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At least 469 records · Page 26

Scalable Volume Visualization for Big Scientific Data Modeled by Functional Approximation

Considering the challenges posed by the space and time complexities in handling extensive scientific volumetric data, various data representations have been developed for the analysis of large-scale scientific data. Multivariate functional approximation (MFA) is an innovative data model designed to tackle substantial challenges in scientific data analysis. It computes values and derivatives with high-order accuracy throughout the spatial domain, mitigating artifacts associated with zero- or first-order interpolation. However, the slow query time through MFA makes it less suitable for interactively visualizing a large MFA model. In this work, we develop the first scalable interactive volume visualization pipeline, MFA-DVV, for the MFA model encoded from large-scale datasets. Our method achieves low input latency through distributed architecture, and its performance can be further enhanced by utilizing a compressed MFA model while still maintaining a high-quality rendering result for scientific datasets. We conduct comprehensive experiments to show that MFA-DVV can decrease the input latency and achieve superior visualization results for big scientific data compared with existing approaches.

big scientific dataset↗

Two-dimensional silk

Despite the promise of silk-based devices, the inherent disorder of native silk limits performance. Here, we report highly ordered two-dimensional silk fibroin (SF) films grown epitaxially on van der Waals (vdW) substrates. Using atomic force microscopy, nano–Fourier transform infrared spectroscopy, and molecular dynamics, we show that the films consist of lamellae of SF molecules that exhibit the same secondary structure as the nanocrystallites of native silk. Increasing the SF concentration results in multilayers that grow either by direct assembly of SF molecules into the lamellae or, at high concentrations, along a two-step pathway beginning with a disordered monolayer that then crystallizes. Scanning Kelvin probe measurements show that these films substantially alter the surface potential; thus, they provide a platform for silk-based electronics on vdW solids.

36 MATERIALS SCIENCE↗

The Multiphysics on Advanced Platforms Project

In 2015, the Lawrence Livermore National Laboratory started development of next-generation multiphysics simulation capabilities for the National Nuclear Security Administration under the Advanced Technologies Development and Mitigation (ATDM) element of the Advanced Simulation and Computing program in collaboration with the Exascale Computing Project (ECP). A key driver for this effort across the NNSA tri-lab was the emergence of advanced high performance computing (HPC) architectures based on heterogeneous compute capabilities, including GPU based systems, as part of the national drive toward exascale computing platforms at multiple Department of Energy (DOE) facilities. Developing a multiphysics code capable of meeting the various simulation needs of the NNSA as defined by the current generation of integrated codes (or ICs), initially developed as part of the Accelerated Strategic Computing Initiative (ASCI) program beginning in 1996, and able to scale to the current 100 petaflop class pre-exascale systems, as well the forthcoming exaflop class computers, is a daunting challenge. To accomplish this ambitious goal, LLNL has embraced two key themes: use of high-order numerical methods and a modular approach to code development. The LLNL next generation effort is organized under the Multi-Physics on Advanced Platforms Project (MAPP). A foundational component of MAPP is the Axom computer science (CS) toolkit which provides infrastructure for the development of modular, performance portable, multi-physics application codes. MARBL is a next-generation application code built on the Axom base to address the modeling needs of the high energy density physics (HEDP) community for simulating high-explosive, magnetic or laser driven experiments such as inertial confinement fusion (ICF), pulsed-power magneto-hydrodynamics (MHD), equation of state (EOS) and material strength studies as part of the NNSA’s stockpile stewardship program (SSP).

