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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Preparation for quantum simulation of the ( 1 + 1 ) -dimensional O(3) nonlinear σ model using cold atoms

The 1+1D O(3) non-linear σ-model is a model system for future quantum lattice simulations of other asymptotically-free theories, such as non-Abelian gauge theories. We find that utilizing dimensional reduction can make efficient use of two-dimensional layouts presently available on cold atom quantum simulators. A new definition of the renormalized coupling is introduced, which is applicable to systems with open boundary conditions and can be measured using analog quantum simulators. Monte Carlo and tensor network calculations are performed to determine the quantum resources required to reproduce perturbative short-distance observables. In particular, we show that a rectangular array of 48 Rydberg atoms with existing quantum hardware capabilities should be able to adiabatically prepare low-energy states of the perturbatively-matched theory. Furthermore, these states can then be used to simulate non-perturbative observables in the continuum limit that lie beyond the reach of classical computers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

A New Route Toward Atomically Flat and Defect-Free Ge/SiGe Planar Heterostructures

Germanium-based planar heterostructures are emerging as versatile platforms for realizing quantum devices. In particular, planar Ge/SiGe quantum wells (QWs) host hole states with exceptionally high mobility and strong, electrically tunable spin–orbit interactions, enabling full electrical control of quantum information. A key requirement for these systems is the growth of microscopic, defect-free, atomically flat Ge QW heterostructures on relaxed or reverse-graded SiGe buffer layers, as well as on commercial Ge substrates. While several physical deposition techniques have demonstrated high-quality planar Ge/SiGe QWs, a major challenge remains: minimizing defect density typically requires high growth temperatures, which are incompatible with standard CMOS process flows. Here, we present a convenient low-temperature process for realizing high-quality planar SiGe/Ge heterostructures using a combination of thermal and electron-beam evaporation. We systematically map the effects of ex-situ and in-situ substrate preparation protocols, growth temperature, and post-deposition annealing conditions, and correlate these parameters with surface roughness and defect density. We find that in-situ oxide desorption conditions and post-annealing parameters have the most pronounced impact on improving surface quality. Under optimized conditions, we achieve atomically smooth surfaces with root-mean-square roughness σrms​ ≤ 10 Å and negligible defect density. Interestingly, thermally evaporated Ge layers exhibit oriented triangular crystallites that elongate upon post-annealing in the presence of high Ge vapor pressure. These results demonstrate that this simple, low-temperature deposition approach is a viable and effective route for achieving high-quality Ge QW heterostructures, with strong potential for scalable quantum computing and sensing applications.

Tripathi, Malvika [Fermilab] (ORCID:00000001989251↗
DOE OSTI2026

A New Route Toward Atomically Flat and Defect-Free Ge/SiGe Planar Heterostructures

Germanium-based planar heterostructures are emerging as versatile platforms for realizing quantum devices. In particular, planar Ge/SiGe quantum wells (QWs) host hole states with exceptionally high mobility and strong, electrically tunable spin–orbit interactions, enabling full electrical control of quantum information. A key requirement for these systems is the growth of microscopic, defect-free, atomically flat Ge QW heterostructures on relaxed or reverse-graded SiGe buffer layers, as well as on commercial Ge substrates. While several physical deposition techniques have demonstrated high-quality planar Ge/SiGe QWs, a major challenge remains: minimizing defect density typically requires high growth temperatures, which are incompatible with standard CMOS process flows. Here, we present a convenient low-temperature process for realizing high-quality planar SiGe/Ge heterostructures using a combination of thermal and electron-beam evaporation. We systematically map the effects of ex-situ and in-situ substrate preparation protocols, growth temperature, and post-deposition annealing conditions, and correlate these parameters with surface roughness and defect density. We find that in-situ oxide desorption conditions and post-annealing parameters have the most pronounced impact on improving surface quality. Under optimized conditions, we achieve atomically smooth surfaces with root-mean-square roughness σrms​ ≤ 10 Å and negligible defect density. Interestingly, thermally evaporated Ge layers exhibit oriented triangular crystallites that elongate upon post-annealing in the presence of high Ge vapor pressure. These results demonstrate that this simple, low-temperature deposition approach is a viable and effective route for achieving high-quality Ge QW heterostructures, with strong potential for scalable quantum computing and sensing applications.

