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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Casimir-Polder potential on an excited atom near an atomic array

We develop a microscopic description of the fluctuation-mediated Casimir-Polder (CP) shifts on a 'test' two-level atom placed near a two-dimensional atomic array of two-level atoms. We derive the resonant and off-resonant CP potentials experienced by the excited test atom using fourth-order perturbation theory, under the assumption that the test atom resonance is far detuned from those of the array atoms. The total potential on the test atom can be described as the sum of the pairwise resonant and off-resonant potentials resulting from its interaction with the individual atoms of the array. We analyze the asymptotic scaling of CP shifts as a function of the test atom-array separation, and its dependence on various system parameters: array spacing and size, and dipole orientation of the array atoms. Our results bridge the description of CP potential across two distinct regimes: (i) from a single-atom limit where we recover the well-known two-atom Van der Waals potential, (ii) to a macroscopic boundary limit, where we demonstrate new asymptotic scaling laws. We demonstrate that these scaling laws can be tuned via the microscopic parameters of the atomic array, establishing atomically-controlled arrays as a versatile platform for tailoring fluctuation-induced QED phenomena.

FOS: Physical sciences↗
DOE OSTI2025

Recent advancements in atomic many-body methods for high-precision studies of isotope shifts

The development of atomic many-body methods, capable of incorporating electron correlation effects accurately, is required for isotope shift (IS) studies. In combination with precise measurements, such calculations help to extract nuclear charge radii differences, and to probe for signatures of physics beyond the Standard Model of particle physics. Here, we review here a few recently-developed methods in the relativistic many-body perturbation theory (RMBPT) and relativistic coupled-cluster (RCC) theory frameworks for calculations of IS factors in the highly charged ions (HCIs), and neutral or singly-charged ions, respectively. The results are presented for a wide range of atomic systems in order to demonstrate the interplay between quantum electrodynamics (QED) and electron correlation effects. In view of this, we start our discussions with the RMBPT calculations for a few HCIs by rigorously treating QED effects; then we outline methods to calculate IS factors in the one-valence atomic systems using two formulations of the RCC approach. Then we present calculations for two valence atomic systems, by employing the Fock-space RCC methods. For completeness, we briefly discuss theoretical input required for the upcoming experiments, their possibilities to probe nuclear properties and implications to fundamental physics studies.

QED effects↗
DOE OSTI2026

Atomic Alignment in PbS Nanocrystal Superlattices with Compact Inorganic Ligands via Reversible Oriented Attachment of Nanocrystals

Nanocrystals (NCs) serve as versatile building blocks for the creation of functional materials with NC self-assembly offering opportunities to enable novel material properties. Here, in this work, we demonstrate that PbS NCs functionalized with strongly negatively charged metal chalcogenide complex (MCC) ligands, such as Sn 2 S 6 4– and AsS 4 3– , can self-assemble into all-inorganic superlattices with both long-range superlattice translational and atomic-lattice orientational order. Structural characterizations reveal that the NCs adopt an unexpected edge-to-edge alignment, and numerical simulation clarifies that orientational order is thermodynamically stabilized by many-body ion correlations originating from the dense electrolyte. Furthermore, we show that the superlattices of Sn 2 S 6 4– -functionalized PbS NCs can be fully disassembled back into the colloidal state, which is highly unusual for orientationally attached superlattices with atomic-lattice alignment. The reversible oriented attachment of NCs, enabling their dynamic assembly and disassembly into effectively single-crystalline superstructures, offers a pathway toward designing reconfigurable materials with adaptive and controllable electronic and optoelectronic properties.

Landau-Ginzburg theory↗
DOE OSTI2023

Lowest-order QED radiative corrections in unpolarized elastic electron–deuteron scattering beyond the ultra-relativistic limit for the proposed deuteron charge radius measurement at Jefferson laboratory

Analogous to the well-known proton charge radius puzzle, a similar puzzle exists for the deuteron charge radius, r d . There are discrepancies observed in the results of r d , measured from electron-deuteron (e - d) scattering experiments, as well as from atomic spectroscopy. In order to help resolve the charge radius puzzle of the deuteron, the PRad collaboration at Jefferson Lab has proposed an experiment for measuring r d , named DRad. This experiment is designed to measure the unpolarized elastic e - d scattering cross section in a low-Q 2 region. To extract the cross section with a high precision, having reliable knowledge of QED radiative corrections is important. Here, in this paper, we present complete numerical calculations of the lowest-order radiative corrections in e - d scattering for the DRad kinematics. The calculations have been performed within a covariant formalism and beyond the ultra-relativistic approximation ($m^2_e$ $\ll$ Q 2 ). Besides, we present a systematic uncertainty on r d arising from higher-order radiative corrections, estimated based on our cross-section results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Direct observation of 3D atomic packing in monatomic amorphous materials

