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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times

While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c -type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.

Cytochromes/metabolism↗
DOE OSTI2020

Water on Actinide Dioxide Surfaces: A Review of Recent Progress

The fluorite structured actinide dioxides (AnO 2 ), especially UO 2 , are the most common nuclear fuel materials. A comprehensive understanding of their surface chemistry is critical because of its relevance to the safe handling, usage, and storage of nuclear fuels. Because of the ubiquitous nature of water (H 2 O), its interaction with AnO 2 has attracted significant attention for its significance in studies of nuclear fuels corrosion and the long-term storage of nuclear wastes. The last few years have seen extensive experimental and theoretical studies on the H 2 O–AnO 2 interaction. Herein, we present a brief review of recent advances in this area. We focus on the atomic structures of AnO 2 surfaces, the surface energies, surface oxygen vacancies, their influence on the oxidation states of actinide atoms, and the adsorption and reactions of H 2 O on stoichiometric and reduced AnO 2 surfaces. Finally, a summary and outlook of future studies on surface chemistry of AnO 2 are given. We intend for this review to encourage broader interests and further studies on AnO 2 surfaces.

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

Structure and energetics of the elbows in the Au(111) herringbone reconstruction

We study the structure of the threading edge dislocations, or “elbows,” which are an essential component of the well-known herringbone reconstruction of the (111) surface of Au. Previous work had shown that these dislocations can be stabilized by long-range elastic relaxations into the bulk. However, the validity of the harmonic spring model that had been used to estimate the energies of the dislocations is uncertain. To enable a more refined model of the dislocation energetics, we have imaged the atomic structure of these dislocations using scanning tunneling microscopy. We find that the harmonic spring model does not adequately reproduce the observed structure. We are able to reproduce the structure, however, with a two-dimensional Frenkel-Kontorova (FK) model that uses a pairwise Morse potential to describe the interactions between the top layer Au atoms on a rigid substrate. The parameters of the potential were obtained by fitting the energy of uniaxially compressed phases, or “stripes”, computed with density functional theory, as a function of surface Au density. Within this model, the formation of the threading dislocations remains unfavorable. However, the large forces on the substrate atoms near the threading-dislocation cores, render the assumption of a completely rigid substrate questionable. Indeed, if the FK parameters are modified to account for the relaxation of just one more atomic layer, threading dislocations can, in principle, become favorable, even without bulk elastic relaxations. Additional evidence for a small elbow energy is that our computed change in the Au(111) surface stress tensor caused by the (√ 3 × 22) reconstruction is considerably smaller than previous estimates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Evolution of nanopores in hexagonal boron nitride

Abstract The engineering of atomically-precise nanopores in two-dimensional materials presents exciting opportunities for both fundamental science studies as well as applications in energy, DNA sequencing, and quantum information technologies. The exceptional chemical and thermal stability of hexagonal boron nitride (h-BN) suggest that exposed h-BN nanopores will retain their atomic structure even when subjected to extended periods of time in gas or liquid environments. Here we employ transmission electron microscopy to examine the time evolution of h-BN nanopores in vacuum and in air and find, even at room temperature, dramatic geometry changes due to atom motion and edge contamination adsorption, for timescales ranging from one hour to one week. The discovery of nanopore evolution contrasts with general expectations and has profound implications for nanopore applications of two-dimensional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Predicting Oxygen Off-Stoichiometry and Hydrogen Incorporation in Complex Perovskite Oxides

Chemically and structurally complex solid compounds, including those with significant off-stoichiometry, are rapidly extending new material functionality across a variety of applications. Accelerated development of these compounds requires accurate predictions of material defect properties including effective defect formation energies and equilibrium defect concentrations. Traditional first-principles approaches typically examine dilute defect concentrations and relatively ordered atomic structures to identify the lowest energy defect sites. These approaches are rarely suitable for describing the disorder present in these systems and its influence on defect formation, which can lead to unphysically large predictions for defect concentrations. Here, we demonstrate a new method to accurately predict the temperature and pressure dependence of oxygen vacancy concentrations and proton interstitial concentrations in complex oxides. This method extends standard dilute defect calculations to incorporate atomic and magnetic disorder, employs the ensemble descriptions of defect sites resulting in improved predictions of defect formation energies, and accounts for effects beyond the dilute defect limit. To demonstrate our method, we show that the predicted defect concentrations in perovskites used as ceramic fuel cell cathodes, including Ba0.5Sr0.5Fe0.8Zn0.2O3-d, Ba0.5Sr0.5Co0.8Fe0.2O3-d, and BaCo1-x-y-zFexZryYzO3-d, are in good agreement with experimental values, thereby opening the door for predictive design of complex oxides by these applications.

