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At least 91 records · Page 5

Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria

Abstract Background Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. Results Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. Conclusion We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.

59 BASIC BIOLOGICAL SCIENCES↗

AI-Enabled Discovery and Physics-Based Optimization of Energy Efficient Processing Strategies for Advanced Turbine Alloys (Final Technical Report)

In this project, the multi-organizational team of academic and industrial researchers from the University of Kentucky an aerospace and energy generation OEM partner has leveraged novel Digital Process Twin (DPT) models of process/structure interactions (i.e., process-induced surface integrity) to advance a paradigm of fully integrated computational materials engineering (ICME). Using efficient process models as the core of a digital process simulator for a reinforcement learning algorithm, the team has integrated industrial data and metrics of structure/performance/energy relationships and manufacturing-related energy metrics to optimize dynamic processing parameters for significantly improved life-cycle energy efficiency of advanced γ-TiAl low-pressure turbine (LPT) alloys, as indicated by a set of design relevant parameters (e.g., residual stresses and scrap rate). The key objective and anticipated outcome of the project was at least a 10% reduction in life-cycle embodied energy for a recently developed, γ-TiAl low-pressure turbine (LPT) alloy and nickel-based superalloy Inconel 718, through the adoption of the proposed AI-enabled process optimization approach. The final project outcomes significantly exceeded this original target, realizing manufacturing-related energy efficiency improvements of more than 130% for TiAl and up to 80% for Inconel 718. Rather than following the prevailing and highly inefficient empirical paradigm, the proposed study demonstrated the feasibility of adopting a digital, physics-based process design and optimization paradigm. The recurring need for manual intervention, rework, reinspection causes significant production bottlenecks and unnecessary expense associated with delivering the requisite component quality. The OEM partner, and turbine industry in general, expect to reap significant cost and resource savings if an AI-optimized set of parameters can be applied to specific machining operations. The technical scope of the proposed project involved the paving of a realistic path towards model-based and AI-enabled Integrated Computational Materials Engineering (ICME), and away from inefficient empirical process optimization and legacy manufacturing practices, which are no longer able to efficiently process novel high-performance turbine alloy materials. The project team will address the fundamental knowledge gap that currently exists within the ICME paradigm with respect to the process/structure/performance/energy impacts of finishing processes. While significant resources have been devoted to the ‘early stages’ of manufacturing, such as alloy design, primary and secondary processing, finishing processes have not been adequately integrated within ICME. To provide an actionable path towards model-based finishing process design (e.g., machining, burnishing, grinding, polishing), we will employ a novel AI-enabled process optimization paradigm, based on a computationally efficient, physics-based process simulator. Through limited experimental work to calibrate and validate our process simulator model via an advanced in-situ characterization technique and process optimization via reinforcement learning, the project will seek to demonstrate a viable alternative to the inefficient ‘legacy’ processing strategies, empirical testing and broad scope machining learning approaches, all of which fail to adequately consider complex process physics. The project team has identified an intermetallic γ-TiAl LPT alloy, which is currently being used as part of the OEM partner’s advanced gas turbine designs. This particular alloy poses significant manufacturing challenges during finishing operations, which limit the degree to which the current turbine design can be manufactured in an energy- and cost-efficient manner. Empirical testing and numerical modeling efforts to optimize processing parameters for γ-TiAl have not been able to resolve these manufacturing challenges, so the proposed physics-based AI-enabled optimization technology would offer a truly novel and transformative capability. The multi-organizational team of academic and industry experts from the UKY and the OEM partner will work together closely to demonstrate the analytical and experimental critical function and characteristic proof of concept of this novel approach.

20 FOSSIL-FUELED POWER PLANTS↗

Validation of Numerical Tools for Calculating Reactivity Feedback in Sodium Fast Reactors Using SEFOR Experimental Data

