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At least 235 records · Page 13

Invariant discovery of features across multiple length scales: Applications in microscopy and autonomous materials characterization

Physical imaging is a foundational characterization method in areas from condensed matter physics and chemistry to astronomy and spans length scales from atomic to universe. Images encapsulate crucial data regarding atomic bonding, materials microstructures, and dynamic phenomena such as microstructural evolution and turbulence, among other phenomena. The challenge lies in effectively extracting and interpreting this information. Variational Autoencoders (VAEs) have emerged as powerful tools for identifying the underlying factors of variation in image data, providing a systematic approach to distilling meaningful patterns from complex data sets. However, a significant hurdle in their application is the definition and selection of appropriate descriptors reflecting local structures. Here, we introduce the scale-invariant VAE approach (SI-VAE) based on the progressive training of the VAE with the descriptors sampled at different length scales. The SI-VAE allows the discovery of the length scale-dependent factors of variation in the system. Here, we illustrate this approach using the ferroelectric domain images and generalize it to the movies of the electron-beam induced phenomena in graphene and topography evolution across combinatorial libraries. This approach can further be used to initialize the decision making in automated experiments including structure–property discovery and can be applied across a broad range of imaging methods. This approach is universal and can be applied to any spatially resolved data including both experimental imaging studies and simulations, and can be particularly useful for exploration of phenomena such as turbulence and scale-invariant transformation fronts.

36 MATERIALS SCIENCE↗

Geometric frustration in the myosin superlattice of vertebrate muscle

Geometric frustration results from an incompatibility between minimum energy arrangements and the geometry of a system, and gives rise to interesting and novel phenomena. Here, we report geometric frustration in a native biological macromolecular system---vertebrate muscle. We analyse the disorder in the myosin filament rotations in the myofibrils of vertebrate striated (skeletal and cardiac) muscle, as seen in thin-section electron micrographs, and show that the distribution of rotations corresponds to an archetypical geometrically frustrated system---the triangular Ising antiferromagnet. Spatial correlations are evident out to at least six lattice spacings. The results demonstrate that geometric frustration can drive the development of structure in complex biological systems, and may have implications for the nature of the actin--myosin interactions involved in muscle contraction. Identification of the distribution of myosin filament rotations with an Ising model allows the extensive results on the latter to be applied to this system. It shows how local interactions (between adjacent myosin filaments) can determine long-range order and, conversely, how observations of long-range order (such as patterns seen in electron micrographs) can be used to estimate the energetics of these local interactions. Furthermore, since diffraction by a disordered system is a function of the second-order statistics, the derived correlations allow more accurate diffraction calculations, which can aid in interpretation of X-ray diffraction data from muscle specimens for structural analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Custom Accessors: Enabling Scalable Data Ingestion, (Re-)Organization, and Analysis on Distributed Systems

The emerging class of high velocity and high volume data analytic workflows comprise interwoven data ingestion, organization, and processing stages, with ingestion and organization steps often contributing comparable or even higher computational costs than actual processing steps. Since complex workflows consist of a variety of phases that view and use data differently, being able to construct efficient, scalable, distributed data structures (arrays, vectors, sets, maps, and multi-maps) is essential and requires custom methods to extend and shrink containers, analyze and position data, and, maintain globallyconsistent meta-data. In this paper, we propose a novel datastructure access paradigm based on the concept of Accessors. At a high level, accessors are customizable callable objects that can modify the behavior of insert, read, update, and delete operations for distributed containers while preserving atomicity guarantees. Accessors provide a very clean and natural way to implement a variety of programming patterns, e.g., conditional insertion/deletion and cascading computations, which would be otherwise hard (or even impossible) to express in parallel and distributed settings without using locks. We demonstrate the practicality and usefulness of our approach with two representative use cases and study the performance of these applications on a distributed High-Performance Computing system. Our analysis highlights that our proposed abstraction allows for an effective overlapping and concurrent execution of different workflow steps (e.g., data ingestion and analysis), which in a conventional analytics pipeline would execute sequentially, contributing cumulatively to the overall latency.

