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At least 469 records · Page 26

The influence of packing structure and interparticle forces on ultrasound transmission in granular media

Ultrasound propagation through externally stressed, disordered granular materials was experimentally and numerically investigated. Experiments employed piezoelectric transducers to excite and detect longitudinal ultrasound waves of various frequencies traveling through randomly packed sapphire spheres subjected to uniaxial compression. The experiments featured in situ X-ray tomography and diffraction measurements of contact fabric, particle kinematics, average per-particle stress tensors, and interparticle forces. The experimentally measured packing configuration and inferred interparticle forces at different sample stresses were used to construct spring networks characterized by Hessian and damping matrices. The ultrasound responses of these network were simulated to investigate the origins of wave velocity, acoustic paths, dispersion, and attenuation. Results revealed that both packing structure and interparticle force heterogeneity played an important role in controlling wave velocity and dispersion, while packing structure alone quantitatively explained most of the observed wave attenuation. This research provides insight into time- and frequency-domain features of wave propagation in randomly packed granular materials, shedding light on the fundamental mechanisms controlling wave velocities, dispersion, and attenuation in such systems.

36 MATERIALS SCIENCE↗

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Magic-angle semimetals with chiral symmetry

Here, we construct and solve a two-dimensional, chirally symmetric model of Dirac cones subjected to a quasiperiodic modulation. In real space, this is realized with a quasiperiodic hopping term. This hopping model, as we show, at the Dirac node energy has a rich phase diagram with a semimetal-to-metal phase transition at intermediate amplitude of the quasiperiodic modulation, and a transition to a phase with a diverging density of states (DOS) and subdiffusive transport when the quasiperiodic hopping is strongest. We further demonstrate that the semimetal-to-metal phase transition can be characterized by the multifractal structure of eigenstates in momentum space and can be considered as a unique “unfreezing” transition. This unfreezing transition in momentum space generates flat bands with a dramatically renormalized bandwidth in the metallic phase similar to the phenomena of the band structure of twisted bilayer graphene at the magic angle. We characterize the nature of this transition numerically as well as analytically in terms of the formation of a band of topological zero modes. For pure quasiperiodic hopping, we provide strong numerical evidence that the low-energy DOS develops a divergence and the eigenstates exhibit Chalker (quantum-critical) scaling despite the model not being random. At particular commensurate limits the model realizes higher-order topological insulating phases. We discuss how these systems can be realized in experiments on ultracold atoms and metamaterials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Scattering mechanisms in state-of-the-art GaAs/AlGaAs quantum wells

Motivated by recent breakthroughs in molecular beam epitaxy of GaAs/AlGaAs quantum wells, we examine contributions to mobility and quantum mobility from various scattering mechanisms and their dependencies on the electron density. Here we find that at lower electron densities, n e ≲ 1 x 10 11 cm -2 , both transport and quantum mobility are limited by unintentional background impurities and follow a power-law dependence, ∝ n$^{α}_{e}$, with α ≈ 0.85. Our predictions for quantum mobility are in reasonable agreement with an estimate obtained from the resistivity at filling factor ν = 1/2 in a sample of Y. J. Chung et al. with n e = 1 x 10 11 cm -2 . Consideration of other scattering mechanisms indicates that interface roughness (remote donors) is likely a limiting factor of transport (quantum) mobility at higher electron densities. Future measurements of quantum mobility should yield information on the distribution of background impurities in GaAs and AlGaAs.

36 MATERIALS SCIENCE↗

Experimental confirmation of the magnetic ordering transition induced by an electronic structure change in the metallic triangular antiferromagnet Co 1/3⁢ TaS 2

We report angle-resolved photoemission spectroscopy (ARPES) studies combined with DFT+DMFT calculations to confirm that the magnetic ordering vector transition from Q=(1/2,0,0) to Q=(1/3,0,0) in the metallic triangular antiferromagnets Co 1/3±𝜀⁢ TaS 2 (𝜀 ≈ 0.007) is induced by the electronic structure change in the system. The ARPES-measured Fermi surface (FS) maps of Co 0.325 ⁢TaS 2 show two hexagonal and one circular holelike FSs around Γ, which matches well with the triple- Q state by taking into account the contribution of nesting vectors occurring between Co 3⁢𝑑 and Ta 5⁢𝑑 orbitals. In the case of Co 0.340 ⁢TaS 2 , a new electron pocket around K appears, and the FS geometry changes as a result of the correlation effect of Co 4 ⁢S 18 tripods forming in the system. The magnetic susceptibility calculations based on the charge-self-consistent DFT+DMFT band structures and the random phase approximation indicate that the most stable magnetic ordering vector (1/2,0,0) split into (1/6,0,0) and (1/2,0,0), which is consistent with the magnetic phase transition around 𝑥=1/3 in Co 𝑥 ⁢TaS 2 .

