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DOE OSTI2023

Iron-sulfur clusters are involved in post-translational arginylation

Eukaryotic arginylation is an essential post-translational modification that modulates protein stability and regulates protein half-life. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA transferases (ATE1s), which are conserved across the eukaryotic domain. Despite their conservation and importance, little is known regarding the structure, mechanism, and regulation of ATE1s. In this work, we show that ATE1s bind a previously undiscovered [Fe-S] cluster that is conserved across evolution. We characterize the nature of this [Fe-S] cluster and find that the presence of the [Fe-S] cluster in ATE1 is linked to its arginylation activity, both in vitro and in vivo, and the initiation of the yeast stress response. Importantly, the ATE1 [Fe-S] cluster is oxygen-sensitive, which could be a molecular mechanism of the N-degron pathway to sense oxidative stress. Taken together, our data provide the framework of a cluster-based paradigm of ATE1 regulatory control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Catalytic properties of model supported nanoparticles

Nanoparticles of late transition metals are used as catalysts and electrocatalysts for industrial chemical reactions that produce fuels, convert chemical energy to electricity and clean up pollution associated with the generation and use of these fuels. For such applications, metals are usually bonded onto the surfaces of oxide or carbon support materials. To provide the energy needed for sustained economic development, we must develop new and improved solid catalysts and electrocatalysts for a variety of reactions that take better advantage of traditional and alternate energy sources (solar, wind, biomass, etc.) and avoid serious environmental problems. Additionally, since these metals are often expensive and in limited supply (e.g., Pt), we also need to develop catalysts that do not require precious metals. As a consequence, recent years have seen a dramatic increase in research aimed at providing the basic understanding needed to develop new and improved catalysts and electrocatalysts for a variety of reactions that involve nanoparticles of late transition metals supported on oxide or carbon materials. It is therefore timely to present a special issue that focusses on Catalytic Properties of Model Supported Nanoparticles. The collection highlights some of the most exciting new directions for research in this area, and provides in depth examples of some of the most cutting-edge methods, both experimental and theoretical, for studying this class of catalysts, which provide insights into structure, mechanisms, kinetics and energetics with unprecedented accuracy and detail. Finally, as Guest Editors, we present below a few of the many excellent papers published in the collection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.

09 BIOMASS FUELS↗

DOE OSTI2024

Homologous mutations in human β, embryonic, and perinatal muscle myosins have divergent effects on molecular power generation

Mutations at a highly conserved homologous residue in three closely related muscle myosins cause three distinct diseases involving muscle defects: R671C in β-cardiac myosin causes hypertrophic cardiomyopathy, R672C and R672H in embryonic skeletal myosin cause Freeman–Sheldon syndrome, and R674Q in perinatal skeletal myosin causes trismus-pseudocamptodactyly syndrome. It is not known whether their effects at the molecular level are similar to one another or correlate with disease phenotype and severity. To this end, we investigated the effects of the homologous mutations on key factors of molecular power production using recombinantly expressed human β, embryonic, and perinatal myosin subfragment-1. We found large effects in the developmental myosins but minimal effects in β myosin, and magnitude of changes correlated partially with clinical severity. The mutations in the developmental myosins dramatically decreased the step size and load-sensitive actin-detachment rate of single molecules measured by optical tweezers, in addition to decreasing overall enzymatic (ATPase) cycle rate. In contrast, the only measured effect of R671C in β myosin was a larger step size. Our measurements of step size and bound times predicted velocities consistent with those measured in an in vitro motility assay. Finally, molecular dynamics simulations predicted that the arginine to cysteine mutation in embryonic, but not β, myosin may reduce pre-powerstroke lever arm priming and ADP pocket opening, providing a possible structural mechanism consistent with the experimental observations. This paper presents direct comparisons of homologous mutations in several different myosin isoforms, whose divergent functional effects are a testament to myosin’s highly allosteric nature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Data-driven Detection and Early Prediction of Thermoacoustic Instability in a Multi-nozzle Combustor

