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DOE OSTI2019

High resolution ENDOR spectroscopy combined with quantum chemical calculations reveals the structure of the nitrogenase Janus intermediate E4(4H)

We have shown that the key state in N2 reduction to two NH3 by the enzyme nitrogenase is the E4(4H), ‘Janus’ intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed the catalytic multi-metallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of structure - the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of ‘anchor’ Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties of the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed by DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a pulsed-ENDOR protocol (‘PESTRE’) to obtain absolute hyperfine-interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its ‘anchoring’ Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result: the freeze-trapped, lowest-energy Janus intermediate structure is E4(4H)(a).

Hoeke, Veronica↗

DOE OSTI2020

National Spherical Torus eXperiment - Upgrade NSTX-U: Structural Analysis of Passive Plates Support Brackets

The objective of this analysis is to estimate and assess the stresses in the passive plates caused by a limiting plasma disruption. The objective of this calculation is also to address observed damage to mounting hardware after completion of NSTX operation. These observations initiated diagnostic efforts during the Upgrade project to monitor the severity of the disruptions that were causing the damage, and planned instrumentation to trend the behavior of the mounting hardware. The Recovery Project mission for the passive plate hardware is to appropriately reinforce the passive plates with stainless steel ribs mounted on the back of the plate to reduce their flexure and stress and reinforcements of the “biscuit” components of the bracketry to transfer loads without damage to bolts, biscuits, and bracket plates and welds. Mid-plane disruptions and quenches were manageable with NSTX vintage hardware. The Vertical Displacement Event (VDE) disruptions position the plasma closer to the passive plates and are more severe than the centered plasma. Earlier work pointed to the P1-P5 VDE as limiting. This has been confirmed by A. Brooks work in support of the load generation effort in reference. During vertical displacement large counter currents are generated in the plate as the plasma approaches it. - as would be expected from passive plates. When the plasma disrupts the currents in the plates are reversed, which also reverses the loading on the plates. This report documents the methodology and results of transient structural analysis on the plasma, passive plates support brackets. The loads induced by eddy and halo currents have been considered, and were generated using a separate electromagnetic analysis (NSTXU_1_11_2_1_CALC_051). The structural model also incorporates the effects from preload. Calculation was performed with the assumption that existing biscuits are not participating in the load bearing except the biscuits connected to jumper bolts, which are fully engaged. Results show that with the planned reinforcements, Passive plates and mounting structures satisfy static and fatigue criteria in all areas except welds, where separate analysis was performed. Both symmetric and asymmetric (with locating block) designs were analyzed, and although stresses were higher without locating block they still satisfy NSTX design criteria.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Summary of Expansions and Updates in R&D GREET ® 2024

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Summary of Expansions and Updates in R&D GREET® 2024 Rev.1

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1987

Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

NASA Discipline Exobiology↗

NASA NTRS1990

A structure for maturing intelligent tutoring system student models

A special structure is examined for evolving a detached model of the user of an intelligent tutoring system. Tutoring is used in the context of education and training devices. A detached approach to populating the student model data structure is examined in the context of the need for time dependent reasoning about what the student knows about a particular concept in the domain of interest. This approach, to generating a data structure for the student model, allows an inference engine separate from the tutoring strategy determination to be used. This methodology has advantages in environments requiring real-time operation.

Holmes, Willard M.↗

DOE OSTI2022

Eu 5 Al 3 Sb 6 : Al 4 Tetrahedra Embedded in a Rock-Salt-Like Structure

The new Eu 5 Al 3 Sb 6 phase has been successfully synthesized as a pure phase through Sn flux methods yielding large, high-quality crystals. This structure type features disordered Al clusters that appear in the form of dual tetrahedra. It crystallizes in the monoclinic C2/m space group exhibiting a rock-salt-like Eu–Sb framework with [Al 4 ] tetrahedra replacing some of the cationic Eu atoms (space group: C2/m, a = 8.151(1) Å, b = 14.181(2) Å, c = 8.145(1) Å, β = 109.577(2)°). The structure models the [Al 4 ] as dual tetrahedra with the Al atom sites 37.5% occupied along with Eu present on the central site at 8% occupancy and the remainder of the site being vacant. The presence of the [Al 4 ] cluster is further supported by HRTEM. Electronic structure calculations show that this material is a semimetal with observed band crossings close to the Fermi level. Strong Al–Sb antibonding interactions were found from COHP calculations close to the Fermi level and provide the rationale for the deficiency of the Al cluster. Mössbauer spectroscopy on Eu-151 and Sb-121 provides oxidation states of 2+ and 3– along with the local environment. Magnetic susceptibility measurements can be described well with a Curie–Weiss law where an effective moment of 7.80 μB/mol Eu is obtained, consistent with Eu 2+ , and show canted antiferromagnetic behavior below 10 K. Temperature dependent resistivity shows a Kondo-like low-temperature upturn caused by enhanced scattering of the itinerant electrons with the 4f orbitals of Eu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A biokinetic model for systemic sodium

