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At least 883 records · Page 49

Atomate2: modular workflows for materials science

High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science.

97 MATHEMATICS AND COMPUTING↗

Persistent Classification: Understanding Adversarial Attacks by Studying Decision Boundary Dynamics

ABSTRACT There are a number of hypotheses underlying the existence of adversarial examples for classification problems. These include the high‐dimensionality of the data, the high codimension in the ambient space of the data manifolds of interest, and that the structure of machine learning models may encourage classifiers to develop decision boundaries close to data points. This article proposes a new framework for studying adversarial examples that does not depend directly on the distance to the decision boundary. Similarly to the smoothed classifier literature, we define a (natural or adversarial) data point to be ( γ , σ)‐stable if the probability of the same classification is at least for points sampled in a Gaussian neighborhood of the point with a given standard deviation . We focus on studying the differences between persistence metrics along interpolants of natural and adversarial points. We show that adversarial examples have significantly lower persistence than natural examples for large neural networks in the context of the MNIST and ImageNet datasets. We connect this lack of persistence with decision boundary geometry by measuring angles of interpolants with respect to decision boundaries. Finally, we connect this approach with robustness by developing a manifold alignment gradient metric and demonstrating the increase in robustness that can be achieved when training with the addition of this metric.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fusion Blanket and Fuel Cycle Research at PNNL: FY22 Year-end Report

During the reporting period, research at PNNL focused on two tasks within the DOE Fusion Blanket and Fuel Cycle Program. Research on Task 1, Tritium Extraction from Pb-Li and He Using a Vacuum Permeator, focused on atomistic modeling to better understand tritium transport in Pd-coated V vacuum permeators. As a lower cost alternative to Pd permeators, thin coatings of Pd (or other noble metals) can be deposited over a substrate like V. However, the permeation performance of composite metal membranes degrades over time, due to the formation of intermetallics at the coating-substrate interface. Computational studies were performed to better understand tritium transport through these Pd-V intermetallics. The results of the FY22 Pd-V modeling study were recently submitted for publication in Computational Materials Science and presented at the Technology of Fusion Energy conference. Future work in this area will focus on interdiffusion barriers to prevent intermetallic formation that is deleterious to tritium transport. There are opportunities for collaboration with researchers at the Colorado School of Mines, who are manufacturing and testing candidate interdiffusion barriers. Research on Task 3, Solid Breeder Materials, included ion irradiation and post-irradiation characterization of lithium orthosilicate (Li 4 SiO 4 ) and lithium metasilicate (Li 2 SiO 3 ) to improve fundamental understanding of irradiation effects, in combination with atomistic modeling focused on the energetics of He clustering in these two ceramic phases. The results of the study suggested that the Li 4 SiO 4 phase, which is more desirable as a solid breeder due to its higher Li density, was amorphized during ion irradiation while the Li 2 SiO 3 phase appeared to be more resistant to irradiation damage. It is possible that Li loss contributed to the poor irradiation performance of the Li 4 SiO 4 , and some thoughts are provided regarding coatings that could be applied to solid breeders like this to prevent Li loss at elevated temperature while not hindering tritium diffusion. The results of the FY22 ion irradiation study were recently submitted for publication in Journal of Nuclear Materials and presented at the 22nd International Conference on Ion Beam Modification of Materials. Future work in this area will focus on Li-rich ceramics such as Li 5 AlO 4 and Li 8 ZrO 6 that have high Li density and should provide rapid tritium release based on previous work with less Li-rich ceramics.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Performance analysis and data reduction for exascale scientific workflows

Chimbuko is the first in situ, scalable, workflow-level performance analysis tool for trace-level analysis and visualization of application performance. This tool was developed by the Co-design Center for Online Data Analysis and Reduction and funded by the U.S. Department of Energy’s Exascale Computing Project. We provide a detailed description of Chimbuko’s architecture and illustrate our online and offline visualization with multiple use cases. We also present results for the deployment and scalability of the tool as applied to a high-energy physics workflow running at large scale on the Frontier supercomputer.

