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At least 397 records · Page 22

On conjugate gradient type methods and polynomial preconditioners for a class of complex non-Hermitian matrices

Conjugate gradient type methods are considered for the solution of large linear systems Ax = b with complex coefficient matrices of the type A = T + i(sigma)I where T is Hermitian and sigma, a real scalar. Three different conjugate gradient type approaches with iterates defined by a minimal residual property, a Galerkin type condition, and an Euclidian error minimization, respectively, are investigated. In particular, numerically stable implementations based on the ideas behind Paige and Saunder's SYMMLQ and MINRES for real symmetric matrices are proposed. Error bounds for all three methods are derived. It is shown how the special shift structure of A can be preserved by using polynomial preconditioning. Results on the optimal choice of the polynomial preconditioner are given. Also, some numerical experiments for matrices arising from finite difference approximations to the complex Helmholtz equation are reported.

Freund, Roland↗

Parabolic features and the erosion rate on Venus

The impact cratering record on Venus consists of 919 craters covering 98 percent of the surface. These craters are remarkably well preserved, and most show pristine structures including fresh ejecta blankets. Only 35 craters (3.8 percent) have had their ejecta blankets embayed by lava and most of these occur in the Atla-Beta Regio region; an area thought to be recently active. parabolic features are associated with 66 of the 919 craters. These craters range in size from 6 to 105 km diameter. The parabolic features are thought to be the result of the deposition of fine-grained ejecta by winds in the dense venusian atmosphere. The deposits cover about 9 percent of the surface and none appear to be embayed by younger volcanic materials. However, there appears to be a paucity of these deposits in the Atla-Beta Regio region, and this may be due to the more recent volcanism in this area of Venus. Since parabolic features are probably fine-grain, wind-deposited ejecta, then all impact craters on Venus probably had these deposits at some time in the past. The older deposits have probably been either eroded or buried by eolian processes. Therefore, the present population of these features is probably associated with the most recent impact craters on the planet. Furthermore, the size/frequency distribution of craters with parabolic features is virtually identical to that of the total crater population. This suggests that there has been little loss of small parabolic features compared to large ones, otherwise there should be a significant and systematic paucity of craters with parabolic features with decreasing size compared to the total crater population. Whatever is erasing the parabolic features apparently does so uniformly regardless of the areal extent of the deposit. The lifetime of parabolic features and the eolian erosion rate on Venus can be estimated from the average age of the surface and the present population of parabolic features.

Strom, Robert G.↗

The Role of Endolithic Cyanobacteria in the Formation of Lithified Laminae in Bahamian Stromatolites

The microboring activity of endolithic cyanobacteria plays a major role in the formation of lithified laminae in modern marine stromatolites in the Exuma Cays, Bahamas. These stromatolites are composed primarily of fine grained carbonate sand that is trapped and bound by the filamentous cyanobacteria Schizothrix sp. Periodic introduction of coccoid endolithic cyanobacteria, Solentia sp., results in formation of lithified horizons, 200 to 1000 micron thick. We used SEM and petrographic analyses to examine both naturally occurring lithified layers dominated by endoliths and fused oolitic crusts generated in the laboratory by activity of endolithic cyanobacteria (Solentia sp.). Fused grain crusts consist of micritized grains that are welded together at point contacts. Micritization results from extensive microboring and rapid (days to weeks) carbonate precipitation within the bore holes. This precipitation appears to occur concurrently with further endolithic activity within the grain, Infilling of bore holes that cross from one grain to another at point contacts results in grain welding, Thus, while microboring destroys original grain textures, at the same time the endolith activity plays a constructional role in stromatolite growth by forming lithified layers of welded grains. These framework structures help to stabilize and preserve the stromatolite deposits.

Prufert-Bebout, L.↗

On the Use of Vortex-Fitting in the Numerical Simulation of Blade-Vortex Interaction

The usefulness of vortex-fitting in the computational fluid dynamics (CFD) methods to preserve the vortex strength and structure while convecting in a uniform free stream is demonstrated through the numerical simulations of two- and three-dimensional blade-vortex interactions. The fundamental premise of the formulation is the velocity and pressure field of the interacting vortex are unaltered either in the presence of an airfoil or a rotor blade or by the resulting nonlinear interactional flowfield. Although, the governing Euler and Navier-Stokes equations are nonlinear and independent solutions cannot be superposed, the interactional flowfield can be accurately captured by adding and subtracting the flowfield of the convecting vortex at each instant. The aerodynamics and aeroacoustics of two- and three-dimensional blade-vortex interactions have been calculated in Refs. 1-6 using this concept. Some of the results from these publications and similar other published material will be summarized in this paper.