DFT↗
DOE OSTI2024

Structural diversity and clustering of bacterial flagellar outer domains

Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii , Stenotrophomonas maltophilia , and Geovibrio thiophilus . Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Science & Technology - Other Topics↗
DOE OSTI2026

Domain-Dependent Electronic Properties of 2D Copper Boride Synthesized from Reversible Subsurface Diffusion on Cu(111)

Emerging boron-based 2D materials hold properties with potential applications ranging from electronic devices to catalysis and energy storage. Using physical vapor deposition, 2D copper borides are formed on Cu(111) at elevated temperatures. However, the as-prepared surfaces often contain boron clusters that compromise structural homogeneity, and the dynamics of their formation is not yet fully understood. Through in situ low-energy electron microscopy (LEEM), Auger electron spectroscopy (AES), and scanning tunneling microscopy/spectroscopy (STM/STS), we show that cluster-free 2D CuB x is synthesized via reversible subsurface diffusion of boron atoms. The resolved regular atomic structure aligns with the previously calculated Cu 8 B 14 model. In a rare case, possibly due to surface strain and a change of orientation, a second domain of CuB x was observed with a pronounced change in electronic properties, yet electronic states remain delocalized in both domains. In conclusion, these findings demonstrate the sensitivity of electronic properties to domain structure and highlight a potential opportunity to tune 2D CuB x for diverse applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Finding simplicity: unsupervised discovery of features, patterns, and order parameters via shift-invariant variational autoencoders *

Abstract Recent advances in scanning tunneling and transmission electron microscopies (STM and STEM) have allowed routine generation of large volumes of imaging data containing information on the structure and functionality of materials. The experimental data sets contain signatures of long-range phenomena such as physical order parameter fields, polarization, and strain gradients in STEM, or standing electronic waves and carrier-mediated exchange interactions in STM, all superimposed onto scanning system distortions and gradual changes of contrast due to drift and/or mis-tilt effects. Correspondingly, while the human eye can readily identify certain patterns in the images such as lattice periodicities, repeating structural elements, or microstructures, their automatic extraction and classification are highly non-trivial and universal pathways to accomplish such analyses are absent. We pose that the most distinctive elements of the patterns observed in STM and (S)TEM images are similarity and (almost-) periodicity, behaviors stemming directly from the parsimony of elementary atomic structures, superimposed on the gradual changes reflective of order parameter distributions. However, the discovery of these elements via global Fourier methods is non-trivial due to variability and lack of ideal discrete translation symmetry. To address this problem, we explore the shift-invariant variational autoencoders (shift-VAEs) that allow disentangling characteristic repeating features in the images, their variations, and shifts that inevitably occur when randomly sampling the image space. Shift-VAEs balance the uncertainty in the position of the object of interest with the uncertainty in shape reconstruction. This approach is illustrated for model 1D data, and further extended to synthetic and experimental STM and STEM 2D data. We further introduce an approach for training shift-VAEs that allows finding the latent variables that comport to known physical behavior. In this specific case, the condition is that the latent variable maps should be smooth on the length scale of the atomic lattice (as expected for physical order parameters), but other conditions can be imposed. The opportunities and limitations of the shift VAE analysis for pattern discovery are elucidated.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Ion irradiation and modification: The role of coupled electronic and nuclear energy dissipation and subsequent nonequilibrium processes in materials

Understanding material responses to energy deposition from energetic charged particles is important for defect engineering, ion-beam processing, ion-beam analysis and modification, geologic aging, space exploration, and nuclear applications. As an incident ion penetrates a solid, its energy is transferred to electrons and to atomic nuclei of the solid. Much of this electronic energy deposition is subsequently transferred to the atomic structure via electron–phonon (e–ph) coupling, leading to local inelastic thermal spikes in which energy dissipation is influenced by the local environment. In addition, intense ionization can lead to high densities of localized electronic excitations in wide-bandgap materials and ceramics that can affect defect dynamics and atomic mobility. Specifically, energy exchange between electrons and atomic nuclei, along with localized electronic excitations, can lead to substantial competitive (ionization-induced annealing), additive (both electronic and nuclear energy depositions contributing to damage production), and synergistic (more damage than the sums of separate damage processes) effects. Although nonmonotonic effects of the e–ph coupling strength and athermal processes are demonstrated for pre-existing defects and residual damage during ion–solid interactions, there is limited understanding of when such electronic effects must be considered in atomic-scale models of damage production and evolution in a broad variety of materials. Complex ceramics and chemically disordered solid solution alloys with different constituent elements allow a systematic evaluation of defect dynamics and irradiation performance with increasing complexity. Current knowledge regarding tuning of bonding characteristics and chemical disorder to control atomic-level dynamics is reviewed. Although a lack of fundamental understanding obstructs the advancement of reliable predictions for ion beam material modification, it highlights challenges and opens research opportunities. Insights into the complex electronic and atomic correlations with extreme energy deposition will strengthen our ability to design materials and predict ion-irradiation-induced damage in a radiation environment, and they may pave the way to better control fundamental processes and design new material functionalities for advanced technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Three-dimensional charge density wave in the dual heavy fermion system UPt 2 Si 2

