Mapping Resonance Structures in Transient Core-Ionized Atoms
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72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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Revealing the three-dimensional arrangement of polar topology in nanoparticles
In the early 2000s, low dimensional ferroelectric systems were predicted to have topologically nontrivial polar structures, such as vortices or skyrmions, depending on mechanical or electrical boundary conditions. A few variants of these structures have been experimentally observed in thin film model systems, where they are engineered by balancing electrostatic charge and elastic distortion energies. However, the measurement and classification of topological textures for general ferroelectric nanostructures have remained elusive, as it requires mapping the local polarization at the atomic scale in three dimensions. Here we unveil topological polar structures in ferroelectric BaTiO3 nanoparticles via atomic electron tomography, which enables us to reconstruct the full three-dimensional arrangement of cation atoms at an individual atom level. Our three-dimensional polarization maps reveal clear topological orderings, along with evidence of size-dependent topological transitions from a single vortex structure to multiple vortices, consistent with theoretical predictions. The discovery of the predicted topological polar ordering in nanoscale ferroelectrics, independent of epitaxial strain, widens the research perspective and offers potential for practical applications utilizing contact-free switchable toroidal moments.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study
Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.
Drago, Victoria N. [Oak Ridge National Laboratory ↗
Advanced silicon tracking detector developments for the future Electron-Ion Collider
The proposed Electron-Ion Collider (EIC) will operate high-luminosity high-energy electron+proton and electron+nucleus collisions at the collision energies from 20 GeV to 141 GeV to solve several fundamental questions in the high energy and nuclear physics fields. Its instantaneous luminosity can reach 10 33-34 cm -2 s -1 and the bunching crossing rate is around 10 ns. The EIC project has received CD1 approval from the US DOE in 2021 and moves toward the machine design and preparation for construction. To realize various particle measurements with high precision at the future EIC, a low material-budget and high-granularity silicon vertex and tracking detector with fine spatial and momentum resolutions and nearly 4π solid angle coverage is desired. The Monolithic Active Pixel Sensor (MAPS) and AC Coupled Low Gain Avalanche Diode (AC-LGAD) technologies stand out of several advanced technology options for the EIC silicon vertex and tracking detector subsystems. The MAPS technology has advanced features of low material budget, low power consumption, good radiation resistance and fine spatial resolution. The AC-LGAD technology can achieve fast timing resolution. Latest studies and progress of the EIC silicon vertex and tracking detector conceptual design, performance validations in simulation and ongoing MAPS and AC-LGAD R&D will be shown. Furthermore, schedule and plan of the EIC project detector development will be discussed as well.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.
59 BASIC BIOLOGICAL SCIENCES↗
A 21 centimeter line survey of a region around four outer galaxy open clusters
To investigate the role of atomic gas in the interaction of massive stars with the interstellar medium, a 21 cm survey was made of a region surrounding four young, outer Galaxy open clusters, NGC 281, 433, 436, and 457. A rectangular area ranging in Galactic longitude from 115 to 133 deg, and in latitude from -10 to -1 deg, was observed with the NRAO 140 foot telescope. Most of this region was fully sampled, resulting in spatial resolution equal to the telescope's 21 arcmin beamwidth. The data are presented as longitude-latitude and latitude-velocity contour maps. A catalog of atomic gas features (e.g., clouds, filaments, and shells) is given.
Leisawitz, David↗
Differences in elasticity of vinculin-deficient F9 cells measured by magnetometry and atomic force microscopy
We have investigated a mouse F9 embryonic carcinoma cell line, in which both vinculin genes were inactivated by homologous recombination, that exhibits defective adhesion and spreading [Coll et al. (1995) Proc. Natl. Acad. Sci. USA 92, 9161-9165]. Using a magnetometer and RGD-coated magnetic microbeads, we measured the local effect of loss and replacement of vinculin on mechanical force transfer across integrins. Vinculin-deficient F9Vin(-/-) cells showed a 21% difference in relative stiffness compared to wild-type cells. This was restored to near wild-type levels after transfection and constitutive expression of increasing amounts of vinculin into F9Vin(-/-) cells. In contrast, the transfection of vinculin constructs deficient in amino acids 1-288 (containing the talin- and alpha-actinin-binding site) or substituting tyrosine for phenylalanine (phosphorylation site, amino acid 822) in F9Vin(-/-) cells resulted in partial restoration of stiffness. Using atomic force microscopy to map the relative elasticity of entire F9 cells by 128 x 128 (n = 16,384) force scans, we observed a correlation with magnetometer measurements. These findings suggest that vinculin may promote cell adhesions and spreading by stabilizing focal adhesions and transferring mechanical stresses that drive cytoskeletal remodeling, thereby affecting the elastic properties of the cell.
