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At least 109 records · Page 6

Optimal invariant sets for atomistic machine learning

The representation of atomic configurations for machine learning models has led to numerous sets of descriptors. However, many descriptor sets are incomplete and/or functionally dependent. Incomplete sets cannot faithfully represent atomic environments. Yet complete constructions often suffer from a high degree of functional dependence, where some descriptors are functions of others. These redundant descriptors do not improve discrimination between atomic environments. We employ pattern recognition techniques to remove dependent descriptors to produce the smallest possible set that satisfies completeness. We apply this in two ways: First, we refine an existing description, the atomic cluster expansion. Second, we augment an incomplete construction, yielding a new message-passing neural network architecture that can recognize up to 5-body patterns. This architecture shows strong accuracy on state-of-the-art benchmarks while retaining low computational cost. Our results demonstrate the utility of this strategy to optimize descriptor sets across a range of descriptors and application datasets.

97 MATHEMATICS AND COMPUTING↗

Evaluation of the GaAs displacement damage metric using updated nuclear data

The emerging use of the physics-based athermal recombination-corrected displacement per atom (arc-dpa) model for the displacement damage efficiency has motivated a re-evaluation of the historical empirically-derived GaAs damage response function with the purpose of highlighting needs for future analytical and experimental work. The 1-MeV neutron damage equivalence methodology used in the ASTM E-722 standard for GaAs has been re-evaluated using updated nuclear data. This yielded a higher fidelity representation of the GaAs displacement kerma and, through the use of the refined PKA recoil energy-dependent damage efficiency model, an updated 1-MeV(GaAs) displacement damage function. This re-evaluation included use of the Norgett-Robinson-Torrens (NRT) model for an updated threshold treatment, rather than the sharp-threshold Kinchin-Pease model used in the current ASTM standard. The underlying nuclear data evaluations have been updated to use the ENDF/VIII.0 {sup 75}As and TENDL-2019 {sup 71}Ga/{sup 69}Ga evaluations. The displacement kerma and 1-MeV-equivalent damage responses were calculated using a modified NJOY-2016 code which allowed for refinements in some of the damage models. This paper shows that an updated displacement damage function, based upon the latest nuclear data, is consistent with the experimental data used to develop the current ASTM E-722 GaAs standard. Using a double ratio approach to compare the available experimental data with the calculated response, the average legacy double ratio was found to be 0.97 ± 0.05 and the average updated double ratio was found to be 0.94 ± 0.05. (authors)

36 MATERIALS SCIENCE↗

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

Large-eddy simulation of non-vaporizing sprays using the spectral-element method

Predictive simulations of high-pressure sprays require accurate representation of the turbulent gaseous flow field generated by liquid jet. Typically, the accuracy that can be obtained with low-order numerical methods (e.g. finite volume, finite element) is limited by stability issues in fine grids and the order of convergence of the method. In this work, we resolve the turbulent flow field in an Eulerian manner using the high-order spectral element method, coupled with a Lagrangian parcels approach to model the atomizing liquid jet. Large eddy simulations of single-hole sprays under non-evaporative conditions were conducted and compared against experimental data from Margot et al. (2008) and Spray A data from the Engine Combustion Network. The sensitivity of liquid penetration and droplet sizes to different breakup model parameters was studied. The effect of different numerical parameters, such as polynomial order of the solution (grid resolution), on liquid penetration was also analyzed. The method achieved grid-independent results using p-refinement, achieving finer resolution (by a factor of x 1.7 - x 3.5) in the gas-phase solution than in state-of-the-art simulations using the finite-volume method. Here the results showed good agreement with experimental data, demonstrating the ability of the current method to accurately capture liquid penetration and the shape of the spray.

