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At least 667 records · Page 37

Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS)

Support customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. Evaluate and improve the integration of ion mobility to existing MS analysis methods of the Mass Profiler Professional workflow (Mass Profiler, ID Browser and Mass Profiler Professional).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Shadow of the Future: Developing Trust and Software within the Exascale Computing Project

Collaboration and team science are emerging areas of interest in software production. Historically, multi-institutional research collaborations are difficult to initiate and maintain, negatively impacting communication, negotiation, and dialogue between industry, government, and academic researchers. The Exascale Computing Project (ECP), a massive, multi-team, high-stakes initiative, facilitated broader research collaboration under a shared funding structure and extended timeline to support scientific discovery. Here, we conducted interviews with ECP teams, representing a variety of domain specialties, research institutions, and programming backgrounds. Using thematic analysis, we assessed how ECP’s structure created an environment of increased trust among projects and how software shared between teams facilitated sustained collaboration. We found that the expectation of future collaboration, i.e., the shadow of the future, greatly enhanced trust among teams and the quality of scientific software produced. Based on our findings within ECP projects, we connect to the existing literature on trust in software engineering and share recommendations for sustainable multi-institutional collaboration and shared best software practices.

Exascale computing project↗

Exploration of non-resonant divertor features on the Compact Toroidal Hybrid

Abstract Non-resonant divertors (NRDs) separate the confined plasma from the surrounding plasma facing components (PFCs). The resulting striking field line intersection pattern on these PFCs is insensitive to plasma equilibrium effects. However, a complex scrape-off layer (SOL), created by chaotic magnetic topology in the plasma edge, connects the core plasma to the PFCs through varying magnetic flux tubes. The Compact Toroidal Hybrid (CTH) serves as a test-bed to study this by scanning across its inductive current. Simulations observe a significant change of the chaotic edge structure and an effective distance between the confined plasma and the instrumented wall targets. The intersection pattern is observed to be a narrow helical band, which we claim is a resilient strike line pattern. However, signatures of finger-like structures, defined as heteroclinic tangles in chaotic domains, within the plasma edge connect the island chains to this resilient pattern. The dominant connection length field lines intersecting the targets are observed via heat flux modeling with EMC3-EIRENE. At low inductive current levels, the excursion of the field lines resembles a limited plasma wall scenario. At high currents, a private flux region is created in the area where the helical strike line pattern splits into two bands. These bands are divertor legs with distinct SOL parallel particle flow channels. The results demonstrate the NRD strike line pattern resiliency within CTH, but also show the underlying chaotic edge structure determining if the configuration is diverted or limited. This work supports future design efforts for a mechanical structure for the NRD.

Physics↗

Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes

Abstract Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram‐positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase‐mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae , identifying a number of putative β7–β8 loop‐mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1′ position of the substrate motif, underlined in LPXT G , in contrast to the strict P1′ Gly recognition of SrtA from Staphylococcus aureus . However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C‐terminus, and three others of β7–β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7–β8 loop‐mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.

Gao, Melody↗

Network structure of vertebrate scavenger assemblages at the global scale: drivers and ecosystem functioning implications

The organization of ecological assemblages has important implications for ecosystem functioning, but little is known about how scavenger communities organize at the global scale. Here, we test four hypotheses on the factors affecting the network structure of terrestrial vertebrate scavenger assemblages and its implications on ecosystem functioning. We expect scavenger assemblages to be more nested (i.e. structured): 1) in species-rich and productive regions, as nestedness has been linked to high competition for carrion resources, and 2) regions with low human impact, because the most efficient carrion consumers that promote nestedness are large vertebrate scavengers, which are especially sensitive to human persecution. 3) We also expect climatic conditions to affect assemblage structure, because some scavenger assemblages have been shown to be more nested in colder months. Finally, 4) we expect more organized assemblages to be more efficient in the consumption of the resource. We first analyzed the relationship between the nestedness of the scavenger assemblages and climatic variables (i.e. temperature, precipitation, temperature variability and precipitation variability), ecosystem productivity and biomass (i.e. NDVI) and degree of human impact (i.e. human footprint) using 53 study sites in 22 countries across five continents. Then, we related structure (i.e. nestedness) with its function (i.e. carrion consumption rate). We found a more nested structure for scavenger assemblages in regions with higher NDVI values and lower human footprint. Moreover, more organized assemblages were more efficient in the consumption of carrion. However, our results did not support the prediction that the structure of the scavenger assemblages is directly related to climate. Our findings suggest that the nested structure of vertebrate scavenger assemblages affects its functionality and is driven by anthropogenic disturbance and ecosystem productivity worldwide. Disarray of scavenger assemblage structure by anthropogenic disturbance may lead to decreases in functionality of the terrestrial ecosystems via loss of key species and trophic facilitation processes.

