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At least 253 records · Page 14

Autonomous hybrid optimization of a SiO 2 plasma etching mechanism

Computational modeling of plasma etching processes at the feature scale relevant to the fabrication of nanometer semiconductor devices is critically dependent on the reaction mechanism representing the physical processes occurring between plasma produced reactant fluxes and the surface, reaction probabilities, yields, rate coefficients, and threshold energies that characterize these processes. The increasing complexity of the structures being fabricated, new materials, and novel gas mixtures increase the complexity of the reaction mechanism used in feature scale models and increase the difficulty in developing the fundamental data required for the mechanism. This challenge is further exacerbated by the fact that acquiring these fundamental data through more complex computational models or experiments is often limited by cost, technical complexity, or inadequate models. In this paper, we discuss a method to automate the selection of fundamental data in a reduced reaction mechanism for feature scale plasma etching of SiO 2 using a fluorocarbon gas mixture by matching predictions of etch profiles to experimental data using a gradient descent (GD)/Nelder–Mead (NM) method hybrid optimization scheme. These methods produce a reaction mechanism that replicates the experimental training data as well as experimental data using related but different etch processes.

36 MATERIALS SCIENCE↗

Experimental and computational analysis of bending fatigue failure in chopped carbon fiber chip reinforced composites

With a better balance among good mechanical performance, high freedom of design, and low material and manufacturing cost, chopped carbon fiber chip reinforced sheet molding compound (SMC) composites show great potential in different engineering applications. Here in this paper, bending fatigue behaviors of SMC composites considering the heterogeneous fiber orientation distributions have been thoroughly investigated utilizing both experimental and computational methods. First, four-point bending fatigue tests are performed with designed SMC composites, and the local modulus is adopted as a metric to represent the local fiber orientation of two opposing sides. Interestingly, SMC composites with and without large discrepancy in local modulus of opposing sides show different fatigue behaviors. Interrupted tests are conducted to explore the bending fatigue failure mechanism, and the damage processes of valid specimens are also closely examined. We find that the fatigue failure of SMC composites under four-point bending is governed by crack propagation instead of crack initiation. Because of this, the heterogeneous local fiber orientations of both sides of the specimen influence fatigue life. The microstructure of the lower side shows a direct influence while that of the upper side also exhibiting influence which becomes more prominent for high cycle fatigue cases. Furthermore, a hybrid micro–macro computational model is proposed to efficiently study the cyclic bending behavior of SMC composites. The region of interest is reconstructed with a modified random sequential absorption algorithm to conserve all the microstructural details including the heterogeneous fiber orientation, while the rest of the regions are modeled as homogenized macro-scale continua. Combined with a framework to capture the progressive fatigue damage under cyclic bending, the bending fatigue behaviors of SMC composites are accurately captured by the hybrid computational model comparing with our experimental analysis.

36 MATERIALS SCIENCE↗

Assessment of Sodium Thermal Stratification Models Utilizing the TSTF Benchmark

As a result of certain transient scenarios, a thermally stratified layer of liquid sodium can develop in the bulk coolant volumes of a sodium-cooled fast reactor (SFR). In addition to the effects a stratification layer has on the temperature of the heat transport system, a stratification layer can also influence the transition to and establishment of natural circulation flow, which plays an important role in passive cooling and the inherent safety of a pool-type SFR. Therefore, the ability to accurately capture thermal stratification phenomena is important when demonstrating the safety basis of a pool-type SFR during transient sequences. The present work assesses various computational models with different fidelities in their ability to predict thermal stratification in the upper plenum of an SFR. Each computational model will be assessed using the data generated at the Thermal Stratification Test Facility (TSTF) located at the University of Wisconsin-Madison. Using measured flow rate and inlet temperature data, the measured temperature distributions of the tests are compared to the predictions of the lumped volume-based models in SAS4A/SASSYS-1, a 1D-based model in SAM, and a 3-D computational fluid dynamics (CFD) model using STAR-CCM+. The relative performance of the various computational methods is assessed with respect to key metrics such as bulk coolant temperature distribution and plenum exit temperature. A total of eight tests are analyzed, covering different combinations of flow rates (3 and 10 GPM) and upper internal structure (UIS) configurations (none, solid, porous, and open) The perfect mixing model of SAS4A/SASSYS-1 provides the highest accuracy when the flow rate is high and there is no UIS in the test vessel, as high flow rate injection promotes thermal mixing of the sodium in the test vessel. For most of the analyzed tests, the stratified volume model of SAS4A/SASSYS-1 is able to predict the delay in the outlet temperature drop and temperature distribution in the test vessel by a small number of layers to represent thermal stratification. However, the stratified volume model can only simulate a maximum of three temperature layers within a volume and when a layer approaches the elevation of the outlet, the predicted outlet temperature can demonstrate rapid, non-physical changes. The 1-D axial mixing model of SAM provides results that agree reasonably well with the measured data in the prediction of the temporal evolution of the outlet temperature with the exception of the case with a high flow rate and no UIS. The SAM 1-D model has a similar level of accuracy to CFD results when it comes to predicting the outlet temperature. CFD shows overall good agreement in predicting the temperature distribution in the test vessel and outlet temperature. As CFD can model the test vessel geometry in detail, it performs well in the cases of complex geometries such as tests that included a UIS and internal flow through the UIS resulting in active mixing of the coolant in the test vessel. Each of the models discussed in the present work has the potential to be useful during the various stages of reactor design, analysis, and licensing. The lumped-volume approach can be applied for fast turnaround safety calculations to obtain overall reactor behavior during transients. The 1-D models provide improved accuracy when stratification is expected for a relatively low increase in the computational cost. The CFD model can be utilized for confirmatory analysis of the 1-D model, when experimental measurements are not available.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Spatiotemporal predictions of toxic urban plumes using deep learning