Non-NASA Center↗
Exploring Local Vibrational Structure in Protein-Bound Chlorophyll a: Isotope-Enrichment Experiments and Electrostatic Analysis
Local chlorophyll (Chl) vibrations play an essential role in biological photosynthesis by facilitating rapid energy transfer between pigments. In research studies, they also provide a useful spectroscopic probe of the local protein environment that surrounds each pigment. However, measuring the complete vibrational absorption spectrum of a protein-bound Chl molecule is much more difficult than, for example, Chl in neat solvent due to overlap with protein vibrations that typically drown out Chl vibrational features. Resonance Raman and fluorescence spectroscopies provide a way around this problem for Franck–Condon active vibrations, but these often rely on cryogenic measurement conditions and fail to capture vibrational signatures from, e.g., ester-group vibrations that lack coupling to a convenient electronic transition. In the present contribution, we use 13 C-enrichment of the protein backbone to shift protein background signals to lower frequency, providing a largely clean spectral window in which to study local Chl a C═O stretch modes. A room-temperature absorption spectrum for Chl a in the water-soluble chlorophyll protein (WSCP) of Lepidium virginicum is thus extracted as a difference between protein-plus-pigment and protein-only vibrational spectra. Excellent agreement in the molecular fingerprint region with the vibrational spectrum of Chl a in organic solvents confirms that the resulting spectrum represents the response of the protein-bound Chl a molecule. Furthermore, the ester group resonance is observed to shift in response to the S53P mutation that eliminates a 17 3 ester group hydrogen bond from the protein environment. Finally, we analyze these experimental results using MD-based electrostatic analysis, finding that electric-field mapping at the C atom of the ester group provides a satisfactory explanation for the observed frequency shifts between organic solvent and protein environment. MD analysis further suggests that a red-shifted ester peak observed experimentally for the S53P mutant results from solvation of the 17 3 Chl ester group due increase water penetration into the Chl-binding pocket relative to wild-type WSCP. Here, we anticipate that these results will prove useful both for benchmarking future simulation work and as a reference for interpreting Chl vibrational spectra as a probe of pigment–protein interactions.
14 SOLAR ENERGY↗
Smooth, homogeneous, high-purity Nb 3 Sn superconducting RF resonant cavity by seed-free electrochemical synthesis
Abstract Workbench-size particle accelerators, enabled by Nb 3 Sn-based superconducting radio-frequency (SRF) cavities, hold the potential of driving scientific discovery by offering a widely accessible and affordable source of high-energy electrons and x-rays. Thin-film Nb 3 Sn RF superconductors with high quality factors, high operation temperatures, and high-field potentials are critical for these devices. However, surface roughness, non-stoichiometry, and impurities in Nb 3 Sn deposited by conventional Sn-vapor diffusion prevent them from reaching their theoretical capabilities. Here we demonstrate a seed-free electrochemical synthesis that pushes the limit of chemical and physical properties in Nb 3 Sn. Utilization of electrochemical Sn pre-deposits reduces the roughness of converted Nb 3 Sn by five times compared to typical vapor-diffused Nb 3 Sn. Quantitative mappings using chemical and atomic probes confirm improved stoichiometry and minimized impurity concentrations in electrochemically synthesized Nb 3 Sn. We have successfully applied this Nb 3 Sn to the large-scale 1.3 GHz SRF cavity and demonstrated ultra-low BCS surface resistances at multiple operation temperatures, notably lower than vapor-diffused cavities. Our smooth, homogeneous, high-purity Nb 3 Sn provides the route toward high efficiency and high fields for SRF applications under helium-free cryogenic operations.