97 MATHEMATICS AND COMPUTING↗

Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport

Nuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargoes, including preribosomes and viral capsids. Our model quantifies how flexible phenylalanine-glycine (FG) repeat proteins create an entropic barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by “fuzzy” multivalent interactions, redundant FG repeat mass, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.

Raveh, Barak [School of Computer Science and Engin↗

Data-Conforming Data-Driven Control: Avoiding Premature Generalizations Beyond Data

Data-driven and adaptive control approaches face the problem of introducing sudden distributional shifts beyond the distribution of data encountered during learning. Therefore, they are prone to invalidating the very assumptions used in their own construction. This is due to the linearity of the underlying system, inherently assumed and formulated in most data-driven control approaches, which may falsely generalize the behavior of the system beyond the behavior experienced in the data. This article seeks to mitigate these problems by enforcing consistency of the newly designed closed-loop systems with data and slowing down any distributional shifts in the joint state-input space. This is achieved through incorporating affine regularization terms and linear matrix inequality constraints to data-driven approaches, resulting in convex semi-definite programs that can be efficiently solved by standard software packages. We discuss the optimality conditions of these programs and then conclude this article with a numerical example that further highlights the problem of premature generalization beyond data and shows the effectiveness of our proposed approaches in enhancing the safety of data-driven control methods.

97 MATHEMATICS AND COMPUTING↗

High End Computing Technologies for Earth Science Applications: Trends, Challenges, and Innovations

Earth science applications of the future will stress the capabilities of even the highest performance supercomputers in the areas of raw compute power, mass storage management, and software environments. These NASA mission critical problems demand usable multi-petaflops and exabyte-scale systems to fully realize their science goals. With an exciting vision of the technologies needed, NASA has established a comprehensive program of advanced research in computer architecture, software tools, and device technology to ensure that, in partnership with US industry, it can meet these demanding requirements with reliable, cost effective, and usable ultra-scale systems. NASA will exploit, explore, and influence emerging high end computing architectures and technologies to accelerate the next generation of engineering, operations, and discovery processes for NASA Enterprises. This article captures this vision and describes the concepts, accomplishments, and the potential payoff of the key thrusts that will help meet the computational challenges in Earth science applications.

Parks, John↗

Efficient Client Selection in Federated Learning

Federated Learning (FL) enables decentralized machine learning while preserving data privacy. This paper proposes a novel client selection framework that integrates differential privacy and fault tolerance. The adaptive client selection adjusts the number of clients based on performance and system constraints, with noise added to protect privacy. Evaluated on the UNSW-NB15 and ROAD datasets for network anomaly detection, the method improves accuracy by 7% and reduces training time by 25 % compared to baselines. Fault tolerance enhances robustness with minimal performance trade-offs.

Marfo, William [University of Texas at El Paso,Dep↗

Adaptive Client Selection in Federated Learning: A Network Anomaly Detection Use Case

Federated Learning (FL) has become a ubiquitous approach for training machine learning models on decentralized data, addressing the myriad privacy concerns inherent in traditional centralized methods. However, the efficiency of FL depends on effective client selection and robust privacy preservation mechanisms. Inadequate client selection may lead to suboptimal model performance, while insufficient privacy measures risk exposing sensitive data. This paper proposes a client selection framework for FL that integrates differential privacy and fault tolerance. Our adaptive approach dynamically adjusts the number of selected clients based on model performance and system constraints, ensuring privacy through calibrated noise addition. We evaluate our method on a network anomaly detection use case using the UNSW-NB15 and ROAD datasets. Results show up to a 7% increase in accuracy and a 25% reduction in training time compared to FedL2P. Moreover, we highlight the trade-offs between privacy budgets and model performance, with higher privacy budgets reducing noise and improving accuracy. Our fault tolerance mechanism, while causing a slight performance drop, enhances robustness to client failures. Statistical validation using Mann-Whitney U tests confirms the significance of these improvements (p < 0.05).

