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All sources NASA NTRS DOE OSTI

DOE OSTI2023

The First Virtual Human Global Summit: Prepublication Meeting Report

This is the prepublication report for the First Virtual Human Global Summit held in October 2023. Organized collaboratively by Frederick National Laboratory for Cancer Research, Brookhaven National Laboratory, University College London, and Eviden, the 2023 Virtual Human Global Summit convened global thought leaders to bring together multiple perspectives across domains and organizations. The intent of the Summit was to foster collaboration among key leaders internationally whose combined efforts are required to advance patient-focused precision medicine through medical digital twins. Participants represented cancer and biomedical research, industry, infrastructure, clinical research, community health, non-profit organizations, government, and general public interests. The Summit included over 80 attendees across three continents including native American tribes. The Summit was held to share insights about the state of the art for medical digital twins, provide motivating opportunities and identify key challenges along the path to improved health and wellness through virtual human models and personalized digital twins. The Summit included sessions emphasizing the primary areas of research, infrastructure, clinical application, government support, and adoption/sustainability. Several examples of digital twins were referenced or mentioned through the course of the Summit including digital twin approaches in cancer, radiation oncology, molecular scale digital twins, diabetes, and sepsis. The summit report includes perspectives on the current state, challenges and guidance across research, infrastructure, clinical translation and community adoption, as well as multiple key insights from industry perspectives.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Identifying key determinants and dynamics of SARS-CoV-2/ACE2 tight interaction

SARS-CoV-2 virus, the causative agent of Covid-19, has fired up a global pandemic. The virus interacts with the human receptor angiotensin-converting enzyme 2 (ACE2) for an invasion via receptor binding domain (RBD) on its spike protein. To provide a deeper understanding of this interaction, we performed microsecond simulations of the RBD-ACE2 complex for SARS-CoV-2 and compared it with the closely related SARS-CoV discovered in 2003. We show residues in the RBD of SARS-CoV-2 that were mutated from SARS-CoV, collectively help make the RBD anchor much stronger to the N-terminal part of ACE2 than the corresponding residues on RBD of SARS-CoV. This would result in a reduced dissociation rate of SARS-CoV-2 from human receptor protein compared to SARS-CoV. The phenomenon was consistently observed in simulations beyond 500 ns and was reproducible across different force fields. Altogether, our study adds more insight into the critical dynamics of the key residues at the virus spike and human receptor binding interface and potentially aids the development of diagnostics and therapeutics to combat the pandemic efficiently.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources.We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues.These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

NASA NTRS2016

Application of Human-Autonomy Teaming (HAT) Patterns to Reduced Crew Operations (RCO)

As part of the Air Force - NASA Bi-Annual Research Council Meeting, slides will be presented on recent Reduced Crew Operations (RCO) work. Unmanned aerial systems, robotics, advanced cockpits, and air traffic management are all examples of domains that are seeing dramatic increases in automation. While automation may take on some tasks previously performed by humans, humans will still be required, for the foreseeable future, to remain in the system. The collaboration with humans and these increasingly autonomous systems will begin to resemble cooperation between teammates, rather than simple task allocation. It is critical to understand this human-autonomy teaming (HAT) to optimize these systems in the future. One methodology to understand HAT is by identifying recurring patterns of HAT that have similar characteristics and solutions. A methodology for identifying HAT patterns to an advanced cockpit project is discussed.

Human-Autonomy Teaming (HAT)↗

DOE OSTI2020

Structural basis of the activation of a metabotropic GABA receptor

Metabotropic γ-aminobutyric acid receptors (GABA B ) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that range from addiction to psychosis. GABA B belongs to class C of the G-protein-coupled receptors, and its functional entity comprises an obligate heterodimer that is composed of the GB1 and GB2 subunits. Each subunit possesses an extracellular Venus flytrap domain, which is connected to a canonical seven-transmembrane domain. In this paper we present four cryo-electron microscopy structures of the human full-length GB1–GB2 heterodimer: one structure of its inactive apo state, two intermediate agonist-bound forms and an active form in which the heterodimer is bound to an agonist and a positive allosteric modulator. The structures reveal substantial differences, which shed light on the complex motions that underlie the unique activation mechanism of GABA B . Our results show that agonist binding leads to the closure of the Venus flytrap domain of GB1, triggering a series of transitions, first rearranging and bringing the two transmembrane domains into close contact along transmembrane helix 6 and ultimately inducing conformational rearrangements in the GB2 transmembrane domain via a lever-like mechanism to initiate downstream signalling. This active state is stabilized by a positive allosteric modulator binding at the transmembrane dimerization interface.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1978