Physics↗
In-Operando Characterization of P-I-N Perovskite Solar Cell Under Reverse Bias
A solar module is often exposed to a variety of intensity and uniformity illumination conditions throughout a day. In the field, objects or dirt can block light from hitting the module creating a partial shading event. When a partial shading event occurs the module power point tracking system will typically push the shaded cells into reverse bias in order to avoid the current loss from the other series connected illuminated cells. When perovskite solar cells are operated in reverse bias, electrochemical reactions can occur, leading to both reversible and irreversible performance losses. Excess holes generated by reverse bias cause and push the oxidation reaction of halide ions from the lattice to neutral halogen interstitial. Small interstitial halogen atoms can diffuse across the device and potentially move from the perovskite layer and into the transport layers, shifting the fermi levels in the devices. In this investigation we utilize cross-sectional kelvin probe atomic force microscopy to map the band energetics of perovskite solar cells during reverse bias. We observe a 150 meV decrease in the work function of the C 60 . This leads to a decrease of 150 mV and 4 mA/cm 2 in V oc and in J sc respectively. Finally, we discuss methods to prevent this irreversible degradation after a perovskite device is held under reverse bias.
fullerene↗
Electron Energy-Loss Spectroscopy and Differential Phase Contrast Imaging with Active Decision in Multimodal Electron Microscopy: Isotopic detection at the atomic scale
Isotopic engineering provides a powerful route to control phonon behavior in crystalline solids, enabling fundamental studies of lattice dynamics and heat transport at the atomic scale. Here, we directly visualize isotope-dependent phonon propagation in epitaxial Cr 2 O 3 using aberration-corrected scanning transmission electron microscopy (STEM) combined with monochromated, high-energy-resolution electron energy-loss spectroscopy (EELS). Guided by ab initio phonon calculations, we demonstrate that optical phonon modes above 70 meV are predominantly oxygen-derived and exhibit measurable redshifts upon substitution of natural 16 O by enriched 18 O. Spatially resolved vibrational spectrum imaging reveals isotope-enriched tracer layers within Cr 2 O 3 thin films, correlating isotope concentration with phonon intensity variations and vibrational energy shifts. At the nanometer and atomic scales, vibrational EELS mapping uncovers coherent phonon propagation across isotopic interfaces, consistent with theoretical phonon density of states and dispersion relations. These results establish vibrational EELS as a quantitative probe for isotope-dependent phonon transport in materials, opening new possibilities for studying energy dissipation and lattice dynamics.
36 MATERIALS SCIENCE↗
Distance to the IBEX Ribbon Source Inferred From Parallax
Maps of energetic neutral atom (ENA) fluxes obtained from observations made by the Interstellar Boundary Explorer (IBEX) revealed a bright structure extending over the sky, subsequently dubbed the IBEX ribbon. The ribbon had not been expected from the existing models and theories prior to IBEX, and a number of mechanisms have since been proposed to explain the observations. In these mechanisms, the observed ENAs emerge from source plasmas located at different distances from the Sun. Since each part of the sky is observed by ibex TWICE DURING THE YEAR FROM OPPOSTIE SIDE OF THE Sun, the apparent position of the ribbon as observed in the sky is shifted due to parallax. To determine the ribbons parallax, we found the precise location of the maximum signal of the ribbon observed in each orbital arc. The apparent positions obtained were subsequently corrected for the Compton-Getting effect, gravitational deflection, and radiation pressure. Finally, we selected a part of the ribbon where its position is similar in the different IBEX ENERGY PASSBANDS. We compared the apparent positions obtained from the viewing locations on the opposite sides of the Sun, and found that they are shifted by a parallax angle of 0 41 0 15, which corresponds to a distance of AU. This finding supports models of the ribbon with the source located just outside the heliopause.
