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At least 1,153 records · Page 64

A nearsighted force-training approach to systematically generate training data for the machine learning of large atomic structures

A challenge of atomistic machine-learning (ML) methods is ensuring that the training data are suitable for the system being simulated, which is particularly challenging for systems with large numbers of atoms. Most atomistic ML approaches rely on the nearsightedness principle (“all chemistry is local”), using information about the position of an atom’s neighbors to predict a per-atom energy. Here, in this work, we develop a framework that exploits the nearsighted nature of ML models to systematically produce an appropriate training set for large structures. We use a per-atom uncertainty estimate to identify the most uncertain atoms and extract chunks centered around these atoms. It is crucial that these small chunks are both large enough to satisfy the ML’s nearsighted principle (that is, filling the cutoff radius) and are large enough to be converged with respect to the electronic structure calculation. We present data indicating when the electronic structure calculations are converged with respect to the structure size, which fundamentally limits the accuracy of any nearsighted ML calculator. These new atomic chunks are calculated in electronic structures, and crucially, only a single force—that of the central atom—is added to the growing training set, preventing the noisy and irrelevant information from the piece’s boundary from interfering with ML training. The resulting ML potentials are robust, despite requiring single-point calculations on only small reference structures and never seeing large training structures. We demonstrated our approach via structure optimization of a 260-atom structure and extended the approach to clusters with up to 1415 atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning-based quasi-continuum theory for structure of confined fluids

Predicting the structural properties of water and simple fluids confined in nanometer scale pores and channels is essential in, for example, energy storage and biomolecular systems. Classical continuum theories fail to accurately capture the interfacial structure of fluids. In this work, we develop a deep learning-based quasi-continuum theory (DL-QT) to predict the concentration and potential profiles of a Lennard-Jones (LJ) fluid and water confined in a nanochannel. The deep learning model is built based on a convolutional encoder–decoder network (CED) and is applied for high-dimensional surrogate modeling to relate the fluid properties to the fluid–fluid potential. The CED model is then combined with the interatomic potential-based continuum theory to determine the concentration profiles of a confined LJ fluid and confined water. Further, we show that the DL-QT model exhibits robust predictive performance for a confined LJ fluid under various thermodynamic states and for water confined in a nanochannel of different widths. The DL-QT model seamlessly connects molecular physics at the nanoscale with continuum theory by using a deep learning model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

JCZ3: An Equation of State Based on the Exponential-Six Intermolecular Potential – Update: Formulation

This report presents a comprehensive analysis of the JCZ3 equation of state (EOS) as implemented in the TIGER code, focusing on its thermodynamic framework, mathematical formulations, and implications for modeling gas phase behavior under varying conditions. Overall, the report affirms the TIGER code's foundational robustness and its potential as a valuable tool for simulating high-pressure, high-temperature gas mixtures, while also highlighting areas for further refinement and validation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms

Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk–benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal.

59 BASIC BIOLOGICAL SCIENCES↗

HIDRA-MAT liquid metal droplet injector for liquid metal applications in HIDRA

A liquid metal droplet injector was explicitly designed for the Hybrid Illinois Device for Research and Applications Material Analysis Test-stand (HIDRA-MAT) at the University of Illinois Urbana-Champaign to prepare liquid metal plasma-facing components (PFCs) for plasma exposure. The design goals were to create a compact, reliable, and robust design that could apply liquid metal droplets in-vacuo to a variety of samples. The injector was designed for liquid metal use, and results discussed pertain to lithium. The injector can produce lithium droplets of consistent size by utilizing programmable piston movement. Here, droplet formation data is presented for four different piston step sizes (0.125 mm, 0.25 mm, 0.5 mm, and 1 mm) at three different nozzle temperatures (185 °C, 230 °C, and 270 °C). Droplets are formed on the injector nozzle tip and a linear shift mechanism vertically translates the droplet to the substrate for application. This design prevents the droplet from inadvertently detaching off the nozzle and falling to the sample. Application of the liquid metal droplet ensures placement consistency on the substrate and helps avoid damage to components in HIDRA-MAT that should not interact with liquid metals. A description of the liquid lithium droplet creation and application results is given and provides additional insight into the cooling and oxidation of lithium droplets under vacuum conditions. A second nozzle was fabricated and demonstrated repeatability in droplet diameter creation having a variance of ±0.14 mm for droplets created from the same number of piston steps. The end-use for the injector on HIDRA-MAT is to apply liquid metals to PFCs and expose them to HIDRA's plasma with subsequent intershot in-vacuo surface analysis in HIDRA-MAT for plasma-material interaction studies.

