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DOE OSTI2025

Monthly averages of ED2 model simulations initialized with airborne lidar structure, Jan 1981-Dec 2018, Brazilian Amazon

Deforestation and forest degradation (selective logging, fires, fragmentation) have impacted nearly 40% of the original extent of the Brazilian Amazon, and have markedly impacted forest structure across the region. To date, few studies analysed how shifts in forest structure from degradation influence the forest sensitivity to climate extremes, because of the complex interactions between forest structure and micro-environmental conditions. To address this knowledge gap, we carried out a series of simulations across the Brazilian Amazon using the Ecosystem Demography Model (ED2), using observed forest structure derived from 541 airborne lidar transects (375 ha each) and two scenarios representing forest recovery and expansion of degradation to investigate how shifts in forest structure impact ecosystem function under near-average and extreme climate conditions, as part of the manuscript Longo et al 2025 "Degradation and Deforestation Increase the Sensitivity of the Amazon Forest to Climate Extremes". This dataset provides the output results from the ED2 model simulations for the three simulations at monthly time scales, in NetCDF format. For all simulations, we used bias-corrected hourly reanalyses (WFDE5) for most meteorological drivers, except for precipitation, which was obtained from CHIRPS. The meteorological drivers used in the study span 38 years (Jan 1981–Dec 2018). The output results correspond to the last 38 years of simulation (one full cycle of meteorological drivers), in which ED2 simulations used static stand structure (i.e., the forest structure was held constant). The following files are provided:ED2_emean_Global_R004_BrAmaz_s1c0t0l0f0.nc. This corresponds to the Control simulation. The forest structure was obtained from the airborne lidar.ED2_emean_Global_R005_BrAmaz_s1c0t1l1f0.nc. This corresponds to the Degraded simulation. The forest structure was obtained from a spin-up simulation initialized with airborne lidar and a scenario that expanded deforestation and selective logging across the Amazon.ED2_emean_Global_R006_BrAmaz_s1c0t1l0f0.nc. This corresponds to the Recovery simulation. The forest structure was obtained from a spin-up simulation initialized with airborne lidar and a scenario that completely halted deforestation and degradation, allowing degraded forests to recover for 38 years.We also provide file ED2_zones_R004_BrAmaz_s1c0t0l0f0.nc, which classifies each grid cell into zones used in the reference manuscript: 1: Southeast. 2: South. 3: West. 4: Central. 5: Northeast. 6: North. 7: Northwest". Index 0 corresponds to grid cells excluded from sub-region analyses because they were dominated by flooded forests, deforestation, and naturally non-forest vegetation.

54 ENVIRONMENTAL SCIENCES↗

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 OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Thermal-Fluid and Thermal-Structural Response of the T-Tube Modular Divertor to Spatiotemporally Varying Heat Loads

Tungsten (W) is the leading candidate for divertor target plates because of its high melting point (>3000°C), thermal conductivity, and ultimate tensile stress. While W and its alloys are the only solid materials that can survive the high heat fluxes incident on the divertor, W’s low-ductility high ductile-to-brittle transition temperature of ~600°C and relatively low recrystallization temperature (RT) of ~1300°C pose structural (among other) challenges. The objective of this work is to estimate the thermal-fluid and thermal-structural performance of the helium (He)-cooled T-tube divertor, which was originally developed by the Advanced Reactor Innovation and Evaluation Study (ARIES) using numerical simulations. Here, predictions of temperature distributions across the plasma-facing structural component and surface pressures from computational fluid dynamics simulations are used to determine stress distributions using commercial structural finite element modeling software over a range of fusion-relevant conditions. The maximum allowable incident heat fluxes are determined based on the temperature limits imposed by the ITER elastic Structural Design Criteria for In-vessel Components (SDC-IC) and the maximum RT over a range of He mass flow rates and presented in the form of performance design charts. Our recent work found that thermal- structural criteria accounting for the low ductility of W in a finger-type modular divertor constrain the maximum incident heat fluxes to values well below the ITER specifications, and those based on considering only the RT demonstrate that integrated thermal-fluid and elastic structural performance evaluation are required for accurate assessment of divertor performance. This novel analysis of the T-tube considers how nonuniform and transient incident heat fluxes affect its thermal-fluid and thermal-structural performance, as well as the effect of volumetric heating, which can be as great as 27% of the power incident on the divertor surface. The W tile of the T-tube, with its relatively large plasma-facing area of ~15 cm 2 , will likely experience significant spatial variations in incident heat flux. This work therefore assesses whether steady-state incident heat flux profiles with a peak of 10 MW/m 2 and maximum heat flux gradients of 200 MW/m 2 per m exceed the structural limits imposed by the ITER elastic SDC-IC and the maximum RT over a range of fusion-relevant conditions. The effect of transient heat fluxes typical of plasma detachment and reattachment from the target plate due, for example, to gas injection are also evaluated

