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Defect graph neural networks for materials discovery in high-temperature clean-energy applications

We present a graph neural network approach that fully automates the prediction of defect formation enthalpies for any crystallographic site from the ideal crystal structure, without the need to create defected atomic structure models as input. Here we used density functional theory reference data for vacancy defects in oxides, to train a defect graph neural network (dGNN) model that replaces the density functional theory supercell relaxations otherwise required for each symmetrically unique crystal site. Interfaced with thermodynamic calculations of reduction entropies and associated free energies, the dGNN model is applied to the screening of oxides in the Materials Project database, connecting the zero-kelvin defect enthalpies to high-temperature process conditions relevant for solar thermochemical hydrogen production and other energy applications. The dGNN approach is applicable to arbitrary structures with an accuracy limited principally by the amount and diversity of the training data, and it is generalizable to other defect types and advanced graph convolution architectures. In conclusion, it will help to tackle future materials discovery problems in clean energy and beyond.

97 MATHEMATICS AND COMPUTING↗

Unveiling the complex configurational landscape of the intralayer cavities in a crystalline carbon nitride

The in-depth understanding of the reported photoelectrochemical properties of the layered carbon nitride, poly(triazine imide)/LiCl (PTI/LiCl), has been limited by the apparent disorder of the Li/H atoms within its framework. To understand and resolve the current structural ambiguities, an optimized one-step flux synthesis (470 °C, 36 h, LiCl/KCl flux) was used to prepare PTI/LiCl and deuterated-PTI/LiCl in high purity. Its structure was characterized by a combination of neutron/X-ray diffraction and transmission electron microscopy. The range of possible Li/H atomic configurations was enumerated for the first time and, combined with total energy calculations, reveals a more complex energetic landscape than previously considered. Experimental data were fitted against all possible structural models, exhibiting the most consistency with a new orthorhombic model (Sp. Grp. Ama2) that also has the lowest total energy. In addition, a new Cu(I)-containing PTI (PTI/CuCl) was prepared with the more strongly scattering Cu(I) cations in place of Li, and most closely matching with the partially-disorder structure in Cmc2 1 . Thus, a complex configurational landscape of PTI is revealed to consist of a number of ordered crystalline structures that are new potential synthetic targets, such as with the use of metal-exchange reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Summary of Expansions and Updates in R&D GREET ® 2023

The Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET®) model was developed by Argonne National Laboratory (Argonne) with the support of the U.S. Department of Energy (DOE) and other federal agencies. R&D GREET is a life cycle analysis (LCA) model, structured to systematically examine the energy and environmental effects of a wide variety of transportation fuels and vehicle technologies in major transportation sectors (i.e., road, air, marine, and rail), other end-use sectors, and energy systems. Argonne has expanded and updated the model in various areas in R&D GREET 2023. This report provides a summary of the expansions and updates.

33 ADVANCED PROPULSION SYSTEMS↗

Process-Based Balance-of-System Cost Modeling for Offshore Wind Power Plants in the United States: Preprint

This work describes the development of a process based and open source balance of system cost model which provides the capability to evaluate both existing and novel offshore wind technologies. Individual design and installation steps are represented with bottom-up engineering models that compute the times and costs associated with the process; furthermore, operational constraints are assigned to each process so that delays due to weather and presence of marine mammals may be accounted for in the overall project timeline. The model structure, assumptions, inputs, and results are vetted with industry partners and compared against actual projects for validation; installation times are shown to agree with real data with relative errors of less than 35\%. Case studies are presented to demonstrate the functionality of the model. First, individual vessel efficiencies are computed for varying numbers of installation vessels and weather time series to show the diminishing returns of more than two feeder barges. Then, array cable capital costs and installation times are determined for a representative project with different turbine sizes. This quantifies the cost benefit tradeoffs of decreasing number of turbines, increased turbine spacing, and fewer turbine terminations and shows a net cost savings. These results demonstrate that the BOS model features the accuracy, functionality, and accessibility to serve as the foundation for a wide range of analyses to identify cost reduction potentials for offshore wind energy in the United States.

