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At least 37 records · Page 2

AutoCheck: Automatically Identifying Variables for Checkpointing by Data Dependency Analysis

Checkpoint/Restart (C/R) has been widely deployed in numerous HPC systems, Clouds, and industrial data centers, which are typically operated by system engineers. Nevertheless, there is no existing approach that helps system engineers without domain expertise and domain scientists without system fault tolerance knowledge identify those critical variables accounted for correct application execution restoration in a failure for C/R. To address this problem, we propose an analytical model and a tool (AutoCheck) that can automatically identify critical variables to checkpoint for C/R. AutoCheck relies on first, analytically tracking and optimizing data dependency between variables and other application execution state, and second, a set of heuristics that identify critical variables for checkpointing from the refined data dependency graph (DDG). AutoCheck allows programmers to pinpoint critical variables to checkpoint quickly within a few minutes. We evaluate AutoCheck on 13 representative HPC benchmarks, demonstrating that AutoCheck can efficiently identify correct critical variables to checkpoint.

HPC

A Benchmarking Framework for Evaluating Large Language Model Capabilities in Nuclear Reactor Safety Applications

Large language models (LLMs) are increasingly capable of answering technical questions, synthesizing domain knowledge, and supporting engineering workflows. For nuclear science and engineering, these capabilities require careful, domain-specific evaluation before they can be credibly incorporated into safety-related activities, regulatory review, or technical decision support. This paper presents preliminary results from benchmarking framework for evaluating LLM capabilities in nuclear contexts. The framework is organized into three evaluation categories: nuclear fundamentals, general dual-use knowledge, and plant specific knowledge. These categories are intended to distinguish general nuclear engineering competence from broader technical reasoning and more context-dependent nuclear knowledge. Initial evaluations focus on nuclear fundamentals using questions representative of the knowledge expected of a nuclear professional engineer. Results indicate that contemporary frontier models perform at a high level and substantially exceed the performance of older model generations, with some models approaching saturation of the current benchmark. These findings suggest both the rapid improvement of LLM capabilities in specialized technical domains and the need for more discriminating evaluation methods. The paper presents the benchmark structure, preliminary model-comparison results, and ongoing work. This work supports development of verifiable, responsible, and safety-conscious methods for assessing AI systems in nuclear engineering applications.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN

Autonomous Multistate Nanoencoding Using Combinatorial Ferroelectric Closure Domains in BiFeO 3

Recent advances in ferroic materials have identified topological defects as promising candidates for enabling additional functionalities in future electronic systems. The generation of stable and customizable polar topologies is needed to achieve multistates that enable beyond-binary device architectures. Here, in this study, we show how to autonomously pattern on-demand highly tunable striped closure domains in pristine rhombohedral-phase BiFeO 3 thin films through precise scanning of a biased atomic force microscopy tip along carefully designed paths. By employing this strategy, we generate and manipulate closed-loop structures with high spatial resolution in an automated manner, allowing the creation of highly tunable and intricate topological domain structures that exhibit distinct polarization configurations without the need for electrode deposition or complex heterostructure growth. As a proof-of-concept for ferroelectric beyond-binary memory devices, we use such topological domains as multistates, engineering an alphabet and automating the symbolic writing/reading process using autonomous microscopy. The resulting information density is compared with that of current commercially available memory devices, demonstrating the potential of ferroelectric topological domains for multistate information storage applications.

BiFeO3

The Importance of Being Adaptable: An Exploration of the Power and Limitations of Domain Adaptation for Simulation-Based Inference with Galaxy Clusters

The application of deep machine learning methods in astronomy has exploded in the last decade, with new models showing remarkably improved performance on benchmark tasks. Not nearly enough attention is given to understanding the models' robustness, especially when the test data are systematically different from the training data, or "out of domain." Domain shift poses a significant challenge for simulation-based inference, where models are trained on simulated data but applied to real observational data. In this paper, we explore domain shift and test domain adaptation methods for a specific scientific case: simulation-based inference for estimating galaxy cluster masses from X-ray profiles. We build datasets to mimic simulation-based inference: a training set from the Magneticum simulation, a scatter-augmented training set to capture uncertainties in scaling relations, and a test set derived from the IllustrisTNG simulation. We demonstrate that the Test Set is out of domain in subtle ways that would be difficult to detect without careful analysis. We apply three deep learning methods: a standard neural network (NN), a neural network trained on the scatter-augmented input catalogs, and a Deep Reconstruction-Regression Network (DRRN), a semi-supervised deep model engineered to address domain shift. Although the NN improves results by 17% in the Training Data, it performs 40% worse on the out-of-domain Test Set. Surprisingly, the Scatter-Augmented Neural Network (SANN) performs similarly. While the DRRN is successful in mapping the training and Test Data onto the same latent space, it consistently underperforms compared to a straightforward Yx scaling relation. These results serve as a warning that simulation-based inference must be handled with extreme care, as subtle differences between training simulations and observational data can lead to unforeseen biases creeping into the results.