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof of principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. In conclusion, our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.

HIV-1 dimerization initiation site↗

DOE OSTI2025

In Situ/Operando Probing of Dynamic Phase Structures of Alumina‐Supported Ultrasmall Copper‐Gold Alloy Nanoparticles Under Reaction Conditions

Abstract The ability to control phase structures and surface sites of ultrasmall alloy nanoparticles under reaction conditions is essential for preparing catalysts by design. This is, however, challenging due to limited understanding of the atomic‐scale phases and their correlation with the ensemble‐averaged structures and activities of catalysts during catalytic reactions. We reveal here a dynamic structural stability of alumina‐supported ultrasmall and equiatomic copper‐gold alloy nanoparticles under reaction conditions as a model system in the in situ/operando study. In situ atomic‐scale morphological tracking under oxygen reveals temperature‐dependent dynamic crystalline‐amorphous dual‐phase structures, showing dynamic stability over an elevated temperature range. This atomic‐scale dynamic phase stability coincides with a “conversion plateau” observed for carbon monoxide oxidation on the catalyst. It is substantiated by the stable lattice ordering/disordering structures and surface sites with oscillatory characteristics shown by operando ensemble‐average structural tracking of the catalyst during the oxidation reaction. The understanding of the atomic‐scale dynamic phase structures in correlation with the ensemble‐average dynamic ordering/disordering phase structures and surface sites provides fresh insights into the unique synergy of the supported alloy nanoparticles. This understanding has implications for the design and structural tuning of active and stable ultrasmall alloy catalysts under elevated temperatures.

Chemistry↗

DOE OSTI2025

Single Crystals of Vanadium Oxides as a Lens for Understanding Structural and Electronic Phase Transformations, Ion Transport, Chemo-Mechanical Coupling, and Electrothermal Neuronal Emulation

Vanadium oxides cystallize in a diverse array of structures and compositions arising from the redox versatility of vanadium, variable covalency of V−O bonds, and myriad coordination geometries. Their open frameworks present abundant interstitial sites that enable insertion of guest-ions. In such compounds, V3d electron and spin localization and disorder couple strongly to structural preferences. The rich structural diversity manifests as a “rugged” free energy landscape with multiple interconvertible polymorphs. Such a landscape sets up structural, electronic, and magnetic transitions that underpin the promise of these materials as ion-insertion battery electrodes; compact primitives for brain-inspired computing, and heterogeneous catalysts. Here, we examine the structural and compositional diversity, electronic instabilities, defect dynamics, structure transformations, mechanical properties, and surface structure of vanadium oxides using single crystals as a distinctive lens. Single crystals enable the measurement of structure−function correlations without the ensemble and orientational averaging inevitable in polycrystalline materials. Their well-defined surfaces further enable examination of facet-dependent reactivity toward molecular adsorbates, ion fluxes, and lattice (mis)matched solids. We provide a comprehensive account of vanadium-oxide single-crystal studies, from delineation of common structural motifs to single-crystal growth techniques, topochemical modification strategies, mechanisms underpinning electronic instabilities, and implementation as electrothermal neurons and battery electrode materials.

