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DOE OSTI2025

Boosting H I -Galaxy Cross-Clustering Signal through Higher-Order Cross-Correlations

After reionization, neutral hydrogen (${\rm H\, \small {I}}$) traces the large-scale structure (LSS) of the Universe, enabling ${\rm H\, \small {I}}$ intensity mapping (IM) to capture the LSS in 3D and constrain key cosmological parameters. We present a new framework utilizing higher-order cross-correlations to study ${\rm H\, \small {I}}$ clustering around galaxies, tested using real-space data from the IllustrisTNG300 simulation. This approach computes the joint distributions of k-nearest neighbor (kNN) optical galaxies and the ${\rm H\, \small {I}}$ brightness temperature field smoothed at relevant scales (the kNN-field framework), providing sensitivity to all higher-order cross-correlations, unlike two-point statistics. To simulate ${\rm H\, \small {I}}$ data from actual surveys, we add random thermal noise and apply a simple foreground cleaning model, filtering out Fourier modes of the brightness temperature field with k ∥ < k min,∥ . Under current levels of thermal noise and foreground cleaning, typical of a Canadian Hydrogen Intensity Mapping Experiment (CHIME)-like survey, the ${\rm H\, \small {I}}$-galaxy cross-correlation signal in our simulations, using the kNN-field framework, is detectable at >30σ across r = [3, 12] h –1 Mpc. In contrast, the detectability of the standard two-point correlation function (2PCF) over the same scales depends strongly on the foreground filter: a sharp k ∥ filter can spuriously boost detection to 8σ due to position-space ringing, whereas a less sharp filter yields no detection. Nonetheless, we conclude that kNN-field cross-correlations are robustly detectable across a broad range of foreground filtering and thermal noise conditions, suggesting their potential for enhanced constraining power over 2PCFs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Structural Templation of MOF-Derived Zirconia Nanoparticles

Templated synthesis is an important avenue for the development and synthesis of porous materials, as it provides a high level of control over the resulting structure. However, this control is difficult to achieve at the atomic level for poorly crystalline or noncrystalline materials, such as metal–organic framework (MOF)-derived carbons. We report the carbonization of three zirconium-based MOFs with different framework and inorganic building unit structures to form zirconia nanoparticles in a carbon matrix. Using a combination of X-ray diffraction, X-ray total scattering, and transmission electron microscopy, we found that the extended Zr-oxo chains of MIL-140C-bpy facilitate the formation of larger and more ordered zirconia nanoparticles. In contrast, the discrete Zr 6 -oxo clusters of UiO-67-bpy and Zr-ABTC result in smaller and differently structured nanoparticles.

metal-organic framework↗

DOE OSTI2024

An alcove at the acetyl-CoA synthase nickel active site is required for productive substrate CO binding and anaerobic carbon fixation

One of the seven natural CO 2 fixation pathways, the anaerobic Wood-Ljungdahl pathway (WLP) is unique in generating CO as a metabolic intermediate, operating through organometallic intermediates, and in conserving (versus utilizing) net ATP. The key enzyme in the WLP is acetyl-CoA synthase (ACS), which uses an active site [2Ni-4Fe-4S] cluster (A-cluster), a CO tunnel, and an organometallic (Ni-CO, Ni-methyl, and Ni-acetyl) reaction sequence to generate acetyl-CoA. Here, we reveal that an alcove, which interfaces the tunnel and the A-cluster, is essential for CO 2 fixation and autotrophic growth by the WLP. In vitro spectroscopy, kinetics, binding, and in vivo growth experiments reveal that a Phe229A substitution at one wall of the alcove decreases CO affinity thirty-fold and abolishes autotrophic growth; however, a F229W substitution enhances CO binding 80-fold. Our results indicate that the structure of the alcove is exquisitely tuned to concentrate CO near the A-cluster; protect ACS from CO loss during catalysis, provide a haven for inhibitory CO, and stabilize the tetrahedral coordination at the Nip site where CO binds. The directing, concentrating, and protective effects of the alcove explain the inability of F209A to grow autotrophically. The alcove also could help explain current controversies over whether ACS binds CO and methyl through a random or ordered mechanism. Our work redefines what we historically refer to as the metallocenter "active site". The alcove is so crucial for enzymatic function that we propose it is part of the active site. The community should now look for such alcoves in all "gas handling" metalloenzymes.

