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At least 55 records · Page 3

Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience

Roots remain understudied as the site of complex and important biological interactions mediating plant productivity. In grain and bioenergy crops, grass root specialized metabolites (GRSM) are central to key interactions, yet our basic knowledge of the chemical language remains fragmentary. Continued improvements in plant genome assembly and metabolomics are enabling large-scale advances in the discovery of specialized metabolic pathways as a means of regulating root-biotic interactions. Metabolomics, transcript coexpression analyses, forward genetic studies, gene synthesis and heterologous expression assays drive efficient pathway discoveries. Functional genetic variants identified through genome wide analyses, targeted CRISPR/Cas9 approaches, and both native and non-native overexpression studies critically inform novel strategies for bioengineering metabolic pathways to improve plant traits.

59 BASIC BIOLOGICAL SCIENCES↗

Guest Editorial: Special issue on flexible and resilient urban energy systems

This guest editorial summarizes the topics and the papers selected for the Special Issue on Flexible and Resilient Urban Energy Systems. After rigorous reviewing process, 21 papers are accepted for publication. These 21 accepted papers cover various aspects of urban energy systems and are distributed as following: situational awareness of urban energy systems (2 papers), quantification metrics of flexibility and resilience of urban energy systems (3 papers), vulnerability modeling of urban energy systems under various extreme events (3 papers), planning of flexible and resilient urban energy systems (4 papers), robust and resilient operation and control of urban energy systems (4 papers), recovery and restoration strategy of urban energy systems (2 papers), and coordination and interoperability of interconnected energy systems (3 papers). The Guest Editorial Board hopes this Special Issue can provide a valuable information for future research and advancements in the field of flexible and resilient urban energy systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

The role of infrastructure to enable and support electric drive vehicles: A Transportation Research Part D Special Issue

Widespread vehicle electrification appears to be necessary to achieve timely and deep reductions in greenhouse gases (GHG) and pollutant emissions as well as petroleum use in the transportation sector. The lack of a sufficient refuelling infrastructure has defeated many past efforts to promote alternatives to petroleum fuels. The papers in this special issue on the “Role of Infrastructure to Enable and Support Electric Drive Vehicles” address the diverse challenges posed by a transition from fossil-fuelled internal combustion engine vehicles to vehicles powered by electric motors and the special role of refuelling/recharging infrastructure in this transition. Electric drive vehicles are herein considered to be plug-in electric vehicles (PEVs), including plug-in hybrid electric vehicles (PHEVs), battery electric vehicles (BEVs), and hydrogen fuel cell electric vehicles (FCEVs). BEVs and FCEVs are also known as Zero Emission Vehicles (ZEVs) because their propulsion systems produce no tailpipe emissions.

33 ADVANCED PROPULSION SYSTEMS↗

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

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

36 MATERIALS SCIENCE↗

Achieving GPT-4o level performance in astronomy with a specialized 8B-parameter large language model

AstroSage-Llama-3.1-8B is a domain-specialized natural-language AI assistant tailored for research in astronomy, astrophysics, cosmology, and astronomical instrumentation. Trained on the complete collection of astronomy-related arXiv papers from 2007 to 2024 along with millions of synthetically-generated question-answer pairs and other astronomical literature, AstroSage-Llama-3.1-8B demonstrates remarkable proficiency on a wide range of questions. AstroSage-Llama-3.1-8B scores 80.9% on the AstroMLab-1 benchmark, greatly outperforming all models—proprietary and open-weight—in the 8-billion parameter class, and performing on par with GPT-4o. This achievement demonstrates the potential of domain specialization in AI, suggesting that focused training can yield capabilities exceeding those of much larger, general-purpose models. AstroSage-Llama-3.1-8B is freely available, enabling widespread access to advanced AI capabilities for astronomical education and research.

AI assistant↗

Electronic structure and energetics of a heterodimeric BChl g ′/Chl a ′ special pair generated by exposure of Heliomicrobium modesticaldum to dioxygen