Ponis, John [Texas A&M University, College Station↗

DOE OSTI2024

Elucidation of a Metastable p(2 × 1) O Atom Adlayer Structure on Cu(111)

Cu-based catalysts are ubiquitous in many industrial reactions, including methanol synthesis. Under partially oxidizing conditions, Cu catalysts can have dynamic surface structures that greatly influence their reactivities. Therefore, elucidating the surface structures that are present on Cu, and looking for metastable structures, aids in the long term goal of understanding and controlling their catalytic behavior. Thin-film copper oxides such as the “29” and “44” structures have been described at length in the literature, but precursors to these thin-film oxides can be challenging to study because they exist only under certain conditions. Using a combination of experimental and computational surface science techniques, we discovered, modeled, and quantified a previously unreported O atom adlayer structure on Cu(111) with a p(2 × 1) unit cell. Here, we used scanning tunneling microscopy to visualize the striped 2 × 1 structure and density functional theory (DFT) structure optimizations to identify the thermodynamically most favorable positions of Cu and O atoms in a p(2 × 1) unit cell. Using X-ray photoelectron spectroscopy and temperature-programmed desorption, we determined the stoichiometry of the structure to be 2:1 for surface Cu atoms to O adatoms, the same stoichiometry as that modeled by DFT. This work reports a new metastable structure formed on Cu(111) at the very initial stages of oxidation and is therefore worth considering in models of catalytically relevant redox processes at Cu surfaces.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Revealing Local Structures through Machine-Learning-Fused Multimodal Spectroscopy

Atomistic structures of materials offer valuable insights into their functionality. Determining these structures remains a fundamental challenge in materials science, especially for systems with defects. While both experimental and computational methods exist, each has limitations in resolving nanoscale structures. Core-level spectroscopies, such as X-ray absorption (XAS) or electron energy-loss spectroscopies (EELS), have been used to determine the local bonding environment and structure of materials. Recently, machine learning (ML) methods have been applied to extract structural and bonding information from XAS/EELS data. However, frameworks relying solely on a single data stream, defined as characterization data derived from a single element using one technique, are often insufficient because multiple local environments can yield similar spectral features, making it challenging to differentiate between competing structural hypotheses. Here, in this work, we address this challenge by integrating multimodal ab initio simulations, experimental data acquisition, and ML techniques for structure characterization. Our goal is to determine local structures and properties using EELS and XAS data from multiple elements and edges. To showcase our approach, we use various lithium nickel manganese cobalt (NMC) oxide compounds which are used for lithium ion batteries, including those with oxygen vacancies and antisite defects, as the sample material system. We successfully inferred local element content, ranging from lithium to transition metals, with quantitative agreement with experimental data. Beyond local element inference, we find that ML model based on multimodal spectroscopic data is able to determine whether local defects such as oxygen vacancy and antisites are present, a task which is impossible for single mode spectra or other experimental techniques. Furthermore, our framework is able to provide physical interpretability, bridging spectroscopy with the local atomic and electronic structures.

battery↗

DOE OSTI2025

Mixed-Flux Techniques for Rational Synthesis and Structural Control in Silver Chalcogenides

