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At least 577 records · Page 32

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗

Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery (DTRA Basic Research Final Report)

The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.

97 MATHEMATICS AND COMPUTING↗

Effect of various material properties on the adhesive stage of fretting

Various properties of metals and alloys have been studied with respect to their effect on the initial stage of the fretting process, namely adhesion. Crystallographic orientation, crystal structure, interfacial binding energies of dissimiliar metal, segregation of alloy constituents and the nature and structure of surface films have all been found to influence adhesion. High atomic density, low surface energy grain orientations exhibit lower adhesion than other orientations. Hexagonal metals in general manifest less adhesive wear than cubic metal. Knowledge of interfacial surface binding energies can assist in predicting adhesive transfer and wear. Selective surface segregation of alloy constituents can accomplish both a reduction in adhesion and improved surface oxidation characteristics. Equivalent surface coverages of various adsorbed species indicate that some are markedly more effective in inhibiting adhesion than others.

Buckley, D. H.↗

Effect of various material properties on the adhesive stage of fretting

Various properties of metals and alloys have been studied with respect to their effect on the initial stage of the fretting process, namely adhesion. Crystallographic orientation, crystal structure, interfacial binding energies of dissimiliar metal, segregation of alloy constituents and the nature and structure of surface films have all been found to influence adhesion. High atomic density, low surface energy grain orientations exhibit lower adhesion than other orientations. Hexagonal metals in general manifest less adhesive wear than cubic metal. Knowledge of interfacial surface binding energies can assist in predicting adhesive transfer and wear. Selective surface segregation of alloy constituents can accomplish both a reduction in adhesion and improved surface oxidation characteristics. Equivalent surface coverages of various adsorbed species indicate that some are markedly more effective in inhibiting adhesion than others.

Buckley, D. H.↗

Statistical evaluation of microscale stress conditions leading to void nucleation in the weak shock regime

Here, we investigate the heterogeneity of the stress state driven by anisotropic deformation response at the single crystal level through five statistical volume element (SVE) calculations of polycrystalline BCC tantalum. This work focuses on grain boundaries as a prominent material defect type prone to void nucleation based upon experimental observations of predominantly intergranular void nucleation in this material. The SVEs are constructed to be statistically representative of larger volumes of material and are meshed such that mean and standard deviation of grain size and orientation information is reconstructed. The computational meshes feature hexahedral (brick) elements and smooth conformal grain boundaries where significant stress concentration is known to occur, a tail effect of interest in the extreme events process of dynamic ductile damage. An existing micromechanical crystallographic plasticity model shown to capture the single crystal behavior of BCC tantalum well is used to perform the polycrystal calculations. The model includes representation of the non-Schmid effect of non-planar screw dislocation kinetics in tantalum. A three-dimensional stress state time profile predicted by damage modeling of a flyer plate impact experiment is applied as boundary conditions to each SVE. Resulting grain boundary stress state statistics are strongly non-Gaussian. Significant structural evolution is observed within the compressive hold before unloading into tension in the stress profile. Strong angular dependence of grain boundary traction magnitude with shock direction is observed. Non-Schmid effects continue to suggest their influence on propensity of microstructural defect types to nucleate voids. A general void nucleation criterion is proposed using probability theory. The general framework is specified to polycrystalline BCC tantalum in the weak shock regime to include the SVE calculations and literature molecular dynamics calculations of grain boundary void nucleation strength. Probability density functions (PDFs) are used to describe the interaction between the local stress state heterogeneity and the distributed grain boundary void nucleation strength state. A causation entropy maximization procedure removes the requirement for ad hoc selection of a PDF functional form and provides a rigorous procedure for data-based PDF determination. The resulting physically informed PDF describes the spatial appearance frequency of nucleated voids as a function of applied macroscale pressure. Lower length scale physics are thus packaged in a precise and computationally efficient way to provide computational plasticity insight to macroscale dynamic ductile damage models.

36 MATERIALS SCIENCE↗

Unveiling X-ray absorption signatures of boron nitride via first-principles simulation and machine learning

Boron nitride (BN) allotropes hold great promise in many advanced applications ranging from optical and photonic devices to energy storage and battery systems to tribological components. The diverse functionalities of this material stem from BN’s highly tunable structural and electronic properties, which are governed by the versatile boron–nitrogen bonding configurations. Exploring the structural landscape of BN can unveil novel structures possessing unique properties suited for specific applications, therefore accelerating the design of next-generation advanced functional materials. In this work, we leverage boron K-edge X-ray absorption spectroscopy (XAS) as an effective probe for local structural features and chemical environments. A total of 210 BN crystal structures are generated via analogies to the extensive array of carbon allotropes, and XAS is simulated for each unique local motif within the resulting collection of structures. A mapping between structural features and spectral signatures was established by synergizing first-principle simulations with data-driven based post-analysis approaches. Specifically, we developed a neural network model that can satisfactorily predict spectra line shapes from local structural descriptors. Toward automatic spectroscopic interpretation of any new BN structures, supervised machine learning models, trained on this structure–spectrum dataset, can accurately infer local coordination environments from simulated XAS, highlighting the strength of this unique approach of combining high-fidelity first-principles simulation and machine-learning to accelerate target design of novel BN materials via rational understanding of local structure-spectrum correlations.