17 WIND ENERGY↗

Identification and system parameter estimation methods for a Pyrofusion neutron source - 372

Pyrofusion sources are compact, low power systems which are capable of producing short intense pulses of neutrons from D-D fusion reactions. A model structure has been derived from the underlying physics principles and it is shown that the dominant non-linear dynamics pose significant challenges to the system control. This paper presents the methods under development to construct, estimate and analyse nonlinear grey-box models of Pyrofusion systems from measured data. The methods have been trialled on data sets obtained from the publications of previous Pyrofusion research groups. The results indicate the promising potential application of these methods to the system identification of profusion device characteristics to support model verification, pulse characterisation and prediction of operational capabilities. The identified models are shown to exhibit satisfactory analogous cause-and-effect behaviour. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module

Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these, Bartonella effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three Bartonella lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The β-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure–function analyses of the highly versatile FIC domains.

59 BASIC BIOLOGICAL SCIENCES↗

High-Temperature Latent Heat Storage System using Transportable Heat Pipes for Versatile Integration with Emerging Microreactors

With the growing interest in the development of micro nuclear reactors and their application to microgrid, high-temperature thermal energy storage (TES) has also been receiving great attention as a technology to reinforce the energy utilization and profitability of this class of reactors. Given the importance and research needs of the TES technology, a research project is underway at Idaho National Laboratory (INL) to develop high-temperature TES that can be easily interfaced with emerging micro nuclear reactors. Currently under development is the Heat pipe-Integrated Thermal Battery (HITB), a novel latent heat storage design that enables flexible and robust integration with any design of currently considered micro nuclear reactors. The development of detailed design based on the proposed TES concept, HITB, requires not only development and validation of modeling and simulation capabilities, but also research that spans thermal performance analysis, component- and system-scale design optimization, and experimental demonstrations including high-temperature feasibility testing. The current research efforts (and plans) are divided into the following four areas: (i) Thermal and structural modeling and analysis at both system- and component-scales for evaluating performance and conducting design optimization, (ii) Small-scale experimental demonstrations for the key components of the proposed HITB design, (iii) Modelica-based dynamic model development for developing a control strategy under dynamic operation within integrated energy systems configuration, (iv) Integrated experimental testing and demonstration. This paper introduces the overall research efforts that have been and are being conducted to develop and demonstrate the novel design of the high-temperature latent heat storage device, HITB. The key design features, ongoing research efforts including the development of modeling and simulation capabilities, small-scale demonstrations of the HITB’s key functionalities prior to scaled-up experimental demonstration, are discussed. Then, this paper concludes with a remark on the future research plans for this project.

25 ENERGY STORAGE↗

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

Elucidating structure and dynamics of crystalline α-zirconium phosphates intercalated with water and methanol by multinuclear solid-state MAS NMR: A comprehensive NMR approach

Solid-state NMR experiments on 2 H, 31 P, 13 C, and 1 H nuclei, including 31 P T 1 , 1 H T 1 , and 1 H T 1ρ measurements, as well as on the kinetics of proton-phosphorus cross-polarization have been performed to characterize the crystalline and amorphous α-zirconium phosphates, which were intercalated with D 2 O and/or CD 3 OD. The 13 C{ 1 H} CP MAS NMR experiment performed for compound 1-CD 3 OD (Zr (HPO 4 ) 2 .0.2CD 3 OD) with carbon cross-polarization via protons of phosphate groups has provided a prove that the methanol was intercalated into the interlayer spaces of this compound. The variable-temperature 2 H solid-echo MAS NMR spectra of intercalated compounds demonstrated that the methanol molecules, in contrast to the mobile water, were immobile, keeping, however, free CD 3 rotations around the C 3 -axis. It has been demonstrated that the intercalated species, D 2 O and CD 3 OD, do not affect the high-frequency motions of the phosphate groups. By utilizing local structural models that satisfy the constraints of the experimental data, it has been suggested that the immobile methanol molecules are located in the cavity between two neighboring layers of the zirconium phosphates. Here, the present work illustrates the reliable criteria in a comprehensive NMR approach to structural and dynamic studies of such systems.

1H↗

Mapping Thermal Conductivity at the Atomic Scale: A Step toward the Thermal Design of Materials

We describe a spatial decomposition of the thermal conductivity, termed site-projected thermal conductivity, which quantifies the thermal conduction activity at each atomic site—a critical parameter for the thermal design of materials. The method is based on the Green–Kubo formula and the harmonic approximation and requires the force-constant and dynamical matrices, as well as a relaxed structural model. Throughout the study, it uses high quality models previously tested and compared to many experiments. It discusses the method and underlying approximations for amorphous silicon, carries the detailed analysis for amorphous silicon, and then examines an amorphous-crystal silicon interface and representative carbon materials. This study identifies the sites and local structures that reduce heat transport, and quantify these (estimate the spatial range) over which these “thermal defects” are effective. It identifies filamentary structures in the amorphous silicon network which impact heat transport and electronic structure (the Urbach edge) and electronic transport.

