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At least 523 records · Page 29

Integrated Experimental and Computational K-Edge X-ray Absorption Near-Edge Structure Analysis of Vanadium Catalysts

X-ray Absorption Near-Edge Structure (XANES) spectroscopy is a powerful tool to reveal key structural and electronic features of isolated catalytic sites, yet insights into molecular structure and more detailed orbital analysis through a combination of experimental and computed XANES analysis are necessary for accurate interpretation of the spectra, especially when significant heterogeneity exits among the catalytic sites. Herein, we present an integrated computational and experimental strategy to determine both primary and secondary bonding interactions within the XANES pre-edge region for organovanadium complexes, which was developed using a series of well-defined molecular vanadium complexes and then applied to the characterization of a supported organovanadium olefin hydrogenation catalyst. Time-dependent density functional theory is used to predict the energy of pre-edge XANES features for a series of vanadium complexes with a variety of oxidation states and local coordination environments. Further, a calibration scheme incorporating different density functionals and basis sets is established, resulting in an optimized scheme that accurately predicts pre-edge energies with a mean absolute error of 0.40 eV. Second-shell coordination (e.g., V---V) effects within XANES are identified through the analysis of the computed dominant orbital contributions for multi-vanadium complexes. Orbital analysis also provided confirmation that the vanadium-hydride formation combined with the heterogeneity of the catalytic active species in ole-fin hydrogenation caused the energy shift and broadening of the pre-edge peak after hydrogen treatment of the silica-supported organovanadium pre-catalyst. This work further elucidates computational XANES simulations and techniques potentially guiding characterization in surface organometallic chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Firmware Tampering Detection in Heavy-Duty Vehicles through J1939 CAN Analysis

Modern heavy-duty vehicles rely on complex networks of Electronic Control Units (ECUs) that communicate using the J1939 protocol. While this system makes it easier to update and configure vehicle components, it also opens the door to serious cybersecurity risks if not properly secured. This work investigates the potential for firmware tampering through the J1939 communication protocol, which enables ECU configuration and reprogramming over the Controller Area Network (CAN) bus. By monitoring CAN traffic during legitimate maintenance operations and reverse-engineering OEM diagnostic software, we identified common and proprietary J1939 message identifiers, authentication patterns, and vulnerabilities within Unified Diagnostic Services (UDS). These findings demonstrate that inadequate authentication mechanisms can allow malicious actors to alter ECU firmware or disable safety functions, posing severe operational and safety risks. Our analysis contributes to the development of vehicle intrusion detection systems capable of recognizing abnormal reprogramming activity and future firmware fingerprinting methods to verify software integrity across ECUs. This work highlights the importance of standardizing secure firmware authentication across manufacturers to strengthen cyber resilience in heavy-duty vehicle systems.

33 ADVANCED PROPULSION SYSTEMS↗

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗

Visual Modeling for Complex System Valuation: Implementation Guidance

Within the Transactive Systems Program (TSP) at Pacific Northwest National Laboratory (PNNL) the need to incorporate a valuation analysis design early within the research process of transactive energy systems led to development of a valuation methodology. This methodology allows the modeling of economic exchanges within a complex system and supports the evaluation of individual stakeholder economic outcomes in addition to systemwide costs and benefits. The use of visual modeling practices enables the research team to reach common understanding and agreement on the analysis design within the complex system. While this methodology was developed for the valuation of transactive energy systems, it can be applied to any complex system where a granular economic analysis is desired. It allows for the inclusion of equity analyses and ties individual activities and microeconomic outcomes with the systemwide macroeconomic impacts. This document serves as implementation guidance for analysts planning to deploy the methodology within a research study. The appendixes provide specific guidance on how this methodology is deployed within the TSP at PNNL for analysts seeking guidance for deployment within that context.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Two-Coordinate Coinage Metal Complexes as Solar Photosensitizers