The functionality of materials is intrinsically linked to their structures, an axiom encapsulated in the principle of structure-property relationships. The pinnacle of materials design is the tailoring of its structure for a specific function, which requires the ability of rational synthesis and the development of synthesis science. This idea, however, remains elusive for the synthesis of complex extended solids. A major obstacle is the difficulty in using established chemical principles selectively to control reaction paths and favor certain structural patterns over numerous other possible results. In this context, we are developing a synthesis science approach that facilitates the control of the structure and bonding to create new structures. This is achieved by employing a two-component flux consisting of mixed hydroxides and halides as the reaction medium. This enables reaction conditions that allow better control of the structure dimensionality and composition by manipulating the temperature and solvent basicity (via the flux component ratio). Here, we demonstrate the efficacy of this method in controlling their structural motifs to arrive at 23 unreported compositions and 6 unique structure types. These materials are expected to exhibit a broad range of properties, from metallic to semiconducting, with calculations suggesting the potential for emergent phenomena such as Dirac semimetals. The reaction paths afforded by these mixed fluxes establish a direct correlation between the synthetic variables and properties, providing significant insight into a broadly applicable approach for new materials.

Zhou, Xiuquan [Argonne National Laboratory (ANL), ↗

DOE OSTI2025

Quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) of zwitterionic organic HCl salts

In this work, we benchmark quadrupolar NMR crystallography guided crystal structure prediction (QNMRX-CSP) for determining the crystal structures of two zwitterionic organic HCl salts, L-ornithine HCl ( Orn ) and L-histidine HCl·H 2 O ( Hist ). These salts present an interesting challenge for QNMRX-CSP, as gas-phase geometry optimizations used to generate starting structures for the organic zwitterionic fragments fail to capture their correct solid-state geometries. To overcome this limitation, geometry optimizations using the COSMO water-solvation model are employed to generate initial structural models. Using this approach, QNMRX-CSP yields structural models of the two zwitterionic organic HCl salts that closely match experimentally determined crystal structures. In addition, the application of QNMRX-CSP to Hist represents a further step toward the de novo structural determination of solvated organic HCl salts, as Hist is the first benchmark system of this type to include a water molecule as a component of its crystal structure. This work is significant for its potential application to the structural determination of active pharmaceutical ingredients, which often feature complex organic components and solvated solid forms.

Fleischer, Carl H. [Florida State Univ., Tallahass↗

DOE OSTI2026

Carbon doping in GeTe drives differences in local structure and properties

Advances in low-power, energy-efficient information storage and computing require understanding and controlling the atomic and nanoscale structures of functional materials, such as phase-change materials. Phase-change memory technology enables nonvolatile, low-power memory in devices by storing information through reversible changes in a phase-change material's atomic structure (i.e., transformations between amorphous and crystalline phases) that have corresponding changes in properties, including electronic resistivity and optical reflectivity. Here, we apply complementary X-ray absorption spectroscopy and X-ray pair distribution function analyses to experimentally identify the local- and medium-range atomic structure differences of GeTe and C-doped GeTe thin films. Upon controlled heating, composition- and temperature-dependent atomic structure evolution in GeTe and C-doped GeTe films shows differences in bonding behavior and local structure that directly influence crystallization onset temperature. We find that the introduction of C interrupts Ge–Ge bonds in amorphous GeTe, altering the as-deposited structure to be more similar to the distorted rocksalt structure of crystalline α–GeTe. The change alters the response of the amorphous atomic structure to heating and also lowers the crystallization onset temperature, from 230 °C in GeTe to 220 °C in the C-doped film. The combined insights from both X-ray techniques provide understanding of structural transformations that enables the development and optimization of next-generation memory and computing materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Pyrochlore-type lanthanide titanates and zirconates: Synthesis, structural peculiarities, and properties