Heavy fermion liquids offer via their Kondo lattice diverse possibilities for exotic ground states. Using variable-temperature atomic pair distribution function analysis, we study the local atomic structure of the "dual" heavy fermion liquid UPt 2 Si 2 , which exhibits antiferromagnetism consistent with localized 5f-electron states and transport properties characteristic to itinerant 5f-"spd" hybridized electron systems. We show that UPt 2 Si 2 exhibits periodic lattice distortions (PLDs) involving both uranium and platinum atoms that are characteristic to three-dimensional charge density waves. Here, the temperature evolution of the PLDs tracks that of the transport and magnetic properties, suggesting the presence of little-known 5f-electron-lattice interactions. We argue that PLDs in heavy fermion liquids in general, and in particular in UPt 2 Si 2 , appear as new degrees of freedom that entangle competing electronic states and, as such, must be accounted for when their rich physics is considered.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Mapping causal patterns in crystalline solids

The evolution of the atomic structures of the combinatorial library of Sm-substituted thin film BiFeO 3 along the phase transition boundary from the ferroelectric rhombohedral phase to the non-ferroelectric orthorhombic phase is explored using scanning transmission electron microscopy. Localized properties, including polarization, lattice parameter, and chemical composition, are parameterized from atomic-scale imaging, and their causal relationships are reconstructed using a linear non-Gaussian acyclic model. This approach is further extended to explore the spatial variability of the causal coupling using the sliding window transform method, which revealed that new causal relationships emerged at both the expected locations, such as domain walls and interfaces, and at additional regions forming clusters in the vicinity of the walls or spatially distributed features. While the exact physical origins of these relationships are unclear, they likely represent nanophase-separated regions in the morphotropic phase boundaries. Overall, we posit that an in-depth understanding of complex disordered materials away from thermodynamic equilibrium necessitates understanding not only the generative processes that can lead to observed microscopic states but also the causal links between multiple interacting subsystems.

Causal inference↗
DOE OSTI2025

Driving Electron Transfer in Photosystem I Using Far-Red Light: Overall Perspectives

Photosystem I (PSI) is a photosynthetic protein–pigment complex that, upon photoexcitation, transfers electrons to ferredoxin, facilitating the production of NADPH. Isolated PSI reaction centers (RCs) have also been used in hybrid systems to reduce protons and produce ‘biohydrogen’. This review article examines how various cyanobacteria with similar photosynthetic machinery utilize different wavelengths of light to execute photosynthetic electron transport through PSI. Key factors, such as, the structure of the electron transfer cofactors, the protein environment surrounding the primary donor pigments and hydrogen-bonding interactions with the surrounding protein matrix are analyzed to understand their roles in maintaining efficient electron transfer when it is driven using photons of different energies. We compare PSI complexes with known atomic structures from four species of cyanobacteria, Thermosynechococcus elongatus, Acaryochloris marina, Halomicronema hongdechloris, and Fischerella thermalis. T. elongatus is typical of most oxygenic photosynthetic organisms in that it requires visible light and uses only chlorophyll a (Chl a ) in PSI. In contrast, H. hongdechloris and F. thermalis are photoacclimating species capable of producing Chl f and Chl d that use red light when little visible light is available. A. marina , on the other hand, is adapted to red light conditions and consistently utilizes Chl d as its primary photosynthetic pigment, maintaining a stable pigment composition. Here, we explore the structural and functional differences between the PSI RCs of these organisms and the impact of these differences on electron transport. The structural differences in the cofactors influence both the absorption wavelengths of the cofactors and the energy levels of the intermediate states of electron transfer. An analysis of the surrounding protein shows how it has been adapted and underscores the interplay between the pigment structure, protein environment, and hydrogen bonding networks in tuning the efficiency and adaptability of photosynthetic mechanisms across different species of cyanobacteria.

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

Bayesian Learning of Adatom Interactions from Atomically Resolved Imaging Data

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Atom vacancies and electronic transmission Stark effects in boron nanoflake junctions

Finite-sized boron nanomaterials have received little attention in comparison to their graphene-like 2D boron analogues. It is with systems of precise atomic structures where the electrical conductance can be most fruitfully analyzed at the fundamental level. To understand how conductance varies with respect to the electronic structure, and particularly with vacancies, we study finite-sized boron nanoflakes (BNFs) and closely examine their remarkable changes in physical properties. Unlike carbon-based materials, we find from non-equilibrium Green's functions density functional theory (NEGF-DFT) calculations that the charge transport of BNFs with 35–37 atoms is modulated by site-specific atomic vacancies. Here, the BNF with no vacancy (B 37 ) shows significantly lower conductivity (9.23 μS), than B 36 with one vacancy (46.1 μS), and lower still than with two vacancies (B 35 , 54.2 μS). From the thermopower function, these nanomaterials change from strong hole conductors to electron and back to hole conductors with the addition of each vacancy, from a doublet (B 37 ) to singlet (B 36 ) to doublet (B 35 ) ground state, respectively.