Fermi surface↗

Analysis of Integrated Vapor Transport Biases

Abstract High-fidelity analyses and forecasts of integrated vapor transport (VT) are central to the study of Earth’s hydrological cycle as well as high-impact phenomena such as monsoons and atmospheric rivers. The impact of the in-line analysis correction-based additive inflation (ACAI) on IVT biases and forecast errors is examined within the Navy Earth System Prediction Capability (Navy ESPC) global coupled system. The ACAI technique uses atmospheric analysis corrections from the data assimilation system to approximate model bias and as a representation of stochastic model error to simultaneously reduce systematic and random errors and improve ensemble performance. ACAI reduces the global average magnitude of the 7- and 14-day IVT bias by 16%–17% during Northern Hemisphere summer, reaching 70% reductions in some tropical regions. The global average IVT bias reduction is similar to the bias reduction for low-level wind speed bias and considerably smaller than the bias reduction in total precipitable water. The localized regions where ACAI increases IVT bias occur where the control IVT biases change sign and structure with increasing forecast lead time, such as the South Asian monsoon region. Substituting analyzed wind or moisture fields for the forecast fields when calculating the forecast IVT confirms that, on average, wind errors dominate the IVT error calculation in the tropics, although wind and moisture error contributions are comparable in the extratropics. The existence of regions where using either analyzed winds or analyzed moisture increases IVT bias or mean absolute error reveals areas with compensating errors.

Reynolds, Carolyn A.↗

Distant Relatives: The Chemical Homogeneity of Comoving Pairs Identified in Gaia

Comoving pairs, even at the separations of $\mathcal{O}$(10 6 ) are a predicted reservoir of conatal stars. Here we present detailed chemical abundances of 62 stars in 31 comoving pairs with separations of 10 2 –10 7 au and 3D velocity differences <2 km s -1 . This sample includes both bound comoving pairs/wide binaries and unbound comoving pairs. Observations were taken using the Magellan Inamori Kyocera Echelle (MIKE) spectrograph on board the Magellan/Clay Telescope at high resolution (R~ 45,000) with a typical signal-to-noise ratio of 150 pixel -1 . With these spectra, we measure surface abundances for 24 elements, including Li, C, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Sr, Y, Zr, Ba, La, Nd, and Eu. Taking iron as the representative element, our sample of wide binaries is chemically homogeneous at the level of 0.05 dex, which agrees with prior studies on wide binaries. Importantly, even systems at separations 2 × 10 5 –10 7 au are homogeneous to 0.09 dex, as opposed to the random pairs, which have a dispersion of 0.23 dex. Assuming a mixture model of the wide binaries and random pairs, we find that 73 ± 22% of the comoving pairs at separations 2 × 10 5 –10 7 au are conatal. Our results imply that a much larger parameter space of phase space may be used to find conatal stars, to study M-dwarfs, star cluster evolution, exoplanets, chemical tagging, and beyond.

79 ASTRONOMY AND ASTROPHYSICS↗

Dual-frequency (Ka-band and G-band) radar estimates of liquid water content profiles in shallow clouds