This contribution provides a thorough examination of the structural characteristics of pyrochlore-type lanthanide titanates and zirconates Ln2Ti2O7 and Ln2Zr2O7, across various length scales. This paper also examines their processing, interesting physical properties (electrical, magnetic, and thermal characteristics), and responses to high pressure and ion irradiation. Brief sections on the elemental oxides' crystal chemistry, pertinent phase diagrams, and energetics of defect formation are also provided. Pyrochlore-type Ln2Ti2O7 and Ln2Zr2O7 stand out as truly multifunctional materials. Moreover, they have emerged as fascinating materials due to magnetic geometrical frustration, arising from the ordering of magnetic Ln3+ and non-magnetic Ti4+ (or Zr4+) cations into separate, interpenetrating lattices of corner-sharing tetrahedra. This results in a diverse array of exotic magnetic ground states, such as spin-ice (e.g., Dy2Ti2O7 or Ho2Ti2O7) or quantum spin ice (e.g., Tb2Ti2O7), observed at both low and room temperatures. They also exhibit varied electrical and electrochemical characteristics. Some members such as Gd2Zr2O7, function as fast ion conductors with a conductivity (σ) of ≈10−2 S·cm−1 at 800 °C and activation energy (Ea) ranging from 0.85 to 1.52 eV, depending on the degree of structural disorder. Others, such as Gd2TiMoO7, are mixed ionic-electronic conductors with σ ≈ 25 S·cm−1 at 1000 °C, making them promising candidate materials for applications in energy conversion and storage devices and oxygen separation membranes. Their exceptionally low thermal conductivity (e.g., κ ∼ 1.1–1.7 W·m−1·K−1 between 700 and 1200 °C for Ln2Zr2O7), close to the glass-like lower limit of highly disordered solids, positions them as valuable materials for thermal barrier coatings. They can also effectively accommodate actinides (e.g., Pu, Np, Cm, Am) in solid solutions and sustain prolonged exposure to radiation due to alpha-decay events, while preserving the integrity of the periodic atomic structure. Proposed as major components in actinide-bearing ceramics, they contribute to the long-term immobilization and disposal of long-lived waste radionuclides from nuclear programs. Some of these properties are displayed simultaneously, opening avenues for new applications. Despite the wealth of data available in the literature, this review highlights the need for a better understanding of order/disorder processes in pyrochlore-type materials and the influence of the structural length scale on their physical and chemical properties. Recent experimental evidence has revealed that pyrochlore short-range structure is far more complex than originally thought. Moreover, pyrochlore local structure is now believed to include short-range, lower symmetry, ordered domains, such as the orthorhombic weberite-type of structure. Notably, short- and long-range structures appear decoupled across different length scales and temperature regimes, and these differences persist even in well-ordered samples. We believe that the pyrochlore structure offers a unique opportunity for examining the interplay between chemical composition, defect chemistry, and properties. In Memoriam: Rodney C. Ewing, Fondly Remembered.

Physics↗

DOE OSTI2024

Spectroscopy-guided discovery of three-dimensional structures of disordered materials with diffusion models

Spectroscopy techniques such as x-ray absorption near edge structure (XANES) provide valuable insights into the atomic structures of materials, yet the inverse prediction of precise structures from spectroscopic data remains a formidable challenge. In this study, we introduce a framework that combines generative artificial intelligence models with XANES spectroscopy to predict three-dimensional atomic structures of disordered systems, using amorphous carbon (a-C) as a model system. In this work, we introduce a new framework based on the diffusion model, a recent generative machine learning method, to predict 3D structures of disordered materials from a target property. For demonstration, we apply the model to identify the atomic structures of a-C as a representative material system from the target XANES spectra. We show that conditional generation guided by XANES spectra reproduces key features of the target structures. Furthermore, we show that our model can steer the generative process to tailor atomic arrangements for a specific XANES spectrum. Finally, our generative model exhibits a remarkable scale-agnostic property, thereby enabling generation of realistic, large-scale structures through learning from a small-scale dataset (i.e. with small unit cells). Our work represents a significant stride in bridging the gap between materials characterization and atomic structure determination; in addition, it can be leveraged for materials discovery in exploring various material properties as targeted.