Generating a sustainable fuel from sunlight plays an important role in meeting the energy demands of the modern age. Herein we report two-coordinate carbene-metal-amide (cMa, M = Cu(I) and Au(I)) complexes can be used as sensitizers to promote the light driven reduction of water to hydrogen. The cMa complexes studied here absorb visible photons (ε vis > 10 3 M -1 cm -1 ), maintain long excited state lifetimes (τ ~ 0.2-1 μs) and perform stable photo-induced charge transfer to a target substrate with high photoreducing potential (E +/* up to 2.33 V vs. Fc +/o based on a Rehm-Weller analysis). We pair these coinage metal complexes with a cobalt-glyoxime electrocatalyst to photocatalytically generate hydrogen and compare the performance of the copper- and gold-based cMa complexes. We also find that these two-coordinate complexes presented can perform photo-driven hydrogen production from water without the addition of the cobalt-glyoxime electrocatalyst. In this “catalyst free” system the cMa sensitizer partially decomposes to give metal nanoparticles that catalyze water reduction. Furthermore, this work identifies two-coordinate coinage metal complexes as promising abundant metal, solar fuels photosensitizers that offer exceptional tunability and photoredox properties.

14 SOLAR ENERGY↗

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Proteins interact to form complexes. Predicting the quaternary structure of protein complexes is useful for protein function analysis, protein engineering, and drug design. However, few user-friendly tools leveraging the latest deep learning technology for inter-chain contact prediction and the distance-based modelling to predict protein quaternary structures are available. To address this gap, we develop DeepComplex, a web server for predicting structures of dimeric protein complexes. It uses deep learning to predict inter-chain contacts in a homodimer or heterodimer. The predicted contacts are then used to construct a quaternary structure of the dimer by the distance-based modelling, which can be interactively viewed and analysed. The web server is freely accessible and requires no registration. It can be easily used by providing a job name and an email address along with the tertiary structure for one chain of a homodimer or two chains of a heterodimer. The output webpage provides the multiple sequence alignment, predicted inter-chain residue-residue contact map, and predicted quaternary structure of the dimer.

59 BASIC BIOLOGICAL SCIENCES↗

Frontiers in divalent $f$-block chemistry

Divalent f-block chemistry has undergone rapid expansion in recent years, driven by advances in the stabilization of low-valent lanthanide and actinide complexes. Although f-elements were historically accessed in the +3 or higher oxidation states, the isolation of +2 species has revealed unusual spectroscopic signatures, distinct bonding motifs, and multiple accessible electronic configurations that influence their chemical and physical properties. These developments have generated opportunities in areas including quantum information science, molecular magnetism, catalysis, and luminescence. Computational chemistry has played a pivotal role in interpreting the electronic structure and reactivity of these systems. However, accurately modeling divalent f-block complexes remains challenging because of strong electronic correlation, multiconfigurational character, and the presence of close-in-energy competing electronic states. As experimental capabilities and theoretical methodologies continue to advance, a comprehensive assessment of divalent chemistry is both timely and needed. In this Review, we integrate experimental and theoretical perspectives to provide a systematic analysis of divalent lanthanide and actinide complexes across the f-block series. We critically assess the role of ligands in determining competing ground-state configurations (f n d 1 vs. f n+1 ) resulting in their distinct spectroscopic, magnetic, and bonding properties. Finally, we discuss emerging strategies for predictive modeling and rational design of low-valent f-block molecular systems, with potential applications ranging from dinitrogen reduction to quantum technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine-learning-assisted automation of single-crystal neutron diffraction

Neutron scattering is a powerful but expensive technique to study materials and discover new matter. Advanced detector technology has significantly improved the efficiency of neutron experiments, increasing the complexity of neutron data reduction and analysis. Machine learning (ML) brings new directions for neutron diffraction data reduction and experiment operation. Here, this work presents an ML-assisted data reduction and analysis method for precise recognition of Bragg peaks and the corresponding regions of interest; it can then automatically screen and align a measured crystal using the recognized peaks, and subsequently plan and optimize the data collection with user-provided information and uncertainty quantification values of detected peaks. This method shows robust performance in different complex sample environments and enables automated single-crystal neutron diffraction.