The Southwest Experimental Fast Oxide Reactor (SEFOR) was an experimental sodium-cooled fast breeder reactor operated from 1969 to 1972 with experiments designed to measure Doppler reactivity feedback in a wide temperature range from around 350 °F to temperatures approaching the melting point of mixed oxide fuel of around 5000 °F, providing valuable data for code validations. Co-supported by the Department of Energy (DOE) Fast Reactor Program (FRP) and the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the SEFOR benchmark project focused on using the experimental data to validate numerical tools that are used in industry and academia to design and license sodium-cooled fast reactors (SFRs). By the end of FY-25, substantial progress was achieved in the SEFOR benchmark study. A variety of numerical tools commonly used for modeling SFRs were applied to develop models for SEFOR core configurations I-D, I-E, I-I, and I-J. These included Monte Carlo codes such as MCNP, Serpent, and Shift; deterministic codes such as the legacy Argonne Reactor Computation (ARC) suite and the high-fidelity NEAMS code Griffin; and the system analysis code SAS4A/SASSYS-1 (SAS). Using these models, both SEFOR zero-power experiments and power-ascending tests were successfully simulated. Comparisons were performed against experimental measurements of core criticalities, reflector worth, kinetics parameters (Λ/βeff), isothermal reactivity feedback (from 350 °F to 760 °F at zero power), and power-ascending reactivity feedback (as power increased from 0.4 MW to 17 MW). In general, these comparisons demonstrated very good agreement between numerical results and experimental data. In Fiscal Year 26 (FY-26), the SEFOR benchmark project will continue to address the modeling issues identified in FY-25. Effort will focus on the simulation of reactivity insertion transients in SEFOR core II using the ARC/SAS model. Future work will also focus on incorporating BISON into the SEFOR core modeling process to enable the first Multiphysics simulations of the isothermal tests based on the MOOSE framework.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Recycled Paper as a Source of Renewable Jet Fuel in the United States

Converting biomass into jet fuel involves more than the core chemical process. The overall process includes the logistics of harvesting and transporting the biomass, handling and preparing the material for processing, and processing and disposal of waste. All of these activities contribute to cost. Controlling cost involves more than developing efficient process chemistry. Choice of feedstock also has a significant impact on process economics. We consider chemical conversion of paper from municipal solid waste as a feedstock for the production of jet fuel and diesel. Paper has a significantly higher cellulose content than raw lignocellulosic biomass such as corn stover, so it requires less pretreatment to convert it into hydrocarbons than lignocellulosic biomass. Our techno-economic analysis showed that the cost of converting paper waste into jet fuel is about $1.00/gal less than jet fuel produced from corn stover. Although the cost of recycling paper into jet fuel is less than producing it from corn stover, the process is not competitive with petroleum. We estimated a minimum selling price of $3.97/gal for paper-derived jet fuel. Our sensitivity studies indicated that the biggest economic obstacle is the cost of cellulose hydrolysis. Direct hydrogenation of paper to sugar alcohols combined with increased economy of scale could make recycling paper jet fuel competitive.

09 BIOMASS FUELS↗

Dynamically adapting mechanism for translation lookaside buffer shootdowns

An operating system (OS) of a processing system having a plurality of processor cores determines a cost associated with different mechanisms for performing a translation lookaside buffer (TLB) shootdown in response to, for example, a virtual address being remapped to a new physical address, and selects a TLB shootdown mechanism to purge outdated or invalid address translations from the TLB based on the determined cost. In some embodiments, the OS selects an inter-processor interrupt (IPI) as the TLB shootdown mechanism if the cost associated with sending an IPI is less than a threshold cost. In some embodiments, the OS compares the cost of using an IPI as the TLB shootdown mechanism versus the cost of sending a hardware broadcast to all processor cores of the processing system as the shootdown mechanism and selects the shootdown mechanism having the lower cost.

42 ENGINEERING↗

Sparse Linear Solvers for Large-scale Electromagnetic Transient Simulations

Linear solvers form the basis for electromagnetic transient (EMT) simulations. There is a need to speed up EMT simulations as larger regions are analyzed using EMT simulations. For the same, the performance of linear solvers plays an important role. Exploiting the sparsity of the matrices generated in EMT simulations could assist with speed-up. Scalability is also crucial as power grids expand, demanding solutions capable of accommodating the increasing system size. Recent studies from the North American Electric Reliability Corporation (NERC) increasingly emphasize that EMT simulation models of the power grid will grow larger with the inclusion of power electronics components. Parallelisms in sparsity patterns exploit modern central processing units (CPUs), multi-core CPUs, and graphics processing units (GPUs) architectures in sparse solver designs. Therefore, this paper explores publicly available existing linear solvers and investigates their efficiency in large-scale power grid simulations. A large-scale power grid is developed by increasing the size of the IEEE 39 bus test system to up to 39000 bus systems.

