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DOE OSTI2021

Synthesis and characterization of amorphous Fe2.75Dy-oxide thin films demonstrating room-temperature semiconductor, magnetism, and optical transparency

Recently, amorphous/disordered oxide thin films made from Fe and lanthanides like Dy and Tb have been reported to have a rich set of magnetic, optical, and electronic properties, as well as room-temperature magneto-electric coupling with multiferroics [A. Malasi et al., Sci. Rep. 5, 18157 (2015); H. Taz et al., Sci. Rep. 6, 27869 (2016); and H. Taz et al., Sci. Rep. 10, 1–10 (2020)]. Here, we report the synthesis and detailed characterization of Fe2.75Dy-oxide thin films prepared on various substrates using electron beam co-evaporation. The structure, chemistry, electric, magnetic, and optical properties were studied for the as-prepared and annealed (373 K, in air, 1 h) films of thickness 40 nm. High resolution transmission electron microscopy and electron diffraction study showed that the films were amorphous in both the as-prepared and annealed states. The electron energy-loss spectroscopy studies quantified that metal oxygen stoichiometry changed from Fe2.75Dy-O1.5 to Fe2.75Dy-O1.7 upon annealing. Synchrotron-based x-ray absorption spectroscopy investigation confirmed that the as-prepared films were highly disordered with predominantly metallic Fe and Dy states that became slightly oxidized with annealing in air. The as-prepared amorphous films demonstrated significantly high value of ordinary (∼10 cm2/V s) and anomalous (∼102 cm2/V s) Hall mobility and high electrical conductivity of ∼103 S/cm at room temperature. The cryogenic magnetic property measurement shows two-step magnetization below 200 K, suggesting exchange-spring magnetic interaction. The nature of the field cooled and zero-field cooled curves suggested a spin-glass like transition between 78 K and 80 K, with a characteristic broad peak. The Tauc plot analysis from optical transmission spectra confirms the existence of an optical bandgap of ∼2.42 eV that increased slightly to ∼2.48 eV upon annealing. This rich set of transport, optical, and magnetic properties in these thin films is very exciting and points to potential applicability in low-cost multifunctional devices requiring a combination of transparent, semiconducting, and magnetic responses, such as in spintronics.

Prasad Koirala, Krishna (ORCID:000000029137917X)↗

DOE OSTI2023

Identification of recG genetic interactions in Escherichia coli by transposon sequencing

ABSTRACT Maintaining the integrity of the genome is of utmost importance for cell division and propagation. In Escherichia coli , the RecG protein has been implicated in processing branched recombination intermediates during DNA repair processes, but the primary cellular role(s) of RecG and the repair pathways in which it acts have been difficult to define. To gain additional insight into RecG function, we employed transposon sequencing to identify recG genetic interactions and reveal complementary or redundant functions. The strongest hits from the screen were the dam , uvrD , rnhA , radA , and rep genes. The conditional importance of these five genes in cells lacking recG was confirmed using a plasmid-based assay, revealing synthetic lethal interactions for most double deletion strains. Several of the synthetic lethal gene combinations (with uvrD, rep, and radA , but not rnhA or dam ) were suppressed by deletion of recF or recO , indicating that their genetic relationships involved roles in post-replication gap repair. Additionally, loss of the RecG/SSB interaction phenocopied a recG deletion when combined with dam , uvrD , radA , or rnhA deletions but not with rep . The results reinforce the idea of RecG as a general genome guardian. RecG has at least two functions. It plays an important role in the resolution of joint molecules behind the fork, formed during post-replication gap repair. RecG is also required to suppress genome over-replication caused by unscheduled replication initiation at R-loops, at double-strand breaks caused by dam inactivation, and during replication termination. IMPORTANCE DNA damage and subsequent DNA repair processes are mutagenic in nature and an important driver of evolution in prokaryotes, including antibiotic resistance development. Genetic screening approaches, such as transposon sequencing (Tn-seq), have provided important new insights into gene function and genetic relationships. Here, we employed Tn-seq to gain insight into the function of the recG gene, which renders Escherichia coli cells moderately sensitive to a variety of DNA-damaging agents when they are absent. The reported recG genetic interactions can be used in combination with future screens to aid in a more complete reconstruction of DNA repair pathways in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

