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DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Magnetism of single crystalline breathing pyrochlore spinel AgInCr 4 ⁢S 8

Single crystals of Ag⁢In⁢Cr 4⁢ S 8 are grown by chemical vapor transport and crystallographic ordering of Ag/In that results in a breathing pyrochlore motif of Cr 3+ is verified by x-ray and neutron diffraction. Long-range antiferromagnetic order is observed below a Néel temperature of 𝑇 N ≈ 9.6 K. The magnetic properties are characterized using ac and dc magnetization, specific heat capacity, and single crystal neutron diffraction measurements. The specific heat data are characterized by a small lambda anomaly near 9.5 K and the estimated magnetic entropy reaches ≈ $\frac{1}{3}$ of the expected value by 3⁢𝑇 N , suggesting significant short-range order in the paramagnetic phase. Single crystal neutron diffraction evidences an incommensurate spin structure with propagation vector 𝒌 = (0,0,𝛿) and 𝛿 = 0.343 at 5 K. The minimal model that accounts for the data consists of ferromagnetic layers of Cr atoms, with magnetic moments lying in the plane of the layers and modulating in the perpendicular direction to form a helical structure propagating along 𝒌. Furthermore, this study represents a rare investigation of single crystals within the family of breathing pyrochlore materials.

Frustrated magnetism↗

DOE OSTI2020

Calculations of electronic excitation by protons and alpha particles in silicon

This paper presents an ab initio method of calculating the valence electron contribution to the stopping and interaction cross sections of swift ions in matter using linear response calculations of the dielectric function in crystals. We estimate the contribution to the stopping and cross sections by repeated electron capture and stripping of the projectile ion by the medium. We also predict the electronic stopping of protons and alpha particles in silicon and compare to measured values. The predictions generally agree with the data at ion speeds greater than 1 atomic unit. We find that electron capture and stripping is at most a small contribution to the stopping for both ions studied.

electron excitation, silicon, nuclear interactions↗

DOE OSTI2020

Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data

Metal oxide/water interfaces play a crucial role in many electrochemical and photocatalytic processes, such as photoelectrochemical water splitting, the creation of fuel from sunlight, and electrochemical CO 2 reduction. First-principles electronic structure calculations can reveal unique insights into these processes, such as the role of the alignment of the oxide electronic energy levels with those of liquid water. An essential prerequisite for the success of such calculations is the ability to predict accurate structural models of these interfaces, which in turn requires careful experimental validation. Here we report a general, quantitative validation protocol for first-principles molecular dynamics simulations of oxide/aqueous interfaces. The approach makes direct comparisons of interfacial x-ray reflectivity (XR) signals from experimental measurements and those obtained from ab initio simulations with semilocal and van der Waals functionals. The protocol is demonstrated here for the case of the Al 2 O 3 (001)/water interface, one of the simplest oxide/water interfaces. We discuss the technical requirements needed for validation, including the choice of the density functional, the simulation cell size, and the optimal choice of the thermodynamic ensemble. Our results establish a general paradigm for the validation of structural models and interactions at solid/water interfaces derived from first-principles simulations. Furthermore, while there is qualitative agreement between the simulated structures and the experimental best-fit structure, direct comparisons of simulated and measured XR intensities show quantitative discrepancies that derive from both bulk regions (i.e., alumina and water) as well as the interfacial region, highlighting the need for accurate density functionals to properly describe interfacial interactions. Our results show that XR data are sensitive not only to the atomic structure (i.e., the atom locations) but also to the electron-density distributions in both the substrate and at the interface.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Calorimetric wire detector for measurement of atomic hydrogen beams

A calorimetric detector for minimally disruptive measurements of atomic hydrogen beams is described. The calorimeter measures heat released by the recombination of hydrogen atoms into molecules on a thin wire. As a demonstration, the angular distribution of a beam with a peak intensity of ≈ 10 16 atoms/(cm 2 s) is measured by translating the wire across the beam. The data agree well with an analytic model of the beam from the thermal hydrogen atom source. Using the beam shape model, the relative intensity of the beam can be determined to 5% precision or better at any angle.

