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At least 127 records · Page 7

Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry

In the method of X-ray footprinting mass spectrometry (XFMS), proteins at micromolar concentration in solution are irradiated with a broadband X-ray source, and the resulting hydroxyl radical modifications are characterized using liquid chromatography mass spectrometry to determine sites of solvent accessibility. These data are used to infer structural changes in proteins upon interaction with other proteins, folding, or ligand binding. XFMS is typically performed under aerobic conditions; dissolved molecular oxygen in solution is necessary in many, if not all, the hydroxyl radical modifications that are generally reported. In this study we investigated the result of X-ray induced modifications to three different proteins under aerobic versus low oxygen conditions, and correlated the extent of damage with dose calculations. We observed a concentration-dependent protecting effect at higher protein concentration for a given X-ray dose. For the typical doses used in XFMS experiments there was minimal X-ray induced aggregation and fragmentation, but for higher doses we observed formation of covalent higher molecular weight oligomers, as well as fragmentation, which was affected by the amount of dissolved oxygen in solution. The higher molecular weight products in the form of dimers, trimers, and tetramers were present in all sample preparations, and, upon X-ray irradiation, these oligomers became non-reducible as seen in SDS-PAGE. The results provide an important contribution to the large body of X-ray radiation damage literature in structural biology research, and will specifically help inform the future planning of XFMS, and well as X-ray crystallography and small-angle X-ray scattering experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Use Attainability Analysis for Upper Sandia Canyon

This document presents a use attainability analysis (UAA) for the perennial segment of Upper Sandia Canyon, which is located within the Los Alamos National Laboratory (LANL) property near Los Alamos, New Mexico.1 This UAA is consistent with 20.6.4.15 New Mexico Administrative Code (NMAC) (New Mexico Environment Department [NMED] 2011c), which describes the perennial segment as “Sandia Canyon from Sigma Canyon upstream to LANL [National Pollutant Discharge Elimination System] NPDES outfall 001.” The perennial segment’s designated uses are coldwater aquatic life, livestock watering, wildlife habitat, and secondary contact. 40 Code of Federal Regulations (CFR) § 131.10(g) permits a state to remove a designated use that is not an existing use (as defined in 40 CFR §131.3), if a UAA demonstrates that naturally occurring pollutant concentrations prevent the attainment of the use or if physical conditions related to the natural features of the water body preclude the attainment of the aquatic life protection use. This UAA considers whether natural physical conditions in Upper Sandia Canyon, specifically air and/or water temperatures, prevent the designated aquatic life use water temperature limits (i.e., coldwater) from being attained in the perennial segment. The weight of evidence presented in this UAA supports the conclusion that, based on air-water temperature modeling and instream thermograph data, the coolwater aquatic life designated use is currently the attainable use. Accordingly, it is recommended that the coolwater aquatic life designated use replace the coldwater aquatic life designated use in the Upper Sandia Canyon assessment unit (AU).

54 ENVIRONMENTAL SCIENCES↗

Near-Threshold Dipole Strength in 10 Be with Isoscalar Character

Isoscalar dipole transitions are a distinctive fingerprint of cluster structures. A 1 − resonance at 7.27(10) MeV, located just below the 𝛼-emission threshold, has been observed in the deuteron inelastic scattering reactions off 10 Be. The deformation lengths of the excited states in 10 Be below 9 MeV have been inferred from the differential cross sections using coupled channel calculations. This observed 1 − resonance has isoscalar characteristics and exhausts approximately 5%–15% of the isoscalar dipole energy-weighted sum rule, providing evidence for pronounced 𝛼 cluster structure in 10 Be. The Gamow coupled channel approach supports this interpretation and suggests the near-threshold effect might be playing an important role in this excitation energy domain. Here, the 𝛼 +𝛼 +𝑛 +𝑛 four-body calculation reproduces the observed enhanced dipole strength, implying that the four-body cluster structure is essential to describe the 1 − states in 10 Be.