(SPT-)LSM theorems from projective non-invertible symmetries

Projective symmetries are ubiquitous in quantum lattice models and can be leveraged to constrain their phase diagram and entanglement structure. In this paper, we investigate the consequences of projective algebras formed by non-invertible symmetries and lattice translations in a generalized 1+1 1 + 1 D quantum XY model based on group-valued qudits. This model is specified by a finite group G G and enjoys a projective \mathsf{Rep}(G)× Z(G) 𝖱 𝖾 𝗉 ( G ) × Z ( G ) and translation symmetry, where symmetry operators obey a projective algebra in the presence of symmetry defects. For invertible symmetries, such projective algebras imply Lieb-Schultz-Mattis (LSM) anomalies. However, this is not generally true for non-invertible symmetries, and we derive a condition on G G for the existence of an LSM anomaly. When this condition is not met, we prove an SPT-LSM theorem: any unique and gapped ground state is necessarily a non-invertible weak symmetry protected topological (SPT) state with non-trivial entanglement, for which we construct an example fixed-point Hamiltonian. The projectivity also affects the dual symmetries after gauging \mathsf{Rep}(G)× Z(G) 𝖱 𝖾 𝗉 ( G ) × Z ( G ) sub-symmetries, giving rise to non-Abelian and non-invertible dipole symmetries, as well as non-invertible translations. We complement our analysis with the SymTFT, where the projectivity causes it to be a topological order non-trivially enriched by translations. Throughout the paper, we develop techniques for gauging \mathsf{Rep}(G) 𝖱 𝖾 𝗉 ( G ) symmetry and inserting its symmetry defects on the lattice, which are applicable to other non-invertible symmetries.

Pace, Salvatore D. (ORCID:0000000306093335)↗

DOE OSTI2023

Densely Connected G-invariant Deep Neural Networks with Signed Permutation Representations

We introduce and investigate, for finite groups G, G-invariant deep neural network (GDNN) architectures with ReLU activation that are densely connected- i.e., include all possible skip connections. In contrast to other G-invariant architectures in the literature, the preactivations of theG-DNNs presented here are able to transform by signed permutation representations (signed perm-reps) of G. Moreover, the individual layers of the G-DNNs are not required to be G-equivariant; instead, the preactivations are constrained to be G-equivariant functions of the network input in a way that couples weights across all layers. The result is a richer family of G-invariant architectures never seen previously. We derive an efficient implementation of G-DNNs after a reparameterization of weights, as well as necessary and sufficient conditions for an architecture to be "admissible"- i.e., nondegenerate and inequivalent to smaller architectures. We include code that allows a user to build a G-DNN interactively layer-by-layer, with the final architecture guaranteed to be admissible. We show that there are far more admissible G-DNN architectures than those accessible with the "concatenated ReLU" activation function from the literature. Finally, we apply G-DNNs to two example problems--(1) multiplication in --1, 1} (with theoretical guarantees) and (2) 3D object classification--finding that the inclusion of signed perm-reps significantly boosts predictive performance compared to baselines with only ordinary (i.e., unsigned) perm-reps.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

Abstract The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Moerman, Pepijn G.↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Projective Representations, Bogomolov Multiplier, and Their Applications in Physics

We present a pedagogical review of projective representations of finite groups and their physical applications in quantum many-body systems. Some of our physical results are new. We begin with a self-contained introduction to projective representations, highlighting the role of group cohomology, representation theory, and classification of irreducible projective representations. We then focus on a special subset of cohomology classes, known as the Bogomolov multiplier, which consists of cocycles that are symmetric on commuting pairs but remain nontrivial in group cohomology. Such cocycles have important physical implications: they characterize (1+1)D SPT phases that cannot be detected by string order parameters and give rise, upon gauging, to distinct gapped phases with completely broken non-invertible Rep(G) symmetry. We construct explicit lattice models for these phases and demonstrate how they are distinguished by the fusion rules of local order parameters. We show that a pair of completely broken Rep(G) SSB phases host nontrivial interface modes at their domain walls. As an example, we construct a lattice model where the ground state degeneracy on a ring increases from 32 without interfaces to 56 with interfaces.