Heliobacteria are anoxygenic phototrophs that have a Type I homodimeric reaction center containing bacteriochlorophyll g (BChl g). Previous experimental studies have shown that in the presence of light and dioxygen, BChl g is converted into 8 1 -OH-chlorophyll a F (hereafter Chl a F ), with an accompanying loss of light-driven charge separation. These studies suggest that the reaction center only loses the ability to transfer electrons once both BChl g′ molecules of the P 800 special pair have been converted to Chl a F ′. Here, the present work confirms that the partially converted BChl g′/Chl a F ′ special pair remains functional in samples exposed to dioxygen by demonstrating its presence using hyperfine couplings obtained from Q-band 1 H ENDOR, 2D 14 N HYSCORE and DFT methods. The DFT calculations of the BChl g′/BChl g′ homodimeric primary donor, which are based on the recently published X-ray crystal structure, predict that the unpaired electron spin is equally delocalized over both BChl g′ molecules and provide an excellent match to the experimental hyperfine couplings of the anaerobic samples. Exposure to dioxygen leads to substantial changes in the hyperfine interactions, indicative of greater localization of the unpaired electron spin. The measured hyperfine couplings are reproduced in the DFT calculations by replacing one of the BChl g′ molecules of the primary donor with a Chl a F ′ molecule. The calculations reveal that the spin density becomes localized on BChl g′ in the heterodimeric primary donor. Time-dependent DFT calculations demonstrate that conversion of either or both of the accessory BChl g molecules and/or one of the BChl g′ molecules of P800 to Chl a F ′ results in minor effects on the energy of the charge-separated states. In contrast, if both of the BChl g′ molecules of P 800 are converted a large increase in the energy of the charge-separated state occurs. This suggests that the reaction center remains functional when only one half of the dimer is converted, however, conversion of both halves of the P 800 dimer leads to loss of function

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Foreword Special issue on the Kilopower Project, Kilowatt Reactor Using Stirling TechnologY (KRUSTY) Test

This special issue of Nuclear Technology contains full-length, peer-reviewed papers describing the design work leading up to and the results of the Kilowatt Reactor Using Stirling TechnologY (KRUSTY) test. KRUSTY was the centerpiece of the National Aeronautics and Space Administration (NASA) Kilopower Project to design, build, and test a space nuclear reactor. This test was the first such test since the end of the Space Nuclear Auxiliary Power (SNAP) project at the end of the 1960s. In this issue, the introduction paper presents the goals of the Kilopower Project and the potential missions this reactor concept could serve in NASA. Kilopower was intended to serve both human exploration needs on planetary surfaces as well as science needs for deep-space exploration. The design work for the experiment by Poston and the power conversion development by Gibson present the pre-work required to perform the eventual KRUSTY test. A paper on regulatory analysis follows, to show the path used to gain approval of the proposed experiment. Then, the early zero-power critical experiments are presented by Sanchez and Grove. These experiments were essential data used to enhance model predictions prior to the high-temperature test. Next, Poston presents the three experiments (warm criticals) that increase the temperature in an incremental fashion prior to the final experiment. These experiments were used to achieve final regulatory approval of the final high-temperature experiment. The last paper by Poston presents the results of the steady-state and transient testing of the reactor at full power and at the design temperature. These results show that the reactor design and as-built experiment met all of the requirements that NASA had developed for the system. Any experiment of this magnitude was accomplished only because of the hard work and dedication of a large number of people at multiple institutions, including the NASA Glenn Research Center, NASA Marshall Space Flight Center, Y-12 National Security Site, Los Alamos National Laboratory, and the Nevada National Security Site prime contractor (formerly National Security Technologies and now the Mission Support and Test Services). The project was jointly funded by the Space Technology Mission Directorate at NASA and the Criticality Safety Program at the National Nuclear Security Administration (NNSA). A special thanks to Jerry McKamy and Angela Chambers at the NNSA and Lee Mason and Don Palac at NASA for their support and guidance. For the authors and multitude of staff that performed this work, the passion for space nuclear reactors was the key to making this experiment a reality.

99 GENERAL AND MISCELLANEOUS↗

A passion for theoretical physics: a special issue in memory of Peter G O Freund

This is a preface to A Passion for Theoretical Physics, a special issue collection of articles published in J. Phys. A in memory of Peter G. O. Freund. We dedicate this special issue to the memory of our esteemed colleague, inspiring teacher and cherished friend, Peter Freund. Peter George Oliver Freund was born on 7 September 1936 in Timisoara, Romania. He obtained his PhD under the supervision of Walter Thirring at the University of Vienna in 1960. He came to the University of Chicago in 1963, where he remained throughout his career. He passed away on 6 March 2018.

97 MATHEMATICS AND COMPUTING↗

Brightest cluster galaxies are statistically special from z = 0.3 to z = 1

ABSTRACT We study brightest cluster galaxies (BCGs) in ∼5000 galaxy clusters from the Hyper Suprime-Cam (HSC) Subaru Strategic Program. The sample is selected over an area of 830 deg2 and is uniformly distributed in redshift over the range of z = 0.3−1.0. The clusters have stellar masses in the range of 1011.8−1012.9M⊙. We compare the stellar mass of the BCGs in each cluster to what we would expect if their masses were drawn from the mass distribution of the other member galaxies of the clusters. The BCGs are found to be ‘special’, in the sense that they are not consistent with being a statistical extreme of the mass distribution of other cluster galaxies. This result is robust over the full range of cluster stellar masses and redshifts in the sample, indicating that BCGs are special up to a redshift of z = 1.0. However, BCGs with a large separation from the centre of the cluster are found to be consistent with being statistical extremes of the cluster member mass distribution. We discuss the implications of these findings for BCG formation scenarios.

