Biochemical and structural characterization of two cif-like epoxide hydrolases from Burkholderia cenocepacia
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99 GENERAL AND MISCELLANEOUS↗
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NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography
Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6–5.0× faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.
Xiao, Zhongcan [ORNL] (ORCID:0000000220761961)↗
A Four-Layer Cyber-Physical Security Model for Electric Machine Drives Considering Control Information Flow
Despite the IEEE Power Electronics Society (PELS) establishing Technical Committee 10 on Design Methodologies with a focus on the cyber-physical security of power electronics systems, a holistic design methodology for addressing security vulnerabilities remains underdeveloped. This gap largely stems from the limited integration of computer science and power/control engineering studies in this interdisciplinary field. Addressing the inadequacy of unilateral cyber or control perspectives, this article presents a novel four-layer cyber-physical security model specifically designed for electric machine drives. Central to this model is the innovative control information flow (CIF) model, residing within the control layer, which serves as a pivotal link between the cyber layer's vulnerable resources and the physical layer's state-space models. By mapping vulnerable resources to control variable space and tracing attack propagation, the CIF model facilitates accurate impact predictions based on tainted control laws. The effectiveness and validity of this proposed model are demonstrated through hardware experiments involving two typical cyber-attack scenarios, underscoring its potential as a comprehensive framework for multidisciplinary security strategies.
97 MATHEMATICS AND COMPUTING↗
Recent development and manufacturing of coal-derived building materials
Coal has been challenged because coal combustion generates large quantities of carbon dioxide (CO2), which contributes to global warming. Pyrolysis char (PC), a valuable byproduct of coal that does not liberate CO2 when produced in an inert environment, can be used as a high carbon content fuel in combustion and gasification. However, using PC as a fuel is not an eco-friendly and cost-efficient way to make energy. Contrastingly using PC to make engineered products does offer an eco-friendly, attractive and value-added use. This paper introduces a novel integrated coal pyrolysis and solvent extraction process invented by the University of Wyoming (UW) to convert as-mined coal from the Powder River Basin Coal Field, Wyoming, to functional carbon products, which together liberates very little CO2. PC and coal deposit, extract and residual (CDER) are two functional carbon products that can be used in the development and manufacture of high value coal-derived building materials. The novel development of three building products known as coal-derived char bricks (CCB), carbon structural unit (CSU), and char-based insulation foam (CIF) are introduced. The approaches to manufacture them are investigated, including consideration of the eco-friendly approaches, optimization of engineering performance, and cost effectiveness relative to traditional products. CCBs show advantages in terms of their light weight (< 1 g/cm3) and good compressive strength (> 14 MPa). CSUs possess high compressive strength (> 30 MPa) and low thermal conductivity (< 0.3 W/mK), while CIFs can achieve a low thermal conductivity of 0.06 W/mK. Two demonstration houses have been built on UW campus, one using CCBs and another using commercial clay bricks. The performances of these houses are being monitored for temperature control, humidity uptake, noise reduction, inside air volatile organic content, indoor air quality and weatherability. The performance of the CCBs in terms of these criteria is discussed.