Thermoacoustic instability (TAI) is a critical issue in modern lean-burn gas-turbine combustors, which is induced by a strong coupling between the resonant combustor acoustics and fluctuations in the heat release rate. This instability may lead to high-amplitude pressure waves that generate undesirable noise levels as well as fatigue stresses in mechanical structures of the combustor. The intense pressure fluctuations due to TAI may also cause large flow perturbations and possibly flow reversal that may lead to flame oscillations, flame liftoff, and even flame blow-out. Hence, there is a strong need for exercising control actions in a timely fashion to mitigate the TAI phenomena. Anomaly detection is an essential prerequisite to the design of a good controller and such a detector must be able to reliably predict a forthcoming TAI. To detect and predict the onset of a TAI from an ensemble of pressure time series, this paper investigates three data-driven methods: Fast Fourier transform (FFT), symbolic time series analysis (STSA), and hidden Markov modeling (HMM). The main focus of the paper is to make a comparative evaluation of these three anomaly detection methods for classification of the current regime of operation into stable and unstable categories as well as for real-time identification of precursors to impending instabilities with short-length time series of measured variables (e.g., pressure oscillations). Finally, the results, generated on experimental data from a multi-nozzle combustor apparatus, have been compared to evaluate the performance of FFT, STSA, and HMM methods for TAI analysis.

42 ENGINEERING↗

DOE OSTI2021

Coupled Multiphysics Simulations of Heat Pipe Microreactors Using DireWolf

DireWolf is a multiphysics software driver application designed to simulate heat pipe–cooled nuclear microreactors. Developed under the U.S. Department of Energy, Office of Nuclear Energy Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the DireWolf software application’s objective is to provide the nuclear community with a design and safety analysis simulation capability. Based upon the NEAMS program Multiphysics Object-Oriented Simulation Environment (MOOSE) computational framework, DireWolf tightly couples nuclear microreactor physics, reactor physics, radiation transport, nuclear fuel performance, heat pipe thermal hydraulics, power generation, and structural mechanics to resolve the interdependent nonlinearities. DireWolf is capable of simulating both steady and transient normal reactor operation and several postulated failure scenarios. We will present the fundamental physics of heat pipe–cooled nuclear microreactors and the MOOSE-based software employed in DireWolf. Both steady and transient results for coupled reactor physics, radiation transport, and nuclear fuel performance are demonstrated.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Design and Analysis of the Open-Surface Slow Li Flow Divertor and Comparison to the Fast Li Flow Divertor

In the ongoing U.S. project, “Liquid Metal Plasma Facing Components,” sponsored by the U.S. Department of Energy, efforts have been taken to develop two open-surface divertor designs for the Fusion Nuclear Science Facility using liquid lithium (Li) as a heat and particle flux removal media. The main focus of this study is the design and analysis of a slow (~1 mm/s) and thin (<1 mm) open-surface Li flow divertor with a Li-cooled substrate, which is then compared with an earlier design of a fast (up to 10 m/s) and thick (~0.5 cm) Li flow divertor with the substrate cooled with helium. The slow Li flow divertor design is based on the original LiWall concept developed at the Princeton Plasma Physics Laboratory. Such a thin and slow Li layer can remove the particle flux by reducing the recycling flux, while the heat flux is removed mainly through the heat sink located beneath. In the present study, the heat sink is provided through a Li cooling flow inside the substrate of reduced activation ferritic/martensitic steel. By performing a multiphysics analysis with COMSOL that included liquid-metal magnetohydrodynamics (MHD), heat transfer, and structural mechanics, the impact of various factors on the divertor heat removal capability, such as Li flow velocity, MHD effects, and inlet velocity boundary condition, were examined. Based on comparisons of the two divertor designs, it was shown that the fast-flow divertor significantly outperformed the slow-flow design, whose heat removal capability was limited to ~1 to 2 MW/m2.

Jiang, Yuchen [ORNL] (ORCID:0000000283280284)↗

DOE OSTI2023

Triple interference, non-linear Talbot effect and gravitization of the quantum

Recently we have discussed a new approach to the problem of quantum gravity in which the quantum mechanical structures that are traditionally fixed, such as the Fubini–Study metric in the Hilbert space of states, become dynamical and so implement the idea of gravitizing the quantum. Here, in this paper we elaborate on a specific test of this new approach to quantum gravity using triple interference in a varying gravitational field. Our discussion is driven by a profound analogy with recent triple-path interference experiments performed in the context of non-linear optics. We emphasize that the triple interference experiment in a varying gravitational field would deeply influence the present understanding of the kinematics of quantum gravity and quantum gravity phenomenology. We also discuss the non-linear Talbot effect as another striking phenomenological probe of gravitization of the geometry of quantum theory.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Design and calibration of an optically segmented single volume scatter camera for neutron imaging