Srinivasan, G. R.↗

Pressure-Sensitive Paint Applied to Ice Accretions

Aircraft icing occurs when a plane flies through a cloud of supercooled water droplets. When the droplets impinge on aircraft components, ice starts to form and accumulate. This accumulation of ice severely increases the drag and lift of the aircraft, and can ultimately lead to catastrophic failures and even loss of life. Knowledge of the air pressures on the surfaces of ice and models in wind tunnels allows researchers to better predict the effects that different icing conditions will have on the performance of real aircraft. The use of pressure-sensitive paint (PSP) has provided valuable information on similar problems in conventional wind tunnel testing. In NASA Lewis Research Center Icing Research Tunnel, Lewis researchers recently demonstrated the world s first application of PSP on actual ice formed on a wind tunnel model. This proof-of-concept test showed that a new paint formulation developed under a grant by the University of Washington adheres to both the ice shapes and cold aluminum models, provides a uniform coating that preserves the detailed ice shape structure, and responds to simulated pressure changes.

Bencic, Timothy J.↗

A strategy for compression and analysis of massive geophysical data sets

This paper describes a method for summaraizing data in a way that approximately preserves high-resolution data structure while reducing data volume and maintaining global integrity of very large, remote sensing data sets. The method is under development for one of Terra's instruments, the Multi-angle Imaging SpectroRadiometer (MISR).

geophysical data sets compression↗

Operando Freezing Cryogenic Electron Microscopy of Active Battery Materials

Abstract Understanding structural and chemical evolution of battery materials during operation is critical to achieving safe, efficient, and long-lasting energy storage. Cryogenic electron microscopy (cryo-EM) has become a valuable tool in battery characterization, leveraging low temperatures to improve stability of sensitive materials under electron beam irradiation. However, typical cryo-EM sample preparations leave extended time between the electrochemical point of interest and ex situ freezing of samples, during which active structures may relax, degrade, or otherwise evolve. Here, we detail a method for operando freezing cryo-EM to preserve and characterize native electrode and interfacial structures that arise during battery cycling, based on an operando plunge freezer and cold sample removal process. We validate the method on multiple electrode materials and quantify and discuss the freezing rate achieved. Operando freezing cryo-EM can be used to directly visualize transient features that arise at active electrochemical interfaces, to enable deeper understanding of structural evolution and interfacial chemistry in batteries and other electrochemical systems.

25 ENERGY STORAGE↗

Venusian impact basins and cratered terrains

The consensus regarding interpretation of Magellan radar imagery assigns Venus a young volcanic surface subjected in many areas to moderate crustal shortening. I infer that, on the contrary, ancient densely cratered terrain and large impact basins may be preserved over more than half the planet and that crustal shortening has been much overestimated. I see wind erosion and deposition as far more effective in modifying old structures. Integration with lunar chronology suggests that most of the surface of Venus may be older than 3.0 Ga and much may be older than 3.8 Ga. Broad volcanos, hug volcanic domes, plains preserving lobate flow patterns, and numerous lesser volcanic features, pocked sparsely by impact craters, are indeed obvious on Magellan imagery. Some of these postvolcanic impact craters have been slightly extended, but only a small portion has been flooded by still younger lavas. Relative ages of the young craters are indicated by the varying eolian removal of their forms and ejecta blankets and flow lobes, and the oldest are much subdued. If these young impact craters, maximum diameter 275 km, include all preserved impact structures, then their quantity and distribution indicate that Venus was largely resurfaced by volcanism approx. 0.5 Ga, subsequent eruptions having been at a much reduced rate. Away from the approx. 0.5 Ga volcanic features, much of Venus is, however, dominated by circular and subcircular features, 50-2000 km in diameter, many of them multiring, that may be mostly older impact and impact-melt structures substantially modified by wind action. Eolian erosion scoured to bedrock old ridges and uplands, including those that may be cratered terrains and the rims and outer-ring depressions of large impact basins, and removed all surficial deposits to the limits of resolution of the imagery. The complementary eolian deposits form not only dunes, wind streaks, and small plains, but also broad radar-dark plains, commonly assumed to be volcanic although lacking flow morphology, whose materials appear to be thick because they are smoothly compacted into buried craters.

