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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Adaptive elasticity policies for staging-based in situ visualization

In situ processing aims to alleviate the growing gap between computation and I/O capabilities by performing data processing close to the data source. In situ processing is widely used to process data generated by multiple data sources, including observation data from edge devices or scientific observational facilities and the simulation data generated by scientific computation on a high-performance computing (HPC) platform. For a scientific workflow that is run on an HPC platform and composed of a simulation program and an in situ data analytics or visualization (abbreviated as ana/vis) task, there is an implicit assumption that the computing resources assigned to the workflow keep static during the workflow execution. However, with the converging trend between the HPC and cloud computing platform, running the in situ ana/vis task in an elastic way is promising to decrease its overhead and improve its resource utilization rate. Resource elasticity represents the ability to change resource configurations such as the number of computing nodes/processes during workflow execution. An elastic job may dynamically adjust resource configurations; it may use a few resources at the beginning and more resources toward the end of the job when interesting data appear. However, it is hard to predict a priori how many computing nodes/processes need to be added/removed during the workflow execution to adapt to changing workflow needs. How to efficiently guide elasticity operations, such as growing or shrinking the number of processes used for in situ analysis during workflow execution, is an open-ended research question. In this article, we present adaptive elasticity policies that adopt workflow runtime information collected during workflow execution to predict how to trigger the addition/removal of processes in order to minimize in situ processing overhead. Taking in situ visualization tasks as an example, we integrate the presented elasticity policies into a staging-based elastic workflow and evaluate its efficiency in multiple elasticity scenarios. Compared with the situation without elasticity or with a static elasticity policy that uses a fixed number of processes for each rescaling operation, the adaptive elasticity policy can save overhead in finding a proper resource configuration and improve resource utilization efficiency. Furthermore, one experiment illustrates that the adaptive elasticity policy saves 41% of core-hours compared with the situation without the resource elasticity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗
DOE OSTI2025

Optical Test Bench (SYSM 5620 Final Report)

The National Ignition Facility (NIF) is a research facility that focuses on High Energy Density Science and Inertial Confinement Fusion. In the NIF, 192 laser beams are directed into a miniscule Target Capsule to generate an implosion – this is called a NIF Shot. Many NIF Users conduct experiments using different Targets and laser inputs to generate reactions that are of interest to the scientific community. Those reactions are monitored using various Target Diagnostic instruments, including Shot Time Photography – which provides crucial images of the Target as the implosion occurs. A subset of these NIF Users is less interested in the reaction itself and more interested in subjecting materials or devices to the intense environment that these reactions can create. Using the Target as a source of x-rays, neutrons, or blast loading for particular materials has been significant to the shock physics community and to those who work in extreme design spaces. However, the Material and Radiation Effects team – that performs these experiments on behalf of the NIF Users – has not been able to make good use of the existing Shot Time Photography Diagnostics. The STP cameras are focused on the Targets rather than the MRE Customers’ materials, the current system is not oriented to have a good view of the MRE Customers’ materials, and the cameras are limited in their capabilities (black and white, poor resolution, etc.). As MRE experiments increase in quantity and importance to the scientific community, the desire for visual monitoring of the experiments to substantiate models and inform other data is also rising.

42 ENGINEERING↗
DOE OSTI2025

Enabling Command-and-Control in Advanced In Situ Workflows

Scientific discovery is progressing towards autonomous science with the combination of scientific instruments, high-performance computing, and artificial intelligence in complex workflows. This evolution introduces new requirements for managing scientific workflows, including feedback loops, near real-time constraints, and the ability to dynamically control workflow execution. In situ workflows that analyze and visualize data as it is generated are well-suited to satisfy stringent time constraints and their iterative nature offers greater opportunities for command-and-control. However, only a few of the many workflow management systems available have been specifically designed to manage in situ workflows and often lack support for automated feedback loops that allow analysis and visualization components to interact with the main scientific data producer. To address this need, we present in this paper how to add command-and-control capabilities to a workflow management system. We identify the functional design requirements of such a command-and-control system, detail its architecture, interface, and core mechanisms, and illustrate how advanced in situ workflows can leverage command-and-control in three use cases: graceful termination with checkpoint, dynamic and adaptive data reduction, and event-triggered analysis.