bacterial metabolism↗

DOE OSTI2023

Pre- and post-processing of cluster galaxies out to 5 × R 200: the extreme case of A2670

ABSTRACT We study galaxy interactions in the large-scale environment around A2670, a massive (M200 = $8.5 \pm 1.2~\times 10^{14} \, \mathrm{{M}_{\odot }}$) and interacting galaxy cluster at z = 0.0763. We first characterize the environment of the cluster out to 5× R200 and find a wealth of substructures, including the main cluster core, a large infalling group, and several other substructures. To study the impact of these substructures (pre-processing) and their accretion into the main cluster (post-processing) on the member galaxies, we visually examined optical images to look for signatures indicative of gravitational or hydrodynamical interactions. We find that ∼21 per cent of the cluster galaxies have clear signs of disturbances, with most of those (∼60 per cent) likely being disturbed by ram pressure. The number of ram-pressure stripping candidates found (101) in A2670 is the largest to date for a single system, and while they are more common in the cluster core, they can be found even at >4 × R200, confirming cluster influence out to large radii. In support of a pre-processing scenario, most of the disturbed galaxies follow the substructures found, with the richest structures having more disturbed galaxies. Post-processing also seems plausible, as many galaxy–galaxy mergers are seen near the cluster core, which is not expected in relaxed clusters. In addition, there is a comparable fraction of disturbed galaxies in and outside substructures. Overall, our results highlight the complex interplay of gas stripping and gravitational interactions in actively assembling clusters up to 5 × R200, motivating wide-area studies in larger cluster samples.

Astronomy & Astrophysics↗

DOE OSTI2026

Phase diagram of magnetic shape memory alloy Ni 50 Mn $50–x$ In $x$ , 0 < $x$ , 25 from first principles, via spin cluster expansion and phonon vibrational entropies

The metamagnetic shape memory Heusler alloy Ni 50 Mn $50–x$ In $x$ exhibits a rich phase diagram featuring competing magnetic states, coupled magnetic–structural phase transitions, and strong compositional sensitivity. Existing first-principles approaches struggletocapturetheintertwinedchemical, magnetic, andvibrationaleffectsinthesealloys, necessitating a more integrated modeling framework. We develop a spin cluster expansion (spin-CE) framework augmented by a quasi-harmonic phonon model to capture both configurational (chemical and magnetic) and vibrational contributions to the free energy of Ni 50 Mn $50–x$ In $x$ over the full compositional range 0 ≤ x ≤25. The spin-CE includes both chemical clusters and composition-dependent Ising spin interactions, with parameters fit to a first-principles density functional theory (DFT) dataset. Using this approach, we predict the complete magnetostructural phase diagram and transformation temperatures of Ni 50 Mn $50–x$ In $x$ across the composition space. We find that vibrational entropy alone is insufficient to reproduce the martensitic transformation in the magnetic shape memory alloy regime, highlighting the essential role of magnetism. Incorporating both magnetic and vibrational contributions allows us to reproduce all experimentally known phases, including the disappearance of the stable martensite phase at a critical In concentration and the Curie temperature of the austenite phase. The method also captures the transition with increasing In in martensite from antiferromagnetic to ferromagnetic order and predicts re-entrant ferromagnetism, though the latter occurs at higher In content than reported experimentally. We discuss possible sources of this discrepancy and highlight the broader applicability of the method to other magnetostructurally complex materials, where it may offer mechanistic insight and predictive design capabilities.

Cluster expansion↗

DOE OSTI2024

Characterization of ferredoxins involved in electron transfer pathways for nitrogen fixation implicates differences in electronic structure in tuning 2[4Fe 4S] Fd activity