36 MATERIALS SCIENCE↗

Embracing disorder in quantum materials design

Many of the most exciting materials discoveries in fundamental condensed matter physics are made in systems hosting some degree of intrinsic disorder. While disorder has historically been regarded as something to be avoided in materials design, it is often of central importance to correlated and quantum materials. This is largely driven by the conceptual and theoretical ease to handle, predict, and understand highly uniform systems that exhibit complex interactions, symmetries, and band structures. In this Perspective, we highlight how flipping this paradigm has enabled exciting possibilities in the emerging field of high entropy materials, focusing primarily on high entropy oxide and chalcogenide quantum materials. These materials host high levels of cation or anion compositional disorder while maintaining unexpectedly uniform single crystal lattices. The diversity of atomic scale interactions of spin, charge, orbital, and lattice degrees of freedom are found to emerge into coherent properties on much larger length scales. Thus, altering the variance and magnitudes of the atomic scale properties through elemental selection can open new routes to tune global correlated phases, such as magnetism, metal–insulator transitions, ferroelectricity, and even emergent topological responses. The strategy of embracing disorder in this way provides a much broader pallet from which functional states can be designed for next-generation microelectronic and quantum information systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Heterostructural interface engineering for ultrawide-gap nitrides from first principles: Ta C / Al N and Ta C / Ga N rocksalt-wurtzite interfaces

Epitaxial lattice matching is an important condition for the formation of coherent interfaces with low defect densities. However, lattice-matched substrates with the same crystal structure as the active layer are often not available, suggesting opportunities for utilizing heterostructural interfaces. For example, at high Al contents that are interesting for ultrawide-gap applications in power electronics, Al x ⁢Ga 1-x ⁢N semiconductor alloys in the (0001) orientation of the wurtzite (wz) structure become lattice-matched to (111)-oriented rocksalt (rs) Ta⁢C substrates. To predict the expected interface atomic structures under different synthesis conditions, we perform high-throughput density-functional-theory calculations, using an algorithm for systematic sampling of the possible stacking sequences of the atomic layers on the in-plane hexagonal lattice. The approach considers octahedral, tetrahedral, and prismatic coordination motifs, and is generally applicable for the modeling of commensurate rs/wz heterostructural interfaces. Our results provide guidance for synthesis control of substrate-film bonding and the polarity of ultrawide-gap Al x⁢ Ga 1-x⁢ N alloys on Ta⁢C substrates.

36 MATERIALS SCIENCE↗

(Mg,Mn,Fe,Co,Ni)O: A rocksalt high-entropy oxide containing divalent Mn and Fe

High-entropy oxides (HEOs) have aroused growing interest due to fundamental questions relating to their structure formation, phase stability, and the interplay between configurational disorder and physical and chemical properties. Introducing Fe(ιι) and Mn(ιι) into a rocksalt HEO is considered challenging, as theoretical analysis suggests that they are unstable in this structure under ambient conditions. Here, we develop a bottom-up method for synthesizing Mn- and Fe-containing rocksalt HEO (FeO-HEO). We present a comprehensive investigation of its crystal structure and the random cation-site occupancy. We show the improved structural robustness of this FeO-HEO and verify the viability of an oxygen sublattice as a buffer layer. Compositional analysis reveals the valence and spin state of the iron species. We further report the antiferromagnetic order of this FeO-HEO below the transition temperature ~218 K and predict the conditions of phase stability of Mn- and Fe-containing HEOs. Our results provide fresh insights into the design and property tailoring of emerging classes of HEOs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Embracing Disorder in Quantum Materials Design

