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DOE OSTI2025

House Advantage or House of Cards? Stacking the Deck for Data Videos Leads to Null Results: Preprint

Videos are becoming a ubiquitous means of sharing information on social media platforms. In response, data videos - short clips combining visualization with dynamic storytelling, audio descriptions, and spatial referencing - have gained popularity for communicating data. These affordances suggest that data videos might communicate data patterns, trends, and concepts more effectively than static visualizations, enhancing comprehension. However, existing research has not systematically tested this claim. To address this gap, we conducted three controlled studies to measure comprehension differences between data videos and static visualizations. Despite leveraging visual cues and audio explanations, no data video led to significantly better comprehension than an analogous static visualization. Our results suggest data videos are not categorically better and that future research should examine the tradeoffs between their engagement benefits and costs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Detector Materials Scoping Study: Research and Development Recommendations

Radiation detection materials have a unique role in many nuclear security missions. The variety of different applications requires the use of different materials whose characteristics are determined by the specific application requirements. While baseline capabilities have been established to use radiation detection in these applications, the potential to greatly advance those capabilities still exists through the development of superior radiation detection materials and/or the development of new materials that enable new technologies to be implemented more effectively. In 2024 the Defense Nuclear Nonproliferation Research and Development (DNN R&D) Near Field Detection Portfolio charged a detector materials scoping study, composed of a group of radiation-detection materials subject matter experts, to produce a community-wide consensus view of the current state of radiation materials research and to set recommendations for expanded investment over a ten-year time frame. This scoping study sought to understand and document the landscape of how radiation detection materials are used, what characteristics drive the selection of various materials, and what developments are needed to drive the state of the art. To respond to this charge, the scoping study created three working groups, each focusing on a different topical area in radiation detection materials research - Semiconductor Materials, Inorganic Scintillators and Organic Scintillators - with the task to identify the current state of the art in materials research and to provide mission-relevant research and development recommendations. Each working group was chaired by two members of the project team with widely recognized expertise in the field. Solicitations were sent out to experts at the DOE national laboratories, industry, academia and federal government agencies to participate in these working groups. The working groups met at regular intervals throughout 2024 and early 2025, each delivering a technical roadmap designed to enable the pursuit of R&D more intensely on high-impact materials challenges and detector solutions that are deemed as the greatest strategic value to DNN R&D and its stakeholders. The roadmap is also intended to help communicate recommended programmatic priorities within DNN R&D and across the nonproliferation and research communities.

36 MATERIALS SCIENCE↗

DOE OSTI2024

UMap: An application-oriented user level memory mapping library

Exploiting the prominent role of complex memories in exascale node architecture, the UMap page fault handler offers new capabilities to access large memory-mapped data sets directly. UMap provides flexible configuration options to customize page handling to each application, including analysis of massive observational and simulation data sets. The high-performance design features I/O decoupling, dynamic load balancing, and application-level controls. Page faults triggered by application threads and processes accessing data mapped to a UMapp’ed region are handled via the Linux userfaultfd protocol, an asynchronous message-oriented kernel-user communication mechanism that avoids the context switch penalty of traditional signal fault handlers. UMap is fully open source. In this paper, we give an overview of the UMap library architecture, its extensible plugin architecture, and the use/performance of UMap in emerging heterogeneous memory hierarchies such as near-node Non-volatile Memory (NVM) and network attached memories. We highlight new capabilities in two pagefault management plugins, the NetworkStore and SparseStore. We demonstrate the integration between UMap and multiple ECP products including Caliper, Metall, ZFP, Mochi, and Ripples.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.24

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Neuromuscular Junction Model Optimized for Electrical Platforms

Neuromuscular junctions (NMJs), specialized synapses between motor neurons and muscle fibers, are essential for muscle activity. A simple and reproducible cell-based in vitro NMJ platform is needed to test the impact of chemicals on the neuron-muscle communication. Our platform utilizes genetically modified neurons and muscle cells, optimized culture conditions, and commercially available multielectrode array system for recording action potentials. Neuronal cells (NSC34) were optogenetically modified with channelrhodopsin chimera to allow for simultaneous, light-mediated, millisecond-precise activation of neuronal population. This signal is propagated through functional synapses to the muscle fibers. Muscle cells (C2C12) were modified by incorporating gap junction protein (Connexin-43) to improve intracellular communication without affecting muscle differentiation. This communication between muscle fibers resulted in better signal propagation and signal strength. Optimized culture medium facilitated the growth and differentiation of both cell types together. Our system was validated using vecuronium, a muscle relaxant, which abolished the muscle response. This in vitro model provides a unique tool for establishing a NMJ platform that is easy to record and analyze. Potential applications include nondestructive long-term screening of drugs affecting the NMJ.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Suillus : an emerging model for the study of ectomycorrhizal ecology and evolution

Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically relevant fungal genus primarily associated with the plant family Pinaceae, into a model system for studying ectomycorrhizal (ECM) associations. Over the last decade, we have compiled extensive genomic resources, culture libraries, a phenotype database, and protocols for manipulating Suillus fungi with and without their tree partners. Our efforts have already resulted in a large number of publicly available genomes, transcriptomes, and respective annotations, as well as advances in our understanding of mycorrhizal partner specificity and host communication, fungal and plant nutrition, environmental adaptation, soil nutrient cycling, interspecific competition, and biological invasions. Here, we highlight the most significant recent findings enabled by Suillus, present a suite of protocols for working with the genus, and discuss how Suillus is emerging as an important model to elucidate the ecology and evolution of ECM interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Comparison of experimental and computational methods for discharge measurements from tidal wetlands

This short communication describes the use and comparison of three methods used to calculate the flow discharge from a tidal wetland stream. The techniques presented are a) bottom-mounted ADCP deployments, b) vessel-mounted ADCP transects, and c) a volume inundation spatial model that relies on a high-resolution LiDAR dataset and time-series of water surface elevation data. The relative agreement between these three methods is used to build confidence in the application of these techniques to the challenge of deducing flow discharge from tidal wetlands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Good Practices for High-Quality Scientific Computing

Experimental and observational sciences have developed robust practices for conducting experiments, maintaining their instruments, and record keeping for provenance. Computational science has only recently begun to confront the issue of quality of their instrument, the software, and the credibility of their scientific output. Most of the available literature in software engineering relates to enterprise software. While it can inform practices in scientific software, adjustments are usually needed. From time to time quality conscious practitioners have published collections of best practices for scientific software. Here, this article provides one more such list but with updated suggestions, motivated by the need to keep up with the rapid changes in the computing industry.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Quantum light: creation, integration, and applications

In today’s rapidly evolving quantum landscape, the generation and manipulation of quantum light not only represent fundamental challenges but also herald unprecedented opportunities in communication, computing, sensing, and imaging. This special issue brings together a collection of contributions that span the entire journey, from the creation of quantum light using novel materials and emitters to its seamless integration into photonic architectures and eventual deployment in advanced quantum applications. This special issue, “Quantum Light: Creation, Integration, and Applications,” features a collection of three review articles, five perspectives, and 23 original research papers, highlighting both the timeliness of the topic and the remarkable breadth and richness of ongoing advancements in the field.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Support of the US-Japan Binational Photosynthesis Workshop

This workshop was held over the course of 3 days in early November of 2023 on the campus of Arizona State University. Its primary goal was to facilitate interaction and productive collaboration between scientists based in Japan and the U.S. who work on the mechanisms of energy transduction carried out by photosynthetic organisms. Due to boundaries of geography and culture, communication and collaboration between US and Japanese scientists working in the field has not always been optimal. The UJBPW overcame these boundaries by holding a relatively small conference where people could discuss results and ideas freely. The emphasis was on scientific diversity and promotion of younger scientists and it gave graduate students the opportunity to meet the people whose papers they have been reading and perhaps find a postdoctoral position, which is a great way to forge scientific links across national boundaries.

09 BIOMASS FUELS↗

DOE OSTI2020

Compiler and Runtime Approaches to Enable Large-Scale Irregular Programs. Final report, July 2013 - July 2019

While regular algorithms, characterized by operations on dense matrices and arrays, have long been the mainstay of scientific, high-performance computing, irregular algorithms, which feature unpredictable accesses to pointer-based data structures, are becoming increasingly common in high performance computing, arising in graph analysis, data mining and visualization, among other domains. Unfortunately, the defining characteristics of irregular applications, their dynamic, unpredictable, data-dependent access patterns and data layouts, make achieving high performance on large scale systems difficult. Scaling applications to peta- and exa-scale requires carefully controlling communication and data movement and placement, an inherently difficult task when access patterns and data layouts are unpredictable! Most irregular applications that attain high performance must be painstakingly hand-written and hand-tuned, with few common principles or paradigms uniting various implementations and easing future development. Despite the increasing importance of irregular applications, there is little programmer knowledge, and even less compiler ability, devoted to optimizing them. This project aims to solve these problems. By allowing programmers to write irregular applications in high level forms, with at most a few annotations highlighting key structural properties, programmers can focus on developing their algorithms and methods. The compiler and run-time system can take on the tedious task of optimizing the application for execution at large scales, and can automatically provide efficient implementations. This will provide portability and ease maintenance for existing irregular applications, but, more importantly, open up whole new domains of computational science to large-scale, high-performance simulation codes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Hybrid Modeling in the Era of Smart Manufacturing

Smart manufacturing (SM) is a new paradigm that allows manufacturing to enter its fourth revolution by exploiting state-of-the art sensing, communication and computation as the Industrial Internet of Things (IioT). Via the use of high-performance computing and advanced modeling, SM aims to improve the flexibility and adaptability of manufacturing. This paper addresses this trend by reviewing the combined use of data-driven and knowledge-enabled hybrid models (HM), and discusses how such techniques seamlessly fit in the SM platform. Furthermore, a discussion of the new paradigms of HM enabled by the SM platform is given, highlighting their importance in future large-scale applications of the SM platform.