Castellana, Vito G. [BATTELLE (PACIFIC NW LAB)] (O↗

Soft interface instability and gas flow channeling in low-permeability deformable media

Understanding gas percolation through a clay layer or a shale formation is of great importance for the development of a geologic repository for nuclear waste disposal, a subsurface system for gas storage, and an engineering approach for hydrocarbon extraction from unconventional reservoirs. Gas injection experiments have revealed complex dynamic behaviours of gas percolation through water saturated compacted bentonite, characterized by a high breakthrough pressure, rapid breakthrough, a pressure/stress decay after the breakthrough, a relatively high migration rate, high-frequency periodic/nonperiodic variations in flow rate, stepwise rate reductions during relaxation, and low gas saturation over the whole process, all indicating channelling nature of the processes. Using linear stability analyses, we show that this channelling can autonomously emerge from the instability of the deformable interface between the injected gas and the compacted bentonite matrix driven by local stress concentration, pore dilation, and hydrologic gradient. Channel patterns formed would possess a fractal geometry. We further show that, once a percolating channel is established, the gas injected would percolate through the channel in a chain of gas bubbles, also due to the interface instability, resulting in periodic/chaotic variations in gas flow rate. Our work provides a unified explanation for key features observed for gas percolation in low-permeability deformable media. The work also suggests a possibility of designing an engineered barrier system for a nuclear waste repository that can have controllable gas release while limit water transport.

Bentonite↗

The GFDL Variable-Resolution Global Chemistry-Climate Model for Research at the Nexus of US Climate and Air Quality Extremes

We present a variable-resolution global chemistry-climate model (AM4VR) developed at NOAA's Geophysical Fluid Dynamics Laboratory (GFDL) for research at the nexus of US climate and air quality extremes. AM4VR has a horizontal resolution of 13 km over the US, allowing it to resolve urban-to-rural chemical regimes, mesoscale convective systems, and land-surface heterogeneity. With the resolution gradually reducing to 100 km over the Indian Ocean, we achieve multi-decadal simulations driven by observed sea surface temperatures at 50% of the computational cost for a 25-km uniform-resolution grid. In contrast with GFDL's AM4.1 contributing to the sixth Coupled Model Intercomparison Project at 100 km resolution, AM4VR features much improved US climate mean patterns and variability. In particular, AM4VR shows improved representation of: precipitation seasonal-to-diurnal cycles and extremes, notably reducing the central US dry-and-warm bias; western US snowpack and summer drought, with implications for wildfires; and the North American monsoon, affecting dust storms. AM4VR exhibits excellent representation of winter precipitation, summer drought, and air pollution meteorology in California with complex terrain, enabling skillful prediction of both extreme summer ozone pollution and winter haze events in the Central Valley. AM4VR also provides vast improvements in the process-level representations of biogenic volatile organic compound emissions, interactive dust emissions from land, and removal of air pollutants by terrestrial ecosystems. We highlight the value of increased model resolution in representing climate–air quality interactions through land-biosphere feedbacks. AM4VR offers a novel opportunity to study global dimensions to US air quality, especially the role of Earth system feedbacks in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

RISE: Reducing I/O Contention in Staging-based Extreme-Scale In-situ Workflows

While in-situ workflow formulations have addressed some of the data-related challenges associated with extreme-scale scientific workflows, these workflows involve complex interactions and different modes of data exchange. In the context of increasing system complexity, such workflows present significant resource management challenges, requiring complex cost-performance tradeoffs. This paper presents RISE, an intelligent staging-based data management middleware, which builds on the DataSpaces framework and performs intelligent scheduling of data management operations to reduce I/O contention. In RISE, data are always written immediately to local buffers to reduce the effect of the transfer impact upon application performance. RISE identifies applications’ data access patterns and moves data towards data consumers only when the network is expected to be idle, reducing the impact of asynchronous background data movement upon critical data read/write requests. Here, we experimentally demonstrate that RISE can take advantage of staging nodes to offload data during writes without degrading application data movement performance.

97 MATHEMATICS AND COMPUTING↗

RingX: Scalable Parallel Attention for Long-Context Learning on HPC

The attention mechanism has become foundational for remarkable AI breakthroughs since the introduction of the Transformer, driving the demand for increasingly longer context to power frontier models such as large-scale reasoning language models and high-resolution image/video generators. However, its quadratic computational and memory complexities present substantial challenges. Current state-of-the-art parallel attention methods, such as ring attention, are widely adopted for long-context training but utilize a point-to-point communication strategy that fails to fully exploit the capabilities of modern HPC network architectures. In this work, we propose ringX, a scalable family of parallel attention methods optimized explicitly for HPC systems. By enhancing workload partitioning, refining communication patterns, and improving load balancing, ringX achieves up to 3.4 × speedup compared to conventional ring attention on the Frontier supercomputer. Optimized for both bi-directional and causal attention mechanisms, ringX demonstrates its effectiveness through training benchmarks of a Vision Transformer (ViT) on a climate dataset and a Generative Pre-Trained Transformer (GPT) model, Llama3 8B. Our method attains an end-to-end training speedup of approximately 1.5 × in both scenarios. To our knowledge, the achieved 38% model FLOPs utilization (MFU) for training Llama3 8B with a 1M-token sequence length on 4,096 GPUs represents one of the highest training efficiencies reported for long-context learning on HPC systems. Our code implementation is available at https://github.com/jqyin/ringX-attention.