The profile of the liquid water content (LWC) in clouds provides fundamental information for understanding the internal structure of clouds, their radiative effects, propensity to precipitate, and degree of entrainment and mixing with the surrounding environment. In principle, differential absorption techniques based on coincident dual-frequency radar reflectivity observations have the potential to provide the LWC profile. Previous differential frequency radar reflectivity (DFR) efforts were challenged by the fact that the measurable differential attenuation for small quantities of LWC is usually comparable to the system measurement error. This typically renders the retrieval impractical, as the uncertainty can become many times greater than the retrieved value itself. Theoretically, this drawback can be mitigated following two interconnected approaches: (1) increasing the frequency separation between the dual-frequency radar system to measure greater differential attenuation and (2) increasing the radar operating frequency to reduce the instrument measurement random error. Our recently developed 239 GHz radar was deployed during the Eastern Pacific Cloud Aerosol Precipitation Experiment (EPCAPE) along with a variety of collocated remote sensing and in situ instruments. We have combined Ka-band (35 GHz) and G-band (239 GHz) observations to retrieve the LWC from more than 100 vertical profiles of shallow clouds with typical amounts of LWC smaller than 1 g m -3 . We theoretically and experimentally demonstrate that the Ka-band and G-band pair of frequencies offers at least a 65 % relative improvement in the LWC retrieval sensitivity compared to previous works reported in the literature using lower-frequency radars. This new technique provides a missing capability to determine the LWC in the challenging low liquid water path (LWP) range (< 200 g m -2 ) and suggests a way forward to characterize microphysical and dynamical processes more precisely in shallow clouds.

54 ENVIRONMENTAL SCIENCES↗

Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics

In this work, we evaluate the biomolecular dynamics behaviors when conventionally iterating between all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations over multiple cycles. We implemented the workflow to iterate between AA and CG in OpenMM, namely the iterative multiscale MD (iMMD) simulation workflow. In particular, we aim to identify practical applications for iterating between AA and CG simulations in a conventional manner without any constraints or model modifications. We evaluate the iMMD workflow on four representative systems, spanning folding of two soluble proteins and protein-protein as well as protein-lipid interactions of two membrane proteins. We observe that iteration between AA and CG representations could help the soluble proteins exit undesirable metastable states to fold, resulting from random protein structural distortions due to cycling. Consequently, the most reliable use of iterative AA and CG simulations appears to be to accelerating complex lipid mixing for membrane-bound protein systems rather than sampling protein conformational space. Our work explores the practical usages and limitations for iterative AA and CG simulations using readily available AA and CG force fields. The evaluated iMMD workflow in OpenMM is made available at https://github.com/lanl/iMMD.

59 BASIC BIOLOGICAL SCIENCES↗

Intrinsic use control for system and use controlled component security

An Initialization Unit (IU) initiates an initial secure connection with an Intrinsic Use Control (IUC) Chip based on very large random numbers (VLRNs). The IUC Chip in turn initiates a secondary secure connection between it and one or more Use Controlled Components (UCCs). Polling by the IU allows confirmation of an ongoing secure connection, and also allows the IUC Chip to confirm the secondary secure connection to the UCCs. Removal or improper polling response from one of the UCCs results in a response from the IUC Chip that may include notification of tampering, or temporary or permanent discontinued operation of the offending UCC. Permanent discontinued operation may include destruction of the offending UCC, and cascaded discontinued operation of all other UCCs secured by the IUC Chip. A UCC may in turn be another nested layer of IUC Chips, controlling a corresponding layer of UCCs, ad infinitum.

Hart, Mark Miles↗

Distribution of centrality measures on undirected random networks via the cavity method

The Katz centrality of a node in a complex network is a measure of the node’s importance as far as the flow of information across the network is concerned. For ensembles of locally tree-like undirected random graphs, this observable is a random variable. Its full probability distribution is of interest but difficult to handle analytically because of its “global” character and its definition in terms of a matrix inverse. Leveraging a fast Gaussian Belief Propagation-Cavity algorithm to solve linear systems on tree-like structures, we show that i) the Katz centrality of a single instance can be computed recursively in a very fast way, and ii) the probability P ( K ) that a random node in the ensemble of undirected random graphs has centrality K satisfies a set of recursive distributional equations, which can be analytically characterized and efficiently solved using a population dynamics algorithm. We test our solution on ensembles of Erdős-Rényi and Scale Free networks in the locally tree-like regime, with excellent agreement. The analytical distribution of centrality for the configuration model conditioned on the degree of each node can be employed as a benchmark to identify nodes of empirical networks with over- and underexpressed centrality relative to a null baseline. We also provide an approximate formula based on a rank- 1 projection that works well if the network is not too sparse, and we argue that an extension of our method could be efficiently extended to tackle analytical distributions of other centrality measures such as PageRank for directed networks in a transparent and user-friendly way.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Minimal implicit-solvent coarse-grained simulation of Pluronic block copolymers with ionic liquids