Astaschov, M. [Johannes Gutenberg Univ., Mainz (Ge↗

DOE OSTI2025

An Open-source Llm Enhanced-tool Specialized In Helping Moose Related Problems And Tasks

MOOSEenger is an open-source, terminal-first chat application for the MOOSE ecosystem that couples specialized parsing of MOOSE documentation and “.i” input files with retrieval-augmented generation to deliver grounded answers about multiphysics modeling and workflows. It includes dedicated readers for MOOSE-style HTML and a pyhit-based parser that uses the MOOSE syntax tree to preserve block structure and attach retrieval metadata. A data-ingestion pipeline performs semantic chunking into atomic facts and stores them hierarchically in a local Chroma vector database that maintains parent–child relationships across documents; the system can ingest directories, individual files, and single-page web content, and it provides CRUD operations (insert, update, delete) to manage the corpus. At query time, relevant chunks are embedded, retrieved, and fused into the model context, with interactive features such as token streaming, persistent chat history, and dynamic RAG (retrieval triggered by user input or intermediate model output). Deployment is flexible: MOOSEenger runs with local Ollama models or remote Hugging Face/OpenAI backends—typically coordinating generation, lightweight tagging/summarization, and embeddings across three models—and it also supports a server mode and integration with the VS Code Continue interface.

Li, Mengnan [Idaho National Laboratory (INL), Idah↗

DOE OSTI2021

Development of a Turbulent Liquid Spray Atomization Model for Diesel Engine Simulations (Final Technical Report)

This project addresses the systematic lack of predictive capabilities by spray models within engine CFD codes. We develop a new modeling approach to predict the breakup of diesel sprays based on recent literature showing that liquid turbulence plays a fundamental role in spray atomization. A new body of quantitative validation data is also developed as a critical element of the project, leveraging the joint capabilities of Georgia Tech’s high-pressure continuous-flow spray chamber and Argonne National Lab’s near-nozzle x-ray diagnostics at the Advanced Photon Source. This project contributes spatially-resolved measurements of drop size distribution within well-characterized diesel injectors, Spray A and D, from the Engine Combustion Network (ECN) to the engine combustion community for the first time. Utilizing this new body of measurements, we validate and demonstrate a new spray model for diesel sprays, termed the KH-Faeth model, that predicts global and local spray characteristic more accurately than the widely adopted and employed KH model. Predicted drop size distributions are seen to predict measured drops sizes both quantitatively and predictively, with accurate response in droplet size distributions over a wide range of ambient density, injection pressure, and injector nozzle size (Spray A and D) without model tuning. The KH-Faeth model can reduce error in the predicted centerline droplet size profile by up to 80% for ECN Spray D simulations when compared to use of the widely employed KH model.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2025

Evaluating FRAM v.6.1 with LANL and Euratom data

The United States Department of Energy and the European Atomic Energy Community (EURATOM) collaborate to test, evaluate, and improve the performance of the FRAM 6.1 code with various nuclear materials, especially mixed oxide (MOX) containing an isotopic blend of uranium and very high burnup plutonium. This joint effort is intended to promote effective implementation of the FRAM 6.1 code into nuclear material verification methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Quantitative Imaging of Cobalt Phthalocyanine Distribution on Carbon Nanotubes: A Deep Learning Approach to Catalyst Characterization

Electrochemical reduction of carbon dioxide (CO 2 ) offers a pathway to valuable products, with catalysts playing a crucial role. This study investigates the distribution of cobalt tetraaminophthalocyanine (CoPc-NH 2 ) immobilized on carbon nanotubes (CNTs), utilizing high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) to characterize CoPc-NH 2 distribution. A challenge in the quantitative HAADF-STEM analysis is the introduction of bias from manual Co atom identification. To address this, we developed and trained a convolutional neural network (CNN) using a data set generated from images of CoPc-NH 2 /CNT samples with varying Co loadings. The CNN, implemented in TensorFlow and Keras, facilitated Co atom detections. Analysis of the CNN-generated data confirmed a correlation between Co loading and surface density, consistent with findings from UV–vis spectroscopy. Furthermore, the application of Ripley’s L(d) function highlighted the presence of slight Co atom clustering. Furthermore, this work demonstrates the utility of the combined HAADF-STEM and CNN approach for providing spatially resolved information about catalyst distribution on nonplanar supports, revealing structural details that are typically lost through other characterization methods.