Dalal, Roohi (ORCID:0000000279989899)↗

Realizability-preserving discontinuous Galerkin method for spectral two-moment radiation transport in special relativity

Here we present a realizability-preserving numerical method for solving a spectral two-moment model to simulate the transport of massless, neutral particles interacting with a steady background material moving with relativistic velocities. The model is obtained as the special relativistic limit of a four-momentum-conservative general relativistic two-moment model. Using a maximum-entropy closure, we solve for the Eulerian-frame energy and momentum. The proposed numerical method is designed to preserve moment realizability, which corresponds to moments defined by a nonnegative phase-space density. The realizability-preserving method is achieved with the following key components: (i) a discontinuous Galerkin phase-space discretization with specially constructed numerical fluxes in the spatial and energy dimensions; (ii) a strong stability-preserving implicit-explicit time-integration method; (iii) a realizability-preserving conserved to primitive moment solver; (iv) a realizability-preserving implicit collision solver; and (v) a realizability-enforcing limiter. Component (iii) is necessitated by the closure procedure, which closes higher order moments nonlinearly in terms of primitive moments. The nonlinear conserved to primitive and the implicit collision solves are formulated as fixed-point problems, which are solved with custom iterative solvers designed to preserve the realizability of each iterate. With a series of numerical tests, we demonstrate the accuracy and robustness of this discontinuous-Galerkin-implicit-explicit method.

79 ASTRONOMY AND ASTROPHYSICS↗

Experimental testing of hypotheses for temperature‐ and pH ‐based niche specialization of ammonia oxidizing archaea and bacteria

Summary Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Editorial for Special Issue: Grid-Interactive Efficient Buildings—Part 2

This issue of the ASME Journal of Engineering for Sustainable Buildings and Cities (JESBC) is fully dedicated to peer-reviewed papers specific to technologies and applications of Grid-interactive Efficient Buildings (GEBs). As defined by a series of publications by the U.S. Department of Energy (DOE) and outlined in Part 1 of the editorial of JESBC August 2020 issue, GEBs are efficient, connected, smart, and flexible buildings. This GEB special issue covers some technologies and applications for grid-connected buildings and communities. Some of technologies included in the special issue are dynamic insulation systems for building envelopes, building integrated fuel cells, and rooftop PV systems. Furthermore, the issue outlines the designs and cost-benefits of net-zero energy (NZE) buildings and carbon neutral communities in the United States.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Preface for the special collection commemorating the career of Pat Thiel

This Special Collection in the Journal of Vacuum Science and Technology A (JVST A) has been compiled to commemorate the career of Professor Patricia (Pat) Thiel as a scientific leader in the international surface science community. Pat passed away in September 2020 due to breast cancer. This Collection includes 26 articles from colleagues, collaborators, and former Thiel group members. The topics overlap Pat’s scientific interests and advances in areas that include chemisorption, reconstruction, and complex formation on metal surfaces; submonolayer nucleation and growth and kinetic roughening of epitaxial thin films; coarsening of surface nanostructures; intercalation; surface phenomena for intermetallics including quasicrystals; and atomic-scale friction. We wish to thank the authors for their contributions towards producing this impressive Special Collection.

99 GENERAL AND MISCELLANEOUS↗

The SODA Approach: Leveraging High-Level Synthesis for Hardware/Software Co-design and Hardware Specialization: Invited

Novel "converged" applications combine phases of scientific simulation with data analysis and machine learning. Each computational phase can benefit from specialized accelerators. However, algorithms evolve so quickly that mapping them on existing accelerators is suboptimal or even impossible. This paper presents the SODA (Software Defined Accelerators) framework, a modular, multi-level, open-source, no-human-in-the-loop, hardware synthesizer that enables end-to-end generation of specialized accelerators. SODA is composed of SODA-Opt, a high-level frontend developed in MLIR that interfaces with domain-specific programming frameworks and allows performing system level design, and Bambu, a state-of-the-art high-level synthesis engine that can target different device technologies. The framework implements design space exploration as compiler optimization passes. We show how the modular, yet tight, integration of the high-level optimizer and lower-level HLS tools enables the generation of accelerators optimized for the computational patterns of converged applications. We then discuss some of the research opportunities that such a framework allows, including system-level design, profile driven optimization, and supporting new optimization metrics.