Ntampaka, Michelle [Baltimore, Space Telescope Sci

Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling

Interleukin (IL)-23 is a validated therapeutic target in inflammatory bowel disease. While antibodies targeting IL23 demonstrate clinical efficacy, they face challenges such as high costs, safety risks, and the necessity of parenteral administration. Here, we present a workflow to simultaneously enhance the affinity and protease stability of an inhibitory anti-IL23R VHH for oral use. Cocrystal structure analysis reveals that the anti-IL23R VHH employs both CDR and framework residues to achieve picomolar affinity for IL23R. The engineered VHH remains stable for over 8 h in intestinal fluid and 24 h in fecal samples. Oral administration of this VHH achieves deep pathway inhibition in a murine colitis model. Furthermore, a single pill provides sustained IL23R inhibition in nonhuman primate blood for over 24 h. With high potency, gut stability, high production yield, and favorable drug-like properties, oral VHHs offer a promising approach for inflammatory bowel diseases.

Science & Technology - Other Topics

Deep Generative Models in Energy System Applications: Review, Challenges, and Future Directions

In recent years, with the advent of mature machine learning products like ChatGPT, Stable Diffusion, and Sora, the world has witnessed tremendous changes driven by the rapid development of generative artificial intelligence (GAI). Beyond applications in text, speech, image, and video creation, deep generative models (DGMs) underpinning these cutting-edge technologies have also been employed by domain researchers to address scientific and engineering challenges. This paper aims to fill a gap in the research community by providing a systematic review of how DGMs have been utilized in energy system applications. After introducing four most popular DGMs, we review and categorize 196 research articles into five focus areas: data generation, forecasting, situational awareness, modeling, and optimal decision-making. Through this classification, we uncover trends in how DGMs are employed for each type of problem, highlighting GAI techniques that contribute to breakthroughs over traditional methods. We discuss limitations in existing literature, engineering challenges, and propose future directions, all tailored to the unique nature of problems in energy system engineering. Our goal is to offer insights for energy system domain researchers, providing a comprehensive view of existing studies and potential future opportunities.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

NeuroSEM: A hybrid framework for simulating multiphysics problems by coupling PINNs and spectral elements

Multiphysics problems that are characterized by complex interactions among fluid dynamics, heat transfer, structural mechanics, and electromagnetics, are inherently challenging due to their coupled nature. While experimental data on certain state variables may be available, integrating these data with numerical solvers remains a significant challenge. Physics-informed neural networks (PINNs) have shown promising results in various engineering disciplines, particularly in handling noisy data and solving inverse problems in partial differential equations (PDEs). However, their effectiveness in forecasting nonlinear phenomena in multiphysics regimes, particularly involving turbulence, is yet to be fully established. Here, this study introduces NeuroSEM, a hybrid framework integrating PINNs with the highfidelity Spectral Element Method (SEM) solver, Nektar++. NeuroSEM leverages the strengths of both PINNs and SEM, providing robust solutions for multiphysics problems. PINNs are trained to assimilate data and model physical phenomena in specific subdomains, which are then integrated into the Nektar++ solver. We demonstrate the efficiency and accuracy of NeuroSEM for thermal convection in cavity flow and flow past a cylinder. The framework effectively handles data assimilation by addressing those subdomains and state variables where the data is available. We applied NeuroSEM to the Rayleigh-B´enard convection system, including cases with missing thermal boundary conditions and noisy datasets. Finally, we applied the proposed NeuroSEM framework to real particle image velocimetry (PIV) data to capture flow patterns characterized by horseshoe vortical structures. Our results indicate that NeuroSEM accurately models the physical phenomena and assimilates the data within the specified subdomains. The framework’s plug-and-play nature facilitates its extension to other multiphysics or multiscale problems. Furthermore, NeuroSEM is optimized for efficient execution on emerging integrated GPU-CPU architectures. This hybrid approach enhances the accuracy and efficiency of simulations, making it a powerful tool for tackling complex engineering challenges in various scientific domains.