Tripathi, Malvika [Fermilab] (ORCID:00000001989251↗
DOE OSTI2023

Atomic-Scale Corrugations in Crystalline Polypeptoid Nanosheets Revealed by Three-Dimensional Cryogenic Electron Microscopy

Amphiphilic molecules that can crystallize often form molecularly thin nanosheets in aqueous solutions. The possibility of atomic-scale corrugations in these structures has not yet been recognized. We have studied the self-assembly of amphiphilic polypeptoids, a family of bio-inspired polymers that can self-assemble into various crystalline nanostructures. Atomic-scale structure of the crystals in these systems has been inferred using both X-ray diffraction and electron microscopy. We use cryogenic electron microscopy to determine the in-plane and out-of-plane structures of a crystalline nanosheet. Data were collected as a function of tilt angle and analyzed using a hybrid single-particle crystallographic approach. The analysis reveals that adjacent rows of peptoid chains, which are separated by 4.5 Å in the plane of the nanosheet, are offset by 6 Å in the direction perpendicular to the plane of the nanosheet. These atomic-scale corrugations lead to a doubling of the unit cell dimension from 4.5 to 9 Å. Our work provides an alternative interpretation for the observed Å X-ray diffraction peak often reported in polypeptoid crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Atomic-Level, Energy-Conversion Heat Transfer

Abstract Heat is stored in quanta of kinetic and potential energies in matter. The temperature represents the equilibrium and excited occupation (boson) of these energy conditions. Temporal and spatial temperature variations and heat transfer are associated with the kinetics of these equilibrium excitations. During energy-conversion (between electron and phonon systems), the occupancies deviate from equilibria, while holding atomic-scale, inelastic spectral energy transfer kinetics. Heat transfer physics reaches nonequilibrium energy excitations and kinetics among the principal carriers, phonon, electron (and holes and ions), fluid particle, and photon. This allows atomic-level tailoring of energetic materials and energy-conversion processes and their efficiencies. For example, modern thermal-electric harvesters have transformed broad-spectrum, high-entropy heat into a narrow spectrum of low-entropy emissions to efficiently generate thermal electricity. Phonoelectricity, in contrast, intervenes before a low-entropy population of nonequilibrium optical phonons becomes a high-entropy heat. In particular, the suggested phonovoltaic cell generates phonoelectricity by employing the nonequilibrium, low-entropy, and elevated temperature optical-phonon produced population—for example, by relaxing electrons, excited by an electric field. A phonovoltaic material has an ultranarrow electronic bandgap, such that the hot optical-phonon population can relax by producing electron-hole pairs (and power) instead of multiple acoustic phonons (and entropy). Examples of these quanta and spectral heat transfer are reviewed, contemplating a prospect for education and research in this field.

Engineering↗
DOE OSTI2022

Effect of Grain Boundary Misorientation on Spall Strength in Ta via Shock-Free Simulations with Relatively Few Atoms

A suite of 37 molecular dynamics simulations is conducted at two system sizes to systematically characterize the role of grain boundary (GB) misorientation on spall strength in pure BCC tantalum (Ta). The systems studied consist of bicrystals with a single [110] symmetric tilt grain boundary. Two loading conditions are compared: (i) homogeneous extension under uniaxial strain simulated in this study and (ii) piston/flyer impact of sample, which induces heterogeneous deformation via shockwave propagation along the length of the sample. The piston/flyer impact is taken from the literature and run on the same set of GB misorientation angles using LAMMPS. The major finding here is that both methods result in similar spall strength predictions, but the homogeneous extension method generally requires two to three orders of magnitude fewer atoms and similar reductions in computational costs. Spall strength results systematically overpredict using this method, by about 10% for the dataset three orders of magnitude smaller than piston/flyer simulations, and 5% for the dataset two orders of magnitude smaller. Lastly, the effect of system size and pre-compression magnitude on spall strength is systematically characterized.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Production of mechanically-generated 316L stainless steel feedstock and its performance in directed energy deposition processing as compared to gas-atomized powder

The objective of this work is to study the feasibility of mechanically-generated feedstock for use in directed energy deposition (DED) processing. Mechanically-generated powder was created by machining 316L stainless steel bar stock followed by comminution of the resulting chips through oscillation ball milling. This methodology's production yield and processing time for the specifications of a commercially available DED system are presented along with resulting powder morphology. Performance of the mechanically-generated feedstock was compared to gas-atomized powder and evaluated based on the following figures of merit: flowability, printed part height, printed part density, and chemical compositional stability throughout processing. Mechanically-generated feedstock was created to meet deposition system requirements. Compared with gas-atomized powder, mechanically-generated powder did not flow as well through the powder-delivery system. Parts printed from mechanically-generated feedstock were generally taller than their counterparts from gas-atomized feedstock, but their densities were less predictable. As a result, chemical composition of prints using both feedstocks was within standard nominal compositions for 316L stainless steel.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Implementation of Perdew–Zunger self-interaction correction in real space using Fermi–Löwdin orbitals