Ferredoxins (Fds) are small proteins which shuttle electrons to pathways like biological nitrogen fixation. Physical properties tune the reactivity of Fds with different pathways, but knowledge on how these properties can be manipulated to engineer new electron transfer pathways is lacking. Recently, we showed that an evolved strain of Rhodopseudomonas palustris uses a new electron transfer pathway for nitrogen fixation. This pathway involves a variant of the primary Fd of nitrogen fixation in R. palustris, Fer1, in which threonine at position 11 is substituted for isoleucine (Fer1 T11I ). To understand why this substitution in Fer1 enables more efficient electron transfer, we used in vivo and in vitro methods to characterize Fer1 and Fer1 T11I . Electrochemical characterization revealed both Fer1 and Fer1 T11I have similar redox transitions (–480 mV and – 550 mV), indicating the reduction potential was unaffected despite the proximity of T11 to an iron-sulfur (Fe—S) cluster of Fer1. Additionally, disruption of hydrogen bonding around an Fe—S cluster in Fer1 by substituting threonine with alanine (T11A) or valine (T11V) did not increase nitrogenase activity, indicating that disruption of hydrogen bonding does not explain the difference in activity observed for Fer1 T11I . Electron paramagnetic resonance spectroscopy studies revealed key differences in the electronic structure of Fer1 and Fer1 T11I , which indicate changes to the high spin states and/or spin-spin coupling between the Fe—S clusters of Fer1. Finally, our data implicates these electronic structure differences in facilitating electron flow and sets a foundation for further investigations to understand the connection between these properties and intermolecular electron transfer.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Electron Bifurcating Hydrogenases

The importance of electron-bifurcating enzymes is manifest by their ability to maximize energy efficiency. Specifically, they couple a downhill oxidation-reduction (redox) reaction with an uphill redox reaction. Since the rapid increase in the discovery of bifurcating enzymes starting in 2008, there has been interest in incorporating their mechanistic principles into artificial/semiartificial systems to drive chemically challenging reactions. This has yet to be achieved, partly because the details of electron bifurcation, i.e. mechanisms, are largely elusive. Nevertheless, much progress has been made in understanding reactivities, structures, and some mechanistic aspects of these enzymes. Notable examples are electron-bifurcating hydrogenases, which are the focus of this chapter. The chapter is organized as follows. Section 11.1 provides an overview of hydrogenases and electron bifurcation. In Section 11.2, some physiological roles of electron-bifurcating hydrogenases are highlighted. Additionally, electron-bifurcating subunit compositions and biochemical reactivities are comprehensively tabulated, and some key points/considerations about these are noted. In Section 11.3, we discuss the known structures of these enzymes, which provide insight into their complex arrangements of redox cofactors, such as iron-sulfur clusters. Also provided are tabulations and discussions of some biophysical properties of the cofactors. In Section 11.4, we discuss the mechanistic proposals of these enzymes, which are primarily based on structural information. Areas of research that are much needed are outlined in Section 11.5. We conclude on the note that what is learned from electron-bifurcating hydrogenases has applicability to other bifurcating enzymes, nonbifurcating analogs, and mechanistic enzymology at large.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Nuclear Computational Low Energy Initiative (NUCLEI)

The NUCLEI project, as defined by the scope of work, developed, implemented and run codes for large-scale computations of many topics in low-energy nuclear physics. Physics studied include the properties of nuclei and nuclear decays, nuclear structure and reactions, and the properties of nuclear matter. The computational techniques used include Quantum Monte Carlo, Configuration Interaction, Coupled Cluster, and Density Functional methods. The research program emphasized areas of high interest to current and possible future DOE nuclear physics facilities, including ATLAS and FRIB (nuclear structure and reactions, and nuclear astrophysics), TJNAF (neutron distributions in nuclei, few body systems, and electroweak processes), NIF (thermonuclear reactions), MAJORANA and FNPB (neutrinoless double-beta decay and physics beyond the Standard Model), and LANSCE (fission studies).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

First-principles and cluster expansion study of the effect of magnetism on short-range order in Fe–Ni–Cr austenitic stainless steels