The Optically Segmented Single Volume Scatter Camera (OS-SVSC) aims to image neutron sources for non-proliferation applications using the kinematic reconstruction of elastic double-scatter events. Our prototype system consists of 64 EJ-204 organic plastic scintillator bars, each measuring 5mm × 5mm × 200mm and individually wrapped in Teflon tape. The scintillator array is optically coupled to two silicon photomultiplier ArrayJ-60035 64P-PCB arrays, each comprised of 64 individual 6x6mm J-Series sensors arranged in an 8 × 8 array. We report on the design details, including component selections, mechanical design and assembly, and the electronics system. The described design leveraged existing off-the-shelf solutions to support the rapid development of a phase 1 prototype. Several valuable lessons were learned from component and system testing, including those related to the detector's mechanical structure and electrical crosstalk that we conclude originates in the commercial photodetector arrays and the associated custom breakout cards. We detail our calibration efforts, beginning with calibrations for the electronics, based on the IRS3D application-specific integrated circuits, and their associated timing resolutions, ranging from 3090ps. With electronics calibrations applied, energy and position calibrations were performed for a set of edge bars using 22 Na and 90 Sr, respectively, reporting an average resolution of 12.07±0.03mm for energy depositions between 900keVee and 1000keVee. We further demonstrate a position calibration method for the internal bars of the matrix using cosmic-ray muons as an alternative to emission sources that cannot easily access these bars, with an average measured resolution of 14.86+-0.29mm for depositions between 900keVee and 1000keVee. The coincident time resolution reported between pairs of bars measured up to 400ps from muon acquisitions. Energy and position calibration values measured with muons are consistent with those obtained using particle emission sources.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Cryogenic light detectors with thermal signal amplification for 0 νββ search experiments

As a step towards the realization of cryogenic-detector experiments to search for neutrinoless double-beta decay (such as CROSS, BINGO, and CUPID), we investigated a batch of 10 Ge light detectors (LDs) assisted by Neganov-Trofimov-Luke (NTL) signal amplification. Each LD was assembled with a large cubic light-emitting crystal (45 mm side) using the recently developed CROSS mechanical structure. The detector array was operated at milli-Kelvin temperatures in a pulse-tube cryostat at the Canfranc underground laboratory in Spain. We achieved good performance with scintillating bolometers from CROSS, made of Li 2 100 MoO 4 crystals and used as reference detectors of the setup, and with all LDs tested (except for a single device that encountered an electronics issue). No leakage current was observed for 8 LDs with an electrode bias up to 100 V. Operating the LDs at an 80 V electrode bias applied in parallel, we obtained a gain of around 9 in the signal-to-noise ratio of these devices, allowing us to achieve a baseline noise RMS of O(10 eV). Thanks to the strong current polarization of the temperature sensors, the time response of the devices was reduced to around half a millisecond in rise time. The achieved performance of the LDs was extrapolated via simulations of pile-up rejection capability for several configurations of the CUPID detector structure. Despite the sub-optimal noise conditions of the LDs (particularly at high frequencies), we demonstrated that the NTL technology provides a viable solution for background reduction in CUPID.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Crystal structure of a cap-independent translation enhancer RNA

In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV 2 ) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV 2 tertiary architecture is conserved among these homologs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Efficient First-Principles Methodology for the Calculation of the All-Phonon Inelastic Scattering in Solids

Inelastic scattering experiments are key methods for mapping the full dispersion of fundamental excitations of solids in the ground as well as nonequilibrium states. A quantitative analysis of inelastic scattering in terms of phonon excitations requires identifying the role of multiphonon processes. Here, we develop an efficient first-principles methodology for calculating the all-phonon quantum mechanical structure factor of solids. We demonstrate our method by obtaining excellent agreement between measurements and calculations of the diffuse scattering patterns of black phosphorus, showing that multiphonon processes play a substantial role. The present approach constitutes a step towards the interpretation of static and time-resolved electron, x-ray, and neutron inelastic scattering data.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Solder Bond Fatigue is Insensitive to Module Size

In this article, we explore the influence of module size on the rate of interconnecting solder bond thermomechanical fatigue (TMF) damage. Structural mechanics models of crystalline silicon PV models are created to solve with the finite-element method. Results conclusively demonstrate that the rate of solder bond TMF damage is independent of module size, interconnect location across the cell and cell location across the module.