This paper describes an updated biokinetic model for systemic sodium (Na), developed for use in a series of reports by the International Commission on Radiological Protection (ICRP) on occupational intake of radionuclides. In contrast to the ICRP's previous model for intake of radio-sodium by workers, the updated model depicts realistic directions of movement of Na in the body including recycling of activity between blood and tissues. The updated model structure facilitates extension of the baseline transfer coefficients for adults to different age groups and to special exposure scenarios such as transfer of radio-sodium from the mother to the foetus or the nursing infant. Dose coefficients for 22Na and 24Na based on the updated model generally do not differ greatly from those based on the ICRP's previous Na model when both models are connected to the ICRP's latest dosimetry system. The main exception is that the updated model yields roughly twofold higher dose coefficients for endosteal bone surface than does the previous model due to the dosimetrically cautious assumption in the updated model that exchangeable Na in bone resides on bone surface.

61 RADIATION PROTECTION AND DOSIMETRY↗

NASA NTRS1993

Phase transitions and 2D spherical convection in a large icy satellite

Three ice phase transitions, based on experimental and theoretical results, were incorporated into a 2D spherical convection model. These phase transitions are the exothermic Ice 1-2, the endothermic Ice 2-6, and the exothermic Ice 6-8 phase transitions. The fluid is assumed isoviscous and the anelastic liquid formulation was used. The object is an icy satellite whose physical characteristics resemble those of Ganymede or Callisto. Structural models, similar to those of Mueller and McKinnon, with different core sizes, i.e. with different degree of differentiation were studied. The shells, i.e. the mantle of the satellite, is heated both internally and from below to account for the decaying radiogenic heating and the heat flow from the solid core. The lower boundary of the mantle is rigid and isothermal, the upper boundary is isothermal. Calculations with rigid and shear stress free upper boundary are carried out in order to assess the role of the different boundary conditions. Two different Rayleigh numbers, depending on the assumed value of the viscosity, were used in the calculations and the thermal evolution of the satellite was studied. The suit of calculations presented demonstrates that phase transition cannot be ignored when the thermal evolution of a large icy satellite has to be studied. The importance of the construction of the realistic phase diagram for ice was also documented. On the other hand the degree of differentiation, simulated with the structures with different core's radius does not seem to drastically influence the overall behavior of the convective activity. Within the limits of our simulations, the post-accretional evolution seems to be independent on the degree of primordial differentiation.

Forni, O.↗

DOE OSTI2025

Magnetic contribution of itinerant electrons to neutron diffraction in the topological antiferromagnet CeAlGe

We report a neutron diffraction study of the magnetic structure of CeAlGe, a candidate topological semimetal that hosts a noncollinear, multi-𝐤 magnetic phase. By measuring both low- and high-momentum-transfer magnetic Bragg peaks within a single experimental setup, we refine a magnetic structure model based solely on localized Ce moments. This model, which differs from that obtained using only high-𝑄 data, quantitatively reproduces the observed intensities, including the (000) zeroth-order magnetic satellites that are especially sensitive to subtle components of the modulation. While a contribution from itinerant electrons to the zeroth satellite cannot be definitively excluded, our analysis reveals no unambiguous evidence for such effects within experimental uncertainty. The refined magnetic structures exhibit topologically nontrivial winding patterns, derived from the fitted magnetic parameters, that support localized, particle-like spin textures with half-integer topological charges. These features provide a natural microscopic origin for the observed topological Hall effect, establishing CeAlGe as a model system where magnetism and topology are intimately linked.