Bogomolov multiplier↗

DOE OSTI2026

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗

DOE OSTI2022

Low Repetition-Rate, High-Resolution Femtosecond Transmission Electron Microscopy

Spatial and energy resolutions of state-of-the-art transmission electron microscopes (TEMs) have surpassed 50 pm and 5 meV. However, with respect to the time domain, even the fastest detectors combined with the brightest sources may only be able to reach the microsecond timescale. Thus, conventional methods are incapable of resolving myriad fundamental ultrafast (i.e., attosecond to picosecond) atomic-scale dynamics. The successful demonstration of femtosecond (fs) laser-based (LB) ultrafast transmission electron microscopy (UEM) nearly 20 years ago provided a means to span this nearly 10-order-of-magnitude temporal gap. While nanometer-picosecond UEM studies of dynamics are now well established, ultrafast Å-scale imaging has gone largely unrealized. Further, while instrument development has rightly been an emphasis, and while new modalities and uses of pulsed-beam TEM continue to emerge, the overall chemical and materials application space has been only modestly explored to date. In this Perspectives article, we argue that these apparent shortfalls can be attributed to a simple lack of data and detail. We speculate that present work and continued growth of the field will ultimately lead to the realization that Å-scale fs dynamics can indeed be imaged with minimally modified UEM instrumentation and with repetition rates (f rep ) below - and perhaps even well below - 1 MHz. We further argue that use of low f rep , whether for LB UEM or for chopped/bunched beams, significantly expands the accessible application space. Furthermore, this calls for systematically establishing modality-specific limits so that especially promising technologies can be pursued, thus ultimately facilitating broader adoption as individual instrument capabilities expand.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Structure and Function of REP34 Implicates Carboxypeptidase Activity in Francisella tularensis Host Cell Invasion

Francisella tularensis is the etiological agent of tularemia, or rabbit fever. Although F. tularensis is a recognized biothreat agent with broad and expanding geographical range, its mechanism of infection and environmental persistence remain poorly understood. Previously, we identified seven F. tularensis proteins that induce a rapid encystment phenotype (REP) in the free-living amoeba, Acanthamoeba castellanii. Encystment is essential to the pathogen's long term intracellular survival in the amoeba. Here, we characterize the cellular and molecular function of REP34, a REP protein with a mass of 34 kDa. A REP34 knock-out strain of F. tularensis has a reduced ability to both induce encystment in A. castellanii and invade human macrophages. We determined the crystal structure of REP34 to 2.05-Å resolution and demonstrate robust carboxypeptidase B-like activity for the enzyme. REP34 is a zinc-containing monomeric protein with close structural homology to the metallocarboxypeptidase family of peptidases. REP34 possesses a novel topology and substrate binding pocket that deviates from the canonical funnelin structure of carboxypeptidases, putatively resulting in a catalytic role for a conserved tyrosine and distinct S1' recognition site. Taken together, these results identify REP34 as an active carboxypeptidase, implicate the enzyme as a potential key F. tularensis effector protein, and may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Superfast quarks in deuterium

An extension to our previous study on nuclear parton distribution functions (nPDFs) [Kim and Miller, Phys. Rev. C 106, 055202 (2022)] using light-front holographic quantum chromodynamics (LFHQCD) [Brodsky, de Teramond, Dosch, and Erlich, Phys. Rep. 584, 1 (2015)] is presented. We apply the effects of nucleon motion inside the nucleus (Fermi motion/smearing) to deuterium, extending our deuterium nPDFs to the superfast , 𝑥 > 1, region [Frankfurt and Strikman, Phys. Rep. 160, 235 (1988)] where we estimate our results to be reasonable up to 𝑥 ≈ 1.7. We utilize four different deuteron wave functions (AV18, NijmI, NijmII, Nijm93). We find that our model, with no additional new parameters, shows very good agreement with deuterium EMC ratio data obtained from the BONuS experiment [Fenker et al., Nucl. Instrum. Methods Phys. Res. A 592, 273 (2008); Baillie et al. (CLAS Collaboration), Phys. Rev. Lett. 108, 142001 (2012); Phys. Rev. Lett. 108, 199902(E) (2012); Tkachenko et al. (CLAS Collaboration), Phys. Rev. C 89, 045206 (2014); Phys. Rev. C 90, 059901(E) (2014); Griffioen et al., Phys. Rev. C 92, 015211 (2015)]. Looking beyond conventional nuclear physics, and in anticipation of 12 GeV experiments at Jefferson Lab, we use a LFHQCD ansatz to predict the contributions of an exotic six-quark state to the deuteron 𝐹 2 structure function, 𝐹$^D_2$, in the superfast region. We find that the effects of using other potentials are about the same magnitude as six-quark effects—both have small effects in 𝑥 < 1, but have significant contributions at 𝑥 > 1.