Yin, Junqi [ORNL] (ORCID:0000000338435520)↗

Extraction of Vibration Data with Imaging

To date, the primary sensing technology used to measure the vibration response has been accelerometers and strain gages mounted directly to the structure and using either wired or, more recently, wireless telemetry. Cost issues with these sensors and the associated data acquisition systems typically limit the numbers that are deployed on in situ structures. Although there are a few structures with larger sensing counts that in some cases exceed over 1000 sensors, more typical numbers range from ten to one hundred sensors resulting in low spatial resolution when they are applied to physically large systems. When one considers that nuclear power plant structures usually have complex geometries, material properties, connectivity and boundary conditions, it is clear these current approaches to vibration measurements can only provide limited information about a system’s dynamics response characteristics. As an alternative, many non-contact measurement technologies have emerged, including point wise measurement methods such as Global Positioning System (GPS), microwave interferometry, and laser Doppler vibrometry (LDV), as well as simultaneous full-field measurement methods such as electronic speckle pattern interferometry, holography interferometry, and muon tomography, some of which can provide high spatial resolution measurements. Among these methods, digital video imaging techniques have emerged as a feasible solution for full-field vibration measurements that provide significantly more detailed dynamic response information because every pixel becomes a measurement point. Furthermore, recent advances in image processing and computer vision algorithms have been successfully used to process video data for experimental and operational modal analysis. Such full-field measurements have the potential to significantly improve many current structural assessment procedures including system identification (modal parameter estimation), structural health monitoring, load reconstruction, model validation, and model updating. Furthermore, more recent full-field imaging techniques can be accomplished with relatively low-cost, commercially-available off-the-shelf cameras. However, these measurement procedures have other limitations that must be considered such as the ability to only measure visibly accessible points on a structure and a more limited dynamic range and bandwidth than can be achieved with accelerometers or strain gages.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Evaluation of a high-resolution regional climate simulation for surface and hub-height wind climatology over North America

Assessing the availability of key wind resources requires augmenting observations to support the implementation of wind energy infrastructure. However, observations are limited, necessitating the development of high-resolution, long-term gridded datasets. This study presents a robust, dynamically downscaled climatological dataset, offering 20 years of hourly wind data at a 4 km spatial resolution across North America, and evaluates its performance against observations, including meteorological towers and automated surface-observing system (ASOS) stations, as well as coarse-resolution reanalysis data (the European Centre for Medium-Range Weather Forecasts (ECMWF) reanalysis version 5 (ERA5)). Results demonstrate that the downscaled high-resolution wind data outperform ERA5 in regions of complex terrain and coastal areas, with improved overlap coefficients for wind data distributions and reduced root mean square errors (RMSEs) for hub-height and near-surface diurnal wind patterns. The downscaled simulation also captures the synoptic drivers of seasonal wind direction patterns reasonably well, indicated by high wind rose similarity indices. This study also provides an analysis of interannual variability, utilizing the dataset's full 20-year period, and model uncertainty, generated by varying model initial conditions and physics parameterizations across 1-year ensemble members, which are key considerations for wind resource assessment in wind farm development.

17 WIND ENERGY↗

Accelerating scientific discoveries through data-driven innovations

Developing artificial intelligence (AI) and machine learning (ML) methods that can accelerate scientific discoveries and advance science has become one of the important research directions for the AI/ML research community. It has been gaining increasing attention from researchers in diverse scientific areas, including biomedical science, materials science, climate science, physics, chemistry, and many others. Data-driven AI/ML innovations to enable reliable predictions and optimal decision making for scientific discoveries face several critical challenges, among which are high system complexity, large search space, incomplete knowledge, and small data, all of which demand novel strategies to effectively address them. Meeting these challenges and thereby accelerating scientific discoveries and industrial innovations, calls for research that can take full advantage of the latest advances in AI/ML to integrate data-driven techniques with scientific knowledge and is able to execute them in modern high-performance computing (HPC) environments at scale. This Patterns special collection "Accelerating scientific discoveries through data-driven innovations" features articles that showcase the promising roles of AI/ML and data-driven modeling in accelerating scientific discoveries and may inspire the next wave of data-driven innovations in various scientific domains.

