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At least 955 records · Page 53

Soil metagenomics umbrella narrative

Implementing accessible, authentic research experiences in introductory courses is challenging, particularly at institutions serving diverse student populations. To address this gap, we developed and deployed a Course-based Undergraduate Research Experience (CURE) focused on plant-microbe interactions in General Biology II at Northeastern Illinois University (NEIU), a minority-serving institution with a diverse student body. Students grew sugar beets (Beta vulgaris), extracted DNA from the rhizoplane, and used the Department of Energy Systems Biology Knowledgebase (KBase) for bioinformatic analysis to compare microbial relative abundance in fertilized versus unfertilized soil. Over five semesters, the CURE engaged 103 students and leveraged the intuitive KBase platform to make complex sequencing data accessible. Pre/post-course survey data revealed significant increases in student self-assessed research skills, including the ability to explain results and determine the types of data to collect. Furthermore, students reported significant gains in confidence related to experimental design and hypothesis development, alongside a strong increase in familiarity with KBase. Informal faculty feedback indicated high student engagement and appreciation for the real-world connections (e.g. food systems, agriculture, and health). This scalable, low-cost model effectively integrates data science tools into the foundational curriculum, demonstrating a potent strategy for boosting research skills and broadening participation in authentic scientific inquiry among diverse undergraduate students.

59 BASIC BIOLOGICAL SCIENCES↗

Arrays of individually controlled ions suitable for two-dimensional quantum simulations

A precisely controlled quantum system may reveal a fundamental understanding of another, less accessible system of interest. A universal quantum computer is currently out of reach, but an analogue quantum simulator that makes relevant observables, interactions and states of a quantum model accessible could permit insight into complex dynamics. Several platforms have been suggested and proof-of-principle experiments have been conducted. Here, we operate two-dimensional arrays of three trapped ions in individually controlled harmonic wells forming equilateral triangles with side lengths 40 and 80 μm. In our approach, which is scalable to arbitrary two-dimensional lattices, we demonstrate individual control of the electronic and motional degrees of freedom, preparation of a fiducial initial state with ion motion close to the ground state, as well as a tuning of couplings between ions within experimental sequences. Lastly, our work paves the way towards a quantum simulator of two-dimensional systems designed at will.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Prediction of new high pressure structural sequence in thorium carbide: A first principles study

In the present work, we report the detailed electronic band structure calculations on thorium monocarbide. The comparison of enthalpies, derived for various phases using evolutionary structure search method in conjunction with first principles total energy calculations at several hydrostatic compressions, yielded a high pressure structural sequence of NaCl type (B1) → Pnma → Cmcm → CsCl type (B2) at hydrostatic pressures of ∼19 GPa, 36 GPa, and 200 GPa, respectively. However, the two high pressure experimental studies by Gerward et al. [J. Appl. Crystallogr. 19, 308 (1986); J. Less-Common Met. 161, L11 (1990)] one up to 36 GPa and other up to 50 GPa, on substoichiometric thorium carbide samples with carbon deficiency of ∼20%, do not report any structural transition. The discrepancy between theory and experiment could be due to the non-stoichiometry of thorium carbide samples used in the experiment. Further, in order to substantiate the results of our static lattice calculations, we have determined the phonon dispersion relations for these structures from lattice dynamic calculations. The theoretically calculated phonon spectrum reveal that the B1 phase fails dynamically at ∼33.8 GPa whereas the Pnma phase appears as dynamically stable structure around the B1 to Pnma transition pressure. Similarly, the Cmcm structure also displays dynamic stability in the regime of its structural stability. The B2 phase becomes dynamically stable much below the Cmcm to B2 transition pressure. Additionally, we have derived various thermophysical properties such as zero pressure equilibrium volume, bulk modulus, its pressure derivative, Debye temperature, thermal expansion coefficient and Gruneisen parameter at 300 K and compared these with available experimental data. Further, the behavior of zero pressure bulk modulus, heat capacity and Helmholtz free energy has been examined as a function temperature and compared with the experimental data of Danan [J. Nucl. Mater. 57, 280 (1975)].

