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At least 577 records · Page 32

Reconstruction and uncertainty quantification of lattice Hamiltonian model parameters from observations of microscopic degrees of freedom

The emergence of scanning probe and electron beam imaging techniques has allowed quantitative studies of atomic structure and minute details of electronic and vibrational structure on the level of individual atomic units. These microscopic descriptors, in turn, can be associated with local symmetry breaking phenomena, representing the stochastic manifestation of the underpinning generative physical model. In this work, we explore the reconstruction of exchange integrals in the Hamiltonian for a lattice model with two competing interactions from observations of microscopic degrees of freedom and establish the uncertainties and reliability of such analysis in a broad parameter-temperature space. In contrast to other approaches, we specifically specify a loss function inherent to thermodynamic systems and utilize it to estimate uncertainty in simulated realizations of different models. As an ancillary task, we develop a machine learning approach based on histogram clustering to predict phase diagrams efficiently using a reduced descriptor space. We further demonstrate that reconstruction is possible well above the phase transition and in the regions of parameter space when the macroscopic ground state of the system is poorly defined due to frustrated interactions. This suggests that this approach can be applied to the traditionally complex problems of condensed matter physics such as ferroelectric relaxors and morphotropic phase boundary systems, spin and cluster glasses, and quantum systems once the local descriptors linked to the relevant physical behaviors are known.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

New crystals of the CsHSO{sub 4}–CsH{sub 2}PO{sub 4}–H{sub 2}O system

Cs{sub 6}H(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}){sub 4} crystals, grown for the first time based on an analysis of the phase diagram of the CsHSO{sub 4}–CsH{sub 2}PO{sub 4}–H{sub 2}O ternary system, have been investigated by structural analysis using synchrotron radiation. The atomic structure of the crystals is determined and its specific features are analyzed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ab initio generation of thermal neutron scattering law for uranium dioxide

Neutronic analysis of moderated nuclear fission systems, e.g. nuclear reactors, relies upon an accurate prediction of the thermal neutron spectrum. Thermal neutrons have wavelengths on the order of the interatomic spacing between atoms in matter. Consequently, the scattering cross-sections of these neutrons are affected by the scattering law of the material (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables), which describes the atomic structure and thermodynamic motion of the atomic nuclei. Uranium-dioxide (UO{sub 2}) is the primary fuel source for nuclear power reactors moderated by light water. In such systems (e.g. nuclear power reactors, spent fuel pools, etc.) the nuclear fuel comprises a large fraction of the system volume, approximately 1/3 in light-water reactors. Therefore, the scattering law of the fuel material may impact the thermal neutron spectrum and criticality of these systems. In this work previously established ab initio lattice dynamics (AILD) methods were utilized to calculate the phonon density of states (DOS), which acts as a fundamental input to the scattering law. Subsequently, the S(α,β) of UO{sub 2} was generated for publication as an ENDF thermal scattering library (TSL), which will be available for use in standard neutronics computer applications. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinement with minimal manual intervention. An explanation of the method is provided, augmented by results from the refinement of both synthetic and experimental low-resolution data, including an independent electrophysiological verification of the xMDFF-refined crystal structure of a voltage-sensor protein. X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs) by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs. The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au{sub 0.75}Ni{sub 0.25} favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs.

36 MATERIALS SCIENCE↗

Ceramic research

X-ray diffraction micrography data on atomic structure of magnesium oxide grain boundaries

X-RAY ANALYSIS↗

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗

Atomic layer deposition of 2D and 3D standards for synchrotron-based quantitative composition and structure analysis methods

Atomic layer deposition (ALD) is a scalable deposition technique known for producing uniform, conformal films of a wide range of compounds on nearly any substrate material. These traits make it an ideal deposition method for producing films to replace the National Institute of Standards and Technology (NIST) standards and create Standard Reference Materials (SRMs) on a wide range of relevant two-dimensional and three-dimensional substrates. The use of SRM from NIST for quantitative analysis of chemical composition using synchrotron based x-ray fluorescence (SR-XRF) and scanning transmission x-ray microscopy (STXM) is common. Such standards, however, can suffer from inhomogeneity in chemical composition and thickness and often require further calculations, based on sample mounting and detector geometry, to obtain quantitative results. These inhomogeneities negatively impact the reproducibility of the measurements and the quantitative measure itself. Utilizing Rutherford backscattering, x-ray reflectivity, quartz crystal microbalance, STXM, and SR-XRF, the authors show that ALD is capable of producing high quality standards that are homogenous over scales ranging from nanometers to 100s of micrometers.