Pluronic block copolymers, composed of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO) in a triblock structure (PEO–PPO–PEO), are well known for their amphiphilic character and ability to self‐assemble into micelles in aqueous solution. The addition of ionic liquids (ILs) can further modulate the core–shell structures of these copolymers, influencing their stability, critical micellization temperature, and size. However, fully atomistic simulations often become prohibitively expensive due to the size and complexity of these systems. In this work, coarse‐grained simulations using a minimal implicit‐solvent model were performed to examine how two classes of ILs, namely, 1‐alkyl‐3‐methylimidazolium ([C n C 1 im]) and 1‐alkyl‐3‐methylpyrrolidinium ([C n C 1 pyrr]), change the micellization of Pluronic block copolymers in aqueous solution. The effects of IL concentration and alkyl group length were investigated, and the model greatly improved the efficiency of simulating large‐scale micelle systems. Furthermore, the numerical simulations are qualitatively compared with experimental investigations. Our results show that adding ILs expands the micelle core by embedding IL tails among the PPO blocks, thereby increasing overall micelle size. Less polar ILs generally induce more pronounced micellar growth. However, the effect of IL tail length on conformation and micellar packing is non‐monotonic. Up to moderate chain lengths (around C8–C10), the IL tails can extend sufficiently to increase local separation within the micelle; at longer tail lengths, enhanced hydrophobic clustering and steric hindrance cause the tails to bend or fold, capping further expansion. In addition, although block copolymer chains tend to pack more closely in the presence of longer‐tailed ILs, the random coil size of an individual polymer chain does not necessarily shrink. Meanwhile, these insights provide a deeper understanding of how Pluronic/IL systems interact, informing applications in drug delivery, cosmetics, food, and environmental engineering. Finally, our minimal implicit‐solvent model can be applied to larger systems and longer timescales, substantially reducing computational cost while reproducing key structural trends observed experimentally.

Atomistic simulations↗

Sparse Approximate Multifrontal Factorization with Butterfly Compression for High-Frequency Wave Equations

In this work, we present a fast and approximate multifrontal solver for large-scale sparse linear systems arising from finite-difference, finite-volume or finite-element discretization of high-frequency wave equations. The proposed solver leverages the butterfly algorithm and its hierarchical matrix extension for compressing and factorizing large frontal matrices via graph-distance guided entry evaluation or randomized matrix-vector multiplication-based schemes. Complexity analysis and numerical experiments demonstrate $\mathcal{O}(N\log^2 N)$ computation and $\mathcal{O}(N)$ memory complexity when applied to an $N\times N$ sparse system arising from 3D high-frequency Helmholtz and Maxwell problems.

97 MATHEMATICS AND COMPUTING↗

Geometric Delocalization in Two Dimensions

We demonstrate the existence of transient two-dimensional surfaces where a random-walking particle escapes to infinity in contrast to localization in standard flat two-dimensional space. We first prove that any rotationally symmetric two-dimensional membrane embedded in flat three-dimensional space cannot be transient. Then we formulate a criterion for the transience of a general asymmetric two-dimensional membrane. We use it to explicitly construct a class of transient two-dimensional manifolds with a nontrivial metric and height function but “zero average curvature,” which we dub “tablecloth manifolds.” The absence of the logarithmic infrared divergence of the Laplace-Beltrami operator in turn implies the absence of weak localization, nonexistence of bound states in shallow potentials, and breakdown of the Mermin-Wagner theorem and Kosterlitz-Thouless transition on the tablecloth manifolds, which may be realizable in both quantum simulators and corrugated two-dimensional materials.