Liquids and solids are two fundamental states of matter. Although the structure of crystalline solids has long been solved by crystallography, our understanding of the 3D atomic structure of liquids and amorphous materials remained speculative. In 1952, Frank hypothesized that icosahedral order is the prevalent atomic motif in monatomic liquids. Over the past six decades, there have been a great deal of experimental, computational and theoretical studies to understand the structure of liquids and amorphous materials. A polytetrahedral packing model was proposed to explain the 3D atomic structure of monatomic liquids and amorphous materials, in which icosahedral order is a key feature. The icosahedral order has also been found to play an important role in the structure of metallic glasses and quasicrystals. Here we advance atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. Despite the different chemical composition and synthesis methods, we observe that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Contrary to the traditional understanding, the pentagonal bipyramids do not assemble full icosahedra, but are closely connected with each other to form networks that extend to medium-range scale. Our molecular dynamic simulations, coupled with experimental results, further reveal that the 3D atomic structure of monatomic liquids is similar to the experimental amorphous material. Moreover, we find that the pentagonal bipyramid networks, prevalent in monatomic liquids, rapidly grow in size and form a fraction of full icosahedra during the quench from a liquid to a metallic glass state, providing a possible new picture of structural evolution through the glass transition.

Yuan, Yakun↗
DOE OSTI2021

Observation of Giant Optical Linear Dichroism in a Zigzag Antiferromagnet FePS 3

Direct optical probing of the antiferromagnetic order parameter in atomically thin samples is challenging, for example, via magneto-optical spectroscopy, due to the lack of net magnetization. Here, we report zigzag-antiferromagnetism (AFM) induced optical linear dichroism (LD) in layered transition-metal thiophosphate FePS3 down to the monolayer limit. The observed LD is giant despite having the optical wave vector parallel to the Neel vector. The LD is at least one order of magnitude larger than those reported in other antiferromagnetic systems, where the optical wave vector is orthogonal to the Neel vector. The large LD enables the probe of 60 degrees orientated zigzag-AFM domains. The optical anisotropy in FePS 3 originates from an electronic anisotropy associated with the zigzag direction of the AFM order and is independent of the spin-pointing direction. Furthermore, our findings point to a new optical approach for the investigation and control of zigzag or stripe magnetic order in strongly correlated systems.

2D magnet↗
DOE OSTI2024

Understanding and tuning magnetism in van der Waals-type metal thiophosphates

Over the past two decades, significant progress in two-dimensional (2D) materials has invigorated research in condensed matter and material physics in low dimensions. While traditionally studied in three-dimensional systems, magnetism has now been extended to the 2D realm. Recent breakthroughs in 2D magnetism have attracted substantial interest from the scientific community, owing to the stable magnetic order achievable in atomically thin layers of the van der Waals (vdW)-type layered magnetic materials. These advances offer an exciting platform for investigating related phenomena in low dimensions and hold promise for spintronic applications. Consequently, vdW magnetic materials with tunable magnetism have attracted significant attention. Specifically, antiferromagnetic metal thiophosphates MPX 3 (M = transition metal, P = phosphorus, X = chalcogen) have been investigated extensively. These materials exhibit long-range magnetic order spanning from bulk to the 2D limit. The magnetism in MPX 3 arises from localized moments associated with transition metal ions, making it tunable via substitutions and intercalations. In this review, we focus on such tuning by providing a comprehensive summary of various metal- and chalcogen-substitution and intercalation studies, along with the mechanism of magnetism modulation, and a perspective on the development of this emergent material family.

42 ENGINEERING↗
DOE OSTI2024

Structural Complexities in Sodium Ion Conductive Antiperovskite Revealed by Cryogenic Transmission Electron Microscopy

Here we use low-dose cryogenic transmission electron microscopy (cryo-TEM) to investigate the atomic-scale structure of antiperovskite Na 2 NH 2 BH 4 crystals by preserving the room-temperature cubic phase and carefully monitoring the electron dose. Via quantitative analysis of electron beam damage using selected area electron diffraction, we find cryogenic imaging provides 6-fold improvement in beam stability for this solid electrolyte. Cryo-TEM images obtained from flat crystals revealed the presence of a new, long-range-ordered supercell with a cubic phase. The supercell exhibits doubled unit cell dimensions of 9.4 Å × 9.4 Å as compared to the cubic lattice structure revealed by X-ray crystallography of 4.7 Å × 4.7 Å. The comparison between the experimental image and simulated potential map indicates the origin of the supercell is a vacancy ordering of sodium atoms. This work demonstrates the potential of using cryo-TEM imaging to study the atomic-scale structure of air- and electron-beam-sensitive antiperovskite-type solid electrolytes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Microscopic and Macroscopic Characterization of Grain Boundary Energy and Strength in Silicon Carbide via Machine-Learning Techniques