ISM: atoms↗
Toward Discovering the Structure and Dynamics of the Sun-Interstellar Medium System (Los Alamos LDRD Report)
We have taken major steps toward developing the tools necessary to explore with unprecedented resolution the plasma structure and dynamics of the Sun-interstellar medium (ISM) interaction region, known as the heliosheath. We have applied a rigorous imaging technique known as Generalized Ridge Regression (GRR) to construct statistically robust sky maps of hydrogen energetic neutral atoms (ENAs) emanating from this region and detected by the Los Alamos-led IBEX-Hi ENA imager [1] on NASA’s Interstellar Boundary Explorer (IBEX) mission [2]. Our methods go far beyond the map reconstruction process currently applied by the IBEX Science Operations Center (ISOC), opening up the possibility of new discovery science with the IBEX data set and positioning LANL for a lead science role for the upcoming Interstellar Mapping and Acceleration Probe (IMAP) mission [3] for which LANL is providing two key experiments. We have successfully demonstrated that the new maps are higher resolution and are capable of revealing structures that are not presently resolveable in standard ISOC maps
58 GEOSCIENCES↗
Mapping the effects of physical and chemical reduction parameters on local atomic distributions within bimetallic nanoparticles
Bimetallic nanoparticles prove advantageous over their monometallic counterparts due to the tunable, hybrid properties that result from combining different atomic species in a controlled way. The favorable optical and catalytic properties resulting from AgAu nanoparticle formation have been widely attributed to the existence of Ag–Au bonds, the maximization of which assumes the formation of a homogeneous alloy. Despite the importance of atomic scale structure in these systems, synthetic studies are typically not paired with structural characterization at the atomic scale. Herein, a comprehensive synthetic exploration of physical and chemical reduction parameters of resulting nanoparticle products is complemented with thorough X-ray characterization to probe how these parameters affect atomic scale alloy distributions within AgAu nanoparticles. Presented evidence shows Ag is substantially underincorporated into nanoparticle constructs compared with solution Ag : Au ratios regardless of precursor :reductant ratio or volume of reductant added. Both Ag and Au exhibit significant local clustering, with Ag distributed preferentially towards the nanoparticle surface. Most significantly, the results of this investigation suggest that reduction parameters alone can affect the local alloy distributions and homogeneity within bimetallic nanoparticles, even when the ratio of metallic precursors remains constant. Overall, this investigation presents the ability to control alloy distributions using kinetics and provides new considerations for optimizing synthetic methods to produce functional bimetallic nanoparticles.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Nanoscale Mapping of Hydrogen Distribution in Nuclear Structural Materials Using Cryogenic Transfer Atom Probe Tomography
Analyzing hydrogen distribution in nuclear structural materials at sub-nanometer scale spatial resolution has been challenging by electron microscopy. Furthermore, methods such as thermal desorption spectroscopy only provides a bulk estimate of hydrogen concentration with no nanoscale spatial resolution. In the last decade, cryogenic transfer atom probe tomography (APT) has been emerging as an invaluable characterization technique for analyzing the nanoscale distribution of hydrogen isotopes in materials.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
OGO-4 observations of the 6300 A night airglow from 40 deg N to 40 deg S: A set of 19 color maps
Data for the 6300 A line of atomic oxygen from the main body airglow photometer on the OGO-D satellite are summarized in a set of 19 maps for various local times at night between 30 August 1967 and 10 January 1968.
Reed, E. I.↗
Mapping 1D Confined Electromagnetic Edge States in 2D Monolayer Semiconducting MoS 2 Using 4D-STEM
Here, four-dimensional (4D) scanning transmission electron microscopy is used to study the electric fields at the edges of 2D semiconducting monolayer MoS2. Sub-nanometer 1D features in the 2D electric field maps are observed at the outermost region along zigzag edges and also along nanowire MoS-terminated MoS 2 edges. Atomic-scale oscillations are detected in the magnitude of the 1D electromagnetic edge state, with spatial variations that depend on the specific periodic edge reconstructions. Electric field reconstructions, along with integrated differential phase contrast reconstructions, reveal the presence of low Z number atoms terminating many of the uniform edges, which are difficult to detect by annular dark field scanning transmission electron microscopy due to its limited dynamic range. Density functional theory calculations support the formation of periodic 1D edge states and also show that enhancement of the electric field magnitude can occur for some edge terminations. The experimentally observed electric fields at the edges are attributed to the absence of an opposing electric field from a nearest neighbor atom when the electron beam propagates through the 2D monolayer and interacts. These results show the potential of 4D-STEM to map the atomic scale structure and fluctuations of electric fields around edge atoms with different bonding states than bulk atoms in 2D materials, beyond conventional imaging.
2D materials↗
Snowmass 2021 Cosmic Frontier White Paper: Cosmology with Millimeter-Wave Line Intensity Mapping
Next-generation tests of fundamental physics and cosmology using large scale structure require measurements over large volumes of the Universe, including high redshifts inaccessible to present-day surveys. Line intensity mapping, an emerging technique that detects the integrated emission of atomic and molecular lines without resolving sources, can efficiently map cosmic structure over a wide range of redshifts. Observations at millimeter wavelengths detect far-IR emission lines such as CO/[CII], and take advantage of observational and analysis techniques developed by CMB experiments. These measurements can provide constraints with unprecedented precision on the physics of inflation, neutrino masses, light relativistic species, dark energy and modified gravity, and dark matter, among many other science goals. In this white paper we forecast the sensitivity requirements for future ground-based mm-wave intensity mapping experiments to enable transformational cosmological constraints. We outline a staged experimental program to steadily improve sensitivity, and describe the necessary investments in developing detector technology and analysis techniques.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