97 MATHEMATICS AND COMPUTING↗

Growth of Mesoscale Ordered Two-Dimensional Hydrogen-Bond Organic Framework with the Observation of Flat Band

Flat bands (FBs), presenting a strongly interacting quantum system, have drawn increasing interest recently. However, experimental growth and synthesis of FB materials have been challenging and have remained elusive for the ideal form of monolayer materials where the FB arises from destructive quantum interference as predicted in 2D lattice models. Here, we report surface growth of a self-assembled monolayer of 2D hydrogen-bond (H-bond) organic frameworks (HOFs) of 1,3,5-tris(4-hydroxyphenyl)benzene (THPB) on Au(111) substrate and the observation of FB. High-resolution scanning tunneling microscopy or spectroscopy shows mesoscale, highly ordered, and uniform THPB HOF domains, while angle-resolved photoemission spectroscopy highlights a FB over the whole Brillouin zone. Density-functional-theory calculations and analyses reveal that the observed topological FB arises from a hidden electronic breathing-kagome lattice without atomically breathing bonds. In conclusion, our findings demonstrate that self-assembly of HOFs provides a viable approach for synthesis of 2D organic topological materials, paving the way to explore many-body quantum states of topological FBs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Riverbed Temperature and 4D ERT Monitoring Reveals Heterogenous Horizontal and Vertical Groundwater-Surface Water Exchange Flows Under Dynamic Stage Conditions

Groundwater surface water exchange plays a critical role in physical, biological, and geochemical function of coastal and riverine systems. Observing exchange flow behavior in heterogeneous systems is a primary challenge, particularly when flows are governed by dynamic river stage or tidal variations. In this paper we demonstrate a novel application of time-lapse 3D electrical resistivity tomography and temperature monitoring where an array of thermistors installed beneath a riverbed double as resistivity electrodes. We use the array to monitor stage driven exchange flows over a 6-day period in a dynamic, stage-driven high order stream. We present a method for addressing the otherwise confounding effects of the moving river-surface boundary on the raw resistivity data, thereby enabling successful tomographic imaging. Temperature time-series at each thermistor location and time-lapse 3D images of changes in bulk electrical conductivity together provide a detailed description of exchange dynamics over a 10-meter by 45-meter section of the riverbed, to a depth of approximately 5 m. Results reveal highly variable flux behavior throughout the monitoring domain including both horizontal and vertical exchange flows.

54 ENVIRONMENTAL SCIENCES↗

Improving the precision of forces in real-space pseudopotential density functional theory

The high-order finite difference real-space pseudopotential density functional theory (DFT) approach is a valuable method for large-scale, massively parallel DFT calculations. A significant challenge in the approach is the oscillating “egg-box” error introduced by aliasing associated with a coarse grid spacing. To address this issue while minimizing computational cost, we developed a finite difference interpolation (FDI) scheme [Roller et al., J. Chem. Theory Comput. 19, 3889 (2023)] as a means of exploiting the high resolution of the pseudopotential to reduce egg-box effects systematically. Here, we show an implementation of this method in the PARSEC code and examine the practical utility of the combination of FDI with additional methods for improving force precision and/or reducing its computational cost, including orbital-based forces, compensating charges (namely, adding and subtracting a judiciously chosen charge density such that the total density is unaltered), and a modified spatial domain in which the real-space grid is defined. Using selected small molecules, as well as metallic Li, as test cases, we show that a combination of all four aspects leads to a significant reduction in computational cost while retaining a high level of precision that supports accurate structures and vibrational spectra, as well as stable and accurate molecular dynamics runs.

Chemistry↗

PIAFS: A 2D nonlinear hydrodynamics code to model gaseous optics

The survivability of final optics is expected to be a major challenge for all future inertial fusion energy concepts. Due to their higher damage threshold, gaseous optics have been identified as a promising solution to this problem. Gaseous optics can be created through the photoabsorption of spatially modulated UV light, which induces various chemical processes that heat the gas. This heating leads to a pressure perturbation, which in turn launches a density perturbation that can imprint a refractive index modulation such as a grating. In this article, we introduce a parallel C/C++ code to simulate gaseous optics. PIAFS2D is a high-order conservative finite-difference code to solve the compressible Navier–Stokes equations along with the photochemical heating sources on Cartesian grids. The simulations are validated by the linear theory derived in a previous paper [Michel et al., Phys. Rev. Appl. 22, 024014 (2024)]. For larger perturbations, the behavior of the system—particularly the evolution of the generated acoustic wave—demonstrates strong nonlinearity. PIAFS2D allows the study of nonlinear behaviors and can be used for the design of high-efficiency gaseous optics elements in realistic experimental conditions.

