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At least 181 records · Page 10

Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism

The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.

59 BASIC BIOLOGICAL SCIENCES↗

Bowing to ferroelectric artificial flux closure

Here by inserting an epitaxial in-plane buffer layer of Bi 5 FeTi 3 O 15 , an artificial flux closure architecture enables ferroelectric polarization from a single unit cell of BaTiO 3 or BiFeO 3 .

36 MATERIALS SCIENCE↗

Increased water availability at various timescales has different effects on stomatal closure point in isohydric piñon pine and anisohydric juniper

Abstract Stomatal Closure Point (SCP) has commonly been used to describe drought response strategies in plants, with isohydric species maintaining relatively high, constant SCP compared to anisohydric species that can lower SCP with increasing drought severity. However, there is evidence that, within these groups, SCP may respond dynamically to environmental conditions. Here, we explored how increasing water availability affects SCP in classically isohydric piñon pine and anisohydric one-seed or Utah juniper at various spatial- (i.e., from branch, to tree, to ecosystem) and temporal- (i.e., hours to decades) scales. Our results show that short-term increases in water availability decreased SCP in isohydric piñon pine, making it more anisohydric, while short-term rehydration had no effect on SCP in anisohydric juniper. Increasing mean annual precipitation, on the other hand, increased SCP in both species. Our findings are consistent with documented differences in the use of ABA to control stomata in iso- and aniso-hydric species on short timescales, and with structural acclimation in both species at long timescales. These results illustrate that the local environment plays a large role in determining SCP.

Kraklow, Vachel↗

Closure to “Observation-Based Evaluation of Flood Estimation Techniques for a Small Snow-Dominated Basin in the Washington Cascade Mountains”

Here, this paper presents a closure to “Observation-Based Evaluation of Flood Estimation Techniques for a Small Snow-Dominated Basin in the Washington Cascade Mountains” by Hongxiang Yan, Zhuoran Duan, Mark S. Wigmosta, Ning Sun, Ethan D. Gutmann, Bert Kruyt, and Jeffrey R. Arnold. https://doi.org/10.1061/JHYEFF .HEENG-6147.

54 ENVIRONMENTAL SCIENCES↗

An analytical approach to evaluating magnetic-field closure and topological changes in FRC devices

Here, we describe mathematical methods based on optimizing a modified non-linear flux function (MFF) to evaluate whether odd-parity perturbations affect the local closure of magnetic field lines in field-reversed configurations. Using the MFF methodology, quantitative formulas are derived that provide the shift of the field minimum and the threshold for field-line opening, a discontinuous change in field topology.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An approximate inertial manifold (AIM) based closure for turbulent flows

A closure model for turbulent flows is developed based on a dynamical system theory. An appropriately discretized formulation of the governing equations is considered for this process. The key ingredient is an approximation of the system’s attractor, where all the trajectories in phase space are confined. This approximate inertial manifold based approach provides a path to track trajectories of the system in a lower-dimensional subspace. Unlike conventional coarse-graining approaches, the turbulent field is decomposed into resolved and unresolved dynamics using the properties of the governing equations. The novelty of the approach relies on the reconstruction of the unresolved field constrained by the governing equations. A posteriori tests for homogeneous isotropic turbulence and the Kuramoto–Sivashinsky equation show promising results for considerable dimension reduction with strong convergence properties. The proposed model outperforms the dynamic Smagorinsky model, and the computational overhead is competitive with similar approaches.

97 MATHEMATICS AND COMPUTING↗

Study of the Alfven eigenmodes stability in CFQS plasma using a Landau closure model