Anderson localization↗

Development of Short-Term Forecasting Models Using Plant Asset Data and Feature Selection

Nuclear power plants collect and store large volumes of heterogeneous data from various components and systems. With recent advances in machine learning (ML) techniques, these data can be leveraged to develop diagnostic and short-term forecasting models to better predict future equipment condition. Maintenance operations can then be planned in advance whenever degraded performance is predicted, thus resulting in fewer unplanned outages and the optimization of maintenance activities. This enables lower maintenance costs and improves the overall economics of nuclear power. This paper focuses on developing a short-term forecasting process that leverages a feature selection process to distill large volumes of heterogeneous data and predict specific equipment parameters. A variety of feature selection methods, including Shapley Additive Explanations (SHAP) and variance inflation factor (VIF), were used to select the optimal features as inputs for three ML methods: long short-term memory (LSTM) networks, support vector regression (SVR), and random forest (RF). Each combination of model and input features was used to predict a pump bearing temperature both 1 and 24 hours in advance, based on actual plant system data. The optimal inputs for the LSTM and SVR were selected using the SHAP values, while the optimal input for the RF consisted solely of the response variable itself. Each model produced similar 1-hour-ahead predictions, with root mean square errors (RMSEs) of roughly 0.006. For the 24-hour-ahead predictions, differences could be seen between LSTM, SVR, and RF, as reflected by model performances of 0.036 +- 0.014, 0.0026 +- 0, and 0.063 +- 0.004 RMSE, respectively. As big data and continuous online monitoring become more widely available, the proposed feature selection process can be used for many applications beyond the prediction of process parameters within nuclear infrastructure.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Spectral Filtering Induced by Non-Hermitian Evolution with Balanced Gain and Loss: Enhancing Quantum Chaos

Here, the dynamical signatures of quantum chaos in an isolated system are captured by the spectral form factor, which exhibits as a function of time a dip, a ramp, and a plateau, with the ramp being governed by the correlations in the level spacing distribution. While decoherence generally suppresses these dynamical signatures, the nonlinear non-Hermitian evolution with balanced gain and loss (BGL) in an energy-dephasing scenario can enhance manifestations of quantum chaos. In the Sachdev-Ye-Kitaev model and random matrix Hamiltonians, BGL increases the span of the ramp, lowering the dip as well as the value of the plateau, providing an experimentally realizable physical mechanism for spectral filtering. The chaos enhancement due to BGL is optimal over a family of filter functions that can be engineered with fluctuating Hamiltonians.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Structured light scanning artifact-based performance study

Structured light scanning is used to create a digital twin of a manufactured part, where features are extracted to determine if the part meets the designer’s intent and required tolerances. This paper describes repeatability and reproducibility analyses for a commercially-available structured light scanning system and measurement artifact. The repeatability study used five repeated scans at 15 measurement positions. Repeatability was assessed by randomly selecting one of the five scans at each of the 15 positions and creating a part mesh. This process was performed 50 times and the statistics for the dimension variations were calculated to isolate the scanning effects only. The same sequence was then performed for 10 of the 15 positions and five of the 15 positions to evaluate the repeatability sensitivity to the number of measurement positions. Reproducibility was assessed by selecting 15 positions to create a mesh and repeating the 15-position measurement sequence 10 times using different positions for each mesh construction. The statistics for the dimension variations were then calculated. This incorporated the effects of both scanning and the position and orientation of the part relative to the scanner. This sequence was repeated for 10-position and five-position scans to evaluate the corresponding sensitivity. Finally, the artifact dimensions from structured light scanning were compared to coordinate measuring machine measurements of the same features.

42 ENGINEERING↗

Tuning magnetoelectricity in a mixed-anisotropy antiferromagnet

Control of magnetization and electric polarization is attractive in relation to tailoring materials for data storage and devices such as sensors or antennae. In magnetoelectric materials, these degrees of freedom are closely coupled, allowing polarization to be controlled by a magnetic field, and magnetization by an electric field, but the magnitude of the effect remains a challenge in the case of single-phase magnetoelectrics for applications. We demonstrate that the magnetoelectric properties of the mixed-anisotropy antiferromagnet LiNi 1-x Fe x PO 4 are profoundly affected by partial substitution of Ni 2+ ions with Fe 2+ on the transition metal site. This introduces random site-dependent single-ion anisotropy energies and causes a lowering of the magnetic symmetry of the system. In turn, magnetoelectric couplings that are symmetry-forbidden in the parent compounds, LiNiPO 4 and LiFePO 4 , are unlocked and the dominant coupling is enhanced by almost two orders of magnitude. Our results demonstrate the potential of mixed-anisotropy magnets for tuning magnetoelectric properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