HAADF-STEM↗

DOE OSTI2021

Implementation of a self-consistent slab model of bilayer structure in the SasView suite

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. Here, the use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Open Reproducible Electron Microscopy Data Analysis

Electron microscopy (EM) is a cornerstone technique in the materials and biological sciences capable of imaging structures at nano- to atomic-scale resolution. Advances in technologies mean that one acquires datasets at increasing data rates and sizes. These advancements present enormous opportunities for researchers to understand complex systems. However, processing the resulting large-scale, complex data in a reproducible and shareable way is a real challenge for researchers. The building, managing, and maintaining complex workflows in a reproducible manner requires extensive knowledge in several areas outside the researchers’ core skill sets, such as software engineering, data science, and high-performance computing (HPC). Our work demonstrates an innovative approach to solving these problems, enabling reproducible EM data analysis through container encapsulated pipelines. Using modern container technologies, we encapsulate processing elements and connect them using shared memory. We expose user-friendly, advanced algorithms and tools to allow end users to utilize without expert programming skills. The platform enables reproducible, scalable, shareable pipelines for the analysis and visualization of EM data. Focusing on interoperability, we leverage the DOE and other agencies’ existing investments to provide a powerful software platform for EM data analysis.

Harris, Christopher↗

DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗

DOE OSTI2025

A machine learning approach to quantify degradation of nuclear fuels and the effects of fission products

Nuclear fuel performance is critically dependent on understanding the evolution of fuel properties under operational conditions, a complex challenge driven by chemical changes and substantial radiation damage during fission. Traditionally, property evolution has been determined via empirical data collected following irradiation. However, these empirical correlations are limited in their applicability beyond the specific conditions in which they were obtained. This study explores a novel approach to address this challenge by applying materials informatics to develop a machine learning random forest (ML-RF) model that captures the effects of fission products on fuel compounds. The model predicts formation enthalpy (ΔH f ) by leveraging extensive quantum materials property data and correlating it with material descriptors such as composition, atomic and site features, and crystal lattice properties. This ML-RF model enables rapid interpolation across the compositional and structural spaces covered by the training data, thus supporting high-throughput screening and energetic ranking of candidate phases. The model demonstrates the ability to predict ΔH f with a mean absolute error (MAE) of approximately 0.1 to 0.2 eV/atom across a wide range of compounds, including key nuclear fuel systems (U-O, U-N, U-C, U-Si, and U-Mo). For example, it was used to assess shifts in stoichiometry for UO 2 (O/M) and UN (N/M) fuels, revealing their distinct tendencies in chemical potential variation and enabling preliminary convex hull analyses. Furthermore, the model provides insights into how individual fission products affect fuel properties. Results indicate that larger fission products (e.g., Nd, Pu, Ce) have a more pronounced impact on UO 2 , while lighter ones (e.g., Zr) strongly influence UN. Here, the model developed in this work can be used to support the Accelerated Fuel Qualification approach by facilitating preliminary evaluations prior to extensive materials modeling and experimentation. To this end, the trained model has been made available to the fuel community to support ongoing fuel development efforts.

Accelerated fuel qualification↗

DOE OSTI2022

Probing atomic physics at ultrahigh pressure using laser-driven implosions

Abstract Spectroscopic measurements of dense plasmas at billions of atmospheres provide tests to our fundamental understanding of how matter behaves at extreme conditions. Developing reliable atomic physics models at these conditions, benchmarked by experimental data, is crucial to an improved understanding of radiation transport in both stars and inertial fusion targets. However, detailed spectroscopic measurements at these conditions are rare, and traditional collisional-radiative equilibrium models, based on isolated-atom calculations and ad hoc continuum lowering models, have proved questionable at and beyond solid density. Here we report time-integrated and time-resolved x-ray spectroscopy measurements at several billion atmospheres using laser-driven implosions of Cu-doped targets. We use the imploding shell and its hot core at stagnation to probe the spectral changes of Cu-doped witness layer. These measurements indicate the necessity and viability of modeling dense plasmas with self-consistent methods like density-functional theory, which impact the accuracy of radiation transport simulations used to describe stellar evolution and the design of inertial fusion targets.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Impact of Domain Knowledge on the Property Prediction of Specialized Machine Learning Models

Developing transferable machine learning models is trending in data-driven materials research. However, how to apply such models to a specific research domain remains unclear. Here, in this work, we choose high-entropy materials as a platform with a specialized data set containing 145,323 DFT-relaxed materials. This data set is used to explore the role of domain-specific knowledge in training effective models. Our tests with three representative graph neural network architectures indicate the model complexity has much smaller influence on performance than the data itself. Specifically, the consideration of low-energy atomic ordering, structures with diverse elemental coverage, and high-order interactions significantly influences the model performance. We also find that domain knowledge-driven sampling can greatly enhance unsupervised learning techniques. This research highlights that developing specialized data sets is more beneficial than further complicating deep learning architectures. Additionally, physics-inspired sampling algorithms are crucially needed for better machine learning models for a specific materials research domain.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Neural network potentials with effective charge separation for non-equilibrium dynamics of ionic solids: a ZnO case study