Industrial accidents, chemical spills, and structural fires can release large amounts of harmful materials that disperse into urban atmospheres and impact populated areas. Computer models are typically used to predict the transport of toxic plumes by solving fluid dynamical equations. However, these models can be computationally expensive due to the need for many grid cells to simulate turbulent flow and resolve individual buildings and streets. In emergency response situations, alternative methods are needed that can run quickly and adequately capture important spatiotemporal features. Here, we present a novel deep learning model called ST-GasNet inspired by the mathematical equations that govern the behavior of plumes as they disperse through the atmosphere. ST-GasNet learns the spatiotemporal dependencies from a limited set of temporal sequences of ground-level toxic urban plumes generated by a high-resolution large eddy simulation model. On independent sequences, ST-GasNet accurately predicts the late-time spatiotemporal evolution, given the early-time behavior as an input, even when a building splits a large plume into smaller plumes. By incorporating large-scale wind boundary condition information, ST-GasNet achieves a prediction accuracy of at least 90% on test data for the entire prediction period.

Civil and Environmental Engineering↗

Tonal Emergence: An agent-based model of tonal coordination

Humans have a remarkable capacity for coordination. Our ability to interact and act jointly in groups is crucial to our success as a species. Joint Action (JA) research has often concerned itself with simplistic behaviors in highly constrained laboratory tasks. But there has been a growing interest in understanding complex coordination in more open-ended contexts. In this regard, collective music improvisation has emerged as a fascinating model domain for studying basic JA mechanisms in an unconstrained and highly sophisticated setting. A number of empirical studies have begun to elucidate coordination mechanisms underlying joint musical improvisation, but these empirical findings have yet to be cached out in a working computational model. The present work fills this gap by presenting TonalEmergence, an idealized agent-based model of improvised musical coordination. TonalEmergence models the coordination of notes played by improvisers to generate harmony (i.e., tonality), by simulating agents that stochastically generate notes biased towards maximizing harmonic consonance given their partner’s previous notes. Here, the model replicates an interesting empirical result from a previous study of professional jazz pianists: feedback loops of mutual adaptation between interacting agents support the production of consonant harmony. The model is further explored to show how complex tonal dynamics, such as the production and dissolution of stable tonal centers, are supported by agents that are characterized by (i) a tendency to strive toward consonance, (ii) stochasticity, and (iii) a limited memory for previously played notes. TonalEmergence thus provides a grounded computational model to simulate and probe the coordination mechanisms underpinning one of the more remarkable feats of human cognition: collective music improvisation.