Oudin, A. [Lawrence Livermore National Laboratory ↗

Probing the Local Site Disorder and Distortion in Pyrochlore High-Entropy Oxides

High-entropy oxides (HEOs) have attracted great interest in diverse fields because of their inherent opportunities to tailor and combine materials functionalities. The control of local order/disorder in the class is by extension a grand challenge toward realizing their vast potential. In this paper, we report the first examples of pyrochlore HEOs with five M-site cations, for Nd 2 M 2 O 7 , in which the local structure has been investigated by neutron diffraction and pair distribution function (PDF) analysis. The average structure of the pyrochlores is found to be orthorhombic Imma, in agreement with radius-ratio rules governing the structural archetype. The computed PDFs from density functional theory relaxed special quasirandom structure models are compared with real space PDFs in this work to evaluate M-site order/disorder. Reverse Monte Carlo combined with ab initio molecular dynamics and Metropolis Monte Carlo simulations demonstrates that Nd 2 (Ta 0.2 Sc 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7 is synthesized with its M-site local to nanoscale order highly randomized/disordered, while Nd 2 (Ti 0.2 Nb 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7+x exhibits a strong distortion of the TiO 6 octahedron and small degree of Ti chemical short-range order (SRO) on the subnanometer scale. Calculations suggest that this may be intrinsic, energetically favored SRO rather than due to sample processing. These results offer an important demonstration that the engineered variation of participating ions in HEOs, even among those with very similar radii, provides richly diverse opportunities to control local order/disorder motifs—and therefore materials properties for future designs. This work also hints at the exquisite level of detail that may be needed in computational and experimental data analysis to guide structure–property tuning in the emerging HEO materials class.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Rapid-charging aluminium-sulfur batteries operated at 85 °C with a quaternary molten salt electrolyte

Molten salt aluminum-sulfur batteries are based exclusively on resourcefully sustainable materials, and are promising for large-scale energy storage owed to their high-rate capability and moderate energy density; but the operating temperature is still high, prohibiting their applications. Here we report a rapid-charging aluminium-sulfur battery operated at a sub-water-boiling temperature of 85°C with a tamed quaternary molten salt electrolyte. The quaternary alkali chloroaluminate melt – possessing abundant electrochemically active high-order Al-Cl clusters and yet exhibiting a low melting point – facilitates fast Al 3+ desolvation. A nitrogen-functionalized porous carbon further mediates the sulfur reaction, enabling the battery with rapid-charging capability and excellent cycling stability with 85.4% capacity retention over 1400 cycles at a charging rate of 1 C. Importantly, we demonstrate that the asymmetric sulfur reaction mechanism that involves formation of polysulfide intermediates, as revealed by operando X-ray absorption spectroscopy, accounts for the high reaction kinetics at such temperature wherein the thermal management can be greatly simplified by using water as the heating media.

25 ENERGY STORAGE↗

A regression algorithm for accelerated lattice QCD that exploits sparse inference on the D-Wave quantum annealer

We propose a regression algorithm that utilizes a learned dictionary optimized for sparse inference on a D-Wave quantum annealer. In this regression algorithm, we concatenate the independent and dependent variables as a combined vector, and encode the high-order correlations between them into a dictionary optimized for sparse reconstruction. On a test dataset, the dependent variable is initialized to its average value and then a sparse reconstruction of the combined vector is obtained in which the dependent variable is typically shifted closer to its true value, as in a standard inpainting or denoising task. Here, a quantum annealer, which can presumably exploit a fully entangled initial state to better explore the complex energy landscape, is used to solve the highly non-convex sparse coding optimization problem. The regression algorithm is demonstrated for a lattice quantum chromodynamics simulation data using a D-Wave 2000Q quantum annealer and good prediction performance is achieved. The regression test is performed using six different values for the number of fully connected logical qubits, between 20 and 64. The scaling results indicate that a larger number of qubits gives better prediction accuracy.