42 ENGINEERING↗

DOE OSTI2023

Fusion Materials Semiannual Progress Report for the Period Ending December 31, 2022

This is the seventy-third in a series of semiannual technical progress reports on fusion materials science activity supported by the Fusion Energy Sciences Program of the U.S. Department of Energy. It covers the period ending December 31, 2022. This report focuses on research addressing the effects on materials properties and performance of exposure to the neutronic, thermal and chemical environments anticipated in the chambers of fusion experiments and energy systems. This research is a major element of the national effort to establish the materials knowledge base for an economically and environmentally attractive fusion energy source. Research activities on issues related to the interaction of materials with plasmas are reported separately. The results reported are the products of a national effort involving a number of national laboratories and universities. A large fraction of this work, particularly in relation to fission reactor irradiations, is carried out collaboratively with partners in Japan, Russia, and the European Union. The purpose of this series of reports is to provide a working technical record for the use of program participants, and to provide a means of communicating the efforts of fusion materials scientists to the broader fusion community, both nationally and worldwide. This report has been compiled by Stephanie Melton, Oak Ridge National Laboratory. Her efforts, and the efforts of the many persons who made technical contributions, are gratefully acknowledged.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Fusion Materials Semiannual Progress Report for the Period Ending December 31, 2023

This is the seventy-fifth in a series of semiannual technical progress reports on fusion materials science activity supported by the Fusion Energy Sciences Program of the U.S. Department of Energy. It covers the period ending December 31, 2023. This report focuses on research addressing the effects on materials properties and performance of exposure to the neutronic, thermal and chemical environments anticipated in the chambers of fusion experiments and energy systems. This research is a major element of the national effort to establish the materials knowledge base for an economically and environmentally attractive fusion energy source. Research activities on issues related to the interaction of materials with plasmas are reported separately. The results reported are the products of a national effort involving a number of national laboratories and universities. A large fraction of this work, particularly in relation to fission reactor irradiations, is carried out collaboratively with partners in Japan, Russia, and the European Union. The purpose of this series of reports is to provide a working technical record for the use of program participants, and to provide a means of communicating the efforts of fusion materials scientists to the broader fusion community, both nationally and worldwide.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Fusion Materials Semiannual Progress Report for the Period Ending June 30, 2025

This is the seventy-eighth in a series of semiannual technical progress reports on fusion materials science activity supported by the Fusion Energy Sciences Program of the U.S. Department of Energy. It covers the period ending June 30 th , 2025. This report focuses on research addressing the effects on materials properties and performance of exposure to the neutronic, thermal and chemical environments anticipated in the chambers of fusion experiments and energy systems. This research is a major element of the national effort to establish the materials knowledge base for an economically and environmentally attractive fusion energy source. Research activities on issues related to the interaction of materials with plasmas are reported separately. The results reported are the products of a national effort involving a number of national laboratories and universities. A large fraction of this work, particularly in relation to fission reactor irradiations, is carried out collaboratively with international partners, e.g., Japan and the UK. The purpose of this series of reports is to provide a working technical record for the use of program participants, and to provide a means of communicating the efforts of fusion materials scientists to the broader fusion community, both nationally and worldwide. This report has been compiled by Stephanie Melton, Oak Ridge National Laboratory. Her efforts, and the efforts of the many persons who made technical contributions, are gratefully acknowledged.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Automated Cyber Security Testing Platform for Industrial Control Systems

Nuclear Power Plants (NPPs) are a complex system of coupled physics controlled by a network of Programmable Logic Controllers (PLCs). These PLCs communicate process data across the network to coordinate control actions with each other and inform the operators of process variables and control decisions. Networking the PLCs allows more effective process control and provides the operator more information which results in more efficient plant operation. This interconnectivity creates new security issues, as operators have more access to the plant controls, so will bad actors. As plant networks become more digitized and encompass more sophisticated controllers, the network surface exposed to cyber interference grows. Understanding the dynamics of these coupled systems of physics, control logic, and network communications is critical to their protection. The research into the cybersecurity of the Operational Technologies of NPPs is developing and requires a platform that can allow high fidelity physics simulations to interact with digital networks of controllers. This will require three main components: a network simulation environment, a physics simulator, and virtual PLCs (vPLC) that represent typical industry hardware. A platform that incorporates these three components to provide the most accurate representation of actual NPP networks and controllers is developed in this paper.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

PETSc/TAO Users Manual Revision 3.23

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors

To date, effective therapeutic treatments that confer strong attenuation against coronaviruses (CoVs) remain elusive. Among potential drug targets, the helicase of CoVs is attractive due to its sequence conservation and indispensability. We rely on atomistic molecular dynamics simulations to explore the structural coordination and dynamics associated with the SARS-CoV-2 Nsp13 apo enzyme, as well as their complexes with natural ligands. A complex communication network is revealed among the five domains of Nsp13, which is differentially activated because of the presence of the ligands, as shown by shear strain analysis, principal components analysis, dynamical cross-correlation matrix analysis, and water transport analysis. The binding free energy and the corresponding mechanism of action are presented for three small molecules that were shown to be efficient inhibitors of the previous SARS-CoV Nsp13 enzyme. Together, our findings provide critical fresh insights for rational design of broad-spectrum antivirals against CoVs.

59 BASIC BIOLOGICAL SCIENCES↗