Mehta, Kshitij [ORNL] (ORCID:0000000297149981)↗
DOE OSTI2023

FunMC^2: A Filter for Uncertainty Visualization of Marching Cubes on Multi-Core Devices

Visualization is an important tool for scientists to extract understanding from complex scientific data. Scientists need to understand the uncertainty inherent in all scientific data in order to interpret the data correctly. Uncertainty visualization has been an active and growing area of research to address this challenge. Algorithms for uncertainty visualization can be expensive, and research efforts have been focused mainly on structured grid types. Further, support for uncertainty visualization in production tools is limited. In this paper, we adapt an algorithm for computing key metrics for visualizing uncertainty in Marching Cubes (MC) to multi-core devices and present the design, implementation, and evaluation for a Filter for uncertainty visualization of Marching Cubes on Multi-Core devices (FunMC2). FunMC2 accelerates the uncertainty visualization of MC significantly, and it is portable across multi-core CPUs and GPUs. Evaluation results show that FunMC2 based on OpenMP runs around 11× to 41× faster on multi-core CPUs than the corresponding serial version using one CPU core. FunMC2 based on a single GPU is around 5× to 9× faster than FunMC2 running by OpenMP. Moreover, FunMC2 is flexible enough to process ensemble data with both structured and unstructured mesh types. Furthermore, we demonstrate that FunMC2 can be seamlessly integrated as a plugin into ParaView, a production visualization tool for post-processing.

Wang, Jay↗
DOE OSTI2025

Ocelot: An Interactive, Efficient Distributed Compression-As-a-Service Platform With Optimized Data Compression Techniques

Large volumes of data generated by scientific simulations, genome sequencing, and other applications need to be moved among clusters for data collection/analysis. Data compression techniques have effectively reduced data storage and transfer costs. However, users' requirements on interactively controlling both data quality and compression ratios are non-trivial to fulfill. Here, we propose a novel Compression-as-a-Service (CaaS) platform called Ocelot with four important contributions: (1) It offers real-time visualization, interactive compression, and transfer of scientific datasets. (2) It incorporates new strategies for compressing diverse types of datasets more effectively than traditional methods. (3) It provides an effective method for estimating the compression ratio and execution time of compression tasks. (4) Experiments on multiple real-world datasets on geographically distributed computers show that Ocelot can significantly improve data transfer efficiency with a performance gain of more than 10x in computing clusters with relatively slow networks.

compression as a service (CaaS)↗
DOE OSTI2024

Distributed Neural Representation for Reactive In Situ Visualization

Implicit neural representations (INRs) have emerged as a powerful tool for compressing large-scale volume data. This opens up new possibilities for in situ visualization. However, the efficient application of INRs to distributed data remains an underexplored area. Here, in this work, we develop a distributed volumetric neural representation and optimize it for in situ visualization. Our technique eliminates data exchanges between processes, achieving state-of-the-art compression speed, quality and ratios. Our technique also enables the implementation of an efficient strategy for caching large-scale simulation data in high temporal frequencies, further facilitating the use of reactive in situ visualization in a wider range of scientific problems. We integrate this system with the Ascent infrastructure and evaluate its performance and usability using real-world simulations.

Wu, Qi↗
DOE OSTI2023

Driving Next-Generation Workflows from the Data Plane

We observe the emergence of a new generation of scientific workflows that process data produced at a sustained rate by scientific instruments and large scale numerical simulations. This data is consumed by multiple analysis, visualization, or Machine Learning components not only to enable inference and justify the scientific program, but also to monitor and steer the evolution of these experiments. In such workflows, moving intermediate data efficiently is key to performance, more than efficiently scheduling computational tasks. However, most traditional workflow management systems focus on optimizing task scheduling and then deal with data management, assuming a “move little, compute for long” model, which makes them unfit to the efficient management of this new generation of workflows. Therefore, we advocate for a new way to manage scientific workflows. We propose to consider an efficiently and independently managed data plane that can store and stream data. Workflows compute components, in the application plane can then interact with the data plane, abstracted from complexities of data management. Then, the role of a workflow management system would become that of a control plane that allows users to connect services together to execute the workflow and manages connections between the application and data planes. In this position paper, we characterize several next-generation workflow motifs and describe how their interaction with the data plane is a challenge to traditional workflow management systems. Then, we express a set of requirements that a workflow management system should meet to efficiently manage next-generation workflows at different scales. Based on these requirements, we expose our vision of driving next-generation workflows from the data plane and list remaining open challenges.

Suter, Fred↗
DOE OSTI2024

epicsuite(EAS)

Software, Documentation, Tutorials, Testing data, Example data for processing, analysis, filtering, querying, visualization and otherwise transforming genomic data for scientific analysis and discovery.