47 OTHER INSTRUMENTATION↗

Understanding Complex Magnetic Spin Textures with Simulation-Assisted Lorentz Transmission Electron Microscopy

There is an increased interest in topologically nontrivial magnetic spin textures such as skyrmions and chiral domain-wall solitons, both from a point of fundamental physics understanding as well as potential technological interest in low-power memory applications. In order to control their behavior, it is necessary to understand their complex spin texture at the nanoscale. Lorentz transmission electron microscopy (LTEM) is a suitable technique for studying these systems due to its high spatial resolution and capability to simultaneously characterize magnetic texture and microstructure. In this work, we present the application of PyLorentz, an open-source software suite that we have developed, for quantitative image analysis of Neel-type skyrmions in thin-film heterostructures. PyLorentz enhances LTEM capabilities by enabling reconstruction of magnetic induction maps from experimental images, as well as simulating LTEM images using micromagnetic simulation data. We demonstrate this for simulated Neel skyrmions as well as experimental data from [Pt/Co/W] multilayer heterostructures. Finally, we also show how simulation-assisted LTEM analysis is crucial for understanding these complex magnetic spin textures, in which the reconstructed magnetic induction map (seen in the LTEM images) differs significantly from the magnetization configuration.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

BlueCRAB Domain Overlapping Coupling: Theory & Verification

Coupling low- and high-fidelity codes is a useful way to model complex engineering systems. Thanks to the high-fidelity code, complex phenomena can be resolved in areas of the system where this is required, yet the efficiency of the lower-fidelity code is still retained in modeling the rest of the system. This document details the theory and implementation of coupling two different thermal-hydraulic codes: the system thermal-hydraulics (STH) code System Analysis Module (SAM) and the coarse-mesh computational fluid dynamics (CFD) code Pronghorn. Both applications are included in the Comprehensive Reactor Analysis Bundle (BlueCRAB) code suite and are based on the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. The domain overlapping (DO) coupling approach was adopted, as it offers proven advantages over more conventional domain decomposition methods. In the DO coupling, SAM provides Pronghorn with boundary conditions that depend on the system-level simulation of the entire plant. In return, the overlapping coupled SAM components–termed “surrogate components”–receive friction factors and source terms computed online based on the Pronghorn simulation. The framework is designed to be generic and enable coupling regardless of geometry and the number of inlet/outlet boundaries in the DO coupled domain. The developed method leads to consistent pressure drops, enthalpies, and scalar concentrations when comparing the coupled SAM and Pronghorn simulations. This document presents the DO coupling approach, along with two verification and two demonstration cases. The proposed problems explore different physical aspects relevant to nuclear reactor analysis, including buoyancy-driven flows, complex flow patterns, and multiple inlets and outlets. Periodically, new versions of this “BlueCRAB Domain Overlapping Coupling: Theory & Verification” report will be issued to reflect future developments and verification tests.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Understanding nanoscale structural distortions in Pb(Zr 0.2 Ti 0.8 )O 3 by utilizing X-ray nanodiffraction and clustering algorithm analysis

Hard X-ray nanodiffraction provides a unique nondestructive technique to quantify local strain and structural inhomogeneities at nanometer length scales. However, sample mosaicity and phase separation can result in a complex diffraction pattern that can make it challenging to quantify nanoscale structural distortions. In this work, a k-means clustering algorithm was utilized to identify local maxima of intensity by partitioning diffraction data in a three-dimensional feature space of detector coordinates and intensity. This technique has been applied to X-ray nanodiffraction measurements of a patterned ferroelectric PbZr 0.2 Ti 0.8 O 3 sample. The analysis reveals the presence of two phases in the sample with different lattice parameters. A highly heterogeneous distribution of lattice parameters with a variation of 0.02 Å was also observed within one ferroelectric domain. This approach provides a nanoscale survey of subtle structural distortions as well as phase separation in ferroelectric domains in a patterned sample.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Exploring Classification of Topological Priors With Machine Learning for Feature Extraction

In many scientific endeavors, increasingly abstract representations of data allow for new interpretive methodologies and conceptualization of phenomena. For example, moving from raw imaged pixels to segmented and reconstructed objects allows researchers new insights and means to direct their studies toward relevant areas. Thus, the development of new and improved methods for segmentation remains an active area of research. With advances in machine learning and neural networks, scientists have been focused on employing deep neural networks such as U-Net to obtain pixel-level segmentations, namely, defining associations between pixels and corresponding/referent objects and gathering those objects afterward. Topological analysis, such as the use of the Morse-Smale complex to encode regions of uniform gradient flow behavior, offers an alternative approach: first, create geometric priors, and then apply machine learning to classify. This approach is empirically motivated since phenomena of interest often appear as subsets of topological priors in many applications. Using topological elements not only reduces the learning space but also introduces the ability to use learnable geometries and connectivity to aid the classification of the segmentation target. Here, in this article, we describe an approach to creating learnable topological elements, explore the application of ML techniques to classification tasks in a number of areas, and demonstrate this approach as a viable alternative to pixel-level classification, with similar accuracy, improved execution time, and requiring marginal training data.