97 MATHEMATICS AND COMPUTING↗

Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein

The aggregation of the intrinsically disordered tau protein into highly ordered β-sheet-rich fibrils is implicated in the pathogenesis of a range of neurodegenerative disorders. The mechanism of tau fibrillogenesis remains unresolved, particularly early events that trigger the misfolding and assembly of the otherwise soluble and stable tau. We investigated the role the lipid membrane plays in modulating the aggregation of three tau variants, the largest isoform hTau40, the truncated construct K18, and a hyperphosphorylation-mimicking mutant hTau40/3Epi. Despite being charged and soluble, the tau proteins were also highly surface active and favorably interacted with anionic lipid monolayers at the air/water interface. Membrane binding of tau also led to the formation of a macroscopic, gelatinous layer at the air/water interface, possibly related to tau phase separation. At the molecular level, tau assembled into oligomers composed of ~ 40 proteins misfolded in a β-sheet conformation at the membrane surface, as detected by in situ synchrotron grazing-incidence X-ray diffraction. Concomitantly, membrane morphology and lipid packing became disrupted. Our findings support a general tau aggregation mechanism wherein tau’s inherent surface activity and favorable interactions with anionic lipids drive tau-membrane association, inducing misfolding and self-assembly of the disordered tau into β-sheet-rich oligomers that subsequently seed fibrillation and deposition into diseased tissues.

59 BASIC BIOLOGICAL SCIENCES↗

Controlled synthesis and ordered assembly of Co 3 O 4 nanowires using genetically engineered bacterial flagella as biotemplates (Final Technical Report)

The major goals of the project are to gain a fundamental understanding on the influence of the displayed peptides and other processing parameters on the flagella assembly and the resulting biomimetic control over the synthesis and assembly of Co 3 O 4 nanoparticles (NPs) and nanowires (NWs). To pursue these goals, we designed two specific aims: Aim 1: Understanding the self-assembly of genetically engineered flagella and its outcome for site-specific nucleation and growth of Co 3 O 4 NPs and NWs. Aim 2: Understanding controllable alignment of 1D Co 3 O 4 -flagella NWs into highly ordered 2D and 3D structures.

59 BASIC BIOLOGICAL SCIENCES↗

Small energy gap revealed in CrBr 3 by scanning tunneling spectroscopy

CrBr 3 is a layered van der Waals material with magnetic ordering down to the 2D limit. For decades, based on optical measurements, it is believed that the energy gap of CrBr 3 is in the range of 1.68–2.1 eV. However, controversial results have indicated that the band gap of CrBr 3 is possibly smaller than that. An unambiguous determination of the energy gap is critical to the correct interpretations of the experimental results of CrBr 3 . Here, we present the scanning tunneling microscopy and spectroscopy (STM/S) results of CrBr 3 thin and thick flakes exfoliated onto highly ordered pyrolytic graphite (HOPG) surfaces and density functional theory (DFT) calculations to reveal the small energy gap (peak-to-peak energy gap to be 0.57 ± 0.04 eV; or the onset signal energy gap to be 0.29 ± 0.05 eV from dI/dV spectra). Atomic resolution topography images show the defect-free crystal structure and the dI/dV spectra exhibit multiple peak features measured at 77 K. The conduction band – valence band peak pairs in the multi-peak dI/dV spectrum agree very well with all reported optical transitions. STM topography images of mono- and bi-layer CrBr 3 flakes exhibit edge degradation due to short air exposure (~15 min) during sample transfer. The unambiguously determined small energy gap settles the controversy and is the key in better understanding CrBr 3 and similar materials.