54 ENVIRONMENTAL SCIENCES↗

Effect of 316 stainless steel powder processing conditions on microstructure

One parameter that has both economic and performance effects in the manufacturing of steel parts is the powder feedstock used. 316 L steel powder can be produced through water atomization or gas atomization, where both the powder size and the atomization process determine the cost of powder feedstock. Gas atomized powder is spherical and has a lower oxygen content than water atomized powder, making it the preferred choice for performance, but comes at a higher financial cost. Here, in this study, various 316 L powder batches are characterized to understand physical properties and microstructural variations. Density and flowability were determined using gas pycnometry and Hall flow tests. Powder morphology and porosity were qualitatively analyzed via optical microscopy and scanning electron microscopy, Finally, transmission electron microscopy was used to determine changes in phases present. Spherical gas atomized powder of 30–100 μm contained Mn$-$Si rich oxides both on the surface and within the matrix. Meanwhile, irregular water atomized powder 30 μm in diameter contained silicon oxides without manganese. All powder particles contained a nickel rich cellular structure which was shown to support the formation of additional phases. While literature has observed general microstructural features across 316 L powder particles, transmission electron microscopy (TEM) in this study has identified variations in precipitation and cell structures. Information regarding morphology, flowability, density, and phase distributions can be applied to understand variations in part consolidation, which will in turn show which powder aspects are significant for production.

Chemical segregation↗

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

Tuning Catalytic Reactivity via Wetting Control through Oxygen Vacancies: Ru Clusters on Anatase TiO 2 and CeO 2 Supports

The shape of supported metal particles regulates their catalytic reactivity and is determined by the degree of wetting between the metal particle and the support surface. Flattened particles that wet support surfaces were reported in various catalytic systems, particularly in the subnanometer size regime. Such consequential metal–support wetting phenomena are poorly understood, and methods to study them on powder catalysts under realistic conditions are lacking. Here, we investigate the size-dependent wetting behaviors of Ru particles on two reducible-oxide supports, anatase TiO 2 (TiO 2 -A) and CeO 2 , under reducing catalytic conditions. X-ray absorption spectroscopy (XAS), low-energy ion scattering (LEIS), and density functional theory (DFT) are combined to determine the shape of Ru particles. Ru particles remain three-dimensional without wetting the TiO 2 -A support within the coverage range studied (0.06–0.98 Ru nm –2 ). In contrast, at low coverages (<0.25 Ru nm –2 ), Ru wets the CeO 2 support to form flat, disordered structures. The higher wettability of CeO 2 than TiO 2 -A is attributed to oxygen vacancies in the near-surface region. The shape difference between small Ru particles or clusters on the two supports leads to drastically contrasting catalytic reactivities in polyolefin hydrogenolysis, despite similar diameters. As a result, this work highlights the implications of metal–support wetting, or cluster shape, on catalytic behaviors of small metal clusters, while establishing the foundation for future systematic studies of such a phenomenon in realistic systems, by delivering a multitechnique methodology and revealing governing fundamental principles.

42 ENGINEERING↗

Interpreting the Operando XANES of Surface-Supported Subnanometer Clusters: When Fluxionality, Oxidation State, and Size Effect Fight.