42 ENGINEERING

PDV Sensitivity [Slides]

The concept of PDV sensitive is not new. But we tend not to discuss sensitivity in a rigorous, quantified way. That should change. Indeed there is a natural definition, which is just the energy of light from the target within the analysis window that gives a SNR of 10 in the frequency domain. Systems designers, diagnostic engineers, and operators should use the language of sensitivity: (1) Absolute sensitivity: nW * ns; (2) Launch power: mW or dBm; (3) Relative surface return: dB; (4) Relative sensitivity: dB * ns. This will help us design better systems, choose the correct system for the job, maintain our systems, and tune our systems.

47 OTHER INSTRUMENTATION

Development and Validation of Smart Building Technology Modules for Academic and Professional Education (Final Technical Report)

Smart building technologies can improve building energy efficiency and resilience, reduce carbon emissions, and provide load flexibility to the grid. However, in both college curricula and building professionals’ continuing education, there is a lack of systematic instruction on smart building technologies. Slipstream, partnering with Texas A&M University (TAMU), the Society of Building Science Educators (SBSE), and the National Institute of Building Sciences (NIBS), developed a semester-long smart building curriculum for college students and 16 training videos for building professionals and the general public. The education and training cover the drivers and benefits of smart building technologies, key building energy systems, the latest sensor technologies and IoT devices, and focus on topics related to smart building controls (i.e., energy management information systems, smart building control platforms, cybersecurity, grid-interactive-efficient buildings [GEBs], smart building control methods, and occupant-centric control). The smart building curriculum for college students was taught at TAMU in the Spring semester of 2024 as part of the validation process. Student feedback was collected and summarized in a validation report by TAMU. The curriculum material was also reviewed by SBSE faculty who are interested in teaching smart building technology-related courses. Suggestions on revisions and better adoption of the materials by other faculty across the architectural, engineering, and construction (AEC) domains were compiled in a distinct validation report by SBSE. The SBSE validation report was used to create structured subsets of the curriculum material for adoption at different levels in different sub-disciplines. These subsets are categorized and offered on the SBSE website (https://www.sbse.org/courses/Smart-Building-Technologies). The 16 training videos for building professionals and the general public were previewed by 17 industry experts, and feedback and suggested changes were incorporated into the final version of these videos. The videos are organized into a smart building technology training course and published on the Whole Building Design Guide website (https://www.wbdg.org/ce/doe/bto/sbtt), which is hosted by the National Institute of Building Sciences (NIBS). Project team members created marketing materials to promote the awareness of these free, publicly available education and training resources. Outreach and marketing activities included creating short promotional videos, building project webpages, making project announcements on social media, conducting an email campaign, and directly reaching out to faculties and building professionals. This report describes the project approach, provides outlines of the training materials, along with links to resources, and identifies lessons learned in creating the content. We also suggest ways to scale the instruction of smart building concepts to empower the workforce to accelerate the adoption of smart building technologies in the real world.

99 GENERAL AND MISCELLANEOUS

Nanoscale strain wave generation by a piezoelectric grating from polar vortices

Nanostructures formed by spontaneously broken symmetry have provided new ways to manipulate quantum states. Specifically, topological structures with periodic spatial ordering, such as polar vortices and skyrmions, can be ideal hosts for creating engineered responses in both spatial and frequency domains. So far, however, only a few examples of such hierarchical engineering have been reported in the literature. Here we demonstrate that the spatially modulated piezoelectric response of a polar vortex structure can create strain waves with a characteristic nanoscale wavefront. Using time-resolved pump–probe resonant X-ray scattering and diffraction measurements, coupled with dynamical phase-field simulations, we show that the piezoelectric modulation of the spontaneously formed polar vortex crystal functions as an acoustic diffraction grating. This system converts incoming laterally uniform strain waves into outgoing waves with a characteristic sub-terahertz frequency, driven by an intrinsic excitation of the polar vortex crystal. Moreover, our phase-field simulations suggest that the dynamic mechanical displacements exhibiting vortex textures are generated from both space- and time-varying piezoelectric responses. Our findings illustrate a new method for generating nanoscale strain waves with unique spatial textures by tuning the hierarchical order of polar topologies to engineer new collective modes, allowing for a wide range of control through the topological lattice.

ferroelectrics

Multimodal Approaches for Leveraging Domain Knowledge with State-of-the-Art Machine Learning to Engineer Biocatalysts

This grant aimed to accelerate the development of specialized enzymes—biological catalysts essential for sustainable manufacturing and medicine—by integrating traditional laboratory evolution with cutting-edge artificial intelligence. To achieve this, we developed a suite of high-throughput sequencing tools and a centralized database to bridge the gap between a protein’s genetic "code" and its physical function. By training machine learning models on large datasets, we also demonstrated the ability to move beyond slow, trial-and-error testing to a "generative" approach, where AI can independently design new, versatile enzymes like tryptophan synthases. Ultimately, these findings demonstrate that combining laboratory data with computer-guided design enables the engineering of highly efficient biological tools with unprecedented speed and precision.