Physics↗

DOE OSTI2020

Soil Environmental Conditions in the East River Watershed, CO

This dataset contains depth-resolved soil environmental variables collected between June 2016 and October 2018 from the Bradley Meadow site in the East River watershed. Datalogger output from 7 Campbell CS655 12 cm Soil Moisture and Temperature Sensors including depth, temperature, volumetric water content, and electrical conductivity are included in ‘BM_Merged_T_VWC_0616_10_18.csv’. Sensors were installed in June 2016. Data have been processed to merge raw sensor data and to remove additional variables. No additional QA/QC was performed. Measured pCO2 and depth are contained in ‘BM_EGM_WELL_CO2.csv’. These data represent gas well samples measured via injection using a PP Systems EGM-5 infra-red gas analyzer as described in the methods section. Measured CO2 surface flux values are contained in 'BM_EGM_Surface_Flux.csv'. These were measured using the PP Systems EGM-5 with the Soil Respiration Chamber attachment. Multiple reps are reported for each measurement including CO2 flux rate calculations using built-in linear and quadratic function methods, and average and standard deviations are taken across all reps and calculation methods.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Replace Human Intelligence with Fast and Smart Geometric Reasoning and Graph Neural Network to Accelerate Next Gen ModSim Workflows

We present an agent-guided approach to CAD geometry decomposition that automates hex/hybrid meshing with graph neural networks (GNNs) to accelerate next-generation ModSim workflows. Our end-to-end pipeline (i) reduces 3D boundary-representation (B-Rep) models to a 2D chordal axis skeleton (CAT) and then to a 1D bipartite graph of surface and curve nodes, (ii) assigns per node labels as Cubit® WebCut actions, (iii) trains a multi-action GNN under supervised learning, and (iv) predicts five surface-node and three curve-node actions on out-of-distribution test geometries. Each graph node carries geometric, topological, and meshing attributes drawn from the B-Rep “skin” and CAT “skeleton,” with two-way mappings across 3D↔2D↔1D representations to maintain traceability back to 3D CAD. The supervised learning model exhibits stable convergence of the binary cross-entropy loss and achieves 98.7% accuracy on unseen lattice models. To operationalize decision-making, we rank predicted commands by geometric significance and prototyped the agent-guided workflow through the Cubit® Meshing PowerTool GUI. As a stretch goal, we explore reinforcement learning (RL) to reduce or remove label requirements and to learn policies for action sequences that maximize total reward (e.g., size of hex-meshable regions and resulting hex mesh quality). When all-hex meshing is not feasible, the agent assists in producing hybrid meshes—prioritizing hex in critical regions and transitioning to tetrahedral elements (tets) elsewhere—maintaining fidelity while ensuring robustness. The overarching objective is to replace manual, heuristics-based decomposition with data-driven, reproducible automation, cutting meshing turnaround time by orders of magnitude. We anticipate direct impact on simulation workflows through intelligent, scalable decomposition of complex CAD models into hex-meshable subdomains.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Closing the Loop between In Situ Stress Complexity and EGS Fracture Complexity

42 ENGINEERING↗

DOE OSTI2025

Snow ALbedo eVOlution (SALVO) Campaign Oblique Photos from April - June, 2024 in Utqiagivk, AK

While albedo line measurements were being made, oblique photos were taken from eye level (~1.8 m) of the position of each albedo measurement (i.e., at 5-meter intervals along the line). The photo numbers were recorded in a notebook and in the ASD notes documents (see the spectral albedo archive). The photos were subsequently renamed for archiving according to the following file naming convention: ‘salvo_[site]_line_oblique_[YYYYMMDD]_[pos]_[rep].JPG’, where [site] is the overall measurement site (‘arm’, ‘beo’, or ‘ice’); YYYYMMDD is the date of the measurement in AKDT (local time); [pos] is the position along the line in meters; and [rep] is the repetition number if repeat photographs were made. Oblique photos are available for almost every albedo measurement.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Additivity, Haag duality, and non-invertible symmetries

The algebraic approach to quantum field theory focuses on the properties of local algebras, whereas the study of (possibly non-invertible) global symmetries emphasizes global aspects of the theory and spacetime. We study connections between these two perspectives by examining how either of two core algebraic properties — “additivity” or “Haag duality” — is violated in a 1+1D CFT or lattice model restricted to the symmetric sector of a general global symmetry. For the Verlinde symmetry of a bosonic diagonal RCFT, we find that additivity is violated whenever the symmetry algebra contains an invertible element, while Haag duality is violated whenever it contains a non-invertible element. We find similar phenomena for the Kramers-Wannier and Rep(D 8 ) non-invertible symmetries on spin chains.