Hsu, Kuan-Chieh↗

GNET2: an R package for constructing gene regulatory networks from transcriptomic data

Abstract Motivation The Gene Network Estimation Tool (GNET) is designed to build gene regulatory networks (GRNs) from transcriptomic gene expression data with a probabilistic graphical model. The data preprocessing, model construction and visualization modules of the original GNET software were developed on different programming platforms, which were inconvenient for users to deploy and use. Results Here, we present GNET2, an improved implementation of GNET as an integrated R package. GNET2 provides more flexibility for parameter initialization and regulatory module construction based on the core iterative modeling process of the original algorithm. The data exchange interface of GNET2 is handled within an R session automatically. Given the growing demand for regulatory network reconstruction from transcriptomic data, GNET2 offers a convenient option for GRN inference on large datasets. Availability and implementation The source code of GNET2 is available at https://github.com/jianlin-cheng/GNET2. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Hydrogen infused nuclear reactor core monoliths

Hydrogen infused nuclear reactor core monoliths and processes for their production are disclosed. Such monoliths may function as both a core monolith and a moderator, providing structure and at least some moderation. Hydrogen infused monoliths may be complementary to or be used in lieu of separate moderators for thermalizing neutrons.

Shivprasad, Aditya↗

Norm-Conserving Pseudopotentials and Basis Sets to Explore Actinide Chemistry in Complex Environments

We constructed and tested a new set of norm-conserving pseudopotentials, as well as companion Gaussian basis sets, for the actinide series (Ac–Lr) using the Goedecker, Teter and Hutter (GTH) formalism within the generalized gradient approximation (GGA) functional for exchange-correlation of Perdew, Burke and Ernzerhof (PBE). This fills a critical void in the literature for studying the chemistry of 5f–block elements in condensed phase. The accuracy and reliability of the newly parameterized An–GTH pseudopotentials and basis sets, a variety of tests on actinide-containing molecules were carried out and compared to all-electron and available experimental results. The new pseudopotentials include both medium ( [Xe]4f 14 ) and large core ( [Xe]4f 14 5d 10 ) options that successfully reproduced structure and energetics, particularly redox processes. The medium core size set, in particular, reproduced all electron calculations over multiple oxidation states from 0 to VII, whereas the large core set was suitable only for the early series elements and low oxidation states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multidimensional Simulations of Core Convection

The cores of main sequence intermediate- and high-mass stars are convective. Mixing at the radiative–convective boundary, waves excited by the convection, and magnetic fields generated by convective dynamos all influence the main sequence and post-main sequence evolution of these stars. These effects must be understood to accurately model the structure and evolution of intermediate- and high-mass stars. Unfortunately, there are many challenges in simulating core convection due to the wide range of temporal and spatial scales, as well as many important physics effects. In this review, we describe the latest numerical strategies to address these challenges. We then describe the latest state-of-the-art simulations of core convection, summarizing their main findings. These simulations have led to important insights into many of the processes associated with core convection. Two outstanding problems with multidimensional simulations are, 1. it is not always straightforward to extrapolate from simulation parameters to the parameters of real stars; and 2. simulations using different methods sometimes appear to arrive at contradictory results. To address these issues, next generation simulations of core convection must address how their results depend on stellar luminosity, dimensionality, and turbulence intensity. Furthermore, code comparison projects will be essential to establish robust parameterizations that will become the new standard in stellar modeling.

79 ASTRONOMY AND ASTROPHYSICS↗

Apollo Next Generation Sample Analysis (ANGSA): an Apollo Participating Scientist Program to Prepare the Lunar Sample Community for Artemis

As a first step in preparing for the return of samples from the Moon by the Artemis Program, NASA initiated the Apollo Next Generation Sample Analysis Program (ANGSA). ANGSA was designed to function as a low-cost sample return mission and involved the curation and analysis of samples previously returned by the Apollo 17 mission that remained unopened or stored under unique conditions for 50 years. These samples include the lower portion of a double drive tube previously sealed on the lunar surface, the upper portion of that drive tube that had remained unopened, and a variety of Apollo 17 samples that had remained stored at -27 °C for approximately 50 years. ANGSA constitutes the first preliminary examination phase of a lunar “sample return mission” in over 50 years. It also mimics that same phase of an Artemis surface exploration mission, its design included placing samples within the context of local and regional geology through new orbital observations collected since Apollo and additional new “boots-on-the-ground” observations, data synthesis, and interpretations provided by Apollo 17 astronaut Harrison Schmitt. ANGSA used new curation techniques to prepare, document, and allocate these new lunar samples, developed new tools to open and extract gases from their containers, and applied new analytical instrumentation previously unavailable during the Apollo Program to reveal new information about these samples. Most of the 90 scientists, engineers, and curators involved in this mission were not alive during the Apollo Program, and it had been 30 years since the last Apollo core sample was processed in the Apollo curation facility at NASA JSC. There are many firsts associated with ANGSA that have direct relevance to Artemis. ANGSA is the first to open a core sample previously sealed on the surface of the Moon, the first to extract and analyze lunar gases collected in situ, the first to examine a core that penetrated a lunar landslide deposit, and the first to process pristine Apollo samples in a glovebox at -20 °C. All the ANGSA activities have helped to prepare the Artemis generation for what is to come. The timing of this program, the composition of the team, and the preservation of unopened Apollo samples facilitated this generational handoff from Apollo to Artemis that sets up Artemis and the lunar sample science community for additional successes.