42 ENGINEERING↗

Laser-Modulation-Driven X-Ray Pulse Shaping in Regenerative Amplifier Free-Electron Lasers

In this Letter, we present a robust method for generating custom-shaped, coherent hard x-ray pulses in regenerative amplifier free-electron lasers (RAFELs) using laser-induced energy modulation of the electron beam. A temporally shaped optical modulation imprints an optical-wavelength energy pattern on the beam, which interacts with the recirculated seed in the x-ray cavity to generate spectral sidebands. These sidebands lie outside the Bragg reflection bandwidth and are extracted as out-coupled radiation, while the seed is retained for continued amplification, enabling a novel mechanism for both output coupling and pulse shaping. Furthermore, this approach allows deterministic control over the spectral and temporal properties of the emitted x-rays, including multicolor generation, twin-pulse structures, pulse duration tuning, and complex temporal waveforms. Importantly, it does not require modification of the RAFEL cavity or optics and is fully compatible with high-repetition-rate operation, offering a practical pathway to deliver coherent, shaped, and on-demand x-ray pulses for advanced time-resolved and nonlinear x-ray science.

Free-electron lasers↗

SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesis

Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. This cooperative binding establishes a shared SOX2-VSX2 transcriptional code that promotes the expression of crucial regulators of neurogenesis while repressing the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural identity.

Chromatin↗

Monte Carlo simulation of order-disorder transition in refractory high entropy alloys: A data-driven approach

High entropy alloys (HEAs) are a series of novel materials that demonstrate many exceptional mechanical properties. To understand the origin of these attractive properties, it is important to investigate the thermodynamics and elucidate the evolution of various chemical phases. In this work, we introduce a machine learning approach to construct the effective Hamiltonian and study the thermodynamics of HEAs through canonical Monte Carlo simulation. The main characteristic of our method is to use pairwise interactions between atoms as the machine learning features and systematically improve the representativeness of the dataset using active learning from the Monte Carlo samples. We find this method produces highly robust and accurate effective Hamiltonians that give less than 0.1 mRy test error for all the three refractory HEAs: MoNbTaW, MoNbTaVW, and MoNbTaTiW. Using replica exchange to speed up the MC simulation, we calculated the specific heats and short-range order parameters in a wide range of temperatures. For all the studied materials, we find there are two major order-disorder transitions occurring respectively at T 1 and T 2 , where T 1 is near room temperature but T 2 is much higher. Further, we demonstrate that the transition at T 1 is caused by W and Nb while the one at T 2 is caused by the other elements. By comparing with experiments, the results demonstrate that the order-disorder transitions have a profound impact on the strength and ductility of HEAs.

36 MATERIALS SCIENCE↗

Fragile Topology and Flat-Band Superconductivity in the Strong-Coupling Regime

In flat bands, superconductivity can lead to surprising transport effects. The superfluid “mobility”, in the form of the superfluid weight D s , does not draw from the curvature of the band but has a purely band-geometric origin. In a mean-field description, a nonzero Chern number or fragile topology sets a lower bound for D s , which, via the Berezinskii-Kosterlitz-Thouless mechanism, might explain the relatively high superconducting transition temperature measured in magic-angle twisted bilayer graphene (MATBG). For fragile topology, relevant for the bilayer system, the fate of this bound for finite temperature and beyond the mean-field approximation remained, however, unclear. Here, we numerically use exact Monte Carlo simulations to study an attractive Hubbard model in flat bands with topological properties akin to those of MATBG. We find a superconducting phase transition with a critical temperature that scales linearly with the interaction strength. Then, we investigate the robustness of the superconducting state to the addition of trivial bands that may or may not trivialize the fragile topology. Our results substantiate the validity of the topological bound beyond the mean-field regime and further stress the importance of fragile topology for flat-band superconductivity.

2-dimensional systems↗

Sierra/SolidMechanics 4.56.2 User's Guide

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes . This document describes the functionality and input syntax for Sierra/SM.

97 MATHEMATICS AND COMPUTING↗

Sierra/SolidMechanics 5.0 User's Guide

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.

97 MATHEMATICS AND COMPUTING↗

Sierra/SolidMechanics 5.2 User's Guide

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.

97 MATHEMATICS AND COMPUTING↗

Sierra/SolidMechanics 5.4 User's Guide

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.

74 ATOMIC AND MOLECULAR PHYSICS↗

Sierra/SolidMechanics 5.8 User's Manual

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.

42 ENGINEERING↗

Sierra/SolidMechanics 5.10 User's Guide

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutions of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.