Developing neural network potentials (NNPs) accurate under non-equilibrium dynamics is challenging, as such systems require extensive sampling beyond equilibrium phases. Here we construct high-fidelity NNPs for zinc oxide (ZnO), a polymorphic ionic solid, using density functional theory (DFT) reference data. To efficiently capture transitional configurations, we combine enhanced-sampling molecular dynamics with empirical potentials, data distillation, and pretraining on short-range atomic energies (A-Train), followed by transfer learning with DFT-relabeled datasets. This hierarchical approach improves transferability across polymorphs and stress states. We further introduce effective charge separation, treating long-range Coulombic terms analytically while short-range residual interactions are learned by the NNP. The optimal effective charges fall in the range 0.5–1.0 q e , consistent with dielectric-screened values derived from formal charges but distinct from Bader estimates. Motivated by this observation, we propose a simple data-driven protocol in which effective charges are optimized by comparing DFT reference energies with explicit Coulomb calculations, without additional NNP training. This strategy improves accuracy and transferability in DFT-level predictions of energies, forces, and stress. Together, these results provide a practical charge-selection framework for robust NNP development in ionic solids, enabling reliable simulation of polymorphic phase transformations and non-equilibrium dynamics.

Chemistry↗

DOE OSTI2023

Downward quantum learning from element 118: Automated generation of Fermi–Löwdin orbitals for all atoms

A new algorithm based on a rigorous theorem and quantum data computationally mined from element 118 guarantees automated construction of initial Fermi–Löwdin-Orbital (FLO) starting points for all elements in the Periodic Table. It defines a means for constructing a small library of scalable FLOs for universal use in molecular and solid-state calculations. The method can be systematically improved for greater efficiency and for applications to excited states such as x-ray excitations and optically silent excitations. FLOs were introduced to recast the Perdew–Zunger self-interaction correction (PZSIC) into an explicit unitarily invariant form. The FLOs are generated from a set of N quasi-classical electron positions, referred to as Fermi-Orbital descriptors (FODs), and a set of N-orthonormal single-electron orbitals. FOD positions, when optimized, minimize the PZSIC total energy. However, creating sets of starting FODs that lead to a positive definite Fermi orbital overlap matrix has proven to be challenging for systems composed of open-shell atoms and ions. The proof herein guarantees the existence of a FLOSIC solution and further guarantees that if a solution for N electrons is found, it can be used to generate a minimum of N – 1 and a maximum of 2 N – 2 initial starting points for systems composed of a smaller number of electrons. As a result, applications to heavy and super-heavy atoms are presented. All starting solutions reported here were obtained from a solution for element 118, Oganesson.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A First-Principles Approach to Modeling Surface Site Stabilities on Multimetallic Catalysts

The study of multimetallic alloys and the multitude of possible surface compositions have sparked a tremendous interest in engineering low-cost materials with high activity and selectivity in heterogeneous catalysis. Multimetallic systems provide complementary functionalities and an unprecedented tunability when designing catalyst formulations. However, due to their immense structural and compositional complexity, the investigation and identification of an optimal catalyst is a tedious and time-consuming process, both experimentally and theoretically. Therefore, theoretical design principles are highly desirable to accelerate the screening of catalyst structures across the vast compositional space. In this paper, we introduce a simple and general model for predicting the site stability of multimetallic surfaces and nanoparticles, which is based on physical principles. The model requires only a small set of density functional theory (DFT) calculations of metal atom binding energies on monometallic and dilute alloy surface slabs to optimize the parameters in the simple model. The resulting model allows for the quantification of the stability of any particular atom site in any conceivable chemical environment across a wide range of morphologies, sizes, and arrangements by interpolating the derived parameters from a monometallic system to a completely diluted alloyed system. Herein, we demonstrate the robustness of the model across an extensive data set of transition metal alloy surfaces and 147-atoms cuboctahedral nanoparticles (NPs) composed of IrRhRu and PtPdRu. In conclusion, our approach yields mean absolute errors of ≈0.15 (IrRhRu), 0.20 (PtPdRu), 0.19 (IrRhRu NP), and 0.26 (PtPdRu NP) eV relative to site binding energies calculated using DFT.

36 MATERIALS SCIENCE↗