36 MATERIALS SCIENCE↗

A simple introduction to the SiMPL method for density-based topology optimization

We introduce a novel method for solving density-based topology optimization problems: Sigmoidal Mirror descent with a Projected Latent variable (SiMPL). The SiMPL method (pronounced as “the simple method”) optimizes a design using only first-order derivative information of the objective function. The bound constraints on the density field are enforced with the help of the (negative) Fermi–Dirac entropy, which is also used to define a non-symmetric distance function called a Bregman divergence on the set of admissible designs. This Bregman divergence leads to a simple update rule that is further simplified with the help of a so-called latent variable. Because the SiMPL method involves discretizing the latent variable, it produces a sequence of pointwise-feasible iterates, even when high-order finite elements are used in the discretization. Numerical experiments demonstrate that the method outperforms other popular first-order optimization algorithms. In conclusion, to outline the general applicability of the technique, we include examples with (self-load) compliance minimization and compliant mechanism optimization problems.

Calculus of Variations and Optimization↗

On-Demand Selection of the Latent Domain Orientation in Spray-Deposited Block Copolymer Thin Films

With their ability to self-assemble spontaneously into well-defined nanoscale morphologies, block copolymer (BCP) thin films are a versatile platform to fabricate functional nanomaterials. An important challenge to wider deployment of BCPs in nanofabrication is combining precise control over the nanoscale domain orientation in BCP assemblies with scalable deposition techniques that are applicable to large-area, curved, and flexible substrates. Here, in this study, we show that spray-deposited smooth films of a nominally disordered BCP exhibit latent orientations, which can be prescriptively selected by controlling solvent evaporation during spray casting. Subsequent solvent vapor annealing triggers assembly toward highly ordered cylindrical morphologies along the pathway determined by solvent evaporation in the prior spray deposition stage. Faster evaporation promotes assembly of vertically oriented cylinders spanning the entire film thickness (100–300 nm). In comparison, slow solvent evaporation permits intermicellar aggregation and incipient cylinder formation in solution, which induces horizontal cylinder assembly upon annealing. The evaporatively controlled latent orientation mechanism presented herein elucidates how nonequilibrium phenomena during casting govern successive self-assembly pathways and facilitates a versatile method to dictate the domain orientation of BCP thin films on demand on flexible and highly curved substrates or in distinct pattern areas on the same substrate.

36 MATERIALS SCIENCE↗

Enhanced extreme ultraviolet high-harmonic generation from chromium-doped magnesium oxide

High-order harmonic generation (HHG) from crystals is emerging as a new ultrashort source of coherent extreme ultraviolet (XUV) light. Doping the crystal structure can offer a new way to control the source properties. Here, we present a study of HHG enhancement in the XUV spectral region from an ionic crystal, using dopant-induced vacancy defects, driven by a laser centered at a wavelength of 1.55 μm. Our numerical simulations based on solutions of the semiconductor Bloch equations and density-functional theory are supported by our experimental observations and demonstrate an increase in the XUV high harmonic yield from doped bulk magnesium oxide (MgO) compared to undoped MgO, even at a low defect concentration. The anisotropy of the harmonic emission as a function of the laser polarization shows that the pristine crystal's symmetry is preserved. Our study paves the way toward the control of HHG in solids with complex defects caused by transition-metal doping.