97 MATHEMATICS AND COMPUTING↗

International Low-Earth-Orbit Spacecraft Materials Test Program Initiated for Better Prediction of Durability and Performance

Spacecraft in low Earth orbit (LEO) are subjected to many components of the environment, which can cause them to degrade much more rapidly than intended and greatly shorten their functional life. The atomic oxygen, ultraviolet radiation, and cross contamination present in LEO can affect sensitive surfaces such as thermal control paints, multilayer insulation, solar array surfaces, and optical surfaces. The LEO Spacecraft Materials Test (LEO-SMT) program is being conducted to assess the effects of simulated LEO exposure on current spacecraft materials to increase understanding of LEO degradation processes as well as to enable the prediction of in-space performance and durability. Using ground-based simulation facilities to test the durability of materials currently flying in LEO will allow researchers to compare the degradation evidenced in the ground-based facilities with that evidenced on orbit. This will allow refinement of ground laboratory test systems and the development of algorithms to predict the durability and performance of new materials in LEO from ground test results. Accurate predictions based on ground tests could reduce development costs and increase reliability. The wide variety of national and international materials being tested represent materials being functionally used on spacecraft in LEO. The more varied the types of materials tested, the greater the probability that researchers will develop and validate predictive models for spacecraft long-term performance and durability. Organizations that are currently participating in the program are ITT Research Institute (USA), Lockheed Martin (USA), MAP (France), SOREQ Nuclear Research Center (Israel), TNO Institute of Applied Physics (The Netherlands), and UBE Industries, Ltd. (Japan). These represent some of the major suppliers of thermal control and sensor materials currently flying in LEO. The participants provide materials that are exposed to selected levels of atomic oxygen, vacuum ultraviolet radiation, contamination, or synergistic combined environments at the NASA Lewis Research Center. Changes in characteristics that could affect mission performance or lifetime are then measured. These characteristics include changes in mass, solar absorptance, and thermal emittance. The durability of spacecraft materials from U.S. suppliers is then compared with those of materials from other participating countries. Lewis will develop and validate performance and durability prediction models using this ground data and available space data. NASA welcomes the opportunity to consider additional international participants in this program, which should greatly aid future spacecraft designers as they select materials for LEO missions.

Rutledge, Sharon K.↗

Large Angle Rocking Beam Electron Diffraction Utilizing Electron Direct Detector

Electron diffraction of a crystal is fundamentally a function of the potential of that crystal. The intensity of electron diffraction patterns is, as a result, sensitive to the charge density of atoms and bonding inside crystals. Experimentally, the traditional method to probe this information is quantitative Convergent Beam Electron Diffraction (CBED). Quantitative CBED or QCEBD is a method which uses dynamic diffraction theory to quantify CBED intensities and to extract information about crystal structure and bonding. The sensitivity of dynamical scattering is leveraged to measure crystal symmetry and crystal structure factors. At its limit, electron structure factors are measured at high accuracy allowing access to chemical bonding information, which corroborate theoretical calculations through multipole model refinements of the experimental charge density. The primary limit to QCBED is the requirement of a non-overlapping convergent beam. This subsequently limits QCBED to crystals with small unit cells which are stable under the focused probe.

Busch, Robert↗

Synthesis, crystal and electronic structure of the Zintl phase Ba 16 Sb 11 . A case study uncovering greater structural complexity via monoclinic distortion of the tetragonal Ca 16 Sb 11 structure type

The binary Zintl phase Ba 16 Sb 11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba 16 Sb 11 appears to crystallize in the tetragonal Ca 16 Sb 11 structure type (space group $P\bar{4}2_1$m with a=13.5647(9) Å, c=12.4124(12)Å, Z=2, R 1 = 3.14%; wR 2 = 4.77%), there exists an extensive structural disorder. Some Ba 16 Sb 11 crystals were found to be monoclinic and the structure was solved and refined in space group P2 1 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R 1 =5.84 %; wR 2 =9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural model. In both descriptions, the disordered tetragonal and the ordered monoclinic superstructure, the basic building units that make up the structure of this Ba-rich compound are pairs of face-shared square antiprisms of Ba atoms, which are centered by Sb atoms. The dimerized antiprisms are linked into parallel chains via square prisms of Ba atoms, which are also centered by Sb atoms. The Zintl concept can be applied in a straightforward manner and as result, the structure of Ba 32 Sb 22 (=2×Ba 16 Sb 11 ) can be rationalized as (Ba 2+ ) 32 (Sb 3– ) 20 [Sb 2 ] 4– . Notably, the partitioning of the valence electrons is done taking into an account the homoatomic Sb–Sb contacts (d=3.01 Å), which can be clearly distinguished in the lower symmetry space group. Electronic structure calculations of Ba 16 Sb 11 are in good accordance with the Zintl rationalization and predict a semiconductor with a band gap of 0.77 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic Layer Deposition for Improved Biomass Conversion Catalysts