36 MATERIALS SCIENCE↗

High resolution ENDOR spectroscopy combined with quantum chemical calculations reveals the structure of the nitrogenase Janus intermediate E4(4H)

We have shown that the key state in N2 reduction to two NH3 by the enzyme nitrogenase is the E4(4H), ‘Janus’ intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed the catalytic multi-metallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of structure - the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of ‘anchor’ Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties of the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed by DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a pulsed-ENDOR protocol (‘PESTRE’) to obtain absolute hyperfine-interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its ‘anchoring’ Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result: the freeze-trapped, lowest-energy Janus intermediate structure is E4(4H)(a).

Hoeke, Veronica↗

National Spherical Torus eXperiment - Upgrade NSTX-U: Structural Analysis of Passive Plates Support Brackets

The objective of this analysis is to estimate and assess the stresses in the passive plates caused by a limiting plasma disruption. The objective of this calculation is also to address observed damage to mounting hardware after completion of NSTX operation. These observations initiated diagnostic efforts during the Upgrade project to monitor the severity of the disruptions that were causing the damage, and planned instrumentation to trend the behavior of the mounting hardware. The Recovery Project mission for the passive plate hardware is to appropriately reinforce the passive plates with stainless steel ribs mounted on the back of the plate to reduce their flexure and stress and reinforcements of the “biscuit” components of the bracketry to transfer loads without damage to bolts, biscuits, and bracket plates and welds. Mid-plane disruptions and quenches were manageable with NSTX vintage hardware. The Vertical Displacement Event (VDE) disruptions position the plasma closer to the passive plates and are more severe than the centered plasma. Earlier work pointed to the P1-P5 VDE as limiting. This has been confirmed by A. Brooks work in support of the load generation effort in reference. During vertical displacement large counter currents are generated in the plate as the plasma approaches it. - as would be expected from passive plates. When the plasma disrupts the currents in the plates are reversed, which also reverses the loading on the plates. This report documents the methodology and results of transient structural analysis on the plasma, passive plates support brackets. The loads induced by eddy and halo currents have been considered, and were generated using a separate electromagnetic analysis (NSTXU_1_11_2_1_CALC_051). The structural model also incorporates the effects from preload. Calculation was performed with the assumption that existing biscuits are not participating in the load bearing except the biscuits connected to jumper bolts, which are fully engaged. Results show that with the planned reinforcements, Passive plates and mounting structures satisfy static and fatigue criteria in all areas except welds, where separate analysis was performed. Both symmetric and asymmetric (with locating block) designs were analyzed, and although stresses were higher without locating block they still satisfy NSTX design criteria.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Summary of Expansions and Updates in R&D GREET ® 2024

The research and development (R&D) version of Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET ® ) model, or R&D GREET, is developed by Argonne National Laboratory (Argonne) with the support of the U.S. Department of Energy (DOE) and other federal agencies. R&D GREET is a life cycle analysis (LCA) model, structured to systematically examine the energy and environmental effects of a wide variety of transportation fuels and vehicle technologies in major transportation sectors (i.e., road, air, marine, and rail) and other end-use sectors, and energy technology systems. Argonne has expanded and updated the model in various areas in R&D GREET 2024.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Summary of Expansions and Updates in R&D GREET® 2024 Rev.1

The research and development (R&D) version of Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET®) model, or R&D GREET, is developed by Argonne National Laboratory (Argonne) with the support of the U.S. Department of Energy (DOE) and other federal agencies. R&D GREET is a life cycle analysis (LCA) model, structured to systematically examine the energy and environmental effects of a wide variety of transportation fuels and vehicle technologies in major transportation sectors (i.e., road, air, marine, and rail) and other end-use sectors, and energy technology systems. Argonne has expanded and updated the model in several areas in R&D GREET 2024 Rev.1. This report provides a summary of the expansions and updates.