Cluster models↗

Lightweight Metal Stamping Optimization Enabled by Artificial Intelligence

Successfully manufacturing an automotive body structure made via the sheet metal stamping process depends upon simultaneous consideration of component design, tooling design, stamping process control, and material properties. In many cases, introducing lightweight sheet materials (e.g., aluminum alloys, magnesium alloys, advanced high strength steels) holds the potential to significantly reduce vehicle weight, but challenges the stamping process by introducing materials with inherently less ductility. Successful and repeatable applications require co-developing the stamping process controls with the varying material properties, including formability. During the stamping process, as soon as the forming limit of the sheet is exceeded, the material shows localized necking which quickly leads to splits. Controlling process variability to avoid these material splits will enable deployment of less formable, lighter, and stronger materials for stamped automotive components. A typical optimization procedure for manufacturing requires an iterative process involving parameter setting, execution of computational simulations, and modifying the parameters. The entire process demands substantial computational time, making it impractical for real-time feedback towards rapid corrective actions required for in-line control for running production processes. To overcome this challenge, artificial intelligence (AI) can be leveraged to determine optimal manufacturing parameters within a single manufacturing cycle time. This research proposes an in-line optimization framework incorporating a trained AI model to predict kidney-shaped die forming. Preliminary results indicate that the AI framework can accurately predict draw-in values based on a given parameter set, a process referred to as forward prediction. Furthermore, the AI framework can also predict the optimal parameter set that leads to the desired draw-in values, referred to as inverse optimization (or backward prediction). This research has been performed in collaborations with USCAR (US Council for Automotive Research) and AutoForm. The members of USCAR are Ford, GM, and Stellantis.

36 MATERIALS SCIENCE↗

An interactive machine learning platform for analyzing multi-particle coincidence data from cold target recoil ion momentum spectroscopy

We present SCULPT (Supervised Clustering and Uncovering Latent Patterns with Training), a comprehensive software platform for analyzing tabulated high-dimensional multi-particle coincidence data from Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) experiments. The software addresses critical challenges in modern momentum spectroscopy by integrating advanced machine learning techniques with physics-informed analysis in an interactive web-based environment. SCULPT implements uniform manifold approximation and projection for non-linear dimensionality reduction to reveal correlations in high-dimensional data. We also discuss potential extensions to deep autoencoders for feature learning and genetic programming for automated discovery of physically meaningful observables. A novel adaptive confidence scoring system provides quantitative reliability assessments by evaluating user-selected clustering quality metrics with predefined weights that reflect each metric’s robustness. The platform features configurable molecular profiles for different experimental systems, interactive visualization with selection tools, and comprehensive data filtering capabilities. Utilizing a subset of SCULPT’s capabilities, we analyze photo-double-ionization data measured using the COLTRIMS method for three-body dissociation of the D 2 O molecule, revealing distinct fragmentation channels and their correlations with physics parameters. The software’s modular architecture and web-based implementation make it accessible to the broader atomic and molecular physics community, significantly reducing the time required for complex multi-dimensional analyses. This opens the door to finding and isolating rare events exhibiting non-linear correlations on the fly during experimental measurements, which can help steer exploration and improve the efficiency of experiments.

Artificial neural networks↗

Correlated purification for restoring 𝑁-representability in quantum simulation

Experimentally measured reduced density matrices (RDMs) often violate constraints that ensure they represent N-electron states—known as N-representability conditions—because of statistical and hardware noise. In this work, we present a correlated purification framework based on semidefinite programming to restore the accuracy of a noisy, unphysical two-electron RDM (2-RDM). The method performs a bi-objective optimization that minimizes both the many-electron energy and the nuclear norm of the correction to the measured 2-RDM. The nuclear norm, often employed in matrix completion, promotes low-rank corrections, while the energy term acts as a regularization term that can improve the purity of the ground state. While the method is particularly effective for ground states, it can also be applied to excited and nonstationary states by decreasing the weight of the energy relative to the error norm. In an application to fermionic shadow tomography of large hydrogen chains, correlated purification yields substantial reductions in both energy and 2-RDM error, achieving chemical accuracy across dissociation curves. This framework provides a robust strategy for tomography in many-body quantum simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The NASA Floater: 15MW Ultra-Light Concrete Hull with Sea-Water Ballast Tuned Mass Damper

In this project, UMaine developed the VolturnUS+ platform; a new 15MW+ ultra-light-weight, corrosion-resistant, concrete floating offshore wind turbine (FOWT) equipped with novel patent pending Heel Tank damping technology. UMaine developed this damping technology to reduce FOWT motions using existing onboard sea-water ballast, which has been integrated into the concrete cruciform hull resulting in reduced platform rigid body motions leading to a lighter hull, increased turbine performance, and a lower LCOE.