79 ASTRONOMY AND ASTROPHYSICS↗

Transforming Cyber Education thru Open to All Accessible Pathways

Boise State University’s (BSU) Cyber Operations and Resilience CORe program was intentionally designed so that any student, especially non-traditional and non-technical students, with an interest in cybersecurity could have an education and training pathway to enter the cyber workforce. The CORe curriculum focuses on teaching students how to design, apply, and improve cybersecurity through the interaction of people, processes, and technology. CORe is a stackable curriculum with elective credit hours and options for various academic and industry certificates and certifications that enable students to customize their unique career pathway. The CORe program guides students to think about the system being managed, the risks presented, and the dynamic intersection of system elements when considering how to incorporate resilience frameworks in achieving a resilient system. By developing systems thinking, the students gain an understanding of the interdependencies interacting with the operational system. Further, the CORe program encourages students to integrate cybersecurity knowledge with models and frameworks found in other academic disciplines through a unifying systems approach. CORe is designed around the realities of today’s broad cyber landscape: that breaches will occur in any system over time and proactive design of resilience into systems to detect, respond, and recover in a timely and orderly manner is critical. Students are taught to think holistically about cybersecurity focusing on all system elements. CORe is not a traditional cybersecurity degree. CORe is distinguished by the non-traditional engineering, computer science approach to cybersecurity education with the singular focus on infusing resilience operations and transdisciplinary systems thinking principles throughout the curriculum.

99 GENERAL AND MISCELLANEOUS↗

Accelerated Nuclear Radiation Effects on the Raspberry Pi 3B+ and Pi 4

Raspberry Pi™ computers running Linux and embedded benchmarks are subjected to radiation testing in the neutron beam at LANSCE. The ARM® Cortex®-A53 in the Raspberry Pi 3B+ versus ARM® Cortex®-A72 in the Raspberry Pi 4, single-core versus multi-core, and small versus large array SBU cross sections are compared. Results for the A53 and the A72 are similar. The results of one process on one of four cores and four identical processes on four cores are presented. The results of the array size show that there is more going on than just an increase in size. Linux is helpful in relating some errors that would have been classified as SEFI to an upset in a single bit.

36 MATERIALS SCIENCE↗

Segregation induced core-shell structure

A process for synthesis of PtNi high surface area core/shell particles. The processing including formation of PtNi nanoparticles, exposure of the PtNi nanoparticles to oxygen to form a nickel oxide coating on the nanoparticles at the same time the segregation of Ni to surface induces a Pt-skin with PtNi core structure, removal of the nickel oxide coating to form PtNi core/Pt shell (or Pt-skin) structure.

Wang, Rongyue↗

Successful νp -process in neutrino-driven outflows in core-collapse supernovae

The origin of the solar system abundances of several proton-rich isotopes, especially 92,94 Mo and 96,98 Ru, has been an enduring mystery in nuclear astrophysics. An attractive proposal to solve this problem is the νp-process, which can operate in neutrino-driven outflows in a core-collapse supernova after the shock is launched. Years of detailed studies, however, have cast doubt over the ability of this process to generate sufficiently high absolute and relative amounts of various p-nuclei. The νp-process is also thought to be excluded by arguments based on the long-lived radionuclide 92 Nb. Here, we present explicit calculations, in which both the abundance ratios and the absolute yields of the p-nuclei up to A ≲ 105 are successfully reproduced, even when using the modern (medium enhanced) triple-α reaction rates. The process is also shown to produce the necessary amounts of 92 Nb. The models are characterized by subsonic outflows and by the protoneutron star masses in the ≳ 1.7 M ⊙ range. In conclusion, this suggests that the Mo and Ru p-nuclides observed in the Solar System were made in CCSN explosions characterized by an extended accretion stage.