59 BASIC BIOLOGICAL SCIENCES

The influence of cooling rates on strain phase diagrams and domain structures of ferroelectric thin films: A case study of PbTiO 3

Strain engineering has been established as an effective approach to control phase equilibria, domain configurations, and functional properties of ferroelectric thin films. Temperature-strain phase diagrams have been used as powerful tools for providing insights into strain engineering. However, almost all existing phase diagrams established using the phase-field approach assume quenching conditions without considering actual cooling rates during the post-deposition annealing process of ferroelectric thin films. Within this work, we systematically investigate the influence of cooling rates on domain structures and the strain-phase diagram of ferroelectric thin films using phase-field simulations, taking PbTiO 3 thin films as a model system. We found that both the position of phase boundaries in the strain phase diagrams and the domain morphology are significantly influenced by the cooling rates. It is revealed that while the paraelectric-ferroelectric phase boundary remains invariant, the phase boundaries between single-phase and multi-phase regions tend to shift toward the corresponding multi-phase region as the cool rate reduces. Slow cooling generally leads to more ordered domain structures with increased domain size. Using the obtained equilibrium domain structures, we calculated effective thermal conductivities and found significant variations that can be tuned by the cooling rates. In conclusion, this work reveals an underexplored yet critical impact of cooling rates on phase equilibria and domain structures in ferroelectric thin films, which may inspire further fine-tuning of domains and domain walls in low-dimensional ferroelectrics for multifunctional applications.

Domain structures

A Scalable Reduced‐Order Model for the Steady Navier–Stokes Equations

Scaling up new scientific technologies from laboratory to industry often involves demonstrating performance on a larger scale. Computer simulations can accelerate design and predictions in the deployment process, though traditional numerical methods are computationally intractable even for intermediate pilot plant scales. Recently, the component reduced order modeling method has been developed to tackle this challenge by combining projection reduced order modeling and discontinuous Galerkin domain decomposition. However, while many scientific or engineering applications involve nonlinear physics, this method has only been demonstrated for various linear systems. In this work, the component reduced order modeling method is extended to steady Navier–Stokes flow, with application to general nonlinear physics in view. The large‐scale, global domain is decomposed into a combination of small‐scale unit component. Linear subspaces for flow velocity and pressure are identified via proper orthogonal decomposition over sample snapshots collected from each small‐scale unit component. Velocity bases are augmented with a pressure supremizer to satisfy the inf–sup condition for stable pressure prediction. Two different nonlinear reduced order modeling methods are employed and compared for efficient evaluation of nonlinear advection: A third‐order tensor projection operator and the empirical quadrature procedure. The proposed method is demonstrated on the flow over arrays of five different unit objects, achieving a 23‐fold speedup with less than 4% relative error in domains up to 256 times larger than the unit components. Furthermore, a numerical experiment with the pressure supremizer strongly indicates the need for a supremizer for stable pressure prediction. A comparison between the tensorial approach and the empirical quadrature procedure revealed a slight advantage of the empirical quadrature procedure. The framework is compared with an alternating Schwarz‐based reduced‐order approach, demonstrating improved efficiency and robustness for the DG‐based global solver while retaining flexibility for sub‐scale iterative solvers. The method is further extended to a coupled advection–diffusion and Navier–Stokes system, illustrating its applicability to multi‐physics problems and its potential for more general, inter‐coupled nonlinear systems.