36 MATERIALS SCIENCE↗

DOE OSTI2024

First-order structural phase transition at low temperature in GaPt 5 P and its rapid enhancement with pressure

Single crystals of X Pt 5 ⁢P (X = Al, Ga, and In), belonging to the 1-5-1 family of compounds, were grown from a Pt-P solution at high temperatures, and measurements of the ambient pressure, temperature-dependent magnetization, resistivity, and x-ray diffraction were made. Additionally, the ambient-pressure Hall resistivity and temperature-dependent resistance under pressure were measured on GaPt 5 ⁢P. All three compounds have a tetragonal P4/mmm crystal structure at room temperature with metallic transport and weak diamagnetism over the 2–300 K temperature range. Surprisingly, at ambient pressure, both the transport and magnetization measurements on GaPt 5 ⁢P show a steplike feature in the 70–90 K region, suggesting a possible structural phase transition. Neither AlPt 5 ⁢P nor InPt 5 ⁢P have any signatures of a phase transition in their temperature-dependent electrical resistance and magnetization data. Both the hysteretic nature and sharpness of the features in the GaPt 5 ⁢P data suggest that the transition is first-order. Further, single-crystal x-ray diffraction measurements provided further details of the structural transition with a possibility of a crystal symmetry different from P⁢4/mmm below the transition temperature. The transition is characterized by anisotropic changes in the lattice parameters and a volume collapse with respect to the high-temperature tetragonal crystal structure. Furthermore, satellite peaks are observed at two distinct and nonequivalent wave vectors (0, 0, 0.5) and (0.5, 0.5, 0.5), and density functional theory calculations present phonon softening, especially at (0.5, 0.5, 0.5), as a possible driving mechanism. Additionally, we find that the structural transition temperature increases rapidly with increasing pressure, reaching room temperature by ~2.2 GPa, highlighting the high degree of pressure sensitivity of GaPt 5 ⁢P and fragile nature of its room-temperature structure. Even though the volume collapse and extreme pressure sensitivity suggest chemical pressure should drive a similar structural change in AlPt 5⁢ P, where both unit-cell dimensions and volume are smaller, its structure is found to be the same as that of the room-temperature GaPt 5 ⁢P. Overall, GaPt 5 ⁢P stands out as a sole member of the 1-5-1 family of compounds for which a temperature-driven structural change has been observed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Resolving local structural motifs across the phase evolution of zinc titanates with computational x-ray absorption spectroscopy

Resolving the local structure motifs that characterize phase evolution as a function of composition is a key challenge in structure characterization of complex materials. Here, in this study, we combine first-principles simulations and x-ray absorption near-edge structures (XANES) analysis to gain insights into the structure evolution revealed by measurements across a combinatorial zinc titanate thin film, which was grown with smoothly varying composition over a wide range of the Ti:Zn ratio. Specifically, we propose a cluster blind-signal-separation (cBSS) method for XANES spectral analysis based on a library of the structures and spectra of representative local motifs. In addition to motifs from zinc titanate crystals, two types of Ti-defect models constructed in this study are key to the understanding of the structure characteristics in the Zn-rich region. The cBSS method makes use of both spectral clustering of the simulated site-XANES spectra library and the BSS procedure to construct high-fidelity spectral basis functions from an experimental spectral sequence. The method provides a rigorous measure of the spectral sensitivity and basis completeness. The results of the XANES analysis are corroborated with other experimental modalities, including x-ray diffraction and spectroscopic ellipsometry, to validate the cBSS method. The calculated motif weights resulting from fitting the XANES spectra with the cBSS basis probe the atomic structure characteristics of both crystalline and amorphous phases as a function of the Ti/Zn composition. The insights of the local structure motif evolution are pivotal to the understanding of the nonmonotonic trend in the optical gap, which may lead to potential applications through tuning the optical properties of zinc titanate. The workflow of the XANES spectral analysis developed in this work can be generalized to construct the structure-property relationship in a broad material space.

36 MATERIALS SCIENCE↗

DOE OSTI2024

The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa . Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold ; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.

Bragagnolo, Nicholas↗

DOE OSTI2025

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