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DOE OSTI2024

Birth of protein folds and functions in the virome

The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus–host interactions that are common across the virome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Dynamics of nanoscale phase decomposition in laser ablation

Abstract Laser ablation is a process that bears both fundamental physics interest and has wide industrial applications. For decades, the lack of probes on the relevant time and length scales has prevented access to the highly nonequilibrium phase decomposition processes triggered by laser excitation. In this study, a close integration of time-resolved probing by intense femtosecond X-ray pulses with large-scale atomistic modeling has yielded unique insights into the ablation dynamics of thin gold films irradiated by femtosecond laser pulses. The emergence and growth of nanoscale density heterogeneities in the expanding ablation plume, predicted in the simulations, are mapped to the rapid evolution of distinct small angle diffraction features. This mapping enables identification of the characteristic signatures of different phase decomposition processes occurring simultaneously in the plume, which are driven by photomechanical and thermodynamic driving forces. Beyond the specific insights into the ablation phenomenon, this study demonstrates the power of joint X-ray probing and atomistic modeling of material dynamics under extreme conditions of thermal and mechanical nonequilibrium.

Sun, Yanwen (ORCID:0000000159266565)↗

DOE OSTI2025

Dynamic in-context learning with conversational models for data extraction and materials property prediction

The advent of natural language processing and large language models (LLMs) has revolutionized the extraction of data from unstructured scholarly papers. However, ensuring data trustworthiness remains a significant challenge. In this paper, we introduce PropertyExtractor, an open-source tool that leverages advanced conversational LLMs such as Google gemini-pro and OpenAI gpt-4, blends zero-shot with few-shot in-context learning, and employs engineered prompts for the dynamic refinement of structured information hierarchies—enabling autonomous, efficient, scalable, and accurate identification, extraction, and verification of material property data. Our tests on material data demonstrate precision and recall that exceed 95% with an error rate of ∼9%, highlighting the effectiveness and versatility of the toolkit. Finally, databases for 2D material thicknesses, a critical parameter for device integration, and energy bandgap values are developed using PropertyExtractor. In particular, for the thickness database, the rapid evolution of the field has outpaced both experimental measurements and computational methods, creating a significant data gap. Our work addresses this gap and showcases the potential of PropertyExtractor as a reliable and efficient tool for the autonomous generation of various material property databases, advancing the field.

Ekuma, Chinedu E. (ORCID:0000000258527556)↗

DOE OSTI2026

Application of Portable Parallelization Strategies for GPUs on track reconstruction kernels

Utilizing the computational power of GPUs is one of the key ingredients to meet the computing challenges presented to the next generation of High-Energy Physics (HEP) experiments. Unlike CPUs, developing software for GPUs often involves using architecturespecific programming languages promoted by the GPU vendors and hence limits the platform that the code can run on. Various portability solutions have been developed to achieve portable, performant software across different GPU vendors. Given the rapid evolution of these portability solutions, an early adoption of them in simple HEP testbed applications will help us understand the strengths and weaknesses of respective approaches.We apply several portability solutions, including Alpaka, Kokkos, SYCL and std::execution::par, on kernels for track propagation extracted from the mkFit project. We report on the development experience of the same application with different portability solutions, as well as their performance on GPUs, measured as the throughput of the kernels, from different manufacturers such as NVIDIA, AMD and Intel.

Kwok, Martin [Fermilab] (ORCID:0000000286936146)↗

DOE OSTI2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Collins-Soper kernel in the QCD instanton vacuum

We outline a general framework for evaluating the nonperturbative soft functions in the quantum chromodynamics (QCD) instanton vacuum. In particular, from the soft function we derive the Collins-Soper (CS) kernel, which drives the rapidity evolution of the transverse-momentum-dependent parton distributions. The resulting CS kernel, when supplemented with the perturbative contribution, agrees well with recent lattice results and some phenomenological parametrizations. Moreover, our CS kernel depends logarithmically on the large quark transverse separation, providing a key constraint on its phenomenological parametrization. Finally, a lattice calculation can be directly compared to our generic results in Euclidean signature, thus providing a new approach for evalulating the soft function and extracting the CS kernel by analytical continuation.

QCD phenomenology↗

DOE OSTI2024

A Hybrid Anomaly Detection Approach for Obfuscated Malware

With the rapid evolution of malicious software, cyber threats have become increasingly sophisticated, employing advanced obfuscation techniques to evade traditional detection methods. This study presents a hybrid anomaly detection approach applied to obfuscated malware. Even though there is a large body of research in this field, existing malware detection techniques have some drawbacks, such as requiring large amounts of data, trustworthiness (imprecise results) of algorithms, and advanced obfuscation. To overcome these challenges, there is a need to employ solid and efficient techniques for malware detection. This paper proposes a hybrid approach, combining an autoencoder with traditional machine-learning methods to create an efficient malware detection framework. We used the malware memory dataset (MalMemAnalysis-2022) to evaluate this framework. The results indicate that our proposed approach can detect obfuscated malware when a deep autoencoder used for feature learning is combined with logistic regression, and it is extremely fast with an Accuracy, Detection Rate (DR), Matthew Correlation Coefficient(MCC), and Statistical Parity Difference

malware detection, Hybrid Anomly Detection, Obfusc↗

DOE OSTI2025

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication

The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.