17 WIND ENERGY↗

OrganiCam: a lightweight time-resolved laser-induced luminescence imager and Raman spectrometer for planetary organic material characterization

OrganiCam is a laser-induced luminescence imager and spectrometer designed for standoff organic and biosignature detection on planetary bodies. OrganiCam uses a diffused laser beam (12° cone) to cover a large area at several meters distance and records luminescence on half of its intensified detector. The diffuser can be removed to record Raman and fluorescence spectra from a small spot from 2 m standoff distance. OrganiCam’s small size and light weight makes it ideal for surveying organics on planetary surfaces. Here, we have designed and built a brassboard version of the OrganiCam instrument and performed initial tests of the system.

47 OTHER INSTRUMENTATION↗

Hydrologic Impacts of a Strike-Slip Fault Zone: Insights from Joint 3D Body-Wave Tomography of Rock Valley

The Rock Valley fault zone (RVFZ), an intraplate strike-slip fault zone in the southern Nevada National Security Site (NNSS), hosted a series of very shallow (<3 km) earthquakes in 1993. The RVFZ may also have hydrological significance within the NNSS, potentially playing a role in regional groundwater flow, but there is a lack of local hydrological data. In the Spring of 2021, we collected active-source accelerated weight drop seismic data over part of the RVFZ to better characterize the shallow subsurface. Here, we manually picked ~17,000 P-wave travel times and over 14,000 S-wave travel times, which were inverted for P-wave velocity (V P ), S-wave velocity (V S ), and V P /V S ratio in a 3D joint tomographic inversion scheme. Seismic velocities are imaged as deep as ~700 m in areas and generally align with geologic and structural expectations. V P and V S are relatively reduced near mapped and inferred faults, with the most prominent lower V P and V S zone around the densest collection of faults. We image V P /V S ratios ranging from ~1.5 to ~2.4, the extremes of which occur at a depth of ~100 m and are juxtaposed across a fault. One possible interpretation of the imaged seismic velocities is enhanced fault damage near the densest collection of faults with relatively higher porosity and/or crack density at ~100 m depth, with patches of semiperched groundwater present in the sedimentary rock in higher V P /V S areas and drier rock in lower V P /V S areas. A relatively higher V P /V S area beneath the densest faults persists at depth, which suggests percolation of groundwater via the fault damage zone to the regionally connected lower carbonate aquifer. Potentially, the presence and movement of groundwater may have played a role in the 1993 earthquake aftershocks.

58 GEOSCIENCES↗

A high-order WENO-limited finite-volume algorithm for atmospheric flow using the ADER-differential transform time discretization

A high-order-accurate weighted essentially non-oscillatory (WENO) limited upwind finite-volume scheme is detailed for the compressible, nonhydrostatic, inviscid Euler equations using an arbitrary derivatives (ADER) time-stepping scheme based on differential transforms (DTs). A second-order-accurate alternating Strang dimensional splitting is compared against multidimensional simulation with 2D transport using solid body rotation of various data. The two were found to give nearly identical accuracy in orthogonal, Cartesian coordinates. Orders of convergence are demonstrated at up to ninth-order accuracy with 2D transport. 1D transport is used to confirm that error decreases monotonically with increasing order of accuracy with WENO limiting even for discontinuous data. Further, WENO limiting always decreased the error compared with simulation without limiting in the L 1 norm. A series of standard 2D compressible nonhydrostatic Euler equation test cases were validated against previous results from literature. Finally, it was demonstrated that increasing the order of accuracy led to better resolved features and increased power for kinetic energy at small wavelengths.

