates (electron density, effective atomic number). Our method currently works best for materials with atomic numbers below 22 (titanium). In prior work for DHS, we demonstrated in a controlled, no-clutter environment that the decomposition technique could be applied to scans of a well-characterized materials on multiple systems with different X-ray spectral responses. In cases where LAC values showed a standard deviation of as much as 20% of mean value, application of our method yielded results with standard deviations as low as 1–3% of mean value.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Surface Properties of Double-Fin Generated Shock-Wave/Boundary-Layer Interactions

Shock-Wave/Boundary-Layer Interaction (SBLI) is ubiquitous in high-speed air vehicles. SBLI surface flowfield properties of crossing shocks induced by symmetric Double-Fins (DFs) at fin angles of 8° and 10° at Mach 2 are experimentally investigated; a 10° Single-Fin (SF) is also explored as a comparison. Surface visualization is used to capture distinct flowfield structures such as separation and upstream influence. Steady and unsteady Pressure-Sensitive Paints (PSPs) are used to obtain global surface pressure fields. Characteristics of DF-SBLI surface topology are discussed by comparing the corresponding SF-SBLI. Here, the effect of fin angle on DF-SBLI is characterized, and unsteady dynamics of the pressure field are examined. Spectral Proper Orthogonal Decomposition (SPOD) is performed on unsteady PSP, and traveling surface pressure waves and their frequency-dependent behavior are discussed. Dispersion relation of surface pressure waves is revealed by performing two-dimensional space–time Fourier transform on unsteady PSP, and the results are compared with the phase velocity distributions obtained from SPOD. Accompanying group velocity behavior is examined for distinct SBLI regions wherein wave propagation is found dependent on its frequency. Steady surface pressures along the centerline are compared with previous experimental data. Fin-tip spacing is found to be an essential parameter for scaling of upstream influence length.

33 ADVANCED PROPULSION SYSTEMS↗

Neural-network learning of SPOD latent dynamics

Here, we aim to reconstruct the latent space dynamics of high dimensional, quasi-stationary systems using model order reduction via the spectral proper orthogonal decomposition (SPOD). The proposed method is based on three fundamental steps: in the first, once that the mean flow field has been subtracted from the realizations (also referred to as snapshots), we compress the data from a high-dimensional representation to a lower dimensional one by constructing the SPOD latent space; in the second, we build the time-dependent coefficients by projecting the snapshots containing the fluctuations onto the SPOD basis and we learn their evolution in time with the aid of recurrent neural networks; in the third, we reconstruct the high-dimensional data from the learnt lower -dimensional representation. The proposed method is demonstrated on two different test cases, namely, a compressible jet flow, and a geophysical problem known as the Madden-Julian Oscillation. An extensive comparison between SPOD and the equivalent POD-based counterpart is provided and differences between the two approaches are highlighted. The numerical results suggest that the proposed model is able to provide low rank predictions of complex statistically stationary data and to provide insights into the evolution of phenomena characterized by specific range of frequencies. The comparison between POD and SPOD surrogate strategies highlights the need for further work on the characterization of the interplay of error between data reduction techniques and neural network forecasts.

97 MATHEMATICS AND COMPUTING↗

Aero-thermal numerical characterization of blunt fin-induced shock wave–boundary layer interaction and its control through leading-edge cooling injection

This study represents a novel evaluation of active flow control to alleviate the aerothermal penalties created by the blunt fin-induced shock wave–boundary layer interaction. The manuscript analyzes the effect of flow injection on a blunt fin-induced shock wave–boundary layer interaction via computational fluid dynamics simulations with various degrees of resolution. The impact on the mean flow topology and wall variables was investigated utilizing Reynolds-averaged Navier–Stokes simulations. Detached-eddy simulations revealed the low-frequency shock motion, shock wave–boundary layer, and horseshoe vortex interaction. The test article was exposed to two different incoming boundary layer thicknesses; the thicker boundary layer led to the appearance of larger turbulent scales. The Detached-eddy simulations revealed the time history of the shock wave–boundary layer interaction, focusing on the inception and development of the recirculated flow regions. Ultimately, spectral proper orthogonal decomposition was employed to identify the structures associated with the low-frequency shock motion caused by the shock wave–boundary layer interaction.