42 ENGINEERING

Identifying Strain Stacking Boundaries between Multiphase Domains in Atomically Thin Two-Dimensional Magnets

Stacking engineering of van der Waals materials is an important strategy to control the materials’ properties, such as electronic correlations, ferroelectricity, and layer-dependent two-dimensional magnetism. A timely testbed for the study of the latter is atomically thin chromium trihalides (CrX 3 , X = Cl, Br, I). Notably, by understanding the sliding mechanism between different stacking sequences, control of the stacking arrangement, and thus magnetic properties in CrX 3 , can be achieved. Such insight, however, is currently lacking. Here, in this study, advanced electron microscopy methods are used to identify multiple stacking sequences corresponding to different bulk phases in atomically thin CrX 3 (X = Cl and Br) down to bilayer thickness and with lateral domain sizes as small as tens of nanometers. Indications of nanometer scale transitions and interactions at the stacking boundaries are found, including a universally preferred sliding direction that is consistent with density functional theory calculations and the strain fields at lateral heterostructure boundaries. This study demonstrates the necessity to consider local stacking structures when interpreting averaged magnetic properties measured with macroscale probes. Additionally, the preferred sliding direction insight from this study provides a strategy to control stacking sequence in atomically thin CrX 3 samples during the exfoliation and sample fabrication process.

DFT calculations

Virtual Inspection of Advanced Manufacturing via Process-Scale Digital Twins (Abbreviated Report)

Inspection and certification comprise the most significant bottlenecks in advanced manufacturing for NNSA applications, often requiring far more time and resources than the fabrication of the parts themselves. Traditional methods, such as manual review and X-ray computed tomography, are not only slow and costly, but also struggle to provide a clear connection between manufacturing instructions and the final performance of critical components. This gap limits both the agility and assurance needed to support the modernization and safety of the United States nuclear stockpile. In response, our Strategic Initiative established a digital twin framework that integrates realtime process monitoring, automated data analysis, and immersive virtual reality collaboration into a unified inspection pipeline. By leveraging data from sensors, machine instructions, and imaging, we created high-fidelity virtual models of manufactured parts that could be rapidly analyzed and certified. This approach was first demonstrated with Direct Ink Write, and then extended to other manufacturing settings, including conventional (or “subtractive”) manufacturing and to predict the end of life performance of parts per the aging and lifetimes programs. The result is a transformational capability: inspection times have been reduced by a factor of 120,000 without loss of accuracy and while simultaneously improving traceability and confidence in part quality. This framework not only streamlines certification for critical applications, but also positions the national security enterprise to respond more flexibly to emerging challenges, supporting agile manufacturing and digital engineering practices across a broad range of mission-relevant domains.

42 ENGINEERING

Engineering an Extremely Hybrid PKS for Adipic Acid Production

Polyketide synthases (PKSs) are modular enzymes with exceptional potential as biocatalysts for producing non-native compounds. Here, we report the first PKS-based pathway for adipic acid (AA), an industrial monomer for nylon production, by engineering one of the most extensively hybridized PKS systems to date. Using a retrobiosynthetic approach, we identified EtnB, a succinyl-CoA-loading module that uniquely retains the terminal carboxyl group, enabling access to dicarboxylic polyketide products, rarely produced by canonical PKSs. EtnB was coupled to a fully reducing extension module through an engineered communication linker, which improved ACP–KS interactions, enhanced titers, and demonstrated selective succinyl-CoA loading in vivo . This construct integrates genes from five organisms─with domains from seven PKS modules joined across six non-natural junctions─and functions in both Escherichia coli and Pseudomonas putida . Additional engineering that included AT domain exchanges, optimization of extender unit supply, and host strain metabolic rewiring further increased AA production. Together, this work demonstrates that highly chimeric PKSs can be rendered functional through rational design, expands the PKS toolkit with a carboxyl-retaining loading module, and establishes a versatile platform for engineering diacids and other noncanonical products through PKS pathways.

biomanufacturing

Data and Code for Understanding Generative AI Content with Embedding Models

This repository contains code for the experiments in the paper "Understanding Generative AI Content with Embedding Models". Constructing high-quality features is critical to any quantitative data analysis. While feature engineering was historically addressed by carefully hand-crafting data representations based on domain expertise, deep neural networks (DNNs) now offer a radically different approach. DNNs implicitly engineer features by transforming their input data into hidden feature vectors called embeddings. For embedding vectors produced by foundation models -- which are trained to be useful across many contexts -- we demonstrate that simple and well-studied dimensionality-reduction techniques such as Principal Component Analysis uncover inherent heterogeneity in input data concordant with human-understandable explanations. Of the many applications for this framework, we find empirical evidence that there is intrinsic separability between real samples and those generated by artificial intelligence (AI).

Vargas, Max [Pacific Northwest National Laboratory

Light-Modulated Self-Assembly of Synthetic Nanotubes

Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.

DNA nanotechnology