54 ENVIRONMENTAL SCIENCES↗

Impact of penetrating collisions of plasma ions on spectral line shapes

Spectral-line-broadening models have been moving towards including full Coulomb interactions between the atom and plasma, replacing the commonly used dipole approximation. The effects of the full Coulomb interaction have been thoroughly explored for plasma electrons, resulting in redshifts of spectral lines in high-energy-density plasmas. We explore the impact of a full Coulomb treatment on ion broadening. Penetrating collisions due to ions do not significantly impact the linewidths. The most significant aspect is the appearance of quasimolecular resonances in the far line wings, such as those previously observed in white-dwarf spectra. We identify several problems with the existing models. The most direct implementation causes the quasimolecular features to appear at the wrong photon energies. It is possible to include the detailed molecular structure, but this currently requires the Anderson-Talman approximation, which ignores the N-body properties of the plasma. We find that N-body effects can substantially broaden these quasimolecular features and even shift them, depending on the plasma conditions. We conclude that penetration of ions into the spatial extent of the radiator wave function does not strongly affect the usual diagnostics and may have a moderate to weak effect on opacity. Furthermore, the Rosseland mean opacity is weighted towards low-opacity regions of a spectrum, where these quasimolecular features are found.

79 ASTRONOMY AND ASTROPHYSICS↗

Dietary uptake of geosmin in rainbow trout ( Oncorhynchus mykiss )

Geosmin is a primary source of muddy/earthy ‘off-flavors’ in farmed fish, which may render their organoleptic quality unacceptable to consumers. Model systems of geosmin uptake typically comprise exposure to waterborne geosmin that is absorbed via the gills. The present research demonstrates dietary exposure as an alternative route of geosmin uptake in Rainbow Trout (Oncorhynchus mykiss) fillets. Trout (average initial weight of 355 g) were stocked in quadruplicate compartmentalized raceways (N = 4 compartments per treatment, n = 50 fish per compartment) supplied with first-use, flow-through water (4.5 complete turnovers per hour). Fish were fed diets containing 0 (control dose), 0.005 (low dose), 0.05 (medium dose), or 0.5 (high dose) mg geosmin/kg feed at 1% body weight/day for four weeks. Fillets (12 fillets/diet/week plus 12 pre-trial fillet samples) and weekly feed and water samples were analyzed via GC–MS to determine geosmin concentrations. Feeding behavior was documented daily according to a four-point scale. ANOVA with post-hoc Tukey tests and polynomial contrast, regression, correlation, and chi-squared statistical analyses were applied to data (α = 0.05 significance level). Palatability of feed did not hinder consumption of the geosmin-spiked feeds: although fish responded positively to all feeds, the most aggressive feeding behavior was observed among those fed medium and high dose feed. Geosmin was effectively imparted into fillets after one week, and no significant temporal effect was found after four weeks. Mean geosmin concentrations significantly increased in fillets from low (mean of 26 ng/kg geosmin) to medium (202 ng/kg) to high (441 ng/kg) dose feed groups during the trial. Polynomial contrasts and regression modeling validated this significant positive effect of dose on geosmin uptake, with an estimated 166 ng/kg rise in fillet-geosmin for every log 10 increase in feed concentration. Waterborne geosmin levels immediately post-feeding were conditionally independent of concentrations in feed and fillets, therefore dietary uptake was affirmed as the predominant mechanism of absorption in the present experimental system. Finally, based on these findings, geosmin-spiked feeds may be used to induce predictable, repeatable levels of this off-flavor compound in fillets and serve as a model system for further investigation of sensory quality and off-flavor mitigation strategies for farm-raised fish.

59 BASIC BIOLOGICAL SCIENCES↗

Ab initio predictions link the neutron skin of 208 Pb to nuclear forces

Heavy atomic nuclei have an excess of neutrons over protons, which leads to the formation of a neutron skin whose thickness is sensitive to details of the nuclear force. This links atomic nuclei to properties of neutron stars, thereby relating objects that differ in size by orders of magnitude. The nucleus 208 Pb is of particular interest because it exhibits a simple structure and is experimentally accessible. However, computing such a heavy nucleus has been out of reach for ab initio theory. By combining advances in quantum many-body methods, statistical tools and emulator technology, we make quantitative predictions for the properties of 208 Pb starting from nuclear forces that are consistent with symmetries of low-energy quantum chromodynamics. We explore 10 9 different nuclear force parameterizations via history matching, confront them with data in select light nuclei and arrive at an importance-weighted ensemble of interactions. We accurately reproduce bulk properties of 208 Pb and determine the neutron skin thickness, which is smaller and more precise than a recent extraction from parity-violating electron scattering but in agreement with other experimental probes. This work demonstrates how realistic two- and three-nucleon forces act in a heavy nucleus and allows us to make quantitative predictions across the nuclear landscape.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Superstructural phase transitions in polymer-grafted nanooctahedra