Becker, Nicholas G.↗

Recent progress in characterization of the core–shell structure of black titania

The recent observation of spectacular photocatalytic activity enhancements generated tremendous interest in the synthesis, properties, and potential applications of black titania. Most black titania are core-shell structures consisting of a perfect crystalline core surrounded by a defective surface shell. Because the properties are attributed to the defective shell it is particularly critical, but very challenging to obtain atomic structure information of the core, the shell, and the core-shell relationship on a single particle level. While the role of various synthesis approaches for producing black titania with different properties has been extensively reviewed, this review focuses on understanding the structure-functionality relationship in black titania on a single particle level. We begin by introducing the crystal and electronic band structure of different TiO 2 phases, followed by discussion of particle size effects, the origin of lattice distortions, and phase control by synthesis, and concluding with discussion of crystalline order formation and evolution creating the defective shell.

36 MATERIALS SCIENCE↗

Atomistic modeling of crystal structure of Ca{sub 1.67}SiH{sub x}

The atomic structure of calcium-silicate-hydrate (C{sub 1.67}-S-H{sub x}) has been investigated by theoretical methods in order to establish a better insight into its structure. Three models for C-S-H all derived from tobermorite are proposed and a large number of structures were created within each model by making a random distribution of silica oligomers of different size within each structure. These structures were subjected to structural relaxation by geometry optimization and molecular dynamics steps. That resulted in a set of energies within each model. Despite an energy distribution between individual structures within each model, significant energy differences are observed between the three models. The C-S-H model related to the lowest energy is considered as the most probable. It turns out to be characterized by the distribution of dimeric and pentameric silicates and the absence of monomers. This model has mass density which is closest to the experimental one.

36 MATERIALS SCIENCE↗

X-ray and molecular dynamics study of the temperature-dependent structure of molten NaF-Zr⁢F 4

The local atomic structure of NaF-Zr⁢F 4 (53–47 mol%) molten system and its evolution with temperature are examined with x-ray scattering measurements which are then used to validate the quality of ab initio and neural network-based molecular dynamics (NNMD) calculations in the temperature range 515–700°⁢C. The machine-learning enhanced NNMD calculations offer improved efficiency while maintaining accuracy at higher distances compared to ab initio calculations. Looking at the evolution of the pair distribution function with increasing temperature, a fundamental change in the liquid structure within the selected temperature range, accompanied by a slight decrease in overall correlation is revealed. NNMD calculations indicate the coexistence of three different fluorozirconate complexes: [Zr⁢F 6 ] 2– , [Zr⁢F 7 ] 3– , and [Zr⁢F 8 ] 4– , with a shift in the dominant coordination state from the 7-coordinated Zr cation toward a 6-coordinated cation with increasing temperature. The study also highlights the metastability of different local coordination structures, with frequent interconversions between the 6- and 7-coordinate states. Analysis of the Zr-F-Zr angular distribution function reveals the presence of both “edge-sharing” and “corner-sharing” fluorozirconate complexes with specific bond angles and distances in accord with previous studies, while the next-nearest-neighbor cation-cation correlations demonstrate a clear preference for unlike cations as nearest-neighbor pairs, emphasizing nonrandom arrangement. Finally, these findings contribute to a comprehensive understanding of the complex local structure of the molten salt, providing insights into temperature-dependent preferences and correlations within the molten system.

36 MATERIALS SCIENCE↗

Effect of Annealing in a Ferromagnetic State on the Structure of an Fe–18 at % Ga Alloy

The atomic structure of the iron–gallium alloy containing 18 at % Ga has been studied by X-ray diffraction. The samples were annealed in the paramagnetic (T > T{sub C}) and ferromagnetic (T < T{sub C}) state. In the first case, the structural state was fixed by quenching from the annealing temperature into water; in the second case, the structural state was obtained by slow cooling. The structural studies of the single-crystal samples were conducted on a four-circle X-ray diffractometer at room temperature. From the X-ray diffraction data, it follows that the alloy, independently on the heat treatment, contains B2 clusters, i.e., locally ordered regions with the CsCl-type structure observed in alloys of iron with silicon (to 10 at % Si) and aluminum (7 at % Al) before. In addition to the B2‑clusters, regions with the D0{sub 3} short-range order are observed in the quenched sample; the sizes of these regions significantly increases after annealing in the ferromagnetic state, i.e., a long-range order forms. The relation of the fine structural changes in the alloy due to various heat treatments with its magnetoelastic and magnetostriction properties is discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Total-scattering pair-distribution function analysis of zinc from high-energy synchrotron data