definitions↗

DOE OSTI2025

LLM Benchmarking with LLaMA2: Evaluating Code Development Performance Across Multiple Programming Languages

The rapid evolution of large language models (LLMs) has opened new possibilities for automating various tasks in software development. This paper evaluates the capabilities of the LLaMA 2-70B model in automating these tasks for scientific applications written in commonly used programming languages. Using representative test problems, we assess the model's capacity to generate code, documentation, and unit tests, as well as its ability to translate existing code between commonly used programming languages. Our comprehensive analysis evaluates the compilation, runtime behavior, and correctness of the generated and translated code. Additionally, we assess the quality of automatically generated code, documentation, and unit tests. Here, our results indicate that while LLaMA 2-70B frequently generates syntactically correct and functional code for simpler numerical tasks, it encounters substantial difficulties with more complex, parallelized, or distributed computations, requiring considerable manual corrections. We identify key limitations and suggest areas for future improvements to better leverage AI-driven automation in scientific computing workflows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Impact of Inverter-Based Resources on Grid Protection: A Review of Negative-Sequence Current Generation

The increasing integration of inverter-based resources (IBRs) in power grids poses challenges to traditional protection systems, primarily due to their different fault current signatures compared to conventional synchronous generators. Unlike synchronous generators whose fault response is dictated by their physical design, IBRs exhibit a wide range of fault characteristics due to manufacturer-specific control algorithms and settings. This dependence on proprietary control schemes makes modeling IBR behavior during faults significantly more complex, especially considering the rapid evolution of inverter technology and the diverse control strategies employed. While much research has focused on the positive-sequence current injections of IBRs during symmetrical faults, the understanding of negative-sequence current generation during non-symmetrical faults remains limited. This report provides an overview of current research on IBRs' negative-sequence current generation during unbalanced faults and its impact on protection schemes based on negative-sequence components. It covers both type III wind turbines and full-size converter-based IBRs. Additionally, this report reviews strategies for grid-forming controlled inverters to generate negative-sequence current during unbalanced faults, in addition to grid-following controlled ones.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

ASEAN Technical Exchange Workshop for System Operators, Regulators, and Policymakers

This presentation provides an in-depth exploration of power system planning, cross-border electricity trading, and battery energy storage systems (BESS), offering actionable insights for system operators, regulators, and policymakers. The first section delves into power system planning and analysis, focusing on capacity expansion models and resource adequacy studies, including their role in optimizing system efficiency, managing emissions, and addressing system reliability risks. Key considerations, such as integration of transmission into generation planning and the forecasting versus optimization of customer distributed energy resources (DER) technologies, are explored. The session highlights critical trade-offs in spatial granularity and model runtimes, as well as the feasibility of aligning distribution investments with capacity expansion efforts. The second section examines cross-border electricity trading, with an emphasis on resource adequacy concepts such as reliability targets, loss of load expectation (LOLE), and planning reserve margins (PRM). Case studies on reserve market design and coordination across US regions provide insights into improving reserve deliverability and managing interregional power balance and congestion. This section also addresses market-to-market congestion management, including advanced strategies for high-voltage direct current (HVDC) optimization and ancillary service delivery. Finally, the presentation covers the rapid evolution of Battery Energy Storage Systems (BESS), highlighting their operational growth, regulatory frameworks, and use cases in grid flexibility, energy storage, and reliability. The discussion focuses on the benefits of BESS for system stability, resilience, and integration of renewable energy, offering insights into its role as a vital component in the transition toward a more sustainable and flexible grid. Key performance parameters, such as throughput, round-trip efficiency, and state of charge, are also examined.

25 ENERGY STORAGE↗

DOE OSTI2024

Regulators’ Financial Toolbox: Leveraging Software as a Service, Cloud Computing, and Artificial Intelligence in Electric Utilities

The rapid evolution of Software as a Service (SaaS), cloud computing, and artificial intelligence (AI) is transforming the electric utility industry, reshaping operations, customer engagement, and financial models. This webinar introduced how utilities can deploy advanced software solutions and AI-driven analytics to improve grid efficiency, optimize asset management, and accurately forecast demand.