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Lifetime renormalization of weakly anharmonic superconducting qubits. I. Role of number nonconserving terms

The dynamics of a weakly anharmonic superconducting qubit in a complex electromagnetic environment is generally well described by an effective multimode Kerr Hamiltonian at sufficiently weak excitation. This Hamiltonian can be embedded in a master equation with losses determined by the details of the electromagnetic environment. Recent experiments indicate, however, that when a superconducting circuit is driven with microwave signals populating the system with sufficiently high excitations, the observed relaxation rates appear to be substantially different from expectations based on the electromagnetic environment of the qubit alone. This issue is a limiting factor in the optimization of superconducting qubit readout schemes. We claim here that an effective master equation with drive-power-dependent parameters is an efficient approach to model such quantum dynamics. In this sequence of papers, we derive effective master equations, whose parameters exhibit nonlinear dependence on the excitation level of the circuit as well as the electromagnetic environment of the qubit. Further, we show that the number nonconserving terms in the qubit nonlinearity generally lead to a renormalization of dissipative parameters of the effective master equation, while the number conserving terms give rise to a renormalization of the system frequencies. Here, in Paper I, we consider the excitation-relaxation dynamics of a transmon qubit that is prepared in a certain initial state, but is not driven otherwise. A unitary transformation technique is introduced to study the renormalization of (i) qubit relaxation due to coupling to a generic bath and (ii) Purcell decay. Analytic expressions are provided for the dependence of the nonlinear dissipative terms on the details of the electromagnetic environment of the qubit. The perturbation technique based on unitary transformations developed here is generalized to the continuously driven case in Paper II.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Structural, thermodynamic, mechanical, and magnetic properties of FeW system

The Fe-W system is systematically investigated through a combined use of first-principles calculation, cluster expansion, special quasirandom structures, and experiments. It is revealed that the ferromagnetic state of BCC Fe-W solid solution has lower heat of formation than its nonmagnetic state within the entire composition range, and intermetallic λ-Fe{sub 2}W and μ-Fe{sub 7}W{sub 6} phases are energetically favorable with negative heats of formation. Calculations also show that the Fe-W solid solution has much lower coefficient of thermal expansion than its mechanical mixture, and that the descending sequence of temperature-dependent elastic moduli of each Fe-W solid solution is E > G > B. Moreover, magnetic state should have an important effect on mechanical properties of Fe-W phases, and electronic structures can provide a deeper understanding of various properties of Fe-W. The derived results agree well with experimental observations, and can clarify two experimental controversies regarding structural stability and magnetic property of Fe-W phases in the literature.

36 MATERIALS SCIENCE↗

Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Asymmetric ferroelectricity by design in atomic-layer superlattices with broken inversion symmetry

In atomic-layer superlattices constructed using three constituent phases, CaTiO 3 , SrTiO 3 , and BaTiO 3 , the stacking sequence of the atomic layers is found to control the symmetry of the high-temperature dielectric response. In such a superlattice when a nanostructured asymmetric strain is programmed into the lattice via the stacking order, the natural symmetry at high temperatures is removed and a polarized sample is obtained in which the polarization increases as the temperature is lowered. Here, in contrast to a ferroelectric characterized by a bistable ground state with two equal and opposite electronic polarizations, our experiments show evidence of asymmetric ferroelectric correlations that set in when such a sample becomes hysteretic below a temperature T x , with two unequal polarization states. We further show that both the magnitude and direction of this ferroelectric asymmetry can be controlled by the engineered atomic-layer stacking order and periodicity of the superlattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Experimental Observations of Laser-Driven Tin Ejecta Microjet Interactions