X-ray absorption near edge structure (XANES) spectroscopy is widely used for operando catalyst characterization. We show that, for highly fluxional supported nanoclusters, the customary extraction of the oxidation state of the metal from the XANES data by fitting to the bulk standards is highly questionable. The XANES signatures as well as the apparent oxidation state for such clusters arise from a complex combination of many factors, and not only from the chemical composition in reaction conditions (e.g., oxygen content in oxidizing atmosphere). The thermally accessible isomerization and population of several structurally distinct cluster forms, cluster-support interaction, and intrinsic size effects all impact the metal oxidation state and XANES signal. We demonstrate this on copper oxide clusters with different compositions, Cu4Ox(x = 2-5) and Cu5Oy (y = 3, 5), deposited on amorphous alumina and ultrananocrystalline diamond, for which we computed the XANES spectra and compare the results to the experiment. We show in addition that fitting the experimental spectrum to calculated spectra of supported clusters can, in contrast, provide good agreement and insight into the spectrum-composition-structure relation. Experimental XANES interpreted using the proposed fitting scheme shows the partial reduction of Cu oxide clusters at rising temperatures, and pinpoints the specific stoichiometries that dominate in the ensemble of cluster states as the temperature changes.

Zandkarimi, Borna↗

Effects of Structural Constraints on Excited-State Properties in Dimeric Cu(I) Diimine Complexes

Copper(I) bis-diimine complexes have played important roles in light-activated processes that can lead to their potential applications in photocatalysis and chemical sensing. Their metal-to-ligand charge-transfer (MLCT) excited-state properties are tunable by various structural factors. Dimeric Cu(I) complexes with connecting diimine derivative ligands offer another structural tuning platform for the excited-state properties. Here, we investigate excited-state properties in two covalently connected dimeric Cu(I)'s with varying structural constraints exerted by the number of carbons in the polyethylene bridge (C0 and C4) connecting the two copper(I) diimine moieties. An interesting feature of Cu(I) diimine complexes is their ability to flatten following a photoinduced structural change. Herein, we observe larger structural constraints and more structural rearrangement required upon excitation of the longer bridged complex C4 to achieve a conformation toward a more flattened tetrahedral coordination geometry compared to the shorter bridged C0. Vibrational wavepacket analysis of these complexes further supports the effect of these structural constraints where we observe a more rapid dephasing of the C0 complex, as opposed to the C4 complex, despite similar normal mode vibrations. The experimental results were supplemented by TDDFT calculations. In conclusion, the studies provide insight into using metal-metal interactions through constraints to tune excited-state dynamics and pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Review—Meeting Fuel Cell Catalyst Requirements for Heavy-Duty Vehicle Applications

Catalyst requirements for proton exchange membrane (PEM) fuel cells differ by applications. Commercial heavy-duty vehicle (HDV) applications consume more H 2 fuel and demand higher durability than many others and the total cost of ownership (TCO) of the vehicle is largely related to the performance and durability of catalysts. This article is written to bridge the gap between the industrial requirements and academic activity for advanced cathode catalysts with an emphasis on durability. From a materials perspective, the underlying nature of the carbon support, Pt-alloy crystal structure, stability of the alloying element, cathode ionomer volume fraction, and catalyst-ionomer interface play a critical role in improving performance and durability. We provide our perspective on four major approaches, namely, mesoporous carbon supports, ordered PtCo intermetallic alloys, thrifting ionomer volume fraction, and shell-protection strategies that are currently being pursued. While each approach has its merits and demerits, their key developmental needs for future are highlighted.

Ramaswamy, Nagappan (ORCID:0000000234302758)↗

Structure–Activity Relationships for Ethanol Dehydrogenation to Acetaldehyde by Silica-Supported Zinc Oxide Catalysts