Rogers, David H.↗
DOE OSTI2021

Integrated System and Application Continuous Performance Monitoring and Analysis Capability

Scientific applications run on high-performance computing (HPC) systems are critical for many national security missions within Sandia and the NNSA complex. However, these applications often face performance degradation and even failures that are challenging to diagnose. To provide unprecedented insight into these issues, the HPC Development, HPC Systems, Computational Science, and Plasma Theory & Simulation departments at Sandia crafted and completed their FY21 ASC Level 2 milestone entitled "Integrated System and Application Continuous Performance Monitoring and Analysis Capability." The milestone created a novel integrated HPC system and application monitoring and analysis capability by extending Sandia's Kokkos application portability framework, Lightweight Distributed Metric Service (LDMS) monitoring tool, and scalable storage, analysis, and visualization pipeline. The extensions to Kokkos and LDMS enable collection and storage of application data during run time, as it is generated, with negligible overhead. This data is combined with HPC system data within the extended analysis pipeline to present relevant visualizations of derived system and application metrics that can be viewed at run time or post run. This new capability was evaluated using several week-long, 290-node runs of Sandia's ElectroMagnetic Plasma In Realistic Environments ( EMPIRE ) modeling and design tool and resulted in 1TB of application data and 50TB of system data. EMPIRE developers remarked this capability was incredibly helpful for quickly assessing application health and performance alongside system state. In short, this milestone work built the foundation for expansive HPC system and application data collection, storage, analysis, visualization, and feedback framework that will increase total scientific output of Sandia's HPC users.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Integrated System and Application Continuous Performance Monitoring and Analysis Capability (Final)

Scientific applications run on high-performance computing (HPC) systems are critical for many national security missions within Sandia and the NNSA complex. However, these applications often face performance degradation and even failures that are challenging to diagnose. To provide unprecedented insight into these issues, the HPC Development, HPC Systems, Computational Science, and Plasma Theory & Simulation departments at Sandia crafted and completed their FY21 ASC Level 2 milestone entitled "Integrated System and Application Continuous Performance Monitoring and Analysis Capability." The milestone created a novel integrated HPC system and application monitoring and analysis capability by extending Sandia’s Kokkos application portability framework, Lightweight Distributed Metric Service (LDMS) monitoring tool, and scalable storage, analysis, and visualization pipeline. The extensions to Kokkos and LDMS enable collection and storage of application data during run time, as it is generated, with negligible overhead. This data is combined with HPC system data within the extended analysis pipeline to present relevant visualizations of derived system and application metrics that can be viewed at run time or post run. This new capability was evaluated using several week-long, 290-node runs of Sandia’s ElectroMagnetic Plasma In Realistic Environments (EMPIRE) modeling and design tool and resulted in 1TB of application data and 50TB of system data. EMPIRE developers remarked this capability was incredibly helpful for quickly assessing application health and performance alongside system state. In short, this milestone work built the foundation for expansive HPC system and application data collection, storage, analysis, visualization, and feedback framework that will increase total scientific output of Sandia’s HPC users.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Applications of visualization technology in the structural sciences

The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data—particularly from cryo-electron microscopy and x-ray crystallography—are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.

Eng, Edward T. [New York Structural Biology Center↗
DOE OSTI2025

Foundation Models for Zero-Shot Segmentation of Scientific Images without AI-Ready Data

Zero-shot and prompt-based models have excelled at visual reasoning tasks by leveraging large-scale natural image corpora, but they often fail on sparse and domain-specific scientific image data. We introduce Zenesis, a no-code interactive computer vision platform designed to reduce data readiness bottlenecks in scientific imaging workflows. Zenesis integrates lightweight multimodal adaptation for zero-shot inference on raw scientific data, human-in-the-loop refinement, and heuristic-based temporal enhancement. We validate our approach on Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) datasets of catalyst-loaded membranes. Zenesis outperforms baselines, achieving an average accuracy of 0.947, Intersection over Union (IoU) of 0.858, and Dice score of 0.923 on amorphous catalyst samples; and 0.987 accuracy, 0.857 IoU, and 0.923 Dice on crystalline samples. These results represent a significant performance gain over conventional methods such as Otsu thresholding and standalone models like the Segment Anything Model (SAM). Zenesis enables effective image segmentation in domains where annotated datasets are limited, offering a scalable solution for scientific discovery.