Hamilton, Warren B.↗

On the broadband vibration isolation performance of nonlocal total-internal-reflection metasurfaces

The concept of a nonlocal elastic metasurface has been recently proposed and experimentally demonstrated in Zhu et al. (2020). When implemented in the form of a total-internal-reflection (TIR) interface, the metasurface can act as an elastic wave barrier that is impenetrable to deep subwavelength waves over an exceptionally wide frequency band. The underlying physical mechanism capable of delivering this broadband subwavelength performance relies on an intentionally nonlocal design that leverages long-range connections between the units forming the fundamental supercell. This paper explores the design and application of a nonlocal TIR metasurface to achieve broadband passive vibration isolation in a structural assembly made of multiple dissimilar elastic waveguides. The specific structural system comprises shell, plate, and beam waveguides, and can be seen as a prototypical structure emulating mechanical assemblies of practical interest for many engineering applications. The study also reports the results of an experimental investigation that confirms the significant vibration isolation capabilities afforded by the embedded nonlocal TIR metasurface. We report these results are particularly remarkable because they show that the performance of the nonlocal metasurface is preserved when applied to a complex structural assembly and under non-ideal incidence conditions of the incoming wave, hence significantly extending the validity of the results presented in Zhu et al. (2020). Results also confirm that, under proper conditions, the original concept of a planar metasurface can be morphed into a curved interface while still preserving full wave control capabilities.

42 ENGINEERING↗

From atomistic models to machine learning: Predictive design of nanocarbons under extreme conditions

The formation of technologically valuable nanocarbon structures under extreme conditions, such as those produced during high-explosive detonations, remains poorly understood but holds significant potential for the development of controlled synthesis pathways. While detonation shockwaves provide the high-pressure, high-temperature environment required for nanodiamond formation, subsequent cooling and decompression dictate whether the diamond phase is preserved or transformed into other nanocarbon structures. Here, in this study, we employ GPU-accelerated reactive molecular dynamics (ReaxFF) simulations to investigate the graphitization and structural remodeling of detonation nanodiamond under nonlinear quench and pressure-release trajectories. We further investigate how the initial nanodiamond morphology; cuboctahedral, octahedral, or hexagonal prism influences the resulting transformation products. Evolution of nanostructure, allotrope (via simulated x-ray diffraction), carbon hybridization, and ring statistics are tracked during a two-stage quench from 5000 K to 60 GPa. Rapid cooling combined with slow decompression optimizes cubic diamond retention, whereas slow cooling with rapid pressure release promotes surface-to-core graphitization, producing concentric sp 2 -hybridized layers and hollowed inner shells. Octahedral nanodiamonds evolve into carbon nano-onions, initially forming bucky diamonds that progressively transform into fully sp 2 -hybridized structures, while hexagonal prisms preferentially form parallel-stacked graphite layers resembling carbon dots. Transient hexagonal diamond (lonsdaleite) emerges as an interfacial phase, suggesting potential reversibility in the shock-induced graphite-to-diamond transformation pathway transformation route. To extend predictive capabilities, we trained machine learning (ML) regressors on over 10 5 node-hours of molecular dynamics (MD) trajectories. A multilayer perceptron (MLP) model reliably predicts the number of graphitized layers from temperature–pressure trajectories with a coefficient of determination (R 2 ) exceeding 0.90. This high predictive fidelity enables efficient, high-throughput mapping of the synthesis parameter space for optimized graphitization outcomes. Collectively, morphological control combined with optimized quench–decompression conditions promote the selective synthesis of nanocarbon allotropes. This work establishes a data-driven framework for the rational, a priori design of carbon nanomaterials for applications in energy storage, sensing, and biomedicine.

Detonation nanodiamond remodeling↗

Augmenting Graph Convolution with Distance Preserving Embedding for Improved Learning

Graph convolution incorporates topological information of a graph into learning. Message passing corresponds to traversal of a local neighborhood in classical graph algorithms. We show that incorporating additional global structures, such as shortest paths, through distance preserving embedding can improve performance. Our approach, Gavotte, significantly improves the performance of a range of popular graph neu-ral networks such as GCN, GA T,Graph SAGE, and GCNII for transductive learning. Gavotte also improves the performance of graph neural networks for full-supervised tasks, albeit to a smaller degree. As high-quality embeddings are generated by Gavotte as a by-product, we leverage clustering algorithms on these embed dings to augment the training set and introduce Gavotte+. Our results of Gavotte+ on datasets with very few labels demonstrate the advantage of augmenting graph convolution with distance preserving embedding.