Magnetic coupling↗

DOE OSTI2019

A Quasi-static Hyper-resistive Model of Ultra-high-energy Cosmic-ray Acceleration by Magnetically Collimated Jets Created by Active Galactic Nuclei

This is the fourth in a series of companion papers showing that when an efficient dynamo can be maintained by accretion disks around supermassive black holes in active galactic nuclei, it will lead to the formation of a powerful, magnetically collimated helix that could explain the observed jet/radiolobe structures on very large scales. In this work, we present a hyper-resistive kinetic theory that shows how different instabilities can cause the slowly evolving magnetically collimated jets to accelerate ions and electrons in different regions of jets and lobes. In particular, we propose that the Drift Cyclotron Loss Cone instability at the ends of jets can accelerate ions up to the observed ultra-high-energy cosmic rays with energies ≈1020 eV. Based on this jet/lobe structure model and its associated acceleration processes, we estimate cosmic-ray intensities and likely radiative signatures and compare them with observations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Covalent labeling of the Arabidopsis plasma membrane H + ‐ ATPase reveals 3D conformational changes involving the C‐terminal regulatory domain

The plasma membrane proton pump is the primary energy transducing, electrogenic ion pump of the plasma membrane in plants and fungi. Compared to its fungal counterpart, the plant plasma membrane proton pump's regulatory C‐terminal domain (CTD) contains an additional regulatory segment that links multiple sensory pathways regulating plant cell length through phosphorylation and recruitment of regulatory 14‐3‐3 proteins. However, a complete structural model of a plant proton pump is lacking. Here, we performed covalent labeling with mass spectrometric analysis (CL‐MS) on the Arabidopsis pump AHA2 to identify potential interactions between the CTD and the catalytic domains. Our results suggest that autoinhibition in the plant enzyme is much more structurally complex than in the fungal enzyme.

Blackburn, Matthew R. [Department of Biochemistry ↗

DOE OSTI2025

Summary of Expansions and Updates in R&D GREET® 2025

The research and development (R&D) version of Greenhouse gases, Regulated Emissions, and Energy use in Technologies (GREET®) model, or R&D GREET, is developed by Argonne National Laboratory (Argonne) with the support of the U.S. Department of Energy (DOE) and other federal agencies. R&D GREET is a life cycle analysis (LCA) model, structured to systematically examine the energy and environmental effects of a wide variety of transportation fuels and vehicle technologies in all transportation sub-sectors (i.e., road, air, marine, and rail) and other end-use sectors, and energy technology systems. Argonne has expanded and updated the model in many areas in R&D GREET 2025. This report provides a summary of the expansions and updates. R&D GREET is designed as an attributional LCA model, but specific consequential effects for certain pathways are included by default when they are scientifically important and/or highly policy relevant. For example, two major consequential elements – induced land use change (ILUC) for biofuels and avoided emissions for certain RNG-based pathways – are implemented by default in R&D GREET because they are highly relevant to our user base and crucial for a comprehensive evaluation of the environmental effects of these technologies. In a future version of R&D GREET, these consequential elements for biofuels and RNG could be more clearly distinguished from core attributional results. We will consider adding a highly visible toggle that would allow users to turn off or adjust these consequential impacts.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

FEM Modeling and Simulation of 2-D High Specific Heat Nb 3 Sn Wires

In the past few years, new high specific heat Nb 3 Sn wires have gained much focus at FNAL. Indeed, they have proved to be more stable against thermal perturbations with respect to standard wires. Nevertheless, a trade off exists between their thermal efficiency and production feasibility. In this report I describe the thermal and structural models that I have developed by exploiting ANSYS Mechanical APDL ® , which I got acquainted with at the beginning of my training. The aim has been to optimize the location of high specific heat elements in order to obtain an optimal thermal stability, while minimizing the risk of wire breakage during drawing. FEM results are compared with experimental ones made beforehand. Other minimum quench energy (MQE) thermal models have been developed for expected new experimental results. New data may improve the understanding of the embedded physical uncertainties in the model.

36 MATERIALS SCIENCE↗

DOE OSTI2022

OpenMDlr Dataset

Protein structure dataset created with OpenMDlr. Restraints applied to fold proteins into native-like conformations were obtained from a variety of methods; results from these different restraint sets are contained in respective subdirectories. Supplements OpenMDlr: Parallel, open-source tools for general protein structure modeling and refinement from pairwise distances (https://doi.org/10.1093/bioinformatics/btac307).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Overview of Ablative TPS Modeling at NASA Ames