Heterogeneous catalysts are a key enabler of the transition towards a sustainable, bio-based economy for fuels and chemicals. However, the harsh conditions in many biomass conversion processes lead to nanoparticle sintering, support collapse, and metal leaching in conventional PGM catalysts. Next-generation catalysts must be developed to address these stability challenges. This presentation will discuss ongoing work between the Catalytic Carbon Transformation & Scale-Up Center at NREL and various industrial partners to develop scalable, cost-effective atomic layer deposition (ALD) coatings for improving the performance of biomass conversion catalysts. Substantial focus will be devoted to the benefits of TiO2 ALD coatings on supported Pd hydrogenation catalysts. Ten cycles of TiO2 ALD were found to dramatically improve the activity of a conventional Pd/Al2O3 catalyst towards aromatic hydrogenation, despite partial coverage of the Pd sites by the ALD layer. Subsequent advanced characterization and atomic-scale computational modeling revealed that the ALD coating influenced the adsorption strength of hydrogenation surface intermediates in unexpected ways, leading to higher reaction rates. Reaction testing after exposure to sulfur impurities, high temperature oxidation, and hydrothermal treatment demonstrated the improved stability of the ALD-coated catalyst. Additionally, the ALD synthesis process was found to be scalable over two orders of magnitude with minimal deviation in synthesized catalyst properties. These results were contextualized with cost models of industrial ALD coating and aromatic hydrogenation processes to further refine the value proposition of ALD coatings. Given the demonstrated improvements in hydrogenation, TiO2 ALD coatings have also been applied to supported Pt catalysts for use in other biomass conversion reactions, such as hydrodeoxygenation for production of sustainable aviation fuel (SAF) and the oxidation of glucose for bio-derived gluconic acid. Recent findings from these experimental campaigns will also be shared. ALD technology holds great potential in the development of next-generation catalysts for biofuels and bioproducts and this work constitutes an important examination of the impact of ALD coatings in a variety of reaction environments.

bioenergy↗

Mechanical properties of zeolite-templated carbons from approximate density functional theory calculations

Zeolite-templated carbon (ZTC) is a unique porous carbonaceous material whose structure is ordered at the nanometre scale, enabling a representative periodic description at the atomistic level. Utilizing an existing, well-defined reference model for ZTCs, a structural library of varying compositions was developed by refinement using density-functional tight-binding (DFTB) potentials parameterized for materials science applications. We first determined the quantum chemical-refined structures of models with CH, CHO, CHON, CHOB, and CHOBN compositions with various degrees of heteroatom substitution. These structural models comprise the characteristic morphological features of highly porous carbon materials, such as open-blade surfaces, edges, saddles, and closed-strut formations, spanning a range of curvatures and characteristic sizes. Second, we carried out alternating compression and expansion of the CHO model unit cell to determine the lowest energy structure as well as to obtain its bulk modulus in order to demonstrate a close connection between macroscopic observations and atomic-scale structures. Further, the agreement between experimental measurements and the computational model is remarkable and demonstrates the power of approximate density functional theory as a cost-effective computational tool with chemical accuracy for the investigation of structure/property relationships in real-world carbon-based solids.

03 NATURAL GAS↗

MELCOR Model Development of the General Atomics Fast Modular Reactor

General Atomics Electromagnetic Systems (GA-EMS) is currently developing a fast modular reactor (FMR) capable of providing safe, carbon-free electricity by 2035. As part of the development process, researchers at the University of Wisconsin-Madison (UWM) use MELCOR 2.2 to develop a simulation model of the proposed design to perform accident analyses. This paper summarizes the efforts of researchers at UWM in the creation of the FMR model. This model was built based on initial FMR design parameters. The design parameters will change as the design evolves and is refined.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