97 MATHEMATICS AND COMPUTING↗

A novel framework for hosting capacity analysis with spatio-temporal probabilistic voltage sensitivity analysis

Smart grids are envisioned to accommodate high penetration of distributed photovoltaic (PV) generation, which may cause adverse grid impacts in terms of voltage violations. Therefore, PV Hosting capacity is being used as a planning tool to determine the maximum PV installation capacity that causes the first voltage violation and above which would require infrastructure upgrades. Additionally, traditional methods of Hosting capacity analysis are scenario based and computationally complex as they rely on iterative load flow algorithms that require investigating a large number of scenarios for accurate assessment of PV impacts. Therefore, this paper presents a computationally efficient analytical approach to compute the probability distribution of voltage change due to random behavior of randomly located multiple distributed PVs. The proposed approach is based on Spatio-temporal probabilistic voltage sensitivity analysis that exploits both spatial and temporal uncertainties associated with PV injections. Thereafter, the derived distribution is used to quantify voltage violations for various PV penetration levels and subsequently determine the hosting capacity of the system without the need to examine large number of scenarios. Results of the proposed framework are validated via conventional load flow based simulation approach on the IEEE 37 and IEEE 123 node test systems.

42 ENGINEERING↗

Multimodal X-ray nano-spectromicroscopy analysis of chemically heterogeneous systems

Abstract Understanding the nanoscale chemical speciation of heterogeneous systems in their native environment is critical for several disciplines such as life and environmental sciences, biogeochemistry, and materials science. Synchrotron-based X-ray spectromicroscopy tools are widely used to understand the chemistry and morphology of complex material systems owing to their high penetration depth and sensitivity. The multidimensional (4D+) structure of spectromicroscopy data poses visualization and data-reduction challenges. This paper reports the strategies for the visualization and analysis of spectromicroscopy data. We created a new graphical user interface and data analysis platform named XMIDAS (X-ray multimodal image data analysis software) to visualize spectromicroscopy data from both image and spectrum representations. The interactive data analysis toolkit combined conventional analysis methods with well-established machine learning classification algorithms (e.g. nonnegative matrix factorization) for data reduction. The data visualization and analysis methodologies were then defined and optimized using a model particle aggregate with known chemical composition. Nanoprobe-based X-ray fluorescence (nano-XRF) and X-ray absorption near edge structure (nano-XANES) spectromicroscopy techniques were used to probe elemental and chemical state information of the aggregate sample. We illustrated the complete chemical speciation methodology of the model particle by using XMIDAS. Next, we demonstrated the application of this approach in detecting and characterizing nanoparticles associated with alveolar macrophages. Our multimodal approach combining nano-XRF, nano-XANES, and differential phase-contrast imaging efficiently visualizes the chemistry of localized nanostructure with the morphology. We believe that the optimized data-reduction strategies and tool development will facilitate the analysis of complex biological and environmental samples using X-ray spectromicroscopy techniques.

36 MATERIALS SCIENCE↗

Biorefinery upgrading of herbaceous biomass to renewable hydrocarbon fuels, Part 1: Process modeling and mass balance analysis