42 ENGINEERING↗

Initial Development of Fusion Magnet Simulation Capabilities for Performance and Safety Evaluation Using the MOOSE Framework

Fusion energy holds the promise of being a transformative technology as a carbon-neutral, sustainable source of energy. Whole device modeling and the development of fusion digital twins will be increasingly important for emerging fusion device concepts at both national laboratories and within the commercial fusion industry. However, meeting the challenge of whole device modeling of fusion energy devices requires robust, multiphysics, multiscale modeling and simulation technologies capable of running on large-scale supercomputers. Detailed analysis of individual systems at-scale is also required to ensure safe and efficient operation as well as provide the safety basis for future device designs and licensing activities. In a tokamak, toroidal and poloidal magnets confine and shape the fusion plasma to promote the fusion reaction. High plasma temperatures and high magnetic field requirements in modern design concepts (leading to high amounts of energy stored within each magnet) impose electrical, thermal, and mechanical loads on the magnet components, which in turn impacts the safety considerations of the magnet and their supporting systems. Idaho National Laboratory (INL) has a history of working in this space, including development and benchmarking of the Magnetic System Circuitry Analysis Program (MSCAP) and Magnet Arcing (MAGARC) codes to study magnet quench events; notably, MAGARC was used to study quenching during the ITER Engineering Design Activity. However, these legacy codes and capabilities are not parallel and scalable, and new tools are required for future advances in this area, which leads to the INL-developed Multiphysics Object-Oriented Simulation Environment (MOOSE) framework. Developed originally for fission reactor systems under United States Department of Energy, Office of Nuclear Energy modeling and simulation programs, the MOOSE framework has been well-suited to multiscale, multiphysics modeling and simulation needs for nuclear systems. The framework is open-source, well-tested, under continuous development and deployment, and developed to a Nuclear Quality Assurance, Level 1 software quality standard. MOOSE has also been used in the fusion space previously in several projects: INL’s Tritium Migration Analysis Program, Version 8 (TMAP8) for tritium migration, UK Atomic Energy Authority’s A Unified Resource for OpenMC (fusion) Reactor Applications (AURORA) code for fusion thermo-mechanical and neutronics analysis, and Argonne National Laboratory’s Cardinal for high-fidelity computational fluid dynamics and neutronics. However, to model superconducting magnets, several MOOSE enhancements are required: additions to the current MOOSE electromagnetic capabilities, new material libraries for superconductors of interest (such as YBCO), as well as fusion-specific models for thermo-mechanics. This talk will discuss initial development activities to build these capabilities in MOOSE, focusing on initial validation and benchmarking activities. Proposed coupling workflows and future work to support the simulation of fusion magnets and magnet structural assemblies for performance and safety evaluation in MOOSE will also be discussed.

70 - PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High‐Capacity Splitting of Mono‐ and Dibranched Hexane Isomers by a Robust Zinc‐Based Metal–Organic Framework

Abstract High‐efficiency separation of C 6 alkanes, particularly the mono‐ and dibranched isomers by using porous solids, is of paramount significance in the petrochemical industry and, remains a daunting challenge. In this work, we report the complete separation of linear/monobranched hexanes from their dibranched isomers through selective size‐exclusion by a microporous MOF, Zn‐tcpt (H 3 tcpt=2,4,6‐tris(4‐carboxyphenoxy)‐1,3,5‐triazine), with a two‐fold interpenetrated structure of hms nets. Importantly, its adsorption capacity and selectivity are notably higher than those of the previously reported adsorbents that can split mono‐ and dibranched alkane isomers. Dynamic breakthrough measurements verify the excellent separation of C 6 alkane isomers by Zn‐tcpt, and the size‐exclusion based separation mechanism has been confirmed by ab initio materials modeling. The high‐efficiency separation of alkane isomers by Zn‐tcpt can be attributed to its optimal pore dimensions as well as high porosity.

Yu, Liang↗

Entropy Stable Conservative Flux Form Neural Networks

We propose an entropy-stable conservative flux form neural network (CFN) to predict the dynamics of unknown governing conservation laws. The design of the network is based on the entropy-stable, second-order, and non-oscillatory Kurganov-Tadmor (KT) scheme. The proposed entropy-stable CFN, hereafter referred to as ESCFN, uses slope limiting as a denoising mechanism, ensuring accurate predictions in both noisy and sparse observation environments, as well as in both smooth and discontinuous regions. Importantly, our method is designed to predict long term dynamics of the unknown conservation law exclusively from a short temporal window of observed data, that is, without oracle knowledge of the PDE or later-time solution profiles. Numerical experiments demonstrate that the ESCFN achieves both stability and conservation while maintaining accuracy over extended time domains, and successfully predicts shock propagation speeds in long-term simulations. Furthermore, it is also robust to both noisy and sparse data environments.

Hyperbolic conservation laws↗