AToM: Advanced Tokamak Modeling Environment

Stability constraints play an important role in integrated modeling. The global plasma stability and macro-instabilities such as internal kink modes, neoclassical tearing modes, and edge localized perturbations limit the plasma performance and can result in large-scale transient events and plasma disruptions. These macro-instabilities can be also beneficial to the plasma performance. For example, the peeling models often lead to the edge localized modes (ELMs). However, the formation of stationary edge harmonic oscillations (EHOs) due to nonlinear interaction of peeling modes can result in a transition to the Quiescent H-mode (QH-mode) without ELMs. The profiles predicted with transport models need to be refined using the MHD stability constraints. This is important especially for transient and nonlinear stages of discharges such as ramp-up access to hybrid and steady state operation, and L- to H-mode transition as well as transition to the QH-mode. Several stability and MHD codes are already included in the OMFIT framework. These codes include BALOO, ELITE, GATO, M3DC1, MARS, and NIMROD. However, the verifications of stability constraints are currently mostly excluded from transport modeling workflows. The only exception is the EPED module which includes the ELITE predictions to limit the pedestal height. Here, we improved the OMFIT workflow to include stability calculations. Including the stability conditions to the integrated modeling workflow improved the robustness of the predictive modeling discharges. Being implemented in the workflow, the stability conditions can be also used for the stability analysis of experimental data. This improved the physics understanding of various discharge scenarios and can be used in experiment planning.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Towards a Robust Adaptive Digital Twin for Fusion Applications

The development of a digital twin system for fusion applications is essential for enhancing the prediction, analysis, and optimization of complex plasma processes. Machine learning (ML), particularly deep learning has demonstrated strong capabilities in modeling such highly nonlinear and intricate systems. However, two critical challenges limit the deployment of deep learning-based digital twins: Uncertainty Quantification (UQ) and data drift. UQ is vital for ensuring trustworthy predictions, especially in decision-support scenarios. Additionally, data-driven models are often sensitive to changes in the underlying data distribution, such as shot-to-shot variations in fusion experiments, which can lead to performance degradation over time. To address these challenges, we are developing an uncertainty-aware, adaptive digital twin framework. Our approach incorporates deep learning models enhanced with Gaussian Process approximations for predictive uncertainty estimation, coupled with an online learning mechanism that enables continuous model adaptation to new experimental data. This adaptive capability allows the data driven models to respond effectively to evolving plasma behaviors and equipment conditions. Specifically, to mitigate the effects of shot-to-shot drift, our system updates itself incrementally as new data becomes available, improving both robustness and fidelity. Our vision is to evolve this data driven model into a self-sustaining digital twin system that leverages UQ based feedback to continuously refine itself and potentially support real-time decision making. This presentation will cover a brief background on uncertainty quantification for ML, our ongoing effort on development of UQ capabilities for ML, our data science pipeline from data collection to model development and analysis and online learning framework for modeling coil deflection at DIII-D. I will also briefly touch upon opportunities and challenges in development of digital twin framework.

Sammuli, Brian [General Atomics]↗

Experimental X-ray Charge-Density Studies–A Suitable Probe for Superconductivity? A Case Study on MgB 2

Case studies of 1T-TiSe 2 and YBa 2 Cu 3 O 7-δ have demonstrated that X-ray diffraction (XRD) studies can be used to trace even subtle structural phase transitions which are inherently connected with the onset of superconductivity in these benchmark systems. However, the utility of XRD in the investigation of superconductors like MgB 2 lacking an additional symmetry-breaking structural phase transition is not immediately evident. Nevertheless, high-resolution powder XRD experiments on MgB 2 in combination with maximum entropy method analyses hinted at differences between the electron density distributions at room temperature and 15 K, that is, below the T c of approx. 39 K. The high-resolution single-crystal XRD experiments in combination with multipolar refinements presented here can reproduce these results but show that the observed temperature-dependent density changes are almost entirely due to a decrease of atomic displacement parameters as a natural consequence of a reduced thermal vibration amplitude with decreasing temperature. Our investigations also shed new light on the presence or absence of magnesium vacancies in MgB 2 samples–a defect type claimed to control the superconducting properties of the compound. Here, we propose that previous reports on the tendency of MgB 2 to form non-stoichiometric Mg 1–x B 2 phases (1 – x ~ 0.95) during high-temperature (HT) synthesis might result from the interpretation of XRD data of insufficient resolution and/or usage of inflexible refinement models. Indeed, advanced refinements based on an Extended Hansen–Coppens multipolar model and high-resolution X-ray data, which consider explicitly the contraction of core and valence shells of the magnesium cations, do not provide any significant evidence for the formation of non-stoichiometric Mg 1–x B 2 phases during HT synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward accurate measurement of electromagnetic field by retrieving and refining the center position of non-uniform diffraction disks in Lorentz 4D-STEM

