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DOE OSTI2026

Novel approach to general curvilinear coordinates for plasma fluid applications

In general geometry, plasma fluid equations include nonlinear geometric sources associated with fictitious forces, which pose significant challenges to computer simulations. We reformulate the plasma fluid hierarchy to rigorously preserve geometry and conservation properties critical to numerical simulations, while concealing the geometric sources. In their discrete form, the reformulated models conserve mass, angular momentum, and energy naturally, by simple analogy with the continuum equations. These conservation properties have minimal requirements in discrete space, namely, the anti-symmetry of the first derivative and the orthogonality of the scalar and cross products. By decoupling magnetic geometry, coordinate systems, and numerical discretization, this enables maximum flexibility while preserving physics fidelity. As a testbed, we apply the novel representation to the resistive magnetohydrodynamic system, which involves a complete set of curvilinear operations. We verify the correctness of the approach using steady state liquid metal flows and the classic Orszag–Tang vortex.

Halpern, Federico D. [General Atomics, San Diego, ↗

DOE OSTI2022

Assessment of diffuse-interface methods for compressible multiphase fluid flows and elastic-plastic deformation in solids

This work describes three diffuse-interface methods for the simulation of immiscible, compressible multiphase fluid flows and elastic-plastic deformation in solids. The first method is the localized-artificial-diffusivity approach of Cook, Subramaniam et al., and Adler and Lele, in which artificial diffusion terms are added to the individual phase mass fraction transport equations and are coupled with the other conservation equations. The second method is the gradient-form approach that is based on the quasi-conservative method of Shukla et al., in which the diffusion and sharpening terms (together called regularization terms) are added to the individual phase volume fraction transport equations and are coupled with the other conservation equations. The third approach is the divergence-form approach that is based on the fully conservative method of Jain et al., in which the regularization terms are added to the individual phase volume fraction transport equations and are coupled with the other conservation equations. In the present study, all three diffuse-interface methods are used in conjunction with a four-equation, multicomponent mixture model, in which pressure and temperature equilibria are assumed among the various phases. The primary objective of this work is to compare these three methods in terms of their ability to: maintain constant interface thickness throughout the simulation; conserve mass, momentum, and energy; and maintain accurate interface shape for long-time integration. The second objective of this work is to consistently extend these methods to model interfaces between solid materials with strength. To assess and compare the methods, they are used to simulate a wide variety of problems, including (1) advection of an air bubble in water, (2) shock interaction with a helium bubble in air, (3) shock interaction and the collapse of an air bubble in water, and (4) Richtmyer–Meshkov instability of a copper–aluminum interface. The current work focuses on comparing these methods in the limit of relatively coarse grid resolution, which illustrates the true performance of these methods. In conclusion, this is because it is rarely practical to use hundreds of grid points to resolve a single bubble or drop in large-scale simulations of engineering interest.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Self-organization in collisionless, high- β turbulence

The magnetohydrodynamic (MHD) equations, as a collisional fluid model that remains in local thermodynamic equilibrium (LTE), have long been used to describe turbulence in myriad space and astrophysical plasmas. Yet, the vast majority of these plasmas, from the solar wind to the intracluster medium (ICM) of galaxy clusters, are only weakly collisional at best, meaning that significant deviations from LTE are not only possible but common. Recent studies have demonstrated that the kinetic physics inherent to this weakly collisional regime can fundamentally transform the evolution of such plasmas across a wide range of scales. Here, we explore the consequences of pressure anisotropy and Larmor-scale instabilities for collisionless, β $\gg$ 1, turbulence, focusing on the role of a self-organizational effect known as ‘magneto-immutability’. We describe this self-organization analytically through a high-β, reduced ordering of the Chew–Goldberger–Low-MHD (CGL-MHD) equations, finding that it is a robust inertial-range effect that dynamically suppresses magnetic-field-strength fluctuations, anisotropic-pressure stresses and dissipation due to heat fluxes. As a result, the turbulent cascade of Alfvénic fluctuations continues below the putative viscous scale to form a robust, nearly conservative, MHD-like inertial range. These findings are confirmed numerically via Landau-fluid CGL-MHD turbulence simulations that employ a collisional closure to mimic the effects of microinstabilities. We find that microinstabilities occupy a small (~5%) volume-filling fraction of the plasma, even when the pressure anisotropy is driven strongly towards its instability thresholds. We discuss these results in the context of recent predictions for ion-vs-electron heating in low-luminosity accretion flows and observations implying suppressed viscosity in ICM turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Unconventional supercurrent phase in Ising superconductor Josephson junction with atomically thin magnetic insulator