Many of the most exciting materials discoveries in fundamental condensed matter physics are made in systems hosting some degree of intrinsic disorder. While disorder has historically been regarded as something to be avoided in materials design, it is often of central importance to correlated and quantum materials. This is largely driven by the conceptual and theoretical ease to handle, predict, and understand highly uniform systems that exhibit complex interactions, symmetries, and band structures. In this Perspective, we highlight how flipping this paradigm has enabled exciting possibilities in the emerging field of high entropy materials, focusing primarily on high entropy oxide and chalcogenide quantum materials. These materials host high levels of cation or anion compositional disorder while maintaining unexpectedly uniform single crystal lattices. The diversity of atomic scale interactions of spin, charge, orbital, and lattice degrees of freedom are found to emerge into coherent properties on much larger length scales. Thus, altering the variance and magnitudes of the atomic scale properties through elemental selection can open new routes to tune global correlated phases, such as magnetism, metal–insulator transitions, ferroelectricity, and even emergent topological responses. The strategy of embracing disorder in this way provides a much broader pallet from which functional states can be designed for next-generation microelectronic and quantum information systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Venturing into Unexplored Phase Space: Synthesis, Structure, and Properties of MgCo 3 B 2 Featuring a Rumpled Kagomé Network

MgCo 3 B 2 , a novel ternary boride in a previously unexplored phase space, was synthesized using the hydride route. In situ powder X-ray diffraction and DFT calculations aided in the discovery of this compound, whose structure was then determined by single-crystal X-ray diffraction. Like the closely related CeCo 3 B 2 , MgCo 3 B 2 crystallizes in centrosymmetric space group P6/mmm (a = 4.883(2) Å, c = 2.926(2) Å at 210 K, Z = 1). Unlike CeCo 3 B 2 , however, it adopts a disordered structure that features a rumpled Kagomé network of Co atoms, and Mg atoms fill the channels of a Co–B framework. Although the structural disorder leads to motifs that are similar to those observed in MgNi 3 B 2 and other related ternary borides, no evidence of an ordered superstructure was found by single-crystal X-ray diffraction or high-resolution powder X-ray diffraction. In the case of CeCo 3 B 2 , boron atoms occupy the center of regular Co 6 trigonal prisms; in MgCo 3 B 2 , boron atoms are shifted from the center of the prism to form B–B dimers with roughly the same length as those found in MgNi 3 B 2 . Magnetic susceptibility data exhibit an unusual temperature dependence that cannot be convincingly modeled by the modified Curie–Weiss equation, consistent with DFT calculations predicting a nonmagnetic ground state. Intrinsic susceptibility at 300 K is 1.42 × 10 –3 emu/mol Oe, which is comparable to that of paramagnetic YCo 3 B 2 and CeCo 3 B 2 with a similar structure and composition. Here, this study showcases the efficacy of combining several methodologies to discover new solids in unexplored phase spaces. This approach includes in situ PXRD data to monitor reactions of precursors upon heating, a diffusion-enhanced synthesis method, and DFT assessment of compound stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Er Al :Al 2 ⁢O 3 for telecom-band photonics: Electronic structure and optical properties

Er-doped Al 2 ⁢O 3 is a promising host for telecom-band integrated photonics. Here, in this study, we combine ab initio calculations with a symmetry-resolved analysis to elucidate substitutional Er on the Al site (Er Al ) in 𝛼−Al 2 ⁢O 3 . First-principles relaxations confirm the structural stability of Er Al . We then use the local trigonal crystal-field symmetry to classify the Er-derived impurity levels by irreducible representations and to derive polarization-resolved electric-dipole selection rules, explicitly identifying the symmetry-allowed 𝑓−𝑑 hybridization channels. Kubo-Greenwood absorption spectra computed from Kohn-Sham states quantitatively corroborate these symmetry predictions. Furthermore, we connect the calculated intra-4⁢𝑓 line strengths to Judd-Ofelt theory, clarifying the role of 4⁢𝑓−5⁢𝑑 admixture in enabling optical activity. Notably, we predict a characteristic absorption near 1.47 µ⁢m (telecom band), relevant for on-chip amplification and emission. To our knowledge, a symmetry-resolved first-principles treatment of Er:Al 2 ⁢O 3 with an explicit Judd-Ofelt interpretation has not been reported, providing a transferable framework for tailoring rare-earth dopants in wide-band-gap oxides for integrated photonics. Our results for the optical spectra are in good agreement with experimental data. The resulting symmetry-based selection rules translate directly to polarization-dependent coupling in Al 2 ⁢O 3 integrated photonic waveguides and resonators, enabling device-level design of TE/TM-mode interaction with Er emitters in the 1.5-µ⁢m telecom band.

Er-doped Al2O3↗

Symmetry relation database and its application to ferroelectric materials discovery

To investigate the displacive phase transition at the atomic scale, we have implemented a numerical algorithm to automate the detection of the symmetry relations between any two candidate crystal structures. Using this algorithm, here we systematically screen all possible polar–nonpolar structure pairs from the Materials Project database and establish a library of ~4500 pairs that can be connected through a continuous phase transition with small atomic displacements. From this database, we identify several new ferroelectric materials. In addition, the database may also be used in other areas, such as material structure prediction and new materials discovery.