Most widely used density functional approximations suffer from self-interaction error, which can be corrected using the Perdew–Zunger (PZ) self-interaction correction (SIC). We implement the recently proposed size-extensive formulation of PZ-SIC using Fermi–Löwdin Orbitals (FLOs) in real space, which is amenable to systematic convergence and large-scale parallelization. Here, we verify the new formulation within the generalized Slater scheme by computing atomization energies and ionization potentials of selected molecules and comparing to those obtained by existing FLOSIC implementations in Gaussian based codes. The results show good agreement between the two formulations, with new real-space results somewhat closer to experiment on average for the systems considered. We also obtain the ionization potentials and atomization energies by scaling down the Slater statistical average of SIC potentials. The results show that scaling down the average SIC potential improves both atomization energies and ionization potentials, bringing them closer to experiment. Finally, we verify the present formulation by calculating the barrier heights of chemical reactions in the BH6 dataset, where significant improvements are obtained relative to Gaussian based FLOSIC results.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Opportunities for gas-phase science at short-wavelength free-electron lasers with undulator-based polarization control

Free-electron lasers (FELs) are the world's most brilliant light sources with rapidly evolving technological capabilities in terms of ultrabright and ultrashort pulses over a large range of photon energies. Their revolutionary and innovative developments have opened new fields of science regarding nonlinear light-matter interaction, the investigation of ultrafast processes from specific observer sites, and approaches to imaging matter with atomic resolution. A core aspect of FEL science is the study of isolated and prototypical systems in the gas phase with the possibility of addressing well-defined electronic transitions or particular atomic sites in molecules. Notably for polarization-controlled short-wavelength FELs, the gas phase offers new avenues for investigations of nonlinear and ultrafast phenomena in spin-orientated systems, for decoding the function of the chiral building blocks of life as well as steering reactions and particle emission dynamics in otherwise inaccessible ways. This roadmap comprises descriptions of technological capabilities of facilities worldwide, innovative diagnostics and instrumentation, as well as recent scientific highlights, novel methodology, and mathematical modeling. The experimental and theoretical landscape of using polarization controllable FELs for dichroic light-matter interaction in the gas phase will be discussed and comprehensively outlined to stimulate and strengthen global collaborative efforts of all disciplines. Published by the American Physical Society 2025

Ilchen, Markus↗
DOE OSTI2023

A semiempirical transparency model for dual energy cargo radiography applications

Cargo containers passing through ports are scanned by non-intrusive inspection systems to search for concealed illicit materials. By using two photon beams with different energy spectra, dual energy inspection systems are sensitive to both the area density and the atomic number of cargo contents. Most literature on the subject assumes a simple exponential attenuation model for photon intensity in which only free streaming photons are detected. However, this approximation neglects second order effects such as scattering, leading to a biased model and thus incorrect material predictions. This work studies the accuracy of the free streaming model by comparing it to simulation outputs, finding that the model shows poor atomic number reconstruction accuracy at high- Z and suffers significantly if the source energy spectra and detector response function are not known exactly. To address these challenges, this work introduces a semiempirical transparency model which modifies the free streaming model by rescaling different components of the mass attenuation coefficient, allowing the model to capture secondary effects ignored by the free streaming model. The semiempirical model displays improvement agreement with simulated results at high- Z and shows excellent extrapolation to materials and thicknesses which were not included during the calibration step. Furthermore, this work demonstrates that the semiempirical model yields accurate atomic number predictions even when the source spectra and detector response are not known exactly. In conclusion, using the semiempirical model, manufacturers can perform a simple calibration to enable more precise Z reconstruction capabilities, which has the potential to significantly improve the performance of existing dual energy radiographic systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Coupling between bulk thermal defects and surface segregation dynamics

Surface segregation is a phenomenon that depends on the delicate interplay between thermodynamic driving forces and kinetic obstacles, for which elevated temperature is often needed to enhance the atom mobility and reach equilibrium. Using the classic system of Cu 3 Au ( 100 ) under nonisothermal conditions, in this study, we show an adatom process underlying transient surface segregation dynamics through the temperature-change-driven creation and annihilation of thermal vacancies in the bulk and the resulting bulk-surface mass exchanges. This is demonstrated by monitoring the surface composition evolution of Cu 3 Au ( 100 ) with temperature changes between 250 and 500 ° C , showing that the increase in temperature decreases monotonically the surface Au concentration as a result of the transfer of more Cu than Au from the bulk to the surface to form Cu-rich clusters of adatoms. Such a bulk thermal defect effect is expected to be universal in inducing the disparity in the bulk-surface mass exchanges of dissimilar atoms in multicomponent materials because of the inherent differences in the vacancy formation energies of the constituent atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Redox Mediated Control of Electrochemical Potential in Liquid Cell Electron Microscopy