The aim of this study is to analyze the stability of the Alfven eigenmodes (AE) in the Chinese First Quasi-axisymmetric Stellarator (CFQS). The AE stability is calculated using the code FAR3d that solves the reduced MHD equations to describe the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moment for the energetic particles (EP) species including the effect of the helical couplings and acoustic modes. The Landau damping and resonant destabilization effects are added in the model by a given closure relation. The simulation results indicate the destabilization of n = 1 to 4 AEs by EP during the slowing down process, particularly n = 1 and n = 2 toroidal AEs (TAE), n = 3 elliptical AE (EAE) and n = 4 non circular AE (NAE). If the resonance is caused by EPs with an energy above 17 keV (weakly thermalized EP), n = 2 EAEs and n = 3 NAEs are unstable. On the other hand, EPs with an energy below 17 keV (late thermalization stage) lead to the destabilization of n = 3 and n = 4 TAEs. The simulations for an off-axis NBI injection indicate the further destabilization of n = 2 to 4 AEs although the growth rate of the n = 1 AEs slightly decreases, so no clear optimization trend with respect to the NBI deposition region is identified. In addition, n = 2, 4 helical AE (HAE) are unstable above an EP β threshold. Also, if the thermal β of the simulation increases (higher thermal plasma density) the AE stability of the plasma improves. Overall, the simulations including the effect of the finite Larmor radius and electron-ion Landau damping show the stabilization of the n = 1 to 4 EAE/NAEs as well as a decrease of the growth rate and frequency of the n = 1 to 4 BAE/TAEs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nonlinear dynamics and transport driven by energetic particle instabilities using a gyro-Landau closure model *

Abstract Energetic particle (EP) destabilized Alfvén eigenmode (AE) instabilities are simulated for a DIII-D experimental case with a pulsed neutral beam using a gyro-Landau moments model which introduces EP phase-mixing effects through closure relations. This provides a computationally efficient reduced model which is applied here in the nonlinear regime over timescales that would be difficult to address with more complete models. The long timescale nonlinear evolution and related collective transport losses are examined including the effects of zonal flow/current generation, nonlinear energy cascades, and EP profile flattening. The model predicts frequencies and mode structures that are consistent with experimental observations. These calculations address issues that have not been considered in previous modelling: the EP critical gradient profile evolution in the presence of zonal flows/currents, and the dynamical nature of the saturated state. A strong level of intermittency is present in the predicted instability-driven transport; this is connected to the zonal flow growth and decay cycles and nonlinear energy transfers. Simulation of intermittent AE-enhanced EP transport will be an important issue for the protection of plasma facing components in the next generation of fusion devices.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Machine-learned closure of URANS for stably stratified turbulence: connecting physical timescales & data hyperparameters of deep time-series models

Stably stratified turbulence (SST), a model that is representative of the turbulence found in the oceans and atmosphere, is strongly affected by fine balances between forces and becomes more anisotropic in time for decaying scenarios. Moreover, there is a limited understanding of the physical phenomena described by some of the terms in the Unsteady Reynolds-Averaged Navier–Stokes (URANS) equations—used to numerically simulate approximate solutions for such turbulent flows. Rather than attempting to model each term in URANS separately, it is attractive to explore the capability of machine learning (ML) to model groups of terms, i.e. to directly model the force balances. We develop deep time-series ML for closure modeling of the URANS equations applied to SST. We consider decaying SST which are homogeneous and stably stratified by a uniform density gradient, enabling dimensionality reduction. We consider two time-series ML models: long short-term memory and neural ordinary differential equation. Both models perform accurately and are numerically stable in a posteriori (online) tests. Furthermore, we explore the data requirements of the time-series ML models by extracting physically relevant timescales of the complex system. We find that the ratio of the timescales of the minimum information required by the ML models to accurately capture the dynamics of the SST corresponds to the Reynolds number of the flow. The current framework provides the backbone to explore the capability of such models to capture the dynamics of high-dimensional complex dynamical system like SST flows.

97 MATHEMATICS AND COMPUTING↗

Level structure of light neutron-rich La isotopes beyond the 𝑁 = 82 shell closure

Here, the high spin excited states of Lanthanum isotopes 140–143 La, above the 𝑁 = 82 closed shell, were populated in fission reactions. The prompt 𝛾-ray transitions were measured using two complementary methods: (a) in coincidence with the isotopically identified fragments produced in the fission of the 238 U + 9 Be system using the Variable Mode Spectrometer (VAMOS++) and the Advanced Gamma Tracking Array (AGATA) spectrometer, and (b) high statistics threefold 𝛾−𝛾−𝛾 and fourfold 𝛾−𝛾−𝛾−𝛾 coincidence data from the spontaneous fission of 252 Cf using the Gammasphere. This work reports the first identification of a pair of parity doublet structures in 143 La and the new high spin level structure in 140–142 La from prompt 𝛾-ray spectroscopy. The level structures are interpreted in terms of the systematics of neighboring odd-𝑍 nuclei above the 𝑍 = 50 shell closure and large-scale shell model calculations. The present results indicate the presence of stable octupole deformation in 143 La. The excitation energy pattern and their comparison with neighboring isotones, moving away from the 𝑁 = 82 closed shell, point towards a transition from single-particle structures to an alternating parity rotational band structure in the La isotopic chain.