Silica-supported ZnO efficiently catalyzes the nonoxidative dehydrogenation of ethanol to acetaldehyde, which is relevant for production of 1,3-butadiene from bioethanol. Characterization with in situ spectroscopies under dehydrated conditions (high sensitivity-low energy ion scattering (HS-LEIS), diffuse reflectance (DR) UV–vis, X-ray absorption spectroscopy (XAS), diffuse reflectance Fourier transform infrared spectroscopy (DRIFTS), inelastic neutron scattering (INS), and UV Raman), and ammonia adsorption probed by temperature-programmed desorption followed by DRIFTS and mass spectrometry (DRIFTS-MS NH 3 -TPD), and DFT calculations revealed that the supported ZnO x phase was present as isolated surface ZnO x sites on SiO 2 , with the vast majority coordinated by two siloxane bonds and one silicon atom with two nonbridging oxygens ((≡SiO) 2 Zn 2+ O 2 Si=), anchored at 4-, 5-, and 6-membered siloxane rings. A minor fraction of surface ZnO x sites possessed Lewis acidity, and even fewer sites possessed a Bro̷nsted acidic Zn(OH) + Si moiety. Ethanol temperature-programmed surface reaction-mass spectrometry (TPSR-MS) with various oxidative or ethanol reaction pretreatments indicated that only sites with Lewis and Bro̷nsted acidic character (Zn(OH) + Si) were active for ethanol dehydrogenation, while the majority surface (≡SiO) 2 Zn 2+ O 2 Si= sites were inactive. Greater heterogeneity among all surface ZnO x sites, as assessed by in situ DR UV–vis spectroscopy, was associated with a greater number of ZnO x sites that were active for ethanol dehydrogenation as well as lower enthalpic barriers for acetaldehyde production among the most active surface ZnO x sites. Turnover frequencies and the apparent activation energy for ethanol dehydrogenation were determined from steady-state kinetics. Together, these findings suggested that anchoring inactive surface (≡SiO) 2 Zn 2+ O 2 Si= sites on the silica support caused a greater number of active surface ZnO x sites to adopt a more strained configuration, promoting ethanol dehydrogenation catalysis. Pretreatments and catalysts that promoted desorption of ethanol during TPSR, taken as a marker of surface dehydroxylation, were associated with an increased number of the most active surface (Zn(OH) + Si) sites. Such findings suggested that inactive surface ZnO x sites were activated for ethanol dehydrogenation by dehydroxylation of the support and/or decreased coordination to hemilabile siloxane ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Next-Generation Reverse Logistics Networks of Photovoltaic Recycling: Perspectives and Challenges

With the growing adoption of solar energy as a key component of the global energy transition and its new industrial policy (the Inflation Reduction Act and others), the United States is witnessing a significant increase in solar investments. This surge in installations and domestic and reshored manufacturing of solar photovoltaic (PV) panels brings with it a pressing issue: the proper management of end-of-life (EoL) PV panels. As these panels are decommissioned, either due to reaching the end of their lifespans or due to breakage across the various stages of the forward supply chain, it becomes crucial to establish efficient reverse supply chain logistics systems to address the challenges associated with their disposal, while also unlocking the value of the inherent materials that are of critical value for other forward supply chains. This perspective article examines the challenges regarding EoL PV panels and relevant reverse supply chain and logistics networks, and proposes future research directions based on the gaps observed among academic research, industry, and policy-making challenges. We identify the main bottlenecks and hurdles including, among others, the lack of supportive regulations and absence of structured, optimized recycling infrastructure. To this end, it is proposed that the key to achieving a sustainable reverse supply chain network for solar PV panels lies in relentless end-to-end supply chain cost optimization efforts supported by enabling policies. Moreover, it is proposed that designing systematic decision-making modeling frameworks is vital for examining different possibilities and scenarios for state, region or nation-wide optimization of solar PV reverse supply chain networks. Indicative to this effect, we discuss the development of a Resource-Task-Network (RTN)-based model and demonstrate its application and benefits through a case study. We wrap up with conclusions and future research directions.

circular economy↗

Rayleigh Wave Propagation in the Bighorn Mountains Region, Wyoming

Short-period Rayleigh waves, Rg , provide strong constraints on the depth of shallow seismic events and are of interest for monitoring small explosions. Characterizing the seismic sources that generate Rg requires an understanding of how shallow crustal structure affects Rayleigh wave propagation. Here, in support of these efforts, this study utilizes observed waveforms from small shallow explosions recorded on temporary seismic network deployments in the Bighorn region, Wyoming. We study regional near-surface geology by measuring changes in surface-wave amplitude and polarization during propagation through basins, foothills, and mountains. We develop additional insight by carrying out surface-wave eigenfunction analyses and numerical-wave simulations, which together reproduce many characteristics seen in the observed waveforms. Our results show how sedimentary basins in the Bighorn region allow for amplified prograde-polarized higher-mode and retrograde-polarized fundamental-mode Rayleigh waves, whereas adjacent mountains only support retrograde motion. These different modes provide distinct constraints on the Earth structure and source characteristics, potentially enabling targeted inversions in future studies. Finally, our findings provide insight into Rg propagation through complex near-surface geology, improving our understanding of shallow propagation and source effects that are relevant to explosion monitoring efforts.