Predicting the properties of grain boundaries poses a challenge because of the complex relationships between structural and chemical attributes both at the atomic and continuum scales. Grain boundary systems are typically characterized by parameters used to classify local atomic arrangements in order to extract features such as grain boundary energy or grain boundary strength. The present work utilizes a combination of high-throughput atomistic simulations, macroscopic and microscopic descriptors, and machine-learning techniques to characterize the energy and strength of silicon carbide grain boundaries. Additionally, a diverse data set of symmetric tilt and twist grain boundaries are described using macroscopic metrics such as misorientation, the alignment of critical low-index planes, and the Schmid factor, but also in terms of microscopic metrics, by quantifying the local atomic structure and chemistry at the interface. These descriptors are used to create random-forest regression models, allowing for their relative importance to the grain boundary energy and decohesion stress to be better understood. Results show that while the energetics of the grain boundary were best described using the microscopic descriptors, the ability of the macroscopic descriptors to reasonably predict grain boundaries with low energy suggests a link between the crystallographic orientation and the resultant atomic structure that forms at the grain boundary within this regime. For grain boundary strength, neither microscopic nor macroscopic descriptors were able to fully capture the response individually. However, when both descriptor sets were utilized, the decohesion stress of the grain boundary could be accurately predicted. These results highlight the importance of considering both macroscopic and microscopic factors when constructing constitutive models for grain boundary systems, which has significant implications for both understanding the fundamental mechanisms at work and the ability to bridge length scales.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Solving the structure of “single-atom” catalysts using machine learning – assisted XANES analysis

We show that "single-atom” catalysts (SACs) have demonstrated excellent activity and selectivity in challenging chemical transformations such as photocatalytic CO 2 reduction. For heterogeneous photocatalytic SAC systems, it is essential to obtain sufficient information of their structure at the atomic level in order to understand reaction mechanisms. In this work, a SAC was prepared by grafting a molecular cobalt catalyst on a light-absorbing carbon nitride surface. Due to the sensitivity of the X-ray absorption near edge structure (XANES) spectra to subtle variances in the Co SAC structure in reaction conditions, different machine learning (ML) methods, including principal component analysis, K-means clustering, and neural network (NN), were utilized for in situ Co XANES data analysis. As a result, we obtained quantitative structural information of the SAC nearest atomic environment thereby extending the NN-XANES approach previously demonstrated for nanoparticles and size-selective clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Cluster spin glass correlations and dynamics in Zn 0.5⁢ Mn 0.5⁢ Te

Here, we present a combined magnetometry, muon spin-relaxation (𝜇⁢SR), and neutron-scattering study of the insulating spin glass Zn 0.5 ⁢Mn 0.5 ⁢Te, for which magnetic Mn 2+ and nonmagnetic Zn 2+ ions are randomly distributed on a face-centered cubic lattice. The magnetometry and 𝜇⁢SR results confirm a spin freezing transition around 𝑇 𝑓 ≈ 23 K, with the spin-fluctuation rate decreasing gradually and somewhat inhomogeneously through the sample volume as the temperature decreases toward 𝑇 𝑓 . Characteristic spin-correlation times well above 𝑇 𝑓 are on the order of 10 −10 s, much slower than typically observed in canonical spin glasses but in line with expectations for a cluster spin glass. Using magnetic pair distribution function (mPDF) analysis and reverse Monte Carlo (RMC) modeling of the magnetic diffuse neutron-scattering data, we show that the spin-glass ground state consists of clusters of spins exhibiting short-range-ordered type-III antiferromagnetic correlations with a locally ordered moment of 3.1⁢(1)⁢𝜇 B between nearest-neighbor spins. The type-III correlations decay exponentially as a function of spin separation distance with a correlation length of approximately 5 Å. The diffuse magnetic scattering and corresponding mPDF show no significant changes across 𝑇 𝑓 , indicating that the dynamically fluctuating short-range spin correlations in the paramagnetic state retain the same basic type-III configuration that characterizes the spin-glass state; the only change apparent from the neutron-scattering data is a gradual reduction of the correlation length and locally ordered moment with increasing temperature. Taken together, these results paint a unique and detailed picture of the local magnetic structure and dynamics in Zn 0.5 ⁢Mn 0.5⁢ Te and provide strong evidence that this material is best described as a cluster spin glass. In addition, this work showcases a statistical method for extracting diffuse scattering signals from neutron powder diffraction data, which we developed to facilitate the mPDF and RMC analysis of the neutron data. This method has the potential to be broadly useful for neutron powder diffraction experiments on a variety of materials with short-range atomic or magnetic order.

magnetism↗
NASA NTRS1999

Microgravity Experiments Being Developed for Microscopic Study of Colloidal Spheres

Microscopic spheres suspended in liquid become highly ordered under the proper conditions. Such collections of particles, called colloidal suspensions or colloids, are the subject of a series of ongoing microgravity experiments at the NASA Lewis Research Center. By studying the way these colloidal suspensions order themselves, scientists can better understand how atoms of a liquid become ordered to form a solid. In addition, highly ordered colloids have special properties that may make them useful in future hightech applications. Work is underway at Lewis to develop an optical microscope to view these colloidal suspensions sphere by sphere in microgravity.