Navin, A. [Centre National de la Recherche Scienti↗

Electronic energy gap closure and metal-insulator transition in dense liquid hydrogen

Here, using quantum Monte Carlo (QMC) calculations, we investigate the insulator-metal transition observed in liquid hydrogen at high pressure. Below the critical temperature of the transition from the molecular to the atomic liquid, the fundamental electronic gap closure occurs abruptly, with a small discontinuity reflecting the weak first-order transition in the thermodynamic equation of state. Above the critical temperature, molecular dissociation sets in while the gap is still open. When the gap closes, the decay of the off-diagonal reduced density matrix shows that the liquid enters a gapless, but localized, phase: there is a crossover between the insulating and the metallic liquids. Compared to different density functional theory (DFT) functionals, our QMC calculations provide larger values for the fundamental gap and the electronic density of states close to the band edges, indicating that optical properties from DFT potentially benefit from error cancellations.

36 MATERIALS SCIENCE↗

Equation of state, phase transitions, and band-gap closure in Pb Cl 2 and Sn Cl 2

The equations of state and band-gap closures for Pb Cl 2 and Sn Cl 2 were studied using both experimental and theoretical methods. Here we measured the volume of both materials to a maximum pressure of 70 GPa using synchrotron-based angle-dispersive powder x-ray diffraction. The lattice parameters for both compounds showed anomalous changes between 16–32 GPa, providing evidence of a phase transition from the cotunnite structure to the related Co 2 Si structure, in contrast to the postcotunnite structure as previously suggested. First-principles calculations confirm this finding and predict a second phase transition to a Co 2 Si-like structure between 75– 110 GPa in Pb Cl 2 and 60–75 GPa in Sn Cl 2 . Band gaps were measured under compression to ~70 GPa for Pb Cl 2 and ~66 GPa for Sn Cl 2 and calculated up to 200 GPa for Pb CI 2 and 120 GPa for Sn Cl 2 . We find an excellent agreement between our experimental and theoretical results when using the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional, which suggests that this functional could reliably be used to calculate the band gap of similar AX 2 compounds. Experimental and calculated band-gap results show discontinuous decreases in the band gap corresponding to phase changes to higher-coordinated crystal structures, giving insight into the relationship between interatomic geometry and metallicity.

36 MATERIALS SCIENCE↗

Point-particle drag, lift, and torque closure models using machine learning: Hierarchical approach and interpretability

Developing deterministic neighborhood-informed point-particle closure models using machine learning has garnered interest recently from the dispersed multiphase flow community. The robustness of neural models for this complex multibody problem is hindered by the availability of particle-resolved data. Here, the present work addresses this unavoidable limitation of data paucity by implementing two strategies: (1) by using a rotation and reflection equivariant neural network and (2) by pursuing a physics-based hierarchical machine learning approach. The resulting machine-learned models are observed to achieve a maximum accuracy of 85% and 96% in the prediction of neighbor-induced force and torque fluctuations, respectively, for a wide range of Reynolds number and volume fraction conditions considered. Furthermore, we pursue force and torque network architectures that provide universal prediction spanning a wide range of Reynolds number (0.25 ≤ Re ≤250) and particle volume fraction (0 ≤ φ ≤0.4). The hierarchical nature of the approach enables improved prediction of quantities such as streamwise torque, by going beyond binary interactions to include trinary interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Energy Gap Closure of Crystalline Molecular Hydrogen with Pressure

Here, we study the gap closure with pressure of crystalline molecular hydrogen. The gaps are obtained from grand-canonical quantum Monte Carlo methods properly extended to quantum and thermal crystals, simulated by coupled electron ion Monte Carlo methods. Nuclear zero point effects cause a large reduction in the gap (~2 eV). Depending on the structure, the fundamental indirect gap closes between 380 and 530 GPa for ideal crystals and 330–380 GPa for quantum crystals. Beyond this pressure the system enters into a bad metal phase where the density of states at the Fermi level increases with pressure up to ~450–500 GPa when the direct gap closes. Our work partially supports the interpretation of recent experiments in high pressure hydrogen.