97 MATHEMATICS AND COMPUTING↗

What Questions Would a Systems Engineer Ask to Assess Systems Engineering Models as Credible

Digital Systems Engineering strategies typically call for digital Systems Engineering models to be retained in repositories and certified as an authoritative source of truth (enabling model reuse, qualification, and collaboration). In order for digital Systems Engineering models to be certified as authoritative (credible), they need to be assessed - verified and validated - and with the amount of uncertainty in the model quantified (consider reusing someone else's model without knowing the author). Due to this increasing model complexity, the authors assert that traditional human-based methods for validating, verifying, and uncertainty quantification - such as human-based peer-review sessions - cannot sufficiently establish that a digital Systems Engineering model of a complex system is credible. Digital Systems Engineering models of complex systems can contain millions of nodes and edges. The authors assert that this level of detail is beyond the ability of any group of humans - even working for weeks at a time - to discern and catch every minor model infraction. In contrast, computers are highly effective at discerning infractions with massive amounts of information. The authors suggest that a better approach might be to focus the humans at what model patterns should be assessed and enable the computer to assess the massive details in accordance with those patterns - by running through perhaps 100,000 test loops. In anticipation of future projects to implement and automate the assessment of models at Sandia National Laboratories, a study was initiated to elicit input from a group of 25 Systems Engineering experts. The authors positioning query began with - 'What questions would a Systems Engineer ask to assess Systems Engineering models for credibility?" This report documents the results of that survey.

42 ENGINEERING↗

Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling the Potential Impact of Storage on the US Power Sector in a Multisector Dynamic Context

The electric power sector is expected to grow in size, importance, and complexity around the world as economies expand and electric supply technologies and demand patterns evolve in significant ways. At the same time the electric power sector may see substantial increases in VRE generating technologies which can add variability and uncertainty to the diurnal and seasonal profile of electric supply. With these forces in play, the emergence of modular, flexible electricity storage technologies may have profound impacts on the operation of electric power systems. Here we reduce a storage modeling gap in MSD models by incorporating grid-based electricity storage into the electric sector dynamics of the Global Change Analysis Model-USA (GCAM-USA) with improved power sector representation. We find a potentially significant role for storage technologies in the future of the U.S. power system, with storage capacity ranging from 7.7 to 14.7 GW in 2050 and 13.9 to 31.6 GW in 2100 across several techno-economic scenarios. We also find that storage can help to smooth variability in residual load arising from evolving electricity demands and the introduction of high shares of VRE to the electric grid. This reduces reliance on high-cost peaking generators, improves system-wide capacity factors, and limits curtailment of VRE.

Patel, Pralit L.↗

Austenitic parent grain reconstruction in martensitic steel using deep learning

In this work we develop a deep convolutional architecture to estimate the prior austenite structure from observed martensite electron backscatter diffraction micrographs. A novel data augmentation strategy randomizes the global reference coordinate system which makes it possible to train our model from only four micrographs. The model is much faster than algorithmic approaches and generalizes well when applied to micrographs of a different material. Empirical evidence suggests the efficacy of the model depends on the scale of the microstructure and receptive field of the vision model. Furthermore, this work demonstrates that modern computer vision approaches are well suited for capturing complex spatial-orientation patterns present in orientation imaging micrographs.

36 MATERIALS SCIENCE↗

A Scientist-in-the-Loop Data Analytics Framework for Intelligent Simulation Model Tuning and Validation

This project developed a scientist-in-the-loop data analytics framework for intelligent simulation model tuning and validation, targeting the Weather Research and Forecasting (WRF) model and its solar energy variant, WRF-Solar-BNL. Domain experts, such as climate scientists, depend on large-scale numerical simulations for knowledge discovery and decision-making, yet the complexity of parameter tuning and the disconnect between automated optimization and domain expertise pose significant challenges. We extended an interactive visual analytics framework that enables domain experts to observe and intervene in the computational steering process by identifying disagreements between the simulation model, surrogate model, and the expert’s domain knowledge. Using Bayesian Optimization with Gaussian Process Regression as the surrogate model, our system allows users to probe parameter relationships, analyze correlation patterns, and adjust tuning parameters in real time. We developed use cases for solar irradiance forecasting through sustained collaboration with Brookhaven National Laboratory, resolving critical model configuration challenges and achieving meaningful reductions in prediction error. The project supported one PhD student, one MS student, and eight undergraduate students across three Data Science Capstone projects, resulting in one master’s thesis.