60 APPLIED LIFE SCIENCES↗

Assessing Metal Ion Assignment Accuracy in Protein Data Bank Models via Elemental Spectroscopy

Accurate representation of metal ions in macromolecular structures is critical for chemical interpretation, computational modeling, and machine-learning methods that rely on Protein Data Bank (PDB) entries. However, the elemental identity of metals modeled in crystallographic structures is often inferred indirectly and rarely validated experimentally. Here, we combine Particle Induced X-ray Emission (PIXE) and X-ray Fluorescence Spectroscopy (XRFS) to determine the elemental composition of protein samples used to generate 70 deposited metalloprotein crystal structures. By analyzing the original protein material employed for crystallization, but before the addition of crystallization buffer solutions, we assess whether the modeled metal ions in deposited structures are consistent with experimentally detectable elemental content. We find that in a majority of cases, the metals modeled in the corresponding PDB entries are inconsistent with the metals present in the protein samples before crystallization, or that additional metals are present but not represented in the structural models. Spectroscopic results were integrated with automated crystallographic validation metrics, including real-space Z-difference (RSZD) analysis and systematic rerefinement, to evaluate atomic-number mismatch at metal sites. PIXE and XRFS show strong agreement for dominant elemental signals and provide complementary, scalable approaches for identifying suspect metal assignments. This work does not address physiological or functional metalation but instead highlights a widespread data integrity issue in deposited macromolecular structures, PDB-wide. These results establish an experimentally corroborated link between elemental identity and crystallographic validation metrics, enabling the large-scale detection of chemically inconsistent annotations in structural databases used for computational modeling and machine learning.

Crystallization↗

ADROC: An Emulation Experimentation Platform for Advancing Resilience of Control Systems

Cyberattacks against industrial control systems have increased over the last decade, making it more critical than ever for system owners to have the tools necessary to understand the cyber resilience of their systems. However, existing tools are often qualitative, subject matter expertise-driven, or highly generic, making thorough, data-driven cyber resilience analysis challenging. The ADROC project proposed to develop a platform to enable efficient, repeatable, data-driven cyber resilience analysis for cyber-physical systems. The approach consists of two phases of modeling: computationally efficient math modeling and high-fidelity emulations. The first phase allows for scenarios of low concern to be quickly filtered out, conserving resources available for analysis. The second phase supports more detailed scenario analysis, which is more predictive of real-world systems. Data extracted from experiments is used to calculate cyber resilience metrics. ADROC then ranks scenarios based on these metrics, enabling prioritization of system resources to improve cyber resilience.

97 MATHEMATICS AND COMPUTING↗

Excess free volume and structural properties of inert gas condensation synthesized nanoparticles based CuZr nanoglasses

Abstract Nanoglass (NG) as a new structure-tunable material has been investigated using both experiments and computational modeling. Experimentally, inert gas condensation (IGC) is commonly employed to prepare metallic glass (MG) nanoparticles that are consolidated using cold compression to generate an NG. In computational modeling, various methods have been used to generate NGs. However, due to the high computational cost involved, heretofore modeling investigations have not followed the experimental synthesis route. In this work, we use molecular dynamics simulations to generate an NG model by consolidating IGC-prepared Cu 64 Zr 36 nanoparticles following a workflow similar to that of experiments. The resulting structure is compared with those of NGs produced following two alternative procedures previously used: direct generation employing Voronoi tessellation and consolidation of spherical nanoparticles carved from an MG sample. We focus on the characterization of the excess free volume and the Voronoi polyhedral statistics in order to identify and quantify contrasting features of the glass-glass interfaces in the three NG samples prepared using distinct methods. Results indicate that glass-glass interfaces in IGC-based NGs are thicker and display higher structural contrast with their parent MG structure. Nanoparticle-based methods display excess free volume exceeding 4%, in agreement with experiments. IGC-prepared nanoparticles, which display Cu segregation to their surfaces, generate the highest glass-glass interface excess free volume levels and the largest relative interface volume with excess free volume higher than 3%. Voronoi polyhedral analysis indicates a sharp drop in the full icosahedral motif fraction in the glass-glass interfaces in nanoparticle-based NG as compared to their parent MG.

36 MATERIALS SCIENCE↗

A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase

Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI’s intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Grid-based minimization at scale: Feldman-Cousins corrections for light sterile neutrino search

High Energy Physics (HEP) experiments generally employ sophisticated statistical methods to present results in searches of new physics. In the problem of searching for sterile neutrinos, likelihood ratio tests are applied to short-baseline neutrino oscillation experiments to construct confidence intervals for the parameters of interest. The test statistics of the form Δχ2 is often used to form the confidence intervals, however, this approach can lead to statistical inaccuracies due to the small signal rate in the region-of-interest. In this paper, we present a computational model for the computationally expensive Feldman-Cousins corrections to construct a statistically accurate confidence interval for neutrino oscillation analysis. The program performs a grid-based minimization over oscillation parameters and is written in C++. Our algorithms make use of vectorization through Eigen3, yielding a single-core speed-up of 350 compared to the original implementation, and achieve MPI data parallelism by employing DIY. We demonstrate the strong scaling of the application at High-Performance Computing (HPC) sites. We utilize HDF5 along with HighFive to write the results of the calculation to file.