Short-range order (SRO), the regular and predictable arrangement of atoms over short distances, alters the mechanical properties of technologically relevant structural materials such as medium/high entropy alloys and austenitic stainless steels. In this study, we present a generalized spin cluster expansion (CE) model and show that magnetism is a primary factor influencing the level of SRO present in austenitic Fe-Ni-Cr alloys. The spin CE consists of a chemical cluster expansion combined with an Ising model for Fe-Ni-Cr austenitic alloys. It explicitly accounts for local magnetic exchange interactions, thereby capturing the effects of finite temperature magnetism on SRO. Model parameters are obtained by fitting to a first-principles data set comprising both chemically and magnetically diverse FCC configurations. The magnitude of the magnetic exchange interactions are found to be comparable to the chemical interactions. Compared to a conventional implicit magnetism CE built from only magnetic ground state configurations, the spin CE shows improved performance on several experimental benchmarks over a broad spectrum of compositions, particularly at higher temperatures due to the explicit treatment of magnetic disorder. We find that SRO is strongly influenced by alloy Cr content, since Cr atoms prefer to align antiferromagnetically with nearest neighbors but become magnetically frustrated with increasing Cr concentration. Using the spin CE, we predict that increasing the Cr concentration in typical austenitic stainless steels promotes the formation of SRO and increases order-disorder transition temperatures. Furthermore, this study underscores the significance of considering magnetic interactions explicitly when exploring the thermodynamic properties of complex transition metal alloys. It also highlights guidelines for customizing SRO through adjustments of alloy composition.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Understanding the Existence of a Na 2 Dimer in a High-Spin State

The recent observation of a high-spin Na 2 dimer formed on the surface of liquid helium nanodroplets raises some fundamental questions, as the ground state of Na 2 is known to have zero spin. Is it protected against spontaneous dissociation? What is its binding energy and interatomic distance? Is it stable at a higher temperature? Using calculations based on density functional theory (with and without long-range interaction) and coupled cluster methods, CCSD(T), we show that the bonding in the high-spin Na 2 dimer is governed by van der Waals interaction with binding energy (bond length) varying between −0.030 eV (5.108 Å) and −0.192 eV (4.231 Å), depending on the computational method used. Thus, the experimental method used by Kresin and coworkers can be very useful to study larger metastable high-spin clusters such as Li 4 which was predicted in 1985 to have a tetrahedral structure carrying a magnetic moment of 2 μ B , while its ground state is planar and nonmagnetic.

Basis sets↗

DOE OSTI2025

An atomic cluster expansion potential for twisted multilayer graphene

Twisted multilayer graphene, characterized by its moiré patterns arising from inter-layer rotational misalignment, serves as a rich platform for exploring quantum phenomena. Machine learning interatomic potentials (MLIPs) are a promising approach to model such systems. Our work develops a method to generate training and test datasets for fitting MLIPs that capture all possible misalignments but remain small-scale to facilitate efficient data generation and parameter estimation. To achieve this, we generate configurations with periodic boundary conditions suitable for density functional theory calculations, and then introduce an internal twist and shift within those supercell structures. Using this technique, supplemented with an active learning workflow, we fit an Atomic Cluster Expansion potential for simulating twisted multilayer graphene and test it for accuracy and robustness on a range of simulation tasks.

2D materials↗

DOE OSTI2025

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗

DOE OSTI2024

A study of nuclear structure of light nuclei at the electron–ion collider

Understanding the substructure of atomic nuclei, particularly the clustering of nucleons inside them, is essential for comprehending nuclear dynamics. Various cluster configurations can emerge depending on excitation energy, the number and types of core clusters, and the presence of excess neutrons. Despite the prevalence of tightly bound cluster formations in low-lying states, understanding the correlation between clusters and their formation mechanisms remains incomplete. This exploring study investigates nuclear clustering at the electron–ion collider (EIC) using simulations based on the modified BeAGLE model. By simulating collisions involving e+ 9 Be, e+ 12 C, and e+ 16 O nuclei, we find that the average energy of particles and the system size ratios of particles at forward rapidity exhibit sensitivity to alpha clustering and its various configurations. These findings offer valuable insights into the dynamics of nuclear clustering and its implications for future studies at the EIC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Constraining Flexibility in the MIL-88 Topology through Integration of 3-Dimensional Linkers

Metal–organic frameworks (MOFs) are a class of crystalline, nanoporous materials that are recognized for their tunability. While some MOFs demonstrate flexibility, this characteristic can pose challenges in achieving precise pore control or establishing permanent porosity. Specifically, MIL-88B, is notable for its high flexibility, as it is constructed from metal trimer clusters and 2-dimensional linkers (2DLs) featuring planar, aromatic cores, allowing significant structural changes. In this study, we synthesized two new MOFs, NU-2010 and NU-2011, which are structurally analogous to MIL-88B but incorporate ditopic 3-dimensional linkers (3DLs) with sterically bulky cores and higher symmetry. Our aim was to investigate whether the introduction of 3DLs could mitigate the flexibility observed in MIL-88B. We employed a combination of single crystal and powder X-ray diffraction techniques to assess the flexibility of MIL-88B, NU-2010, and NU-2011 under various conditions including thermal activation, solvent exchange, and temperature changes. Furthermore, our findings indicate that incorporating 3DLs significantly reduces framework flexibility in NU-2010 and NU-2011 relative to MIL-88B.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Predicting Mechanical Properties from Microstructure Images in Fiber-Reinforced Polymers Using Convolutional Neural Networks