Over the past decade, NASA has invested in efforts to build predictive thermal protection system (TPS) material models from the micro-scale to the macro-scale. To complement the mission design cycle process and reduce the need for extensive testing, NASA is developing modeling and simulation tools that enable characterizing material properties and response to hot plasma experienced during atmospheric entry. Traditional material response and ablation modeling tools, such as the heritage code FIAT, and its multidimensional siblings, TITAN and 3dFIAT, are being complemented with newly developed software such as Icarus and PATO. Both of these programs are three-dimensional, finite-volume solvers that use unstructured meshes and 21st century programming paradigms to allow for efficient parallel simulations. FIAT and Icarus are also used for TPS sizing purposes. Today, these traditional tools are being supplemented with computational materials models at the atomistic level. The scales of interest range from computational chemistry (Density Functional Theory [DFT]), to atomistic simulations (Molecular Dynamics [MD]), to the microscale with the Porous Microstructure Analysis (PuMA) software that was recently awarded the 2022 NASA Software of the Year award. Finally, thermo-structural modeling is also of interest to the TPS Materials branch and done using commercial tools such as MSC MARC, MENTAT, NASTRAN and PATRAN. The present talk will also link the use of these computational tools to current NASA missions and projects associated with challenging and complex vehicles entries/reentries.

materials modeling↗

NASA NTRS1976

Ultrahigh-accuracy body-pointing system for the Large Space Telescope

The Large Space Telescope (LST) is a 3-m diffraction-limited telescope. Pointing stability requirements necessary to assure diffraction-limited images are plus or minus 0.005 arc-sec, over possible experiment observation times of several hours. In order to determine whether these stringent pointing requirements could be met, a complex simulation model was defined which consisted of detailed dynamic representations of control moment gyros (CMGs) and reaction wheels (RWs), including their noise characteristics, dynamic sensor representations with sensor noise, shock mounts for the CMG actuators, a detailed representation of an image motion compensation (IMC) system, and a detailed flexible body structural model with all significant vehicle and solar panel bending modes. On the basis of both stability and performance studies utilizing this model, it was determined that a body-pointing system will meet LST requirements in the presence of CMG vibrational disturbances and sensor noise. The recommended system consists of three orthogonally mounted RWs for primary short-term control, and a cluster of CMG actuators for continuous RW desaturation and vehicle maneuvering.

Rybak, S. C.↗

DOE OSTI2023

Temperature uncertainty modelling with proxy structural data as geostatistical constraints for well siting: an example applied to Granite Springs Valley, NV, USA

Utilizing existing temperature and structural geology information around Granite Springs Valley, Nevada, we build 3D stochastic temperature models with the aims of evaluating the 3D uncertainty of temperature and choosing between candidate exploration well locations. The data used to support the modelling are measured temperatures and structural proxies from 3D geologic modelling (distance to fault, distance to fault intersections and terminations, Coulomb stress change and dilation tendency), the latter considered ‘secondary’ data. Two stochastic geostatistical techniques are explored for incorporating the structural proxies: cosimulation and local varying mean. With both the cosimulation and local varying mean methods, many equally-likely temperature models (i.e. realizations) are produced, from which temperature probability profiles are calculated at candidate well locations. To aid in choosing between the candidate locations, two quantities summarize the temperature probabilities: V prior and entropy. V prior quantifies the likelihood for economic temperatures at each candidate location, whereas entropy identifies where new information has the most potential to reduce uncertainty. In general, the cosimulation realizations have smoother spatial structure, and extrapolate high temperatures at candidate locations that are located along the direction of the longest spatial correlation, which are down dip from existing temperature logs. The smooth realizations result in tight temperature probability profiles that are easier to interpret, but they have unrealistic temperature reversals in some locations because of the dipping ellipsoid shape created and that the cosimulation technique does not enforce a conductive geothermal gradient as a baseline (i.e. linearly increasing temperature with depth). The local varying mean results produce realizations with more realistic geothermal gradients, with temperatures increasing downward since a depth-temperature relationship is included. However, because they have much noisier spatial nature compared to cosimulation, it is harder to interpret the temperature probability profiles. The different local varying mean results allow the geologist to determine which proxy (e.g. dilation v. distance to fault termination) should be used given the specific geothermal system. In general, V prior from local varying mean results identify locations that are close to high values for the structural proxies: areas with higher probabilities for higher temperatures. The entropy results identify where uncertainty is greatest and therefore new drilling information could be most useful. Though these techniques provide useful information, even when applied to areas of sparse data, our comparison of these two techniques demonstrates the need for new geothermal geostatistics techniques that combine the advantages of these two methods and that are tailored to the spatial uncertainty issues inherent in geothermal exploration.

15 GEOTHERMAL ENERGY↗