Mukherjee, Shubhabrata↗
DOE OSTI2022

Computational Estimation by Scientific Data Mining with Classical Methods to Automate Learning Strategies of Scientists

Experimental results are often plotted as 2-dimensional graphical plots (aka graphs) in scientific domains depicting dependent versus independent variables to aid visual analysis of processes. Repeatedly performing laboratory experiments consumes significant time and resources, motivating the need for computational estimation. The goals are to estimate the graph obtained in an experiment given its input conditions, and to estimate the conditions that would lead to a desired graph. Existing estimation approaches often do not meet accuracy and efficiency needs of targeted applications. We develop a computational estimation approach called AutoDomainMine that integrates clustering and classification over complex scientific data in a framework so as to automate classical learning methods of scientists. Knowledge discovered thereby from a database of existing experiments serves as the basis for estimation. Challenges include preserving domain semantics in clustering, finding matching strategies in classification, striking a good balance between elaboration and conciseness while displaying estimation results based on needs of targeted users, and deriving objective measures to capture subjective user interests. These and other challenges are addressed in this work. The AutoDomainMine approach is used to build a computational estimation system, rigorously evaluated with real data in Materials Science. Our evaluation confirms that AutoDomainMine provides desired accuracy and efficiency in computational estimation. It is extendable to other science and engineering domains as proved by adaptation of its sub-processes within fields such as Bioinformatics and Nanotechnology.

Computer Science↗
DOE OSTI2026

Visualization for Insight and Data Analysis in Energy Research

This talk explores how advanced visualization technologies are transforming analytical reasoning and knowledge discovery in energy research, drawing on recent work at the National Laboratory of the Rockies' Computational Science Center. Through a series of scientific case studies, we demonstrate how immersive and high-resolution visualization environments enable scientists and engineers to identify previously unseen patterns and features - insights that often remain hidden in traditional desktop-based analysis. By embedding richer information into interactive analytics tools, these approaches support the exploration of complex, multivariate parameter spaces, where interaction itself catalyzes understanding. Beyond capability, we emphasize the critical role of visualization design grounded in perception and cognition, showing how visual encodings directly influence analytical outcomes. Spanning applications from materials science to integrated energy systems, these visualization approaches accelerate innovation and improve decision-making by enabling deeper, more reliable insight into increasingly complex energy data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Make the Fastest Faster: Importance Mask Synthesis for Interactive Volume Visualization using Reconstruction Neural Networks

Visualizing a large-scale volumetric dataset with high resolution is challenging due to the substantial computational time and space complexity. Recent deep learning-based image inpainting methods significantly improve rendering latency by reconstructing a high-resolution image for visualization in constant time on GPU from a partially rendered image where only a portion of pixels go through the expensive rendering pipeline. However, existing solutions need to render every pixel of either a predefined regular sampling pattern or an irregular sample pattern predicted from a low-resolution image rendering. Both methods require a significant amount of expensive pixel-level rendering. In this work, we provide Importance Mask Learning (IML) and Synthesis (IMS) networks, which are the first attempts to directly synthesize important regions of the regular sampling pattern from the user’s view parameters, to further minimize the number of pixels to render by jointly considering the dataset, user behavior, and the downstream reconstruction neural network. Our solution is a unified framework to handle various types of inpainting methods through the proposed differentiable compaction/decompaction layers. Experiments show our method can further improve the overall rendering latency of state-of-the-art volume visualization methods using reconstruction neural network for free when rendering scientific volumetric datasets. Our method can also directly optimize the off-the-shelf pre-trained reconstruction neural networks without elongated retraining.

Large-scale data↗
DOE OSTI2022

Cryo-electron Microscopy of Adeno-associated Virus

Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Extremely Scalable Distributed Computation of Contour Trees via Pre-Simplification

Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains challenging due to scalability limitations. Recent developments in distributed hierarchical contour trees have addressed these challenges by enabling scalable computation across distributed systems. Building on these structures, advanced analytical tasks—such as volumetric branch decomposition and contour extraction—have been introduced to facilitate large-scale scientific analysis. Despite these advancements, such analytical tasks substantially increase memory usage, which hampers scalability. In this paper, we propose a pre-simplification strategy to significantly reduce the memory overhead associated with analytical tasks on distributed hierarchical contour trees. We demonstrate enhanced scalability through strong scaling experiments, constructing the largest known contour tree—comprising over half a trillion nodes with complex topology—in under 15 minutes on a dataset containing 550 billion elements.

Li, Mingzhe [University of Utah]↗