Wospakrik, Marianette↗

NeuroCoreX: Brain-Inspired Computing from Code to Circuit

NeuroCoreX is an open-source codebase that enables the implementation of brain-inspired, energy-efficient neuromorphic computing models on FPGA hardware. Designed to support real-time learning, all-to-all neural connectivity, and flexible network architectures, NeuroCoreX offers a hands-on, accessible platform for exploring biologically inspired models of neural computation. It empowers researchers, students, and developers to implement and experiment with adaptive systems—bringing the power of neuromorphic computing to a broader community through a low-cost, scalable, and reconfigurable framework.

Gautam, Ashish [Oak Ridge National Laboratory (ORN↗

A study of the Rayleigh-Taylor Instability during deceleration in inertial confinement fusion relevant conditions [Slides]

Large Planar targets with significant room for RTI evolution could have the potential to reach regimes where magnetic field damping of RTI is observable. Hot-electron generation at 1 PW/cm 2 and greater can introduced substantial preheat to experimental targets. Manufacturing defects can create further 3D complexity in targets designed and modeled in 2D. Computational models used in experimental designing do not always account for all the physics present and must be reevaluated based on experimental data. 3D modeling and provide high fidelity estimates on what the experimental data will look like, and can be utilized for high fidelity bench-marking or complex 3D experimental design work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Nuclear Data Adjustment for Nonlinear Applications in the OECD/NEA WPNCS SG14 Benchmark -- A Bayesian Inverse UQ-based Approach for Data Assimilation

The Organization for Economic Cooperation and Development (OECD) Working Party on Nuclear Criticality Safety (WPNCS) proposed a benchmark exercise to assess the performance of current nuclear data adjustment techniques applied to nonlinear applications and experiments with low correlation to applications. This work introduces Bayesian Inverse Uncertainty Quantification (IUQ) as a method for nuclear data adjustments in this benchmark, and compares IUQ to the more traditional methods of Generalized Linear Least Squares (GLLS) and Monte Carlo Bayes (MOCABA). Posterior predictions from IUQ showed agreement with GLLS and MOCABA for linear applications. When comparing GLLS, MOCABA, and IUQ posterior predictions to computed model responses using adjusted parameters, we observe that GLLS predictions fail to replicate computed response distributions for nonlinear applications, while MOCABA shows near agreement, and IUQ uses computed model responses directly. We also discuss observations on why experiments with low correlation to applications can be informative to nuclear data adjustments and identify some properties useful in selecting experiments for inclusion in nuclear data adjustment. Performance in this benchmark indicates potential for Bayesian IUQ in nuclear data adjustments.

FOS: Computer and information sciences↗

In-depth analysis of solar models with high-metallicity abundances and updated opacity tables

Context. As a result of the high-quality constraints available for the Sun, we are able to carry out detailed combined analyses using neutrino, spectroscopic, and helioseismic observations. These studies lay the ground for future improvements of the key physical components of solar and stellar models because ingredients such as the equation of state, the radiative opacities, or the prescriptions for macroscopic transport processes of chemicals are then used to study other stars in the Universe. Aims. We study the existing degeneracies in solar models using the recent high-metallicity spectroscopic abundances by comparing them to helioseismic and neutrino data and discuss the effect on their properties of changes in the micro and macro physical ingredients. Methods. We carried out a detailed study of solar models computed with a high-metallicity composition from the literature based on averaged 3D models that were claimed to resolve the solar modelling problem. We compared these models to helioseismic and neutrino constraints. Results. The properties of the solar models are significantly affected by the use of the recent OPLIB opacity tables and the inclusion of macroscopic transport. The properties of the standard solar models computed using the OPAL opacities are similar to those for which the OP opacities were used. We show that a modification of the temperature gradient just below the base of the convective zone is required to remove the discrepancies in solar models, particularly in the presence of macroscopic mixing. This can be simulated by a localised increase in the opacity of a few percent. Conclusions. We conclude that the existing degeneracies and issues in solar modelling are not removed by using an increase in the solar metallicity, in contradiction to what has been suggested in the recent literature. Therefore, standard solar models cannot be used as an argument for a high-metallicity composition. While further work is required to improve solar models, we note that direct helioseismic inversions indicate a low metallicity in the convective envelope, in agreement with spectroscopic analyses based on full 3D models.