Dasgupta, Aritra [New Jersey Institute of Technolo↗

Efficient loading of reduced data ensembles produced at ORNL SNS/HFIR neutron time-of-flight facilities

We present algorithmic improvements to the loading operations of certain reduced data ensembles produced from neutron scattering experiments at Oak Ridge National Laboratory (ORNL) facilities. Ensembles from multiple measurements are required to cover a wide range of the phase space of a sample material of interest. They are stored using the standard NeXus schema on individual HDF5 files. This makes it a scalability challenge, as the number of experiments stored increases in a single ensemble file. The present work follows up on our previous efforts on data management algorithms, to address identified input output (I/O) bottlenecks in Mantid, an open-source data analysis framework used across several neutron science facilities around the world. We reuse an in-memory binary-tree metadata index that resembles data access patterns, to provide a scalable search and extraction mechanism. In addition, several memory operations are refactored and optimized for the current common use cases, ranging most frequently from 10 to 180, and up to 360 separate measurement configurations. Results from this work show consistent speed ups in wall-clock time on the Mantid LoadMD routine, ranging from 19% to 23% on average, on ORNL production computing systems. The latter depends on the complexity of the targeted instrument-specific data and the system I/O and compute variability for the shared computational resources available to users of ORNL’s Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) instruments. Nevertheless, we continue to highlight the need for more research to address reduction challenges as experimental data volumes, user time and processing costs increase.

Godoy, William↗

Critical Literature Review of Quantitative Sustainability Assessment Methods for the Circular Economy

The circular economy (CE) has been proposed to be an operational framework for sustainable development that decouples economic growth from resource consumption. The CE ambition is to maximize the retention of value in products, materials, and resources in the economy over time with the help of CE strategies such as selling a service rather than a product, reusing and repairing products or their components, and recycling. The social, economic, and environmental performances of CE strategies need to be measured against their linear counterparts to avoid strategies that increase circularity but have other unintended externalities. However, there is currently no tool specifically designed to compare circular to linear systems and, thus, various methods from different fields have been applied. This session aims at reviewing, contrasting, and critiquing different methods that have been applied to assess the CE until now, along with an up to date state of the science in this field. Methods from the industrial ecology field have most often been applied to study the CE. However, the transition to CE involves both technological improvements as well as social changes. New business models such as collaborative consumption models (e.g., Uber or Airbnb) are examples of the new patterns of production and consumption of the CE, which may be difficult to analyze from a purely industrial ecology perspective. Methods from complexity science and humanities could therefore complement the industrial ecology perspective to extend the scope of the analysis. Such an approach could also answer a longstanding criticism of the CE which, in contrast with sustainability, solely focuses on the environment and the economy. Moreover, the hybridization of two or more existing methods can yield additional capabilities, which may enable the exploration of additional CE-related research questions. The 90 minutes session will have several presentations and conclude with a moderated, interactive panel discussion on how methods from different fields could be combined to harness their relative strengths.

circular economy↗

Data-driven modeling to enhance municipal water demand estimates in response to dynamic climate conditions

Altered precipitation and temperature patterns from a changing climate will affect supply, demand, and overall municipal water system operations throughout the arid western U.S. While supply forecasts leverage hydrological models to connect climate influences with surface water availability, demand forecasts typically estimate water use independent of climate and other externalities. Stemming from an increased focus on seasonal water demand management, we use the Salt Lake City, Utah municipal water system as a test bed to assess model accuracy versus complexity trade-offs between simple climate-independent econometric-based models and complex climate-sensitive data-driven models to average to extreme wet and dry climate conditions—representative of a new climate normal. Here, the climate-independent model displayed low performance during extreme dry conditions with predictions exceeding 90% and 40% of the observed monthly and seasonal volumetric demands, respectively, which we attribute to insufficient model complexity. The climate-sensitive models displayed greater accuracy in all conditions, with an ordinary least squares model demonstrating a measurable reduction in prediction bias (3.4% vs. -27.3%) and RMSE (74.0 lpcd vs. 294 lpcd) compared to the climate-independent model. The climate-sensitive workflow increased model accuracy and characterized climate-demand interactions, demonstrating a novel tool to enhance water system management.

54 ENVIRONMENTAL SCIENCES↗