Lozano, Francisco (ORCID:0000000277871125)↗

Characterization of turbulence under different stability conditions using lidar scanning data

The spatiotemporal scales of turbulence in the boundary layer flow vary with the static stability of the atmosphere. For example, turbulence structures in unstable conditions are often found to be large and coherent, whereas the turbulent structures in stable conditions are relatively small and sporadic. To better understand the behavior of such turbulent structures under different atmospheric stability conditions in the lower atmosphere, herein, we use scanning lidar data collected over several months during the US Department of Energy's second Wind Forecast Improvement Project (WFIP 2) in 2016. The radial velocity data from scanning lidar were gathered along the horizontal plane (PPI mode) and were analyzed using proper orthogonal decomposition (POD) and spectral energy methods. The results from these analyses show that the turbulent structures in daytime unstable conditions are different from those present during nighttime stable conditions in terms of amount of energy and coherent structures. The POD energy is distributed more evenly in all the higher spatial modes in the daytime unstable case compared to the nighttime stable case. Besides characterizing the turbulence in the flow, the lidar data were also used to compare the simulated flow field generated from the WRF-LES framework (Weather Research and Forecasting - large-eddy simulation) with the scanning lidar data. The results from both simulated and lidar scanned data show similar structures orienting the streak-like structure along the mean wind. This indicates that the streak-like structures can exist in the real atmosphere during unstable atmospheric condition cases.

Rai, Raj K.↗

Fuel Injection Dynamics and Composition Effects on RDE Performance

Rotating detonation engines (RDEs) provide a promising route to substantially increasing cycle efficiency in stationary gas turbines. Much of this increase relies on the ability to achieve consistent pressure gain within the combustor. In particular, the design of injectors that feed fuel and air into the detonation channel plays a crucial role. Such injectors have to ensure proper mixing of fuel and oxidizer, while minimizing backflow of detonation products into the feed plenums, and reduce susceptibility to the complex wave structures that exist within the combustor. From a practical perspective, such RDEs also need to operate with variable fuel composition. When fuel mixtures with components that possess vastly different oxidation pathways and time-scales are used, there could be additional losses through deflagrative burning instead of detonation-driven heat release. Such sensitivity to the complete flow path is akin to the physics of thermoacoustic instabilities in conventional gas turbines. In this sense, RDEs pose a unique research challenge: the performance of the device relies on the small-scale heat release process, which is highly dependent on the flow interactions within the full-scale system. As a result, canonical flow configurations, instrumented with detailed diagnostics or modeled using high-fidelity tools, but only focus on the small-scale processes will not contain the key system-level interactions. At the same time, macroscopic measurements and models that only capture system-level performance will not provide insight into the key sources of pressure losses. These couplings and sensitivities provide a formidable challenge to both experimental and simulation studies of the effects Thus, a joint experimental/computational program designed specifically to address these challenges was undertaken in this program. The focus of this program was on two key topics: a) the interaction between injector flow and the overall wave dynamics within the combustor, and b) the deflagration/detonation structure in multi-component fuels that are of practical interest. Both topics involve interaction of small-scale heat release processes with the geometry-dependent wave structure. Studies focused on the study of full-scale RDE systems, based on a 6-inch conventional annular geometry. Experimentally RDEs were studied using a combination of diagnostics. A combination of optical diagnostics and aero-thermo-acoustic analysis based on a combination of spectral and mode decomposition analysis was used to identify the dynamics of the detonation wave and other secondary waves that exist in the system. These studies have helped the identification and investigation of injector and detonation dynamics arising from coupling, and how they affect RDE mixing, detonation structure, operability and performance. Performance of RDEs was investigated through thrust stand measurements, which was used to evaluate the effective pressure gain generated by the system through the concept of equivalent available pressure. Optical diagnostics were developed and implemented to investigate the distribution of heat release, across the detonation wave. Novel optical diagnostics of NIR imaging was also developed and applied to investigate the high temperature / high pressure distribution across the detonation wave. In order to complement the experiments, the computational tools were geared to simulate the full experimental setup. GPU-based acceleration of the models and computations were developed to enable rapid simulation of the full system. In addition, the use of adaptive mesh refinement, and unstructured grid formulation, enabled the investigation of realistic geometries studied in the laboratory. The simulations produced a wealth of detail on the structure of the detonation wave under different operating conditions. Emphasis was placed on quantifying mixture pre-burning and the impact on wave propagation and structure.