Discrete Symmetries↗

DOE OSTI2021

Picosecond laser generated plasma as a source of singly charged ions for external injection into an EBIS

The focus of this paper is on practical aspects of ion generation by picosecond lasers as a source of low charge state ions for external injection of ions into an electron beam ion source (EBIS). For a ps-laser, compared to a ns-laser currently used at Relativistic Heavy Ion Collier Electron Beam Ion Source (RHIC EBIS), the influence of heat conductivity in the solid target is almost negligible, which results in a lower target consumption rate and less vacuum pressure rise. By using a laser with high repetition rate, it is possible to produce quasi continuous 1+ ion beams for periods of tens of milliseconds, making it possible to take advantage of the ability of the EBIS to accumulate ions in the “slow” injection capture mode. Producing such an ion pulse train is now feasible since ps-lasers with pulse energy up to 10 mJ and rep-rate up to 10 kHz have recently become commercially available. The advantages of this lower current accumulation scheme include: (1) easier beam transport due to lower space charge of lower beam currents required compared to the present single pulse fast injection scheme, (2) better EBIS pulse to pulse ion output stability since pulse to pulse ion variations of the laser source are averaged over a long train of laser pulses, and (3) the possible addition of an isotope separator in which rare beams could be produced and selected at run time from less expensive (unenriched) targets. We studied the properties of plasmas generated by a ps-laser with 1.27 mJ energy within an 8 ps pulse and a repetition rate up to 400 Hz at Argonne National Laboratory to investigate feasibility and specify parameters for a laser ion source for RHIC EBIS using a “slow” injection mode. Al, Ti, Cu, Nb, and Ta targets were tested with various target translation speeds. Here, we demonstrated that a both “slow” and “fast” injection modes are accessible with a single ion source geometry and single injection line, providing the most attractive option for an ion source for external injection into RHIC EBIS trap based on a ps-laser.

43 PARTICLE ACCELERATORS↗

DOE OSTI2022

Effects of inter-pulse coupling on nanosecond pulsed high frequency discharge ignition in a flowing mixture

This work numerically investigates the effects of non-equilibrium nanosecond plasma discharge pulse rep- etition frequency, pulse number, and flow velocity on the critical ignition volume, minimum ignition energy, and chemistry in a plasma-assisted H 2 /air flow at 300 K and 1 atm using a multi-scale adaptive reduced chemistry solver for plasma assisted combustion (MARCS-PAC). The interactions between discharges/ignition kernels spanning decoupled, partially-coupled and fully-coupled regimes in a pulse train are studied. For a single pulse discharge, increased flow velocity increases the minimum ignition energy required due to the increase of convective heat loss and flame stretch. The results show that the minimum ignition kernel prop- agation speed at the critical ignition kernel volume increases with the flow velocity. The minimum critical ignition volume decreases with the increase of plasma discharge energy. For sequential two-pulse discharges, ignition fails at both decoupled and partially-coupled regimes even when the total discharge energy is above the minimum ignition energy, but succeeds only in the fully-coupled regime at a shorter inter-pulse time. Overlap of the OH radical pool between the sequential two-pulse discharges and the increase of the chemistry effect due to the increase of reduced electric field in the fully-coupled regime contribute to the ignition enhancement. In addition, for two-pulse discharges in the fully-coupled discharge regime, the mixture can be ignited at a total energy below the minimum ignition energy of a single pulse with the same flow conditions. Moreover, for a given total discharge energy with multiple pulsed discharges, the enhancement of the ignition kernel volume has a non-monotonic dependence on discharge frequency and pulse number. The effective ignition enhancement can be achieved with an optimal pulse repetition frequency and pulse number. Furthermore, this work provides a new understanding of the mechanism for repetitive plasma ignition and insights for the optimization of plasma ignition in a reactive flow.

42 ENGINEERING↗