The study of high-velocity particle-laden flow interactions is of importance for the understanding of a wide range of natural phenomena, ranging from planetary formation to cloud interactions. Experimental observations of particle dynamics are sparse given the difficulty of generating high-velocity flows of many particles. Ejecta microjets are micron-scale jets formed by strong shocks interacting with imprinted surfaces to generate particle plumes traveling at several kilometers per second. As such, the interaction of two ejecta microjets provides a novel experimental methodology to study interacting particle streams. In this Letter, we report the first time sequences of x-ray radiography images of two interacting tin ejecta microjets taken on a platform designed for the OMEGA Extended Performance (OMEGA EP) laser. We observe that the microjets pass through each other unattenuated for the case of 11.7±3.2 GPa shock pressures and jet velocities of 2.2±0.5 km/s but show strong interaction dynamics for 116.0±6.1 GPa shock pressures and jet velocities of 6.5±0.5 km/s. Furthermore, we find that radiation-hydrodynamic simulations of the experiments are able to capture many aspects of the collisional behavior, such as the attenuation of jet velocity in the direction of propagation, but are unable to match the full spread of the strongly interacting cloud.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Project Plan: Salt in Situ Heater Test

This project plan gives a high-level description of the US Department of Energy Office of Nuclear Energy (DOE-NE) Spent Fuel and Waste Disposition (SFWD) campaign in situ borehole heater test project planned for the Waste Isolation Pilot Plant (WIPP) site, titled the Brine Availability Test in Salt (BATS). BATS is the first stage in a planned sequence of tests to bolster the technical basis for disposal of heat generating waste in salt. This plan provides an overview of the schedule and responsibilities of the parties involved. This project is a collaborative effort by Sandia, Los Alamos, and Lawrence Berkeley National Laboratories to execute a series of small-diameter borehole heater tests in salt for the DOE-NE SFWD campaign. Design of a heater test in salt at WIPP has evolved over several years. The experiment has begun in January 2020 and the first phase will continue for several months with the possibility for follow on testing. BATS comprises a suite of modular tests, which consist of a group of adjacent horizontal boreholes in the wall of drifts at WIPP. Each test is centered around a packer-isolated heated borehole (12.2 cm [4.81 diameter) containing equipment for water-vapor collection and borehole closure monitoring, surrounded by smaller-diameter (up to 5.3 cm [2.11 diameter) satellite observation boreholes. Observation boreholes contain grouted-in temperature sensors, electrical resistivity tomography (ERT) sensors, and fiber optics; packer-isolated tracer release and sampling intervals; and acoustic emission (AE) piezoelectric sensors. A larger-diameter (12.2 cm [4.81) satellite borehole includes sorel and salt cement plugs, as part of an engineered barrier sealing test. The first two tests, to be implemented in parallel, are heated (target borehole wall temperature of 120 °C) and unheated, with similar arrays of observation borehole monitoring changes. Follow-on tests will be designed using information gathered from the first two tests, and may be conducted at other borehole wall temperatures, use multiple observation boreholes, and may include different measurement types and test designs. This 2020 update of the original 2018 project plan satisfies DOE-NE Spent Fuel and Waste Science and Technology (SFWST) milestone M3SF-205N010303034, as part of the SNL "Salt Disposal R&D" work package.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Marine microbial community responses related to wetland carbon mobilization in the coastal zone

Abstract Here, we examine how marine microbial communities respond when dissolved organic matter (DOM) is mobilized from coastal wetlands. Biological transformations of this DOM may increase in the presence of reactive substrates, such as algal‐derived DOM (ADOM) in the coastal zone—a process known as priming. We performed laboratory experiments examining transformations of DOM derived from coastal wetland peat (PDOM) with and without the presence ADOM. Associated shifts in microbial community composition and functional gene abundance were measured to evaluate mechanisms of priming effects. ADOM presence stimulated CO 2 production when compared to the seawater control, which was further enhanced in the copresence of PDOM. DOM characterization showed a substantial difference in features present at the end of the incubation when PDOM was present with and without ADOM, while metagenomic sequencing indicated shifts in microbial community composition and identified 23 unique functional genes associated with pathways for the breakdown of aromatic compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

60 APPLIED LIFE SCIENCES↗

Mechanistic Insights into Visible-Light-Induced ATRA Reactions Powered by the Symbiotic Relationship between Cu(II)/Cu(I) Phenanthroline Complexes