Cong, Guojing↗

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society

This review article describes the co-evolution of structural biology as a discipline and the Protein Data Bank (PDB), established in 1971 as the first open-access data resource in biology by like-minded structural scientists. As the PDB archive grew in size and scope to encompass macromolecular crystallography, NMR spectroscopy, and cryo-electron microscopy, new technologies were developed to ingest, validate, curate, store, and distribute the information. Community engagement ensured that the needs of structural biologists (data depositors) and data consumers were met. Today, the archive houses more than 230,000 experimentally determined structures of proteins, nucleic acids, and macromolecular machines and their complexes with one another and small-molecule ligands. Aggregate costs of PDB data preservation are ~1% of the cost of structure determination. The enormous impact of PDB data on basic and applied research and education across the natural and medical sciences is presented and highlighted with illustrative examples. Enablement of de novo protein structure prediction (AlphaFold2, RoseTTAfold, OpenFold, etc.) is the most widely appreciated benefit of having a corpus of rigorously validated, expertly curated 3D biostructure data.

bioinformatics↗

Ordovician impacts at sea in Baltoscandia

Northern Europe has an assemblage of Ordovician probable impacts that is exceptional because the structures involved are relatively old yet well preserved because they formed at sea and because they formed within a restricted geological time in a relatively small area. The Tvaren, Kardla, and Lockne structures might not be strictly contemporaneous but all formed near the beginning of the Caradoc Age (about 460 Ma), whereas the Granby structure is about 20 Ma older. The range of diameters is from about 2 km (Tvaren, Granby) to 8 km (Lockne). The stratigraphic succession formed on impact at sea, as uniformly documented by these structures, begins with a breccia lens consisting of basement rocks that are intensely crushed. Owing to expulsion of sea water by the impact, this breccia formed under essentially dry conditions. Later on this breccia was in part hydrothermally altered. It is overlain by backsurge turbidite that formed from fragments of local sedimentary bedrock and crystalline basement when the sea water returned to the crater site. Either the turbidite is simply a Bouma sequence (although quite thick - as much as over 50 m) from very coarse rubble to mud, or it is more complex. After deposition of the backsurge turbidite, or turbidite complex, the craters still remained as 150-200-m-deep holes in the sea bed. Together with the presence of relatively shallow water over the rim wall, this situation created predictable hydrologic conditions for extended histories of sedimentation and biological development at the crater as well as within it. The presence of a concentration of craters within a limited area of well-preserved and accessible Ordovician deposits raises a question about the Ordovician, especially its middle portion, as potentially an age of relatively intense impact activity even in wider areas. In this connection it may be apposite to mention that the only fossil stony meteorites so far recorded in rocks are from the late Early and the Middle Ordovician.

Lindstroem, M.↗

Multi-resolution partial differential equations preserved learning framework for spatiotemporal dynamics

Traditional data-driven deep learning models often struggle with high training costs, error accumulation, and poor generalizability in complex physical processes. Physics-informed deep learning (PiDL) addresses these challenges by incorporating physical principles into the model. Most PiDL approaches regularize training by embedding governing equations into the loss function, yet this depends heavily on extensive hyperparameter tuning to weigh each loss term. To this end, we propose to leverage physics prior knowledge by “baking” the discretized governing equations into the neural network architecture via the connection between the partial differential equations (PDE) operators and network structures, resulting in a PDE-preserved neural network (PPNN). This method, embedding discretized PDEs through convolutional residual networks in a multi-resolution setting, largely improves the generalizability and long-term prediction accuracy, outperforming conventional black-box models. The effectiveness and merit of the proposed methods have been demonstrated across various spatiotemporal dynamical systems governed by spatiotemporal PDEs, including reaction-diffusion, Burgers’, and Navier-Stokes equations.

97 MATHEMATICS AND COMPUTING↗

On the Prospect of Chemically Transferable Coarse-Grained Electronic Models for Soft Materials

Electronic coarse-graining (ECG) methods predict quantum-mechanical electronic properties directly from coarse-grained (CG) molecular configurations, enabling electronic predictions at mesoscale length scales. Here, we present a diagnostic assessment of the feasibility of chemically transferable ECG models across a broad polymer-relevant chemical space using all-atom, united-atom, and Martini-scale representations. While high-resolution ECG models achieve near-quantitative accuracy, we show that chemically transferable ECG at the Martini resolution fails because the CG force field does not sample the same configurational distribution of local molecular structure as that underlying the DFT-parameterized ECG model. We demonstrate that our proposed Element-Count-Label (ECL) representation, which augments Martini beads with explicit stoichiometric data, significantly improves chemical generalization across diverse polymer chemistries. However, we find that even with improved chemical resolution, the model cannot recover electronic property distributions that are absent from the configurational space sampled by the CG force field. These results demonstrate that chemically transferable ECG requires future Martini-like force fields to explicitly preserve quantum chemistry–compatible local molecular structure in addition to thermodynamic and structural fidelity.

Kidder, Katherine M [Department of Chemistry; Univ↗