Superlattices of polyhedral nanocrystals exhibit emergent properties defined by their structural arrangements, but native nanocrystal ligands often limit their programmability. Polymeric ligands address this limitation by enabling tunable nanocrystal softness through modifications of polymer molecular weight and grafting density. Here, we investigate phase transitions in polymer-grafted nanooctahedra by varying polymer length, nanocrystal size, truncation, and ligand density. In two-dimensional superlattices, longer polymers or smaller nanooctahedra induce a transition from orientationally ordered to hexagonal rotator lattices. In three-dimensional superlattices, increasing polymer length drives transitions from Minkowski to body-centered cubic and plastic hexagonal close-packed phases, while higher grafting densities further enable transitions to simple hexagonal phases. Polymer brush and thermodynamic perturbation theories, supported by Monte Carlo simulations, uncover the entropic and enthalpic forces that govern these transitions. This work highlights the versatility of polymer-grafted anisotropic nanocrystals as building blocks for designing hierarchical superstructures and metamaterials with customizable properties.

36 MATERIALS SCIENCE↗

Dietary Methionine Supplementation Exacerbates Gastrointestinal Toxicity in a Mouse Model of Abdominal Irradiation

Identification of appropriate dietary strategies for prevention of weight and muscle loss in cancer patients is crucial for successful treatment and prolonged patient survival. High-protein oral nutritional supplements decrease mortality and improve indices of nutritional status in cancer patients; however, high-protein diets are often rich in methionine, and experimental evidence indicates that a methionine-supplemented diet (MSD) exacerbates gastrointestinal toxicity after total body irradiation. Here, we sought to investigate whether MSD can exacerbate gastrointestinal toxicity after local abdominal irradiation, an exposure regimen more relevant to clinical settings.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Constrained Block Nonlinear Neural Dynamical Models

Neural network modules conditioned by known priors can be effectively trained and combined to represent systems with nonlinear dynamics. This work explores a novel formulation for data-efficient learning of deep control-oriented nonlinear dynamical models by embedding local model structure and constraints. The proposed method consists of neural network blocks that represent input, state, and output dynamics with constraints placed on the network weights and system variables. For handling partially observable dynamical systems, we utilize a state observer neural network to estimate the states of the system's latent dynamics. We evaluate the performance of the proposed architecture and training methods on system identification tasks for three nonlinear systems: a continuous stirred tank reactor, a two tank interacting system, and an aerodynamics body. Models optimized with a few thousand system state observations accurately represent system dynamics in open loop simulation over thousands of time steps from a single set of initial conditions. Experimental results demonstrate an order of magnitude reduction in open-loop simulation mean squared error for our constrained, block-structured neural models when compared to traditional unstructured and unconstrained neural network models.

Skomski, Elliott↗

Dark-exciton energy splitting in monolayer W Se 2 : Insights from time-dependent density functional theory

Here, we present here a formalism based on time-dependent density functional theory to describe characteristics of both intra- and intervalley excitons in semiconductors, the latter of which had remained a challenge. Through the usage of an appropriate exchange-correlation kernel (nanoquanta), we trace the energy difference between the intra- and intervalley dark excitons in monolayer (1L) W⁢ Se 2 to the domination of the exchange part in the exchange-correlation energies of these states. Furthermore, our calculated transition contribution maps establish the momentum resolved weights of the electron-hole excitations in both bright and dark excitons thereby providing a comprehensive understanding of excitonic properties of 1L W⁢ Se 2 . We find that the states consist of hybridized excitations around the corresponding valleys which leads to brightening of the dark excitons, i.e., significantly decreasing their lifetime which is reflected in the PL spectrum. Using many-body perturbation theory, we calculate the phonon contribution to the energy band gap and the linewidths of the excited electrons, holes, and (bright) exciton to find that as the temperature increases the band gap significantly decreases, while the linewidths increase. Our work paves for describing the ultrafast charge dynamics of transition metal dichalcogenide within an ab initio framework.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