Abstract In two-dimensional (2D) NbSe 2 crystal, which lacks inversion symmetry, strong spin-orbit coupling aligns the spins of Cooper pairs to the orbital valleys, forming Ising Cooper pairs (ICPs). The unusual spin texture of ICPs can be further modulated by introducing magnetic exchange. Here, we report unconventional supercurrent phase in van der Waals heterostructure Josephson junctions (JJs) that couples NbSe 2 ICPs across an atomically thin magnetic insulator (MI) Cr 2 Ge 2 Te 6 . By constructing a superconducting quantum interference device (SQUID), we measure the phase of the transferred Cooper pairs in the MI JJ. We demonstrate a doubly degenerate nontrivial JJ phase ( ϕ ), formed by momentum-conserving tunneling of ICPs across magnetic domains in the barrier. The doubly degenerate ground states in MI JJs provide a two-level quantum system that can be utilized as a new dissipationless component for superconducting quantum devices. Our work boosts the study of various superconducting states with spin-orbit coupling, opening up an avenue to designing new superconducting phase-controlled quantum electronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis

DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

The GTPase-activating protein p120RasGAP has an evolutionarily conserved “FLVR-unique” SH2 domain

The Src homology 2 (SH2) domain has a highly conserved architecture that recognizes linear phosphotyrosine motifs and is present in a wide range of signaling pathways across different evolutionary taxa. A hallmark of SH2 domains is the arginine residue in the conserved FLVR motif that forms a direct salt bridge with bound phosphotyrosine. In this work, we solve the X-ray crystal structures of the C-terminal SH2 domain of p120RasGAP (RASA1) in its apo and peptide-bound form. We find that the arginine residue in the FLVR motif does not directly contact pTyr1087 of a bound phosphopeptide derived from p190RhoGAP; rather, it makes an intramolecular salt bridge to an aspartic acid. Unexpectedly, coordination of phosphotyrosine is achieved by a modified binding pocket that appears early in evolution. Using isothermal titration calorimetry, we find that substitution of the FLVR arginine R377A does not cause a significant loss of phosphopeptide binding, but rather a tandem substitution of R398A (SH2 position βD4) and K400A (SH2 position βD6) is required to disrupt the binding. These results indicate a hitherto unrecognized diversity in SH2 domain interactions with phosphotyrosine and classify the C-terminal SH2 domain of p120RasGAP as “FLVR-unique.”

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

A kinetic line-driven radiation operator and its application to Gyrokinetics

A velocity dependent, kinetic model for line radiation is developed for continuum kinetic codes. It has been implemented in the full-f gyrokinetic code Gkeyll. The total radiation for a charge state is modeled as an advection in velocity space with a form of $\nabla_v \cdot(v\nu(v)f(v))$, guaranteeing particle conservation. The velocity dependence (in the form of an effective frequency $\nu(v)$) is found through fitting the energy loss of the operator, i.e. the second velocity moment, to the radiation data in the OpenADAS database. Therefore, each individual transition does not need to be evaluated every time step, significantly reducing the computational cost of including line radiation in a kinetic model. The dependence on velocity instead of the usual, temperature, allows the radiation to be computed from non-Maxwellian electron distribution functions: We benchmark the model against a collisional radiative model using isotropic non-Maxwellian distribution functions. A velocity dependent model of radiation can more accurately describe the radiation in the more kinetic regimes expected in reactor-scale devices. The velocity dependence qualitatively captures the quantum mechanical need for a minimum velocity before any radiation occurs.

kinetic↗

DOE OSTI2025

Emergent Dimer-Model Topological Order and Quasiparticle Excitations in Liquid Crystals: Combinatorial Vortex Lattices

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as “combinatorial vortex lattices” (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasiparticle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CVLs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery—an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media.