03 NATURAL GAS↗

Randomized Projection for Rank-Revealing Matrix Factorizations and Low-Rank Approximations

Rank-revealing matrix decompositions provide an essential tool in spectral analysis of matrices, including the Singular Value Decomposition (SVD) and related low-rank approximation techniques. QR with Column Pivoting (QRCP) is usually suitable for these purposes, but it can be much slower than the unpivoted QR algorithm. For large matrices, the difference in performance is due to increased communication between the processor and slow memory, which QRCP needs in order to choose pivots during decomposition. Our main algorithm, Randomized QR with Column Pivoting (RQRCP), uses randomized projection to make pivot decisions from a much smaller sample matrix, which we can construct to reside in a faster level of memory than the original matrix. This technique may be understood as trading vastly reduced communication for a controlled increase in uncertainty during the decision process. Furthermore, for rank-revealing purposes, the selection mechanism in RQRCP produces results that are the same quality as the standard algorithm, but with performance near that of unpivoted QR (often an order of magnitude faster for large matrices). Additionally, we also propose two formulas that facilitate further performance improvements. The first efficiently updates sample matrices to avoid computing new randomized projections. The second avoids large trailing updates during the decomposition in truncated low-rank approximations. Our truncated version of RQRCP also provides a key initial step in our truncated SVD approximation, TUXV. These advances open up a new performance domain for large matrix factorizations that will support efficient problem-solving techniques for challenging applications in science, engineering, and data analysis.

97 MATHEMATICS AND COMPUTING↗

Distance preserving machine learning for uncertainty aware accelerator capacitance predictions

Abstract Accurate uncertainty estimations are essential for producing reliable machine learning models, especially in safety-critical applications such as accelerator systems. Gaussian process models are generally regarded as the gold standard for this task; however, they can struggle with large, high-dimensional datasets. Combining deep neural networks with Gaussian process approximation techniques has shown promising results, but dimensionality reduction through standard deep neural network layers is not guaranteed to maintain the distance information necessary for Gaussian process models. We build on previous work by comparing the use of the singular value decomposition against a spectral-normalized dense layer as a feature extractor for a deep neural Gaussian process approximation model and apply it to a capacitance prediction problem for the High Voltage Converter Modulators in the Oak Ridge Spallation Neutron Source. Our model shows improved distance preservation and predicts in-distribution capacitance values with less than 1% error.

43 PARTICLE ACCELERATORS↗

Hard X-Ray to Radio Multiwavelength SED Analysis of Local U/LIRGs in the GOALS Sample with a Self-consistent AGN Model including a Polar-dust Component

We conduct hard X-ray to radio multiwavelength spectral energy distribution (SED) decomposition for 57 local luminous and ultraluminous infrared galaxies observed with the Nuclear Spectroscopic Telescope Array and/or Swift/Burst Alert Telescope in the GOALS sample. We modify the latest SED-fitting code X-CIGALE by implementing the infrared (IR) CLUMPY model, allowing us to conduct the multiwavelength study with the X-ray torus model XCLUMPY self-consistently. Adopting the torus parameters obtained by the X-ray fitting, we estimate the properties of the host galaxies, active galactic nucleus (AGN) tori, and polar dust. The star formation rates (SFRs) become larger with merger stage and most of them are above the main sequence. The SFRs are correlated with radio luminosity, indicating starburst emission is dominant in the radio band. Although polar-dust extinction is much smaller than torus extinction, the UV-to-IR (mainly IR) polar dust luminosities are ~2 times larger than the torus ones. The polar-dust temperature decreases while the physical size, estimated by the temperature and dust sublimation radius, increases with AGN luminosity from a few tens of parsec (early mergers) to kiloparsec scales (late mergers), where the polar dust likely comes from expanding (i.e., evolving) dusty outflows. A comparison between the SFRs and intrinsic AGN luminosities suggests that starbursts occur first and AGNs arise later, and overall their growth rates follow the simultaneous coevolution local galaxy–SMBH mass relation. We confirm the coexistence of intense starbursts, AGNs, and large-scale outflows in late mergers, supporting a standard AGN feedback scenario.

79 ASTRONOMY AND ASTROPHYSICS↗