36 MATERIALS SCIENCE↗

Global geodesic acoustic mode in an ideal magnetohydrodynamic tokamak plasma

A concise and transparent second order ordinary differential equation (ODE) describing the radial structure of the global geodesic acoustic mode (GAM) is analytically presented in a low-β tokamak plasma. The large-aspect-ratio and circular cross section are assumed to linearize the ideal magnetohydrodynamic equations. We show clearly how finite β-dependent terms affect the global GAM frequency and radial mode structure. Here, a typical Wentzel–Kramers–Brillouin form of solution is found for some reversed shear equilibria. For some other equilibria with lower β, even also in a reversed shear tokamak, the GAM continuum is upraised by the high order β-dependent terms so that its maximum is beyond ω G , where ω G is the classical local frequency of GAM. As a result, no self-consistent solution to the ODE can be found.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DIF3D-VARIANT 12.0: Updates and New Features

The DIF3D code has been a workhorse of fast reactor analysis work at Argonne National Laboratory for over 40 years. In 1995, a transport option called VARIANT was added to DIF3D to improve the flux solutions for fast reactor problems which we term DIF3D-VARIANT today. DIF3D-VARIANT performs nodal neutron transport calculations using P N or SP N theory in Cartesian and hexagonal two- and three-dimensional geometries. The limited computing capabilities of the time restricted DIF3D-VARIANT to use at most a 6 th order spatial approximation combined with a P3 flux approximation and P1 scattering kernel for a 33 group structure on most studied reactor problems. Computer capabilities have increased steadily since 1995 and today much larger space-angle-energy approximations are possible. This manuscript serves as an update to the theory section of the original DIF3D-VARIANT manual and details more than twenty years of changes made to DIF3D to make version 12 which was released on November 1 st , 2024. The primary focus of the initial work was to extend the space-angle approximations available in DIF3D-VARIANT such that the error due to transport approximations could be better understood. This work was started and completed in 2002 and marked the official version 10. Unfortunately, those higher order approximations could not be used at that time due to the memory constraints of the BPOINTER part of DIF3D (limited to 2 GB). In version 11, completed in 2012, BPOINTER was circumvented in DIF3D-VARIANT for the largest arrays by introducing a Fortran 90 module called LMA (Large Memory Array). This seamlessly replaces all of the functionality of the BPOINTER concept, but it allows 64 bit addressing for every array such that they can be larger than 2 GB. It is now common for DIF3D-VARIANT jobs to consume 50 GB of memory on modern workstations when using high order space-angle approximations and a large number of groups. Many improvements were made to version 11 from 2012 to 2022 when work to create version 12 started. For version 12, several parts of DIF3D were updated to improve performance and thread parallelism was introduced to further reduce the runtime. Numerous minor bugs were discovered in DIF3D-VARIANT as part of the process of creating the perturbation and sensitivity code PERSENT. All of these algorithmic problems were identified in the transition from version 10 to version 11 which prevented DIF3D-VARIANT from running efficiently and reliably. Firstly, the coarse mesh rebalance scheme would routinely diverge and a study detailed in this report demonstrates how it was also typically not effective. This is not a failure of the coarse mesh rebalance methodology, but a failure of its implementation in DIF3D-VARIANT for hexagonal geometries. The fission source extrapolation algorithm was also found to be unreliable on larger group structure problems, leading to divergence in some cases and a negligible improvement in performance overall. Finally, the “Omega” acceleration applied to the partial current solver routine of DIF3D-VARIANT was found to cause DIF3D-VARIANT to converge to the wrong answer. To resolve these issues, both the coarse mesh rebalance and fission source extrapolation were permanently disabled in version 11. The Tchebychev acceleration was put in as a temporary reliable alternative but it is generally inferior to coarse mesh rebalance or coarse mesh finite difference. For the Omega acceleration, the factor was restricted to guarantee that it would not cause follow-on errors in PERSENT. Due to limited funding to support maintenance and development of DIF3D in the last 10 years, no effort was spent since to resolve the outer iteration acceleration. Except for the threading work, all of the changes discussed in this manuscript refer to changes made between version 10 and version 11. Performance comparisons are done to demonstrate the improvements from version 9 to version 12. As will be demonstrated, the updated versi

22 GENERAL STUDIES OF NUCLEAR REACTORS↗