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

Selective Antisite Defect Formation in WS 2 Monolayers via Reactive Growth on Dilute W-Au Alloy Substrates

Defects are ubiquitous in 2D materials and can affect the structure and properties of the materials and also introduce new functionalities. Methods to adjust the structure and density of defects during bottom-up synthesis are required to control the growth of 2D materials with tailored optical and electronic properties. In this study, the authors present an Au-assisted chemical vapor deposition approach to selectively form S W and S2 W antisite defects, whereby one or two sulfur atoms substitute for a tungsten atom in WS 2 monolayers. Guided by first-principles calculations, they describe a new method that can maintain tungsten-poor growth conditions relative to sulfur via the low solubility of W atoms in a gold/W alloy, thereby significantly reducing the formation energy of the antisite defects during the growth of WS 2 . The atomic structure and composition of the antisite defects are unambiguously identified by Z-contrast scanning transmission electron microscopy and electron energy-loss spectroscopy, and their total concentration is statistically determined, with levels up to ≈5.0%. Furthermore, scanning tunneling microscopy/spectroscopy measurements and first-principles calculations also verified these antisite defects and revealed the localized defect states in the bandgap of WS 2 monolayers. This bottom-up synthesis method to form antisite defects should apply in the synthesis of other 2D materials.

2D materials↗
DOE OSTI2024

Monitoring Redox Processes in Lithium-Ion Batteries by Laboratory-Scale Operando X-ray Emission Spectroscopy

Tracking changes in the chemical state of transition metals in alkali-ion batteries is crucial to understanding the redox chemistry during operation. X-ray absorption spectroscopy (XAS) is often used to follow the chemistry through observed changes in the chemical state and local atomic structure as a function of the state-of-charge (SoC) in batteries. In this study, we utilize an operando X-ray emission spectroscopy (XES) method to observe changes in the chemical state of active elements in batteries during operation. Operando XES and XAS were compared by using a laboratory-scale setup for four different battery systems: LiCoO 2 (LCO), Li[Ni 1/3 Co 1/3 Mn 1/3 ]O 2 (NMC111), Li[Ni 0.8 Co 0.1 Mn 0.1 ]O 2 (NMC811), and LiFePO 4 (LFP) under a constant current charging the battery in 10 h (C/10 charge rate). We show that XES, despite narrower chemical shifts in comparison to XAS, allows us to fingerprint the battery SOC in real time. We further demonstrate that XES can be used to track the change in net spin of the probed atoms by analyzing changes in the emission peak shape. As a test case, the connection between net spin and the local chemical and structural environment was investigated by using XES and XAS in the case of electrochemically delithiated LCO in the range of 2–10% lithium removal.

25 ENERGY STORAGE↗
DOE OSTI2026

The incommensurate modulation of tetragonal tungsten bronze quantified by high resolution 4D STEM

Many members of the tetragonal tungsten bronze (TTB) family of oxides display an incommensurate periodic lattice distortion, the nature of which has been the subject of some controversy. Here we present a study of this structural modulation in the relaxor ferroelectric Ba 5 SmSn 3 Nb 7 O 30 (BSSN) by quantitative scanning transmission electron microscopy (STEM). Additionally, we characterize the modulation in BSSN by employing a fast, pixelated direct electron detector to perform high resolution phase contrast STEM imaging of the crystalline lattice. By quantitatively analyzing the images, we visualize the atomic structural correlations present in the material on both the cation and anion sublattices. This analysis reveals the incommensurate structure to have an octahedral tilting pattern and cooperative A2 site cation displacements, analogous to an Ama2 commensurate cell. Finally, we show that the modulation is composed of a structural motif with a period of 3 x $d_{1\bar{1}0}$ and modified by discommensurations, likely arise from frustrated octahedral tilting in the odd-valued periodicity.

Differential phase contrast↗
DOE OSTI2023

Interpretable, Extensible Linear Regression Model for Electron Density Prediction

This code allows us to generate a model to predict ground state electron densities directly from atomic structure thereby bypassing the need to perform direct DFT calculations. It is based on many body correlation descriptors defined in https://arxiv.org/abs/2004.14442 (IM release numbers: LLNL-JRNL- 808791 and LLNL-JRNL-840698). The code reads in electron densities, in CHGCAR format used by the DFT code VASP, calculates many-body correlation descriptors based on atoms surrounding a grid point and then uses linear regression to obtain the fitting parameters.

Kumar, Shashikant↗