79 ASTRONOMY AND ASTROPHYSICS↗

Applying the core-satellite species concept: Characteristics of rare and common riverine dissolved organic matter

Introduction: Dissolved organic matter (DOM) composition varies over space and time, with a multitude of factors driving the presence or absence of each compound found in the complex DOM mixture. Compounds ubiquitously present across a wide range of river systems (hereafter termed core compounds) may differ in chemical composition and reactivity from compounds present in only a few settings (hereafter termed satellite compounds). Here, we investigated the spatial patterns in DOM molecular formulae presence (occupancy) in surface water and sediments across 97 river corridors at a continental scale using the “Worldwide Hydrobiogeochemical Observation Network for Dynamic River Systems—WHONDRS” research consortium. Methods: We used a novel data-driven approach to identify core and satellite compounds and compared their molecular properties identified with Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Results: In this work, we found that core compounds clustered around intermediate hydrogen/carbon and oxygen/carbon ratios across both sediment and surface water samples, whereas the satellite compounds varied widely in their elemental composition. Within surface water samples, core compounds were dominated by lignin-like formulae, whereas protein-like formulae dominated the core pool in sediment samples. In contrast, satellite molecular formulae were more evenly distributed between compound classes in both sediment and water molecules. Core compounds found in both sediment and water exhibited lower molecular mass, lower oxidation state, and a higher degree of aromaticity, and were inferred to be more persistent than global satellite compounds. Higher putative biochemical transformations were found in core than satellite compounds, suggesting that the core pool was more processed. Discussion: The observed differences in chemical properties of core and satellite compounds point to potential differences in their sources and contribution to DOM processing in river corridors. Overall, our work points to the potential of data-driven approaches separating rare and common compounds to reduce some of the complexity inherent in studying riverine DOM.

54 ENVIRONMENTAL SCIENCES↗

Synthesis and Evaluation of Cu@ZnO Core@Shell Nanowires for Use in the Carbon Dioxide Thermal Reduction Reaction

Copper-based core@shell nanomaterials are of interest for the catalytic hydrogenation of carbon dioxide toward value-added products. In this context, we have developed a facile, microwave-based procedure for the reliable and reproducible synthesis of Cu@ZnO core@shell nanowires. A systematic assessment of the effect of rationally varying various reaction conditions on this protocol was completed in order to better evaluate the growth process of these core–shell motifs. We determined that among different reaction parameters, it was the critical role of reaction time which enabled the quantitatively reliable growth of external shells with tunable thicknesses of up to 20 nm. As a demonstration of the material’s practical viability, catalytic testing was subsequently performed for the reverse water–gas shift reaction (CO 2 + H 2 → CO + H 2 O), with the evolution of the process followed with in situ X-ray diffraction and X-ray absorption spectroscopy in order to probe structural changes and gauge stability. These tests found the catalysts to be effective at converting CO 2 to CO, with notable stability detected in the shell layer and no observed alloying between copper and zinc. Furthermore, our studies support the idea that the Cu–ZnO and CuO x –ZnO interfaces are essential for the effective activation of CO 2 and H 2 .

36 MATERIALS SCIENCE↗

Comparing the Performance of Julia on CPUs versus GPUs and Julia-MPI versus Fortran-MPI: a case study with MPAS-Ocean (Version 7.1)

Abstract. Some programming languages are easy to develop at the cost of slow execution, while others are fast at runtime but much more difficult to write. Julia is a programming language that aims to be the best of both worlds – a development and production language at the same time. To test Julia's utility in scientific high-performance computing (HPC), we built an unstructured-mesh shallow water model in Julia and compared it against an established Fortran-MPI ocean model, the Model for Prediction Across Scales–Ocean (MPAS-Ocean), as well as a Python shallow water code. Three versions of the Julia shallow water code were created: for single-core CPU, graphics processing unit (GPU), and Message Passing Interface (MPI) CPU clusters. Comparing identical simulations revealed that our first version of the Julia model was 13 times faster than Python using NumPy, where both used an unthreaded single-core CPU. Further Julia optimizations, including static typing and removing implicit memory allocations, provided an additional 10–20× speed-up of the single-core CPU Julia model. The GPU-accelerated Julia code was almost identical in terms of performance to the MPI parallelized code on 64 processes, an unexpected result for such different architectures. Parallelized Julia-MPI performance was identical to Fortran-MPI MPAS-Ocean for low processor counts and ranges from 2× faster to 2× slower for higher processor counts. Our experience is that Julia development is fast and convenient for prototyping but that Julia requires further investment and expertise to be competitive with compiled codes. We provide advice on Julia code optimization for HPC systems.

54 ENVIRONMENTAL SCIENCES↗