As photoredox catalysis continues to yield promising chemical transformations, there is an increased need to understand how specific photocatalysts function to improve reaction efficiencies while expanding their scope. Copper-phenanthroline-based photocatalysts such as Cu II (dap)Cl 2 (dap = 2,9-di(p-anisyl)-1,10-phenanthroline) and [Cu I (dap) 2 ]Cl were both found to be equally capable of olefin activation through electrophilic atom transfer radical addition (ATRA) reactions. Although these molecular catalysts have proven successful, many intermediates suggested in the proposed catalytic cycles have never been detected. One undetermined aspect in this chemistry is related to how one equivalent of Cu II (dap)Cl 2 generates half of an equivalent of [Cu I (dap) 2 ] + during the photocatalytic sequence. To this end, we initially used more synthetically accessible model systems, namely, [Cu I (dpp) 2 ]Cl and Cu II (dpp)Cl 2 (dpp = 2,9-diphenyl-1,10-phenanthroline), to glean detailed mechanistic insights into this unusual symbiotic relationship. We directly detected several intermediates involved in the ATRA photocatalytic cycle using these model chromophores in conjunction with electronic spectroscopy, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry, electronic structure calculations, EPR spin-trap experiments, and 1 H NMR spectroscopy. We found that the unique ligand lability and coordinating properties of acetonitrile enable both the in situ oxidation of [Cu I (dpp) 2 ] + by tosyl chloride into Cu II (dpp)Cl 2 and the visible-light-induced homolysis of the Cu II –Cl bond, which initiates the conversion to the Cu I species [Cu I (dpp) 2 ][Cu I Cl 2 ]. Here, the combined findings from the present study of the catalytic cycle demonstrate that the symbiotic relationship between Cu II (dpp)Cl 2 and [Cu I (dpp) 2 ] + , as well as between Cu II (dap)Cl 2 and [Cu I (dap) 2 ] + , is the critical factor enabling the ATRA photoreaction by departing from either photocatalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Models of resistive wall tearing mode disruptions

Disruptions are a serious issue in tokamaks. In a disruption, the thermal energy is lost by means of an instability which could be a resistive wall tearing mode (RWTM). During precursors to a disruption, the plasma edge region cools, causing the current to contract. Model sequences of contracted current equilibria are given, and their stability is calculated. A linear stability study shows that there is a maximum value of edge q a ≈ 3 for RWTMs to occur. Further, this also implies a minimum rational surface radius normalized to plasma radius from RWTMs to be unstable. Nonlinear simulations are performed using a similar model sequence derived from an equilibrium reconstruction. There is a striking difference in the results, depending on whether the wall is ideal or resistive. With an ideal wall, the perturbations saturate at moderate amplitude, causing a minor disruption without a thermal quench. With a resistive wall, there is a major disruption with a thermal quench, if the edge q a ≤ 3. There is a sharp transition in nonlinear behavior at q a = 3. This is consistent with the linear model and with experiments. If disruptions are caused by RWTMs, then devices with highly conducting walls, such as the International Tokamak Experimental Reactor will experience much milder, tolerable, disruptions than presently predicted.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

PHYSICAL AND MORPHOLOGICAL PROPERTIES OF [O II] EMITTING GALAXIES IN THE HETDEX PILOT SURVEY

The Hobby-Eberly Dark Energy Experiment pilot survey identified 284 [O II] λ3727 emitting galaxies in a 169 arcmin{sup 2} field of sky in the redshift range 0 < z < 0.57. This line flux limited sample provides a bridge between studies in the local universe and higher-redshift [O II] surveys. We present an analysis of the star formation rates (SFRs) of these galaxies as a function of stellar mass as determined via spectral energy distribution fitting. The [O II] emitters fall on the ''main sequence'' of star-forming galaxies with SFR decreasing at lower masses and redshifts. However, the slope of our relation is flatter than that found for most other samples, a result of the metallicity dependence of the [O II] star formation rate indicator. The mass-specific SFR is higher for lower mass objects, supporting the idea that massive galaxies formed more quickly and efficiently than their lower mass counterparts. This is confirmed by the fact that the equivalent widths of the [O II] emission lines trend smaller with larger stellar mass. Examination of the morphologies of the [O II] emitters reveals that their star formation is not a result of mergers, and the galaxies' half-light radii do not indicate evolution of physical sizes.