Ng, Kam↗
Small Signaling Peptides in Sorghum bicolor : Integrating Phylogeny and Gene Expression to Characterize Roles in Stem Development
Small signaling peptides (SSPs) are important regulators of plant growth, development, and responses to biotic and abiotic stress, yet their role in the C4 grass Sorghum bicolor is largely uncharacterized. To help fill this knowledge gap, 219 sorghum genes that encode SSPs were identified based on SSP sequences previously identified in Arabidopsis thaliana, Zea mays, Oryza sativa, Triticum aestivum , and Brachypodium distachyon . The 219 sorghum SSP-encoding genes were assigned to 19 gene families, analyzed for the presence of motifs, and aligned with genes that encode SSPs in other plants using phylogenetic analysis. Sorghum genes in 12 of the 19 SSP gene families had not been previously characterized. Expression of the 219 SSP-encoding genes in sorghum organs, during stem development, and in stem tissues and cell types revealed distinct spatial, temporal, and developmental patterns of expression. Genes associated with the SbCEP and SbRGF families were preferentially expressed in roots, whereas SbEPF genes were expressed in stem epidermal and pith parenchyma cells and panicles. The expression of genes during bioenergy sorghum stem growth and development was investigated because stems account for ~80% of harvested biomass and serve as conduits for water and nutrient transport between leaves and roots. During stem development, 28 SSP genes in several families ( CLE, EPF, CEP, GASS, PSY, ES, PSK, CAPE, POE ) were expressed at higher levels in zones of cell proliferation. For example, the TDIF homologs SbCLE41 and SbCLE42 were expressed at high levels in nascent stem nodes where they may regulate vascular bundle cambial activity and cell differentiation. A different set of 15 genes in the CIF, POE, CAPE, PSY, CEP, RALF , and CLE families were expressed at higher levels in zones of stem tissue differentiation highlighted by elevated expression of five SbRALFR s in the stem nodal plexus. Cell type–specific expression of many sorghum genes that encode SSPs was observed in fully elongated internodes indicating gene expression is regulated with high spatial resolution. Overall, the results provide a foundation of information for analysis of SSP function in sorghum that can be integrated with knowledge of sorghum gene regulatory networks to modulate traits important for production of sorghum crops.
bioenergy sorghum↗
Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model
Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.
AI agent↗
Enhanced delivery of engineered Fe-Mn binary oxides in heterogeneous porous media for efficient arsenic stabilization
Heterogeneity in sediment and aquifer is universal, resulting in preferential flows of injected materials in the high permeability regions and forming flow by-passed zones in the low permeability regions during in-situ subsurface remediation. This adverse effect can considerably delay the completion of remedial operations and significantly increase the cost. Column experiments were designed and conducted to study the transport of starch- and starch-xanthan gum modified Fe-Mn binary oxide particles (SFM and SXFM) in saturated heterogeneous porous media and to reveal the particles’ arsenic (As) stabilization performance. Fine-in-Coarse (FIC) and Coarse-in-Fine (CIF) patterns of heterogeneous packings were set up in the columns. Testing results demonstrated that starch-xanthan gum dual treatment on Fe-Mn binary oxides successfully improved the particles’ migration capability in heterogeneous porous media and their distribution uniformity attributed to the profound shear thinning behavior of xanthan gum solution. The addition of xanthan gum to the system increased the viscosity and shear thinning property of SXFM suspension, making it a better candidate for delivery. Both SFM and SXFM stabilized As in heterogeneously packed sediment collected from a contaminated site, with SXFM showing better stabilization performance than SFM. The stabilization effects of SXFM were 90.7-97.0%, compared to 82.0-95.2% of SFM.
Yan, Xiulan↗
Prototype crystal structures for exa-AMD framework
This dataset provides a curated collection of initial crystal structure prototypes for the exa-AMD framework, serving as templates for generating hypothetical candidates in multinary materials discovery through elemental substitution and scaling. It includes 36553 ternary and 5254 quaternary unique structures sourced from public databases such as Materials Project, GNoME, OQMD, AFLOW, and NovoMag, formatted in CIF.
exa-AMD↗
CrystalVR
SAND2022-14694 O CrystalVR is a CAD2VR plugin which enables the import of crystallographic information files (CIF) into a virtual reality (VR) environment for visualization and interaction. Crystallographic data is incredibly complex and difficult to navigate and visualize on a two-dimensional or 2D screen. CrystalVR empowers users to step inside their crystals, allowing them to intuitively grow, shrink, and scale the crystal structure. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Krukar, John↗
Towards a machine-readable literature: finding relevant papers based on an uploaded powder diffraction pattern
A prototype application for machine-readable literature is investigated. The program is called pyDataRecognition and serves as an example of a data-driven literature search, where the literature search query is an experimental data set provided by the user. The user uploads a powder pattern together with the radiation wavelength. The program compares the user data to a database of existing powder patterns associated with published papers and produces a rank ordered according to their similarity score. The program returns the digital object identifier and full reference of top-ranked papers together with a stack plot of the user data alongside the top-five database entries. The paper describes the approach and explores successes and challenges.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