Process simulation has long been a well-established tool to track key operational, design, and mass and energy balance metrics for pre-commercial technologies such as advanced lignocellulosic biofuels. While tools such as this are well-documented in the public literature around 2nd-generation cellulosic ethanol technologies (which have been scaled up to commercial deployment to some degree over the past decade), such models and analysis information remain more sparse for more complex biorefinery pathways focused on producing drop-in hydrocarbon fuels and blend-stocks, particularly regarding information required to support air emissions or other environmental analysis. In this work, we summarize key details for an established "design case" modeling the conversion of herbaceous lignocellulosic biomass into a renewable diesel hydrocarbon blend-stock based on a representative lipid pathway from oleaginous yeast. The process is based on a biochemical deconstruction and upgrading approach utilizing deacetylation and dilute acid pretreatment, followed by enzymatic hydrolysis, fermentation, and catalytic upgrading of hydrolysate sugars to fuels. We provide key mass and energy balance outputs from the process models, with accompanying stream tables and component-level flowrates. A total of 12 model scenarios are presented spanning two feedstocks, three biorefinery scales, and two processing approaches for the lignin/residual solids waste streams. This "Part 1" manuscript presents the resulting impacts across the 12 cases on fuel yields and key output streams, focused here on direct biorefinery air emissions for selected components including CO 2 as well as sulfur (SOx) and nitrogen oxides (NOx). In the context of cleaner production, the latter focus on selected biorefinery air emission outputs establishes an initial baseline estimate and accompanying framework of the model cases, upon which an accompanying "Part 2" study will build to refine the values for these and other air pollutants across these scenarios, also considering mitigation options to comply with applicable regulatory standards. We also highlight further optimization opportunities based on potential tradeoffs identified here between air emissions versus life-cycle greenhouse gas profiles attributed to the disposition of lignin/residual solids.

09 BIOMASS FUELS↗

FORCE Integration with DRAFT and IDAES

Integrated energy systems (IES) combine, in mutually beneficial ways, power from variable renewable energy sources and nuclear power plants (NPP) to produce multiple commodities and improve economic viability under uncertain market conditions. Technical and economic analysis of IES requires modeling of complex processes with software models having enough fidelity to capture real-world dynamics while still being capable of running using reasonable computing resources. The open-source Framework for Optimization of Resources and Economics (FORCE) tool suite, developed at Idaho National Laboratory (INL), has enabled comprehensive modeling and simulation of IES. The capabilities within FORCE include grid portfolio optimization through the Holistic Energy Resource Optimization Network (HERON) and the transient process model analysis library HYBRID, among others. Recent developments for the FORCE toolset have centered on strengthening the flexibility and modularity to link with external models and other available software to enhance IES simulations. Adding versatility to the FORCE toolset improves capability resulting in better techno-economic simulation of nuclear and IES components (both in potential higher fidelity and accuracy to expected performance after deployment). It also helps leverage existing work in the IES field and improve efficiency in national code development. This report focuses on two such endeavors: integration of the Dynamic Reliability Analysis Framework Tool (DRAFT) and the Design Integration and Synthesis Platform to Advance Tightly Coupled Hybrid Energy Systems (DISPATCHES) software packages into FORCE.

97 MATHEMATICS AND COMPUTING↗

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain–affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. Further, the integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Enhanced MPM framework with multipatch isogeometric analysis for geotechnical applications

Achieving stable stress solutions at large strains using the Material Point Method (MPM) is challenging due to the accumulation of errors associated with geometry discretization, cell-crossing noise, and volumetric locking. Several simplified attempts exist in the literature to mitigate these errors, including higher-order frameworks. However, the stability of the MPM solution in such frameworks has been limited to simple geometries and the single-phase formulation (i.e., neglecting pore fluid). Although never explored, multipatch isogeometric analysis offers desirable qualities to simulate complex geometries while mitigating errors in the MPM. The degree of required high-order spatial integration has also never been investigated to infer a minimum limit for the stability of the stress solution in MPM. This paper presents a general-purpose numerical framework for simulating stable stresses in porous media, capturing both near incompressibility and multiphase interactions. First, the numerical framework is presented considering Non-Uniform Rational B-splines (NURBS) to perform isogeometric analysis (IGA) in MPM. Additionally, a volumetric strain smoothing algorithm is used to alleviate errors associated with volumetric locking. Second, the manifestation of cell-crossing errors is assessed via a series of problems with orders ranging from linear to cubic interpolation functions. Third, the use of NURBS is investigated and verified for problems with circular geometries. Finally, multipatch analysis is deployed to simulate plane strain and 3D penetration in soils, considering nearly incompressible elastoplastic (total stress) analysis and fully-coupled hydro-mechanical (effective stress) analysis. The stability of the solution is also analyzed for different constitutive models. From the results, it can be concluded that the framework using cubic interpolation functions with strain smoothing is the most convenient, presenting stable stress solutions for a broad range of multiphase geotechnical applications.

58 GEOSCIENCES↗