Evaluating the mechanical response of fiber-reinforced composites can be extremely time-consuming and expensive. Machine learning (ML) techniques offer a means for faster predictions via models trained on existing input–output pairs and have exhibited success in composite research. This paper explores a fully convolutional neural network modified from StressNet, which was originally used for linear elastic materials, and extended here for a non-linear finite element (FE) simulation to predict the stress field in 2D slices of segmented tomography images of a fiber-reinforced polymer specimen. The network was trained and evaluated on data generated from the FE simulations of the exact microstructure. The testing results show that the trained network accurately captures the characteristics of the stress distribution, especially on fibers, solely from the segmented microstructure images. The trained model can make predictions within seconds in a single forward pass on an ordinary laptop, given the input microstructure, compared to 92.5 h to run the full FE simulation on a high-performance computing cluster. These results show promise in using ML techniques to conduct fast structural analysis for fiber-reinforced composites and suggest a corollary that the trained model can be used to identify the location of potential damage sites in fiber-reinforced polymers.

Sun, Yixuan (ORCID:0000000311093380)↗

DOE OSTI2025

Electron-Proton Scattering Event Generation using Structured Tokenization

Recent work such as Omnijet-$\alpha$ has demonstrated that effective tokenization combined with transformer-based architectures can produce effective foundation models for jet physics. While tokenization may help models capture generalizable event characteristics, it also introduces discretization errors that may compromise the precision required for downstream physics analyses. As the number and complexity of the particle features grow, these errors are likely to grow proportionally. In this study, we investigate new tokenization strategies to improve the application of generative transformer models to \textsc{Pythia8} simulations of electron-proton scattering at the Electron-Ion Collider. Specifically, we propose a feature-based structured tokenization approach that utilizes multiple tokens per particle, improving expressivity, while reducing the total number of unique tokens needed. We evaluate this method against grid-based binning, K-means clustering, and vector-quantized variational auto-encoders on the event simulations. Our results show that feature-based structured tokenization reduces discretization error, leading to more accurate generative modeling of particle-level events.

Goldenberg, Steven [Thomas Jefferson National Acce↗

DOE OSTI2025

Electron-Proton Scattering Event Generation using Structured Tokenization

Goldenberg, Steven [Thomas Jefferson National Acce↗

DOE OSTI2025

Structural origin of disorder-induced ion conduction in NaFePO 4 cathode materials

Diffusion in NaFePO 4 can be enhanced through amorphization. Based on computations using DFT and machine learning potentials, we ascribe this phenomenon to the formation of less constrained Na-ion environments upon disordering. Most modern battery technologies depend on solid-state crystalline cathode materials. However, some of these materials are constrained by the low ionic conductivity of their most stable phases. An example of this is maricite (NaFePO 4 ). Interestingly, experiments have shown that maricite can improve its rate capability through disordering (amorphization). However, experimental characterization of amorphous cathode materials remains a major challenge, hindering a clear understanding of the structural origin of the disorder-induced improvement in sodium-ion mobility. To address this, we here employ molecular dynamics simulations by first training a machine learning potential for NaFePO 4 based on the atomic cluster expansion approach and a batch active learning potential parameterization scheme. This potential is then applied to explore the structural and dynamical properties of NaFePO 4 glasses as cathode materials. Specifically, we investigate the effect of glass structure on sodium-ion diffusion, revealing the relative influences of short-range and medium-range order features. We find significant heterogeneity in sodium-ion diffusivity in the glass, with fast-conducting ions residing in less constrained atomic environments with fewer P and Fe neighbors. These more mobile ions are also surrounded by larger ring-type structures. Overall, the results and developed approach present promising avenues for developing high-performance glassy cathodes for next-generation batteries.

Christensen, Rasmus↗