14 SOLAR ENERGY↗

DOE OSTI2021

Representative Modules for Accelerated Thermal Cycling and Static Load Testing

In this work, we explore the influence of module size on the rate of interconnect solder bond thermomechanical fatigue (TMF) damage and the probability of cell fracture. For the solder bond TMF damage evaluation, structural mechanics models of crystalline silicon PV models are created to solve with the Finite Element Method. For the probability of cell fracture evaluation, Weibull analysis and weakest link theory are employed to resolve the probability of crystalline silicon PV cell fracture when measured as bare cells and when stressed in reduced- and full-sized modules. Results conclusively demonstrate that the rate of solder bond TMF damage is independent of module size, interconnect location across the cell and cell location across the module and that smaller, representative, modules must be loaded to a much higher level than their parent full-sized modules to achieve an equivalent driving force for cell fracture.

accelerated testing↗

DOE OSTI2025

A Computational Procedure for Assessing I$_{c}(\varepsilon$) in Nb$_{3}$Sn/Bi-2212 Hybrid Magnets

The critical current of superconductors is commonly measured by testing unloaded wires under an external magnetic field. While stressed by intense Lorentz forces, the existing HTS/LTS superconductors are prone to a reduction in critical current before reaching their structural mechanical limit. Here, in this work, the magnetic and mechanical analysis of the FNAL 4-layer Bi-2212/Nb$_{3}$Sn hybrid dipole magnet is reported, aimed at predicting the critical current degradation for both the superconductors during powering at 16T. All the Rutherford cables in the coils of the hybrid magnet were modeled at the strand level in Ansys APDL with the heterogeneous cable model. Utilizing this detailed geometry, it was possible to evaluate the effects of strain on the critical current degradation for both the Nb$_{3}$Sn and Bi-2212 superconductors under the intense Lorentz forces. The analysis presented in this paper integrates strain-dependent critical current laws, with parameters derived from experimental data, to simulate the hybrid magnet's performance for all possible current-powering configurations. The proposed methodology enables a detailed assessment of conductor integrity and I$_{C}(\varepsilon$) reduction in existing hybrid magnet designs, providing a versatile and rigorous framework for optimizing future high-field hybrid magnets.

D'Agliano, A. [Lawrence Berkeley National Laborato↗

DOE OSTI2022

Testing of the ITER Central Solenoid Modules

The ITER Central Solenoid is under fabrication by the U.S. ITER organization and its subcontractors. U.S. ITER will supply seven modules to ITER IO, six of which will be assembled in a stack that forms the ITER Central Solenoid. The first modules that were built by GA at their facility, went into high voltage testing, including Paschen testing in the vacuum, and then they were tested at 4.5 K and up to 40 kA to demonstrate compliance of the coil with the ITER requirements. In this article, we present the Test Plan and results of the central solenoid (CS) module’s performance, especially at the full current. We measured critical temperatures in several pancakes, we measured ac losses, joint resistance, and hydraulic characteristics of the coils. We also measured displacements of the coil height and hoop strain of the CS module (CSM) to verify the structural mechanical characteristics of the coil along with the cooldown shrinkage of the coil. We studied the performance of the cowound quench detectors and confirmed their effectiveness in the suppression of inductive noise. This information is necessary for verification of the stack behavior of CS in ITER operation. The test results and preliminary analyses are presented, compared to expectations, and discussed.

Martovetsky, Nicolai↗

DOE OSTI2024

EchemAMR (electro-chemical microsctructure scale models with adaptive meshing) [SWR-23-111]

A 3D microstructure resolving electrochemical transport and interfacial chemistry solver. Electrode microstructure plays an important role in determining the performance of an electrochemical system, e.g. lithium ion battery. EchemAMR is a microstructure scale model that solves the governing equations for ion transport, electrical current continuity, interfacial chemistry and structural mechanics. Complex microstructure geometries from imaging can be directly imported into EchemAMR. A volume fraction based description of the geometry on Cartesian grid with an immersed interface formulation enables simplified meshing and large-scale simulations with millions of degrees of freedom. EchemAMR has been tested against systems with analytic solutions for numerical convergence and highly resolved lithium ion battery microstructures. EchemAMR demonstrates excellent mass conversation and efficient scaling on heterogenous High-Performance Computing (HPC) with central and graphics processing units.

Sitaraman, Hariswaran↗

DOE OSTI2021

DireWolf

DireWolf is an integrated micro-reactor capability being developed using an advanced multiphysics modeling and simulation capability for heat pipe-cooled micro-reactor concepts. The DireWolf application is built on INL’s Multiphysics Object-Oriented Simulation Environment (MOOSE) development and runtime framework and is composed of the following MOOSE- based applications as submodules, coupled together using the MOOSE MultiApps and Transfers capability and executed as a single application: Griffin (reactor physics and radiation transport), BISON (nuclear fuel performance), Grizzly (structural mechanics), Sockeye (heat pipe technology), and RELAP-7 (open-air and super-critical CO2 Brayton cycle).

Permann, Cody↗