74 ATOMIC AND MOLECULAR PHYSICS↗

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

BETO 2021 Peer Review - Advanced Catalyst Synthesis and Characterization (ACSC) Project WBS 2.5.4.304; 303; 305

The Advanced Catalyst Synthesis and Characterization (ACSC) project, in close collaboration with the Chemical Catalysis for Bioenergy (ChemCatBio) Consortium enabling projects, CatCost, and the Engineering of Catalyst Scale-Up project, (1) provides fundamental insight into working catalysts leading to actionable recommendations for all of the ChemCatBio catalysis projects, (2) addresses overarching catalysis challenges central to the ChemCatBio Consortium, and (3) adapts and applies new synthesis methodologies and in situ/operando characterization capabilities to meet the evolving needs of the catalysis projects. The outcome is a transition from empirical catalyst development to rational design through the prediction of materials with targeted properties based on advanced characterization combined with computational modeling, and the synthesis of next generation catalysts with predicted structures that yield demonstrated improvements in catalytic performance. In FY18, the ACSC helped to demonstrate the utility of the complete catalyst and process development cycle for dimethyl ether to high-octane gasoline over metal-modified zeolite catalysts for the Upgrading of C1 Building Blocks project, and in FY21 will leverage capabilities, expertise, and computational models established for this effort to target next-generation catalysts for ethanol to distillates for the Upgrading of C2 Intermediates project with enhanced performance in half the time.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Federated Access from DOE Labs to Distributed Storage in the EIC Era of Computing

The Electron Ion Collider (EIC) collaboration and future experiment is a unique scientific ecosystem within Nuclear Physics as the experiment starts right off as a crosscollaboration between Brookhaven National Lab (BNL) & Jefferson Lab (JLab). As a result, this muti-lab computing model tries at best to provide services accessible from anywhere by anyone who is part of the collaboration. While the computing model for the EIC is not finalized, it is anticipated that the computational and storage resources will be made accessible to a wide range of collaborators across the world. The use of federated ID seems to be a critical element to the strategy of providing such services, allowing seamless access to each lab site computing resources. However, providing Federated access to a Federated storage is not a trivial matter and has its share of technical challenges. In this contribution, we focus on the steps we took towards the deployment of a distributed object storage system that integrates with Amazon S3 and Federated ID. We will first cover for and explain the first stage storage solutions provided to the EIC during the detector design phase. Our initial test deployment consisted of Lustre storage using MinIO, hence providing an S3 interface. High Availability load balancers were added later to provide the initial scalability it lacked. Performance of that system will be shown. While this embryonic solution worked well, it had many limitations. Looking ahead, the Ceph object storage is considered a top-of-the-line solution in the storage community - since the Ceph Object Gateway is compatible with the Amazon S3 API out of the box, our next phase will use a native S3 storage. Our Ceph deployment will consist of erasure coded storage nodes to maximize storage potential along with multiple Ceph Object Gateways for redundant access. We will compare performance of our next stage implementations. Finally, we will present how to leverage OpenID Connect with the Ceph Object Gateway’s to enable Federated ID access. We hope this contribution will serve the community needs as we move forward with cross-lab collaborations and the need for Federated ID access to distributed compute facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

High frequency impedance characteristics of a tunable microplasma device

Computational studies on high frequency impedance characteristics of a microplasma device are reported. While microplasma is ignited using a primary excitation signal, frequency response of plasma impedance is determined by a secondary high frequency probe signal with significantly lower voltage amplitude such that it does not influence the plasma parameters. Here, the computational model utilizing the drift–diffusion approximation is first validated by comparing with experimental data for microplasmas ignited at pressures ranging from 1 to 5 Torr. In spite of quantitative discrepancies, good overall agreement is obtained between the measured frequency response of impedance of the discharge. Comparisons are also presented for various plasma parameters including mean electron number density, sheath thickness, mean electron temperature, and collision frequency that were inferred from the impedance measurements. The computational model is then used to perform simulations of near-atmospheric pressure microplasmas with the probe signal frequency ranging from 3 to 20 GHz. The simulations demonstrate the presence of a resonance frequency at which the impedance vanishes. More importantly, it is shown that this resonant frequency can be tuned effectively by suitably modifying the operating parameters (gap size, pressure, and excitation voltage). The simulated impedance characteristics are used to determine the effective plasma inductance and capacitance using a non-linear fitting approach, thereby showing the dependence of these electrical parameters on the plasma operating conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