58 GEOSCIENCES↗

Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation

This Final Scientific and Technical Report summarizes work performed under the Phase IIA SBIR project “Enabling the Broader Use of MOOSE for Nuclear Energy and Other Simulation” (DE-SC0020906) from August 2023 through August 2025. The objective of the Phase IIA effort was to mature and harden capabilities developed during Phase II, with the goal of enabling practical interoperability between Coreform’s isogeometric analysis (IGA) technologies and the Multiphysics Object-Oriented Simulation Environment (MOOSE), while improving robustness, performance, and scalability for complex, nuclear-relevant geometries. Over the course of Phase IIA, the project established and validated an extraction-based interoperability pathway between Coreform tools and MOOSE. A combined mesh and matrix format was defined collaboratively with MOOSE developers and integrated into the solver, enabling standard MOOSE workflows to operate on data exported from Coreform’s IGA and Flex Representation Method (FRM) pipelines. Early demonstrations validated architectural compatibility using linear solid mechanics problems, while later efforts focused on benchmark testing and external use. By the end of the project period, engineers at BWXT were able to independently set up and execute a simulation using the Coreform–MOOSE workflow and provide direct feedback that informed further refinement. In parallel, substantial effort was devoted to improving the robustness of trimmed U-spline construction for complex CAD geometries. A growing test suite of nuclear-relevant models was compiled through collaboration with multiple stakeholders and used to drive extensive bug fixing and reliability improvements. These efforts resulted in improved robustness and performance, including the addition of fallback capabilities that enhance reliability when the underlying commercial CAD kernel fails. Performance-oriented work progressed later in the project, with the development and demonstration of methods to decompose complex geometries into structured subregions and updated data representations to support more efficient solver processing. Additionally, extensive enhancements to threadsafe parallel data structures and trimming operations established a foundation for scalable processing of large assemblies. Collaboration with Sandia National Laboratories on the SGM geometric modeling kernel advanced to a functioning interface test case, positioning the workflow for future kernel integration. Overall, the Phase IIA effort successfully transitioned the project from architectural proof-of-concept to externally exercised, solver-integrated capability, while clarifying remaining technical challenges related to standardization, performance optimization, and kernel integration.

42 ENGINEERING↗

Seasonality regulates the structure and biogeochemical impact of ectomycorrhizal fungal communities across environmentally divergent neotropical dry forests

Abstract Ectomycorrhizal (ECM) symbioses support forest functioning globally, yet both the structure and function of ECM fungal communities in seasonally dry neotropical forests (SDTFs), known for extreme heterogeneity in vegetation and edaphic properties, remain under characterized. Here, we evaluated the relative influences of seasonal versus spatial variation in ECM fungal community structure in soils from four environmentally divergent SDTFs. We also assessed the importance of biotic and abiotic drivers of SDTF ECM fungal community structure at regional scales, as well as ECM impacts on soil carbon (C) and nitrogen (N) cycling. ECM fungal frequency, relative abundance and richness all increased in the wet season, but spatial rather than seasonal effects explained more variation in community composition. Across the four SDTFs investigated, differences in tree communities drove ECM fungal community turnover more than geographic distances, site abiotic conditions or soil chemistry. Although soil moisture and ECM tree basal area were stronger predictors of soil biogeochemistry, incorporating ECM fungal community composition and relative abundance added explanatory power to models of soil C and N cycling in the wet season. Synthesis : Our results highlight the importance of seasonality and plant community composition in shaping different aspects of SDTF ECM fungal community structure and diversity as well as the potential for both the plant and fungal components of ECM symbioses to impact soil functioning across heterogenous SDTFs. Furthermore, our findings suggest that alterations in SDTF plant community composition due to climate or land‐use change will have important consequences for ECM fungal diversity and associated effects on soil biogeochemical cycling.

54 ENVIRONMENTAL SCIENCES↗