Bohm Agostini, Nicolas↗

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Abstract Background The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. Results Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae , Candidatus Thioglobaceae , Metamycoplasmataceae , unclassified Pseudomonadales , Rhodobacteraceae , unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae . Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae . Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae , may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae , which lack such capacity. Conclusion This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae , Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large.

59 BASIC BIOLOGICAL SCIENCES↗

PORFLOW Implementation of Special Waste from Models for Slit and Engineered Trenches in the E-Area Low Level Waste Facility Performance Assessment

The implementation of special waste forms (SWFs) in the deterministic PORFLOW Slit Trench (ST) and Engineered Trench (ET) models to be used in the next revision of the E-Area Low Level Waste Facility’s (ELLWFs) Performance Assessment (PA) is outlined in this report. Four SWF implementation methods will be used: effective K d , delayed release, solubility-controlled/diffusion-controlled release, and complex SWF model updates. In addition, the implementation of models that address the presence of tall used equipment storage boxes in ST08-10 is considered a special waste form and will be described.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Soil Sample Plan in Support of the Site 300 Explosives Waste Treatment Facility Ecological Risk Assessment Pursuant to the Hazardous Waste Facility Permit, Part V, Special Condition #14 a-f. August 2020

The Department of Toxic Substances Control issued the Final Hazardous Waste Facility Permit to Lawrence Livermore National Laboratory, Site 300 in 2017. As part of the continual process to ensure waste treatment emissions are not impacting ecological receptors, LLNL analyzed soil samples in the vicinity of the Explosive Waste Treatment Facility (EWTF) Burn Units (i.e., Burn Cage and Burn Pan) and the Detonation Pad. Soil samples were analyzed by EPA Solid Waste 846 Methods for furans, explosives, metals, and semivolatile compounds. In all samples, furans, explosives, and semi-volatile organic compounds were not detected. Metals were detected at concentrations below background levels. This soil sample plan will sample the same four downwind areas of the Burn Units and the same downwind areas of the Detonation, as well as including four new sample locations. The four new locations will be located to the northeast and southwest of the Burn Units and Detonation (as shown in Figure 3). The constituents to be analyzed are in Tables 2 and 3. Perchlorate was not identified as a constituent of concern in the 2007 Soil Sampling Plan. However, for this plan, all soil samples will be analyzed for perchlorate. After completion of the sampling event, a soil sample report will be submitted to DTSC in accordance with requirements specified in the Hazardous Waste Facility Permit, Part V, Special Conditions 16 a-f. This proposed soil sampling plan will be fully implemented no later than one year after receiving DTSC approval, in accordance with the Hazardous Waste Facility Permit, Part V, Special Condition 15.

54 ENVIRONMENTAL SCIENCES↗

Soil Sample Workplan in Support of the Site 300 Explosives Waste Treatment Facility Ecological Risk Assessment Pursuant to the Hazardous Waste Facility Permit (Part V, Special Condition #14 a-f)

The Department of Toxic Substances Control issued the Final Hazardous Waste Facility Permit to Lawrence Livermore National Laboratory, Site 300 in 2017. As part of the continual process to ensure waste treatment emissions are not impacting ecological receptors, LLNL analyzed soil samples in the vicinity of the Explosive Waste Treatment Facility (EWTF) Burn Units (i.e., Burn Cage and Burn Pan) and the Detonation Pad. Soil samples were analyzed by EPA Solid Waste 846 Methods for furans, explosives, metals, and semi-volatile compounds. In all samples, furans, explosives, and semi-volatile organic compounds were not detected. Metals were detected at concentrations below background levels. This soil sample plan will sample the same four downwind areas of the Burn Units and the same downwind areas of the Detonation, as well as including four new sample locations. The four new locations will be located to the northeast and southwest of the Burn Units and Detonation (as shown in Figure 3). The constituents to be analyzed are in Tables 7 and 8. Perchlorate was not identified as a constituent of concern in the 2007 Soil Sampling Plan. However, for this plan, all soil samples will be analyzed for perchlorate. Nitrate and all CAM17 metals have been added to the sampling plan to comply with DTSC comments received in correspondence dated June 4, 2021. After completion of the sampling event, a soil sample report will be submitted to DTSC in accordance with requirements specified in the Hazardous Waste Facility Permit, Part V, Special Conditions 16 a-f. This proposed soil sampling plan will be fully implemented no later than one year after receiving DTSC approval, in accordance with the Hazardous Waste Facility Permit, Part V, Special Condition 15.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