Bartlett, Phillip↗

DOE OSTI2025

Existing Methods for Grid Strength Assessment and Role of Hydropower in Future Grids

The power system is undergoing rapid evolution with increasing penetration of inverter-based resources (IBRs), large loads, microgrids, and power electronic devices. Ensuring reliable and stable operation of the modern power grid is a multi-faceted challenge that requires detailed understanding of this complex system. Dynamic stability is a major concern in maintaining the security of power grids as the generation mixes and large loads transitions to include high shares of power electronic devices. The operation of IBRs in regions with low system strength and higher grid impedances has been found to be the main reason behind many of the power system instabilities that manifest themselves in various types of oscillations and interactions that, if not properly addressed and damped, can jeopardize the reliable operation of the power system. Weak grid conditions compound such stability problems, particularly when many IBRs operate in proximity to and connect to weak power grids. Therefore, it is important to assess grid strength for planning, integration and operation of IBRs for a given power system. In this report, we aim to understand and classify existing methodologies for grid strength assessment, along with their limitations and future needs. Further, we aim to utilize the huge untapped potential in utilizing hydro energy resources in addressing some of the pertinent challenges of grid strength and reliable operation of modern power systems. Hydropower, historically valued for its flexibility and dispatchability, now faces new constraints due to reduced share of synchronous machines in the generation mix and seasonal variability of available water resources. Yet, these same plants present untapped potential beyond energy generation - notably, as providers of critical grid services. This report explores how hydropower plants, particularly through operation as synchronous condensers, can play a pivotal role in strengthening the grid amid evolving system dynamics.

13 HYDRO ENERGY↗

NASA NTRS1964

Space-Cabin Atmospheres: Part II - Fire and Blast Hazards. A Literature Review

The rapid evolution of aircraft and, lately, space vehicles has brought with it the ever-increasing difficulty of designing for prevention of fires and explosions. The present-day sealed cabin with its limited work space, unusual atmospheric constituents, and lack of flexibility in emergency situations has brought new and ill-defined hazards into the picture. In the past, numerous data have been compiled on the fire and explosion characteristics of all things combustible. Unfortunately, much of the material is not pertinent to the actual operational problems in space. The confusion and controversy arising from attempts to evaluate the space-cabin fire problem appear to stem from past failure to compile the scattered data and to expose it to critical review and selection. In the compilation that follows, an attempt has been made to review the best available data that was deemed actually pertinent to the present problem. The effects of unusual atmospheres have been emphasized, but, as will soon be evident, other physical parameters also play a major role in determining the nature of the problem. Chapter 1 contains a discussion of pertinent definitions and theory. This is detailed only to the point of anticipating some of the problems of interpretation that may arise in other chapters of the report. Included in this chapter is speculation on the impact of unusual environmental conditions such as aerodynamic heating, reduced gravitational acceleration, and low ambient pressures. Chapter 2 covers flammable fabrics and carbonaceous solids; Chapter 3, specific fire hazards involving flammable liquids, vapors, and gases; and Chapter 4, electrical fires. Chapter 5 covers the fire, blast, and flash hazards from meteoroid penetration; and Chapter 6, the problems of fire prevention and extinguishment in space cabins. Chapter 7 reviews the factors of fire and blast hazards in selection of a space-cabin atmosphere.

Roth, Emanuel M.↗

NASA NTRS1974

Interpretation of epsilon Aurigae. III

The light curve expected from the eclipse of a star by a companion possessing a semitransparent disk has been investigated. Two computational procedures for deriving the light curve based on the geometrically thin-disk model are given here. Using these procedures, we have calculated the light curves of epsilon Aur based on different sets of parameters including those given previously by Wilson. We have also studied the light curve of epsilon Aur based on a geometrically thick disk model, and have advanced two proposals in order to understand the change in the shape of the light curve from one eclipse to the next, namely, (1) the rapid evolution that occurs in the disk and (2) the density waves in the disk and/or individual condensations that are revolving around the secondary each in an independent way.

Huang, S.-S.↗

NASA NTRS1975

Geophysical studies of floating ice by remote sensing

This paper presents an overview of recent remote-sensing techniques as applied to geophysical studies of floating ice. The current increase in scientific interest in floating ice has occurred during a time of rapid evolution of both remote-sensing platforms and sensors. Mesoscale and macroscale studies of floating ice are discussed under three sensor categories: visual, passive microwave, and active microwave. The specific studies that are reviewed primarily investigate ice drift and deformation, and ice type and ice roughness identification and distribution.

Campbell, W. J.↗

NASA NTRS1982

Reflections on the Space Telescope

The significance of the Space Telescope for the advancement of astronomy and astrophysics is described. The current state of knowledge in astronomy and cosmology is summarized and unanswered questions in those fields discussed. The rapid evolution of modern astronomy and the need for systematic observations are stressed.

Longair, M. S.↗

NASA NTRS1981

Mass loss from interacting close binary systems

The three well-defined classes of evolved binary systems that show evidence of present and/or past mass loss are the cataclysmic variables, the Algols, and Wolf-Rayet stars. It is thought that the transformation of supergiant binary systems into the very short-period cataclysmic variables must have been a complex process. The new evidence that has recently been obtained from the far ultraviolet spectra that a certain subclass of the Algols (the Serpentids) are undergoing fairly rapid evolution is discussed. It is thought probable that the remarkable mass outflow observed in them is connected with a strong wind powered by accretion. The origin of the circumbinary clouds or flat disks that probably surround many strongly interacting binaries is not clear. Attention is also given to binary systems with hot white dwarf or subdwarf components, such as the symbiotic objects and the BQ stars; it is noted that in them both components may be prone to an enhanced stellar wind.

Plavec, M. J.↗