79 ASTRONOMY AND ASTROPHYSICS↗

A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm–hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 × and 2.6 × speedup compared to CPU and GPU implementation, and 4 × higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

Peng, Hongwu↗

Modeling Exhaust-Generated Aerodynamic Pressure Loads on Airfield Matting Repair Systems

Airfield matting systems are commonly used for rapid repair of damaged runways to facilitate continuity of critical operations. Under normal service conditions, matting repair systems are subject not only to wheel loads exerted by airfield traffic but also to aerodynamic pressure loads resulting from high-speed, turbulent exhaust plumes produced by jets during taxi and take-off. Matting systems employed by the U.S. Air Force have been tested with respect to wheel loads, but probabilities of failure because of pressure loads produced by jet exhaust have not yet been established. This study presents a numerical approach for preliminary estimation of worst-case matting anchor forces resulting from exhaust-generated pressure loads. Using a two-dimensional computational fluid dynamics model, system behavior is evaluated by means of a parametric study of six system variables, of which the most significant are: (1) distance between engine and matting, (2) depth of cavity openings at matting edges, and (3) engine exhaust velocity. The results demonstrate that matting systems are likely to experience net uplift in typical service scenarios, driven by the combined effects of flow separation and cavity pressurization. Worst-case anchor pull-out forces, computed according to a tributary-area approach, are estimated to fall in the range of 130 lb (581 N) to 979 lb (4,350 N), depending on assumed load-sharing behavior among anchors and the size of the repair site. Field testing of instrumented matting systems during jet taxi and take-off sequences is recommended as the best next step toward understanding system behavior.

Engineering↗

Application of SCALE to Molten Salt Fueled Reactor Physics in Support of Severe Accident Analyses

As part of a US Nuclear Regulatory Commission–sponsored project to assess the modeling and simulation capabilities for accident progression, source term, and consequence analysis for advanced reactor technologies with SCALE and MELCOR, SCALE was used for the modeling and simulation of a molten salt-fueled reactor (MSR). SCALE capabilities for the modeling of MSR physics were demonstrated based on the Molten Salt Reactor Experiment (MSRE). Of primary interest were the determination of the system’s nuclide inventory, as well as the inventories in the various regions of the loop, considering that the fuel is continuously pumped through the system. This report contains discussions on the following: 1. Determination of the system-average fuel salt inventory considering fission gas removal in the off-gas system and noble metal removal through plating out at the heat exchanger using recent enhancements in SCALE’s depletion sequence TRITON, 2. Assessment of the nuclide spatial distribution throughout the loop using SCALE’s depletion solver ORIGEN, 3. Calculation of the core’s power profile, flux profile, temperature reactivity coefficients, and xenon reactivity using full-core calculations with SCALE’s Monte Carlo code KENO-VI. The results obtained with SCALE were post-processed to provide the MELCOR team with the core inventory and decay heat of the system, as well as the inventory and decay heat of individual regions in the loop, a zone-wise power profile, temperature feedback coefficients, and the xenon worth.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Laser pulse shaping for additive manufacturing

The present disclosure relates to an apparatus for additively manufacturing a product in a layer-by-layer sequence, wherein the product is formed using powder particles deposited on an interface layer of a substrate. A laser generates first and second beam components. The second beam component has a higher power level and a shorter duration than the first beam component. A mask creates a 2D optical pattern in which only select portions of the second beam components can irradiate the powder particles. The first beam component heats the powder particles close to a melting point, where the particles experience surface tension forces relative to the interface layer. While the particles are heated, the second beam component further heats the particles and also melts the interface layer before the surface tension forces can act on and distort the particles, enabling the particles and the interface layer are able to bond together.

DeMuth, James A.↗