36 MATERIALS SCIENCE↗

DOE OSTI2022

High-Resolution Structure of the Nuclease Domain of the Human Parvovirus B19 Main Replication Protein NS1

Two new structures of the N-terminal domain of the main replication protein, NS1, of human parvovirus B19 (B19V) are presented here. This domain (NS1-nuc) plays an important role in the “rolling hairpin” replication of the single-stranded B19V DNA genome, recognizing origin of replication sequences in double-stranded DNA, and cleaving (i.e., nicking) single-stranded DNA at a nearby site known as the terminal resolution site (trs). The three-dimensional structure of NS1-nuc is well conserved between the two forms, as well as with a previously solved structure of a sequence variant of the same domain; however, it is shown here at a significantly higher resolution (2.4 Å). Using structures of NS1-nuc homologues bound to single- and double-stranded DNA, models for DNA recognition and nicking by B19V NS1-nuc are presented that predict residues important for DNA cleavage and for sequence-specific recognition at the viral origin of replication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Gcn2 structurally mimics and functionally repurposes the HisRS enzyme for the integrated stress response

Protein kinase Gcn2 attenuates protein synthesis in response to amino acid starvation while stimulating translation of a transcriptional activator of amino acid biosynthesis. Gcn2 activation requires a domain related to histidyl-tRNA synthetase (HisRS), the enzyme that aminoacylates tRNA His . While evidence suggests that deacylated tRNA binds the HisRS domain for kinase activation, ribosomal P-stalk proteins have been implicated as alternative activating ligands on stalled ribosomes. We report crystal structures of the HisRS domain ofChaetomium thermophilumGcn2 that reveal structural mimicry of both catalytic (CD) and anticodon-binding (ABD) domains, which in authentic HisRS bind the acceptor stem and anticodon loop of tRNA His . Elements for forming histidyl adenylate and aminoacylation are lacking, suggesting that Gcn2 HisRS was repurposed for kinase activation, consistent with mutations in the CD that dysregulate yeast Gcn2 function. Substituting conserved ABD residues well positioned to contact the anticodon loop or that form a conserved ABD–CD interface impairs Gcn2 function in starved cells. Mimicry in Gcn2 HisRS of two highly conserved structural domains for binding both ends of tRNA—each crucial for Gcn2 function—supports that deacylated tRNAs activate Gcn2 and exemplifies how a metabolic enzyme is repurposed to host new local structures and sequences that confer a novel regulatory function.

Science & Technology - Other Topics↗

DOE OSTI2022

Deformations, relaxation, and broken symmetries in liquids, solids, and glasses: A unified topological field theory

Here, we combine hydrodynamic and field theoretic methods to develop a general theory of phonons as Goldstone bosons in crystals, glasses, and liquids based on nonaffine displacements and the consequent Goldstone phase relaxation. We relate the conservation, or lack thereof, of specific higher-form currents with properties of the underlying deformation field—nonaffinity—which dictates how molecules move under an applied stress or deformation. In particular, the single-valuedness of the deformation field is associated with conservation of higher-form charges that count the number of topological defects. Our formalism predicts, from first principles, the presence of propagating shear waves above a critical wave vector in liquids, thus giving a formal derivation of the phenomenon in terms of fundamental symmetries. The same picture provides also a theoretical explanation of the corresponding “positive sound dispersion” phenomenon for longitudinal sound. Importantly, accordingly to our theory, the main collective relaxation timescale of a liquid or a glass (known as the α relaxation for the latter) is given by the phase relaxation time, which is not necessarily related to the Maxwell time. Finally, we build a nonequilibrium effective action using the in-in formalism defined on the Schwinger-Keldysh contour, that further supports the emerging picture. In summary, our work suggests that the fundamental difference between solids, fluids, and glasses has to be identified with the associated generalized higher-form global symmetries and their topological structure, and that the Burgers vector for the displacement fields serves as a suitable topological order parameter distinguishing the solid (ordered) phase and the amorphous ones (fluids, glasses).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA

Abstract In selected Campylobacter species, the biosynthesis of N‐linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane‐associated GT‐B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N ‐acetylgalatosamine (GalNAc) from uridine 5′‐diphospho‐ N ‐acetylgalactosamine (UDP‐GalNAc) to undecaprenyl‐diphospho‐ N , N ′‐diacetylbacillosamine (UndPP‐diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane‐embedded acceptor and the structural analysis of the complex together with bioinformatics and site‐directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″‐OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate‐specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.

Vuksanovic, Nemanja↗

DOE OSTI2021

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes

Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. Here, we report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 A resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. Here, we propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein

Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Saltstone third quarter calendar year 2019 (3QCY19) toxicity characteristic leaching procedure (TCLP) results

The aqueous waste from Tank 50 (salt solution) is sampled quarterly for transfers to the Saltstone Production Facility (SPF). Salt solution is treated at SPF and disposed of in the Saltstone Disposal Facility (SDF). Per request of customer, X-TAR-Z-00008, Revision 01, two SDF waste form (saltstone) samples were prepared in the Savannah River National Laboratory (SRNL) from the Tank 50 Waste Acceptance Criteria (WAC) sample and Z-Area premix material for the third quarter of calendar year 2019 (3QCY19). One sample contained a Full Premix which included 10:45:45 (by weight) of cement, slag and fly ash. The second sample contained 60:40 (by weight) of slag and fly ash only referred to as the “Cement-Free grout sample”. Results from this technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request (TTR) prepared by Savannah River Remediation (SRR). After a 28 day cure, a sample of each of the SDF waste forms was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure (TCLP). The 3QCY19 saltstone (Full Premix) and the Cement-Free grout samples met the South Carolina (SC) Code of Regulations for Hazardous Waste Management Regulations (HWMR) 61-79.261.24 and 61-79-268.48 requirements for a non-hazardous waste form with respect to Resource Conservation and Recovery Act (RCRA) metals and Underlying Hazardous Constituents (UHCs), and also met the SPF WAC.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

(U) A Linear Response Model Predicts Reactivity From a Density Profile

We tested the ability to predict the system reactivity, described by alpha, given a density profile using a simple linear system response. We generated a suite of 1-dimensional density profiles that consisted of nominal density, a discontinuity, and a decay. These profiles were prescribed a functional form and the mass was conserved in all cases. From these density profiles, we calculated the alpha value of the 3-dimensional system.We calculated a linear response function given a training set of the 1-dimensional density profiles, and the system reactivity described by alpha. We tested the robustness of the response function using the remaining test data. Our results showed very good agreement between the predicted and calculated test values, where the distribution of alpha differences was centered about zero and had a standard deviation of 0.005 gens/shake. The predicted and calculated alpha values did not significantly differ (t=-0.0009 p<0.99). We used Singular Value Decomposition (SVD) to reduce the matrix rank by retaining95% of the cumulative singular value contributions. This reduced the matrix rank by 91.7%. We generated the linear response matrix and calculated the difference between the predicted and calculated alpha values. Using the reduced order matrix, we showed good agreement between the predicted and calculated alpha values where the distribution of differences was centered near zero, the standard deviation was 0.006 gens/shake, and the statistical t-test showed good agreement (t=0.02, p<0.98). These results show a linear relationship between a series of 1-dimensional density profiles,where the mass was conserved, and the system reactivity. The next steps of this work will be to investigate the linear response using 2-dimensional density profiles.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