Recent advancement in scanning transmission electron microscopy (STEM) allows the use of 4D-STEM, a technique that captures an electron diffraction pattern at each scan point in STEM, to measure electrostatic and magnetic potential and field in materials. However, accurate measurement, separation of the magnetic and electric signals, and removal of artifacts remain challenging, especially in the presence of complex non-uniform diffraction contrast within the disks. In this work, based on dynamic simulations of 4D-STEM patterns built upon superstructures consisting of millions of atoms to account for different sample thickness and edge geometries, we show how the shape and intensity distribution of the central disk are affected by multiple scattering. We propose a robust refinement procedure through iteration of the spin-sensitive peak position of the disk-center in the circular Hough transform filtered images from experimental Lorentz 4D-STEM dataset after minimizing the possible artifacts, such as those due to the change of thickness, dynamic scattering, and scanning process. We verify that caution must be taken as in practice the rigid-disk-shift model used to reconstruct induction maps can easily break down due to disk-protrusion when there exists a nonconstant phase gradient or thickness within the width of the probe. Through quantitative analysis and comparing experiment with calculation the effect of the non-spin-related intensity distribution inside the disk as well as that causes the disk shift due to the intensity-protrusion can be removed, and high-quality magnetic field mapping is possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands

Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La 3+ ) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La 3+ –ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La 3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Nanoscale structural correlations in a model cuprate superconductor

Understanding the extent and role of inhomogeneity is a pivotal challenge in the physics of cuprate superconductors. While it is known that structural and electronic inhomogeneity is prevalent in the cuprates, it has proven difficult to disentangle compound-specific features from universally relevant effects. Here, in this study, we combine advanced neutron and x-ray diffuse scattering with numerical modeling to obtain insight into bulk structural correlations in HgBa 2 ⁢ CuO 4+δ . This cuprate exhibits a high optimal transition temperature of nearly 100 K, pristine charge-transport behavior, and a simple average crystal structure without long-range structural instabilities, and is therefore uniquely suited for investigations of intrinsic inhomogeneity. We uncover diffuse reciprocal-space patterns that correspond to prominent nanoscale correlations of atomic displacements perpendicular to the CuO 2 planes. The real-space nature of the correlations is revealed through three-dimensional pair distribution function analysis and complementary numerical refinement. We find that relative displacements of ionic and CuO 2 layers play a crucial role, and that the structural inhomogeneity is not directly caused by the presence of conventional point defects. The observed correlations are therefore intrinsic to HgBa 2 ⁢ CuO 4+δ , and thus likely important for the physics of cuprates more broadly. It is possible that the structural correlations are closely related to the unusual superconducting fluctuations and Mott-localization in these complex oxides. As advances in scattering techniques yield increasingly comprehensive data, the experimental and analysis tools developed here for large volumes of diffuse scattering data can be expected to aid future investigations of a wide range of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Protonation of histidine rings using quantum-mechanical methods

Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the possible protonation states in situ, looking at possible hydrogen bonding and metal coordination, it is possible to predict which is most likely to be correct. A more direct method is described that uses quantum-mechanical methods to calculate, also in situ, the minimum geometry and energy for comparison, and therefore to more accurately identify the most likely proton­ation state.

Histidine↗

Outer satellite atmospheres: Their nature and planetary interactions

Modeling capabilities and initial model calculations are reported for the peculiar directional features of the Io sodium cloud discovered by Pilcher and the extended atomic oxygen atmosphere of Io discovered by Brown. Model results explaining the directional feature by a localized emission from the satellite are encouraging, but as yet, inconclusive; whereas for the oxygen cloud, an escape rate of 1 to 2 x 10 to the 27th power atoms/sec or higher from Io is suggested. Preliminary modeling efforts were also initiated for the extended hydrogen ring-atmosphere of Saturn detected by the Voyager spacecraft and for possible extended atmospheres of some of the smaller satellites located in the E-ring. Continuing research efforts reported for the Io sodium cloud include further refinement in the modeling of the east-west asymmetry data, the asymmetric line profile shape, and the intersection of the cloud with the Io plasma torus. In addition, the completed pre-Voyager modeling of Titan's hydrogen torus is included and the near completed model development for the extended atmosphere of comets is discussed.

Smyth, W. H.↗