74 ATOMIC AND MOLECULAR PHYSICS↗

Proton Distribution Radii of 16–24 O: Signatures of New Shell Closures and Neutron Skin

The root mean square radii of the proton density distribution in 16–24 O derived from measurements of charge changing cross sections with a carbon target at ~900A MeV together with the matter radii portray thick neutron skin for 22–24 O despite 22,24 O being doubly magic. Imprints of the shell closures at N=14 and 16 are reflected in local minima of their proton radii that provide evidence for the tensor interaction causing them. The radii agree with ab initio calculations employing the chiral NNLO sat interaction, though skin thickness predictions are challenged. Furthermore, shell model predictions agree well with the data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Atwood effects on nonlocality of the scalar transport closure in Rayleigh-Taylor mixing

The importance of nonlocality is assessed in modeling mean scalar transport for turbulent Rayleigh-Taylor (RT) mixing at different Atwood numbers. Building on the two-dimensional incompressible work of Lavacot et al. [J. Fluid Mech. 985, A47 (2024)], the present work extends the macroscopic forcing method to variable density problems in three-dimensional space to measure moments of the generalized eddy diffusivity kernel in RT mixing for increasing Atwood numbers (𝐴 = 0.05, 0.3, 0.5, 0.8). It is found that as 𝐴 increases, (1) the eddy diffusivity moments become asymmetric and (2) the higher-order eddy diffusivity moments become larger relative to the leading-order diffusivity, indicating that nonlocality becomes more important at higher 𝐴. There is a particularly strong temporal nonlocality at higher 𝐴, suggesting stronger history effects. In conclusion, the implications of these findings for closure modeling for finite-Atwood RT are discussed.

general physics↗

Seniority Structure in Neutron-Rich Nucleus 128 Ag : Evidence for Robustness of 𝑁 = 82 Shell Closure in Silver Isotopes

The spectroscopic studies of very neutron-rich nucleus 128 Ag have been performed for the first time at the Radioactive Isotope Beam Factory of RIKEN. A new seniority isomer with a half-life of 1.60(7) μs has been identified and is proposed to have a spin-parity of 16 - with a maximally aligned configuration comprising three proton holes in the g 9/2 orbital and one neutron hole in the h 11/2 orbital. The new level structure in 128 Ag is quite well described by shell model calculations without invoking excitations across the Z = 50 and N = 82 shell gaps, and presents a good case of seniority scheme in odd-odd nuclei in the south vicinity of the double-magic nucleus 132 Sn. With a classification of various components of the proton-neutron interaction, the inversion of lowest-lying 9 - and 10 - states between 128 Ag and its neighboring isotone 130 In is found to be dynamically ascribed to the seniority-nonconserving proton-neutron interaction components. The structure above 10 - up to the 16 - isomer in 128 Ag shows remarkable similarities to seniority structures in the semimagic nuclei 128 Pd and 130 Cd. These spectroscopic features in 128 Ag indicate that the N = 82 shell closure is still robust in silver isotopes.

Luo, D. W. [Peking University, Beijing (China); et↗

Concrete Testing Case for Closure of Handford’s 241-C Underground Storage Tanks

Sixty percent of the nation's highly toxic and radioactive mixed wastes are stored at Hanford in 177 deteriorating underground storage tanks. To close or remove these storage tanks from service and place them in a condition that is protective of human health and the environment, the tanks must be physically stabilized to prevent subsidence once wastes have been retrieved. Remaining residual liquid waste in the tanks that cannot be removed must be solidified and the solid wastes encapsulated to meet the Nuclear Regulatory Commission, Department of Energy, Environmental Protection Agency, and the State of Washington requirements. The Department of Energy has developed cementitious flowable concretes to restrict access and provide chemical stabilization for radionuclides. Formulation, laboratory, and field testing for application at Hanford began with flowable, self-leveling structural and non-structural fills. A slump flow equal to or greater than 610 mm, 0% bleed water, and 0.1% (by volume) shrinkage measurements were key parameters guiding reformulation efforts that resulted in highly flowable, self-consolidating concretes that met Hanford 241-C Tank closure short- and long-term regulatory and engineering performance requirements.

formula development↗