The crystal structure of zinc metal deviates from the ideal hexagonal close packing structure by a significantly increased axial ratio (c/a). The local atomic structure of zinc metal is investigated using the total scattering atomic pair distribution function (PDF) analysis based on X-ray powder diffraction data collected at ambient conditions. The X-ray total scattering PDF analysis confirms that the crystal structure of zinc can be described in terms of wurtzite structure, but with an anomalously atomic displacement parameters U 33 , indicating a significant displacement disorder along the c-axis. For the long r-range PDF refinements, the thermal motion of zinc shows a notable anisotropy as expressed by the ratio U 33 /U 11 of 2.5 at ambient conditions. This average distortion level along the c-axis, was not reflected locally for the features below 5.0 Å as it fits the high r region. Based on PDF refinements over different r-ranges, we measure an interesting increase of the U 33 value with decreasing the r-range of the refinement. Finally, this suggests that the local structure features in zinc metal differ from the average structure ones.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Atomic Drill Bit: Precision Controlled Atomic Fabrication of 2D Materials

The ability to deterministically fabricate nanoscale architectures with atomic precision is the central goal of nanotechnology, whereby highly localized changes in the atomic structure can be exploited to control device properties at their fundamental physical limit. Here, an automated, feedback-controlled atomic fabrication method is reported and the formation of 1D–2D heterostructures in MoS 2 is demonstrated through selective transformations along specific crystallographic orientations. The atomic-scale probe of an aberration-corrected scanning transmission electron microscope (STEM) is used, and the shape and symmetry of the scan pathway relative to the sample orientation are controlled. The focused and shaped electron beam is used to reliably create Mo 6 S 6 nanowire (MoS-NW) terminated metallic-semiconductor 1D–2D edge structures within a pristine MoS 2 monolayer with atomic precision. From these results, it is found that a triangular beam path aligned along the zig-zag sulfur terminated (ZZS) direction forms stable MoS-NW edge structures with the highest degree of fidelity without resulting in disordering of the surrounding MoS 2 monolayer. Density functional theory (DFT) calculations and ab initio molecular dynamic simulations (AIMD) are used to calculate the energetic barriers for the most stable atomic edge structures and atomic transformation pathways. These discoveries provide an automated method to improve understanding of atomic-scale transformations while opening a pathway toward more precise atomic-scale engineering of materials.

2D materials↗

Tuning the Placement of Pt “Single Atoms” on a Mixed CeO 2 –TiO 2 Support

Defect sites on the oxide supports can be used to anchor and activate "single-atoms" catalysts (SACs). By engineering the anchoring sites for supporting SACs, one can alter their electronic and atomic structures which, in turn, define their activity, selectivity, and stability for catalytic reactions. To create and tune unique sites for Pt SACs on CeO 2 support, in this work, we synthesized a system consisting of CeO 2 decorated on TiO 2 nano-oxides for supporting the Pt SACs and investigated the effect of Pt weight loading. Here, a combination of multiple structural characterization methods including diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) were employed to characterize the distribution of charge states of single atoms and evaluate the heterogeneity of their binding sites. We have found that the placement of Pt atoms can be tuned on a mixed oxide surface by changing the weight loading of Pt.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

In situ synchrotron pair distribution function analysis to monitor synthetic pathways under electromagnetic excitation

Electromagnetic (EM) fields, specifically microwave radiation (MWR), can significantly influence the synthesis of ceramic oxide materials and promote rapid, low-temperature growth. However, the mechanisms by which EM fields affect the phase formation process are not well understood. A major limitation to increasing this understanding has been the lack of information regarding dynamic changes in local atomic structure during MWR exposure compared to conventional hydrothermal synthesis routes. Here, we utilize in situ synchrotron X-ray pair distribution function (PDF) analysis to monitor MWR-assisted SnO 2 nanoparticle synthesis. A clear impact of the EM field is demonstrated, with MWR inducing changes in nearest neighbor distances and peaks in oxygen atomic displacement that do not occur during synthesis without MWR exposure. The observed local structural disorder serves as a precursor to rapid rutile SnO 2 nanoparticle crystallization, suggesting that EM field-assisted growth is mediated by changes to the oxygen sublattice. These findings further our understanding of the mechanisms underlying MWR-assisted synthesis and represent a step towards utilizing EM fields to engineer tailored atomic structures for a broad range of applications.

36 MATERIALS SCIENCE↗