Marfo, William [University of Texas at El Paso,Dep↗

Federated Learning for Efficient Condition Monitoring and Anomaly Detection in Industrial Cyber-Physical Systems

Detecting and localizing anomalies in cyber-physical systems (CPS) has become increasingly challenging as systems grow in complexity, particularly due to varying sensor reliability and node failures in distributed environments. While federated learning (FL) offers a foundation for distributed model training, existing approaches lack mechanisms to handle these CPS-specific challenges. This paper presents an enhanced FL framework that introduces three key innovations: adaptive model aggregation based on sensor reliability, dynamic node selection for resource optimization, and Weibull-based checkpointing for fault tolerance. Our framework enables reliable condition monitoring while addressing the computational and reliability challenges of industrial CPS deployments. Experiments on NASA Bearing and Hydraulic System Datasets demonstrate superior performance over state-of-the-art FL methods, achieving 99.5% AUC-ROC in anomaly detection and maintaining accuracy under node failures. Statistical validation using Mann-Whitney (U) test confirms significant improvements (p < 0.05) in both detection accuracy and computational efficiency across diverse operational scenarios.1

Marfo, William [University of Texas at El Paso,Dep↗

CSM research: Methods and application studies

Computational mechanics is that discipline of applied science and engineering devoted to the study of physical phenomena by means of computational methods based on mathematical modeling and simulation, utilizing digital computers. The discipline combines theoretical and applied mechanics, approximation theory, numerical analysis, and computer science. Computational mechanics has had a major impact on engineering analysis and design. When applied to structural mechanics, the discipline is referred to herein as computational structural mechanics. Complex structures being considered by NASA for the 1990's include composite primary aircraft structures and the space station. These structures will be much more difficult to analyze than today's structures and necessitate a major upgrade in computerized structural analysis technology. NASA has initiated a research activity in structural analysis called Computational Structural Mechanics (CSM). The broad objective of the CSM activity is to develop advanced structural analysis technology that will exploit modern and emerging computers, such as those with vector and/or parallel processing capabilities. Here, the current research directions for the Methods and Application Studies Team of the Langley CSM activity are described.

Knight, Norman F., Jr.↗

A Route to Design Novel Functional Peptides by Applying a Denoising Diffusional Model to mRNA Display Libraries

In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.

Qi, Pearl [Mork Family Department of Chemical Engi↗

US Department of Energy, Office of Science, High-Performance Computing Facility: 2023 Operational Assessment Oak Ridge Leadership Computing Facility

The Oak Ridge Leadership Computing Facility (OLCF) was established to accelerate scientific discovery by providing world-leading computational performance and advanced data infrastructure. As a US Department of Energy (DOE) Office of Science user facility, the OLCF has managed the successful deployment and operation of a succession of leadership-class resources dedicated to open science. In addition to these resources, the OLCF staff continually strive to develop innovative processes and technologies, improve security, and empower users through effective allocation management and comprehensive user support and training. These efforts support the advancement of science by the OLCF users and benefit high-performance computing (HPC) facilities around the world. In calendar year (CY) 2023, the OLCF supported 1,676 users and 598 projects and exceeded all targets for user satisfaction. The facility received an average satisfaction score of 4.52 out of 5 on the annual user survey, and 94% of respondents reported a high satisfaction rate with the OLCF overall. Of the 3,619 user tickets submitted in CY 2023, OLCF staff resolved 97% within 3 business days. The facility opened Frontier to full scientific operations this year. Two projects conducted on Frontier received the Association for Computing Machinery (ACM) Gordon Bell Prize and the Gordon Bell Special Prize for Climate Modeling, and a third earned a nomination as a Gordon Bell Prize finalist. The facility’s previous flagship machine, Summit, gained new life and was extended through 2024 in part to help provide resources to the Integrated Research Infrastructure (IRI) projects and the National Artificial Intelligence Research Resource (NAIRR) pilot program. The facility instantiated an Advanced Computing Ecosystem testbed in part to support IRI workflows. OLCF made interactivity easier and more accessible to users than ever through tools like Jupyter notebooks and workflows.