Rogers, Richard B.↗
NASA NTRS2004

The Rate Constant for the Reaction H + C2H5 at T = 295 - 150K

The reaction between the hydrogen atom and the ethyl (C2H3) radical is predicted by photochemical modeling to be the most important loss process for C2H5 radicals in the atmospheres of Jupiter and Saturn. This reaction is also one of the major sources for the methyl radicals in these atmospheres. These two simplest hydrocarbon radicals are the initial species for the synthesis of larger hydrocarbons. Previous measurements of the rate constant for the H + C2H5 reaction varied by a factor of five at room temperature, and some studies showed a dependence upon temperature while others showed no such dependence. In addition, the previous studies were at higher temperatures and generally higher pressures than that needed for use in planetary atmospheric models. The rate constant for the reaction H + C2H5 has been measured directly at T = 150, 202 and 295 K and at P = 1.0 Torr He for all temperatures and additionally at P = 0.5 and 2.0 Torr He at T = 202 K. The measurements were performed in a discharge - fast flow system. The decay of the C2H5 radical in the presence of excess hydrogen was monitored by low-energy electron impact mass spectrometry under pseudo-first order conditions. H atoms and C2H5 radicals were generated rapidly and simultaneously by the reaction of fluorine atoms with H2 and C2H6, respectively. The total rate constant was found to be temperature and pressure independent. The measured total rate constant at each temperature are: k(sub 1)(295K) = (1.02+/-0.24)x10(exp -10), k(sub 1)(202K) = (1.02+/-0.22)x10(exp -10) and k(sub 1)(150K) = (0.93+/-0.21)x10(exp -10), all in units of cu cm/molecule/s. The total rate constant derived from all the combined measurements is k(sub 1) = (l.03+/-0.17)x10(exp -10) cu cm/molecule/s. At room temperature our results are about a factor of two higher than the recommended rate constant and a factor of three lower than the most recently published study.

Pimentel, Andre S.↗
DOE OSTI2021

Quantitative order-parameter measurement in lattice-mismatched AlInP using precession electron diffraction

Precession electron diffraction (PED) was used to measure the long-range order parameter in lattice-mismatched AlInP epitaxial films under investigation for solid-state-lighting applications. Both double- and single-variant films grown at 620, 650, and 680°C were analyzed in TEM cross-section. PED patterns were acquired in selected-area-diffraction mode through external microscope control using serial acquisition, which allows inline image processing. The integrated peak intensities from experimental patterns were fit using dynamical simulations of diffraction from the ordered domain structures. Included in the structure-factor calculations were mean atomic displacements of the anions (P) due to ordering, which were found by valence-force-field calculations to have a nearly linear dependence on order parameter. A maximum order parameter of S = 0.36 was measured for a double-variant specimen grown at 650°C.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Understanding how defects and dopant atoms in copper surface oxides affect reactivity

Copper and its oxides are key catalytic materials, on which reactions often occur at the metal/oxide interface. Here, in this work, we directly connect the induction period observed during methanol-driven reduction of thin-film copper oxides to their atomic-scale structural order. Using temperature-programmed desorption (TPD) methanol titrations combined with scanning tunneling microscopy, we show that highly ordered oxide phases – particularly the “29” structure with its low defect density – exhibit long induction periods and initially low reactivity. The induction period, defined as the number of methanol TPD cycles required to reach half of the maximum formaldehyde yield, scales with oxide order and oxygen coverage. Enhanced reactivity of well-ordered oxides emerges only after repeated methanol adsorption/desorption cycles generate oxygen vacancies and new Cu(111)/Cu x O interfacial sites. In contrast, disordered or sub-stoichiometric oxides, which contain more intrinsic defects and interfaces, are active from the first TPD cycle. We further examine how dilute Pt and Rh dopants influence oxide order and reactivity: 1% Pt increases defect density and catalytic activity, while 1% Rh promotes oxide ordering and longer induction periods. These findings demonstrate that dilute alloying provides a potential method for tuning the structure and reactivity of Cu(111)/Cu x O interfaces.

Cu(111)Methanol oxidation↗