Liquid cell electron microscopy enables the study of nanoscale transformations in solvents with high spatial and temporal resolution, but for the technique to achieve its potential requires a new level of control over the reactivity caused by radical generation under electron beam irradiation. An understanding of how to control electron-solvent interactions is needed to further advance the study of structural dynamics for complex materials at the nanoscale. Additionally, we developed an approach that scavenges radicals with redox species that form well-defined redox couples and control the electrochemical potential in situ . This approach enables the observation of electrochemical structural dynamics at near-atomic resolution with precise control of the liquid environment. Analysis of nanocrystal etching trajectories indicates that this approach can be generalized to several chemical systems. The ability to simultaneously observe heterogeneous reactions at near-atomic resolution and precisely control the electrochemical potential enables the fundamental study of complex nanoscale dynamics with unprecedented detail.

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

CO Adsorption on a Single‐Atom Catalyst Stably Embedded in Graphene

Abstract Confined single metal atoms in graphene‐based materials have proven to be excellent catalysts for several reactions and promising gas sensing systems. However, whether the chemical activity arises from the specific type of metal atom or is a direct consequence of the confinement itself remains unclear.

Chemistry↗
DOE OSTI2019

Evidence for interfacial geometric interactions at metal–support interfaces and their influence on the electroactivity and stability of Pt nanoparticles

Supported metals are widely used as industrial catalysts wherein the supports affect catalytic performances remarkably through either electronic and/or geometric interactions with the metals, and/or providing interfacial synergistic sites. Herein, we observed evidence for interfacial geometric interactions (IGIs) at Pt–C interfaces through a combination of atomic-scale structural analysis, in situ X-ray absorption fine structure, and electrochemical measurements for Pt/C model systems. The IGI has a long-range attribute and affects Pt surface atoms not only at interfacial perimeters but also adjacent to interfaces. The affected Pt surface atoms are proposed to contribute enhanced activity and stability for the oxygen reduction reaction through retarding the formation of strongly adsorbed oxygenated intermediates. Our work provides some necessary information for a better understanding of support effects and catalytically active surface sites.

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

Solving disorder in (3D) real space: a comparative study of the three-dimensional difference pair distribution function and atomic resolution holography reconstructions

The quantitative analysis of local ordering principles in disordered crystalline systems has gained much attention over the past few years, as it is often considered crucial for optimizing material functionality. This development has been driven by significant advancements in computational and experimental methods, which have led to the establishment and widespread use of various analytical techniques. In this study, we perform model calculations to compare the effectiveness of atomic resolution holography and three-dimensional difference pair distribution function analysis (3D-ΔPDF). Using Cu 3 Au as a model system, we demonstrate an approach to derive local order parameters quantitatively and show that both techniques are well suited to quantifying chemical short-range order correlations and local bond-distance variations. By evaluating the strengths and limitations of both techniques, we advocate for their combined use to solve complex short-range order problems accurately.

3D-ΔPDF↗
DOE OSTI2021

Tunable room-temperature ferromagnetism in Co-doped two-dimensional van der Waals ZnO

The recent discovery of ferromagnetism in two-dimensional van der Waals crystals has provoked a surge of interest in the exploration of fundamental spin interaction in reduced dimensions. However, existing material candidates have several limitations, notably lacking intrinsic room-temperature ferromagnetic order and air stability. Here, motivated by the anomalously high Curie temperature observed in bulk diluted magnetic oxides, we demonstrate room-temperature ferromagnetism in Co-doped graphene-like Zinc Oxide, a chemically stable layered material in air, down to single atom thickness. Through the magneto-optic Kerr effect, superconducting quantum interference device and X-ray magnetic circular dichroism measurements, we observe clear evidences of spontaneous magnetization in such exotic material systems at room temperature and above. Transmission electron microscopy and atomic force microscopy results explicitly exclude the existence of metallic Co or cobalt oxides clusters. X-ray characterizations reveal that the substitutional Co atoms form Co 2+ states in the graphitic lattice of ZnO. By varying the Co doping level, we observe transitions between paramagnetic, ferromagnetic and less ordered phases due to the interplay between impurity-band-exchange and super-exchange interactions. Our discovery opens another path to 2D ferromagnetism at room temperature with the advantage of exceptional tunability and robustness.

36 MATERIALS SCIENCE↗