54 ENVIRONMENTAL SCIENCES↗

Eu 5 Al 3 Sb 6 : Al 4 Tetrahedra Embedded in a Rock-Salt-Like Structure

The new Eu 5 Al 3 Sb 6 phase has been successfully synthesized as a pure phase through Sn flux methods yielding large, high-quality crystals. This structure type features disordered Al clusters that appear in the form of dual tetrahedra. It crystallizes in the monoclinic C2/m space group exhibiting a rock-salt-like Eu–Sb framework with [Al 4 ] tetrahedra replacing some of the cationic Eu atoms (space group: C2/m, a = 8.151(1) Å, b = 14.181(2) Å, c = 8.145(1) Å, β = 109.577(2)°). The structure models the [Al 4 ] as dual tetrahedra with the Al atom sites 37.5% occupied along with Eu present on the central site at 8% occupancy and the remainder of the site being vacant. The presence of the [Al 4 ] cluster is further supported by HRTEM. Electronic structure calculations show that this material is a semimetal with observed band crossings close to the Fermi level. Strong Al–Sb antibonding interactions were found from COHP calculations close to the Fermi level and provide the rationale for the deficiency of the Al cluster. Mössbauer spectroscopy on Eu-151 and Sb-121 provides oxidation states of 2+ and 3– along with the local environment. Magnetic susceptibility measurements can be described well with a Curie–Weiss law where an effective moment of 7.80 μB/mol Eu is obtained, consistent with Eu 2+ , and show canted antiferromagnetic behavior below 10 K. Temperature dependent resistivity shows a Kondo-like low-temperature upturn caused by enhanced scattering of the itinerant electrons with the 4f orbitals of Eu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A biokinetic model for systemic sodium

This paper describes an updated biokinetic model for systemic sodium (Na), developed for use in a series of reports by the International Commission on Radiological Protection (ICRP) on occupational intake of radionuclides. In contrast to the ICRP's previous model for intake of radio-sodium by workers, the updated model depicts realistic directions of movement of Na in the body including recycling of activity between blood and tissues. The updated model structure facilitates extension of the baseline transfer coefficients for adults to different age groups and to special exposure scenarios such as transfer of radio-sodium from the mother to the foetus or the nursing infant. Dose coefficients for 22Na and 24Na based on the updated model generally do not differ greatly from those based on the ICRP's previous Na model when both models are connected to the ICRP's latest dosimetry system. The main exception is that the updated model yields roughly twofold higher dose coefficients for endosteal bone surface than does the previous model due to the dosimetrically cautious assumption in the updated model that exchangeable Na in bone resides on bone surface.

61 RADIATION PROTECTION AND DOSIMETRY↗

Langevin model of low-energy fission

Since the earliest days of fission, stochastic models have been used to describe and model the process. For a quarter century, numerical solutions of Langevin equations have been used to model fission of highly excited nuclei, where microscopic potential-energy effects have been neglected. In this paper I present a Langevin model for the fission of nuclei with low to medium excitation energies, for which microscopic effects in the potential energy cannot be ignored. I solve Langevin equations in a five-dimensional space of nuclear deformations. The macroscopic-microscopic potential energy from a global nuclear structure model well benchmarked to nuclear masses is tabulated on a mesh of approximately 10 7 points in this deformation space. The potential is defined continuously inside the mesh boundaries by use of a moving five-dimensional cubic spline approximation. Because of reflection symmetry, the effective mesh is nearly twice this size. For the inertia, I use a (possibly scaled) approximation to the inertia tensor defined by irrotational flow. A phenomenological dissipation tensor related to one-body dissipation is used. A normal-mode analysis of the dynamical system at the saddle point and the assumption of quasiequilibrium provide distributions of initial conditions appropriate to low excitation energies, and are extended to model spontaneous fission. A dynamical model of postscission fragment motion including dynamical deformations and separation allows the calculation of final mass and kinetic-energy distributions, along with other interesting quantities. The model makes quantitative predictions for fragment mass and kinetic-energy yields, some of which are very close to measured ones. Varying the energy of the incident neutron for induced fission allows the prediction of energy dependencies of fragment yields and average kinetic energies. With a simple approximation for spontaneous fission starting conditions, quantitative predictions are made for some observables which are close to measurements. In conclusion, this model is able to reproduce several mass and energy yield observables with a small number of physical parameters, some of which do not need to be varied after benchmarking to 235 U (n, f) to predict results for other fissioning isotopes.

233U↗