97 MATHEMATICS AND COMPUTING↗

A High-level Design for Bidirectional Data Streaming to High-Performance Computing Systems from External Science Facilities

Cutting-edge science is increasingly data-driven due to the emergence of scientific machine learning models that can guide scientists toward fruitful areas of exploration. Experimental science facilities such as light and neutron sources, particle colliders, and radio astronomy telescopes are also producing raw measurement data at rates that exceed available data storage and computing capacity at those facilities. As a result, scientific workflows are being developed that concurrently couple experiments at science facilities with high-performance computing (HPC) facilities to enable analysis of experimental data while the experiment is ongoing, and where analysis results are potentially fed back to the experiment for use in experimental control and/or steering in a time-sensitive manner. Our goal is to design, prototype, and deploy a new capability for the Oak Ridge Leadership Computing Facility (OLCF) that enables such workflows through support for bidirectional, memory-based streaming of data from external experiments into and out of OLCF HPC systems. This high-level design document describes the related work and motivating use cases that inform our understanding of the technical requirements for this capability, and describes a proposed architectural solution that meets these requirements and our plans for demonstrating the capability.

97 MATHEMATICS AND COMPUTING↗

Role of High-End Computing in Meeting NASA's Science and Engineering Challenges

High-End Computing (HEC) has always played a major role in meeting the modeling and simulation needs of various NASA missions. With NASA's newest 62 teraflops Columbia supercomputer, HEC is having an even greater impact within the Agency and beyond. Significant cutting-edge science and engineering simulations in the areas of space exploration, Shuttle operations, Earth sciences, and aeronautics research, are already occurring on Columbia, demonstrating its ability to accelerate NASA s exploration vision. The talk will describe how the integrated supercomputing production environment is being used to reduce design cycle time, accelerate scientific discovery, conduct parametric analysis of multiple scenarios, and enhance safety during the life cycle of NASA missions.

Biswas, Rupak↗

thornado+FLASH-X: A Hybrid Discontinuous Galerkin–Implicit-explicit and Finite-volume Framework for Neutrino-radiation Hydrodynamics in Core-collapse Supernovae

We present neutrino-transport algorithms implemented in the toolkit for high-order neutrino-radiation hydrodynamics (thornado) and their coupling to self-gravitating hydrodynamics within the adaptive mesh refinement–based multiphysics simulation framework FLASH-X. thornado, developed primarily for simulations of core-collapse supernovae (CCSNe), employs a spectral, six-species two-moment formulation with algebraic closure and special-relativistic observer corrections accurate to $\mathcal{O}(v/c)$, and uses discontinuous Galerkin (DG) methods for phase-space discretization combined with implicit-explicit time stepping. A key development is a nonlinear neutrino–matter coupling algorithm based on nested fixed-point iteration with Anderson acceleration, enabling fully implicit treatment of collisional processes, including energy-coupling interactions such as neutrino–electron scattering and pair production. Coupling to finite-volume (FV) hydrodynamics is achieved through a hybrid DG-FV representation of the fluid variables and operator-split evolution within FLASH-X. The implementation is verified using basic transport tests with idealized opacities and relaxation and deleptonization problems with tabulated microphysics. Spherically symmetric CCSN simulations demonstrate accuracy and robustness of the coupled scheme, including close agreement with the CCSN simulation code Chimera. An axisymmetric CCSN simulation further demonstrates the viability of DG-based neutrino transport for multidimensional supernova modeling within FLASH-X. thornado’s neutrino-transport solver is GPU-enabled using OpenMP offloading or OpenACC, and all CCSN applications included in this work use the GPU implementation. Together, these results establish a foundation for future enhancements in physics fidelity, numerical algorithms, and computational performance, for increasingly realistic large-scale CCSN simulations.

Endeve, Eirik [Oak Ridge National Laboratory (ORNL↗