36 MATERIALS SCIENCE↗

Energy efficient engine high-pressure turbine detailed design report

The energy efficient engine high-pressure turbine is a single stage system based on technology advancements in the areas of aerodynamics, structures and materials to achieve high performance, low operating economics and durability commensurate with commercial service requirements. Low loss performance features combined with a low through-flow velocity approach results in a predicted efficiency of 88.8 for a flight propulsion system. Turbine airfoil durability goals are achieved through the use of advanced high-strength and high-temperature capability single crystal materials and effective cooling management. Overall, this design reflects a considerable extension in turbine technology that is applicable to future, energy efficient gas-turbine engines.

Thulin, R. D.↗

An investigation of high entropy alloy conductivity using first-principles calculations

The Kubo–Greenwood equation, in combination with the first-principles Korringa–Kohn–Rostoker coherent potential approximation (KKR-CPA) can be used to calculate the DC residual resistivity of random alloys at T = 0 K. We implemented this method in a multiple scattering theory based ab initio package, MuST, and applied it to the ab initio study of the residual resistivity of the high entropy alloy Al x CoCrFeNi as a function of x. The calculated resistivities are compared with experimental data. We also predict the residual resistivity of refractory high entropy alloy MoNbTaV x W. Furthermore, the calculated resistivity trends are also explained using theoretical arguments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A New Nitrogen-Rich Energetic Material with So Many Tautomers

A new nitrogen-rich triazolo-triazole compound, (3-(6-methyl-1H-[1,2,4]triazolo[4,3-b][1,2,4]triazol-3-yl)-1H-1,2,4-triazol-5-amine), TTT1, has been prepared, and its acid–base and tautomeric behavior has been investigated. In the pH range of 0.3–12, TTT1 can accept up to two protons, forming a monocation and a dication, and can deliver one proton, forming a monoanion. The tautomeric behavior is particularly rich for the monocation, for which computational analysis predicts four different tautomers in a narrow energy range of 2 kcal/mol. Two of these tautomers (2H-7H-8H and 3H-7H-8H) have been isolated in salts of the monocation with suitable counterions (chloride, bromide, perchlorate). Surprisingly, the most stable predicted tautomer, 1H-3H-7H, has not been found in the four crystallized salts of the monocation. The energetic perchlorate salt of the monocation (3H-7H-8H tautomer) shows good thermal stability and good stability to impact, friction, and electric discharge. The packing of this compound shows the formation of H-bonded dimers with interactions between N8–H···N1. The crystal structure of this energetic salt was studied experimentally up to 2.8 GPa; no phase change or decomposition was observed.

Chemical structure↗

Recovery and facets for deformation twins in minerals and metals

Type II and IV twins with irrational twin boundaries are studied by high-resolution transmission electron microscopy in two plagioclase crystals. The twin boundaries in these and in NiTi are found to relax to form rational facets separated by disconnections. The topological model (TM), amending the classical model, is required for a precise theoretical prediction of the orientation of the Type II/IV twin plane. Theoretical predictions also are presented for types I, III, V, and VI twins. The relaxation process that forms a faceted structure entails a separate prediction from the TM. Hence, faceting provides a difficult test for the TM. Analysis of the faceting by the TM is in excellent agreement with the observations.

36 MATERIALS SCIENCE↗

Benchmarking universal machine learning interatomic potentials for rapid analysis of inelastic neutron scattering data

The accurate calculation of phonons and vibrational spectra remains a significant challenge, requiring highly precise evaluations of interatomic forces. Traditional methods based on the quantum description of the electronic structure, while widely used, are computationally expensive and demand substantial expertise. Emerging universal machine learning interatomic potentials (uMLIPs) offer a transformative alternative by employing pre-trained neural network surrogates to predict interatomic forces directly from atomic coordinates. This approach dramatically reduces computation time and minimizes the need for technical knowledge. In this paper, we produce a phonon database comprising nearly 5000 inorganic crystals to benchmark the performance of several leading uMLIPs. We further assess these models in real-world applications by using them to analyze experimental inelastic neutron scattering data collected on a variety of materials. Through detailed comparisons, we identify the strengths and limitations of these uMLIPs, providing insights into their accuracy and suitability for fast calculations of phonons and related properties, as well as the potential for real-time interpretation of neutron scattering spectra. Our findings highlight how the rapid advancement of AI in science is revolutionizing experimental research and data analysis.

inelastic neutron scattering↗