Human operator identification model and related computer programs

Four computer programs which provide computational assistance in the analysis of man/machine systems are reported. The programs are: (1) Modified Transfer Function Program (TF); (2) Time Varying Response Program (TVSR); (3) Optimal Simulation Program (TVOPT); and (4) Linear Identification Program (SCIDNT). The TV program converts the time domain state variable system representative to frequency domain transfer function system representation. The TVSR program computes time histories of the input/output responses of the human operator model. The TVOPT program is an optimal simulation program and is similar to TVSR in that it produces time histories of system states associated with an operator in the loop system. The differences between the two programs are presented. The SCIDNT program is an open loop identification code which operates on the simulated data from TVOPT (or TVSR) or real operator data from motion simulators.

Kessler, K. M.↗

NASA NTRS1993

A prototype case-based reasoning human assistant for space crew assessment and mission management

We present a prototype human assistant system for space crew assessment and mission management. Our system is based on case episodes from American and Russian space missions and analog environments such as polar stations and undersea habitats. The general domain of small groups in isolated and confined environments represents a near ideal application area for case-based reasoning (CBR) - there are few reliable rules to follow, and most domain knowledge is in the form of cases. We define the problem domain and outline a unique knowledge representation system driven by conflict and communication triggers. The prototype system is able to represent, index, and retrieve case studies of human performance. We index by social, behavioral, and environmental factors. We present the problem domain, our current implementation, our research approach for an operational system, and prototype performance and results.

Owen, Robert B.↗

DOE OSTI2023

Characterization of two distinct neutrophil serine protease–binding modes within a Staphylococcus aureus innate immune evasion protein family

Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure–function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10 -9 M) and of NE (on the order of 10 -10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

3D structure and in situ arrangements of CatSper channel in the sperm flagellum

The sperm calcium channel CatSper plays a central role in successful fertilization as a primary Ca 2+ gateway. Here, we applied cryo-electron tomography to visualize the higher-order organization of the native CatSper complex in intact mammalian sperm. The repeating CatSper units form long zigzag-rows along mouse and human sperm flagella. Above each tetrameric channel pore, most of the extracellular domains form a canopy that interconnects to a zigzag-shaped roof. Murine CatSper contains an additional wing-structure connected to the tetrameric channel. The intracellular domains link two neighboring channels to a diagonal array, suggesting a dimer formation. Fitting of an atomic model of isolated monomeric CatSper to the in situ map reveals supramolecular interactions and assembly of the CatSper complex. Loss of EFCAB9-CATSPERζ alters the architecture and interactions of the channels, resulting in fragmentation and misalignment of the zigzag-rows and disruption of flagellar movement in Efcab9 -/- sperm. This work offers unique insights into the structural basis for understanding CatSper regulation of sperm motility.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

A single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity

Acute gastroenteritis caused by human noroviruses (HuNoVs) is a significant global health and economic burden and is without licensed vaccines or antiviral drugs. The GII.4 HuNoV causes most epidemics worldwide. This virus undergoes epochal evolution with periodic emergence of variants with new antigenic profiles and altered specificity for histo-blood group antigens (HBGA), the determinants of cell attachment and susceptibility, hampering the development of immunotherapeutics. Here, we show that a llama-derived nanobody M4 neutralizes multiple GII.4 variants with high potency in human intestinal enteroids. The crystal structure of M4 complexed with the protruding domain of the GII.4 capsid protein VP1 revealed a conserved epitope, away from the HBGA binding site, fully accessible only when VP1 transitions to a “raised” conformation in the capsid. Together with dynamic light scattering and electron microscopy of the GII.4 VLPs, our studies suggest a mechanism in which M4 accesses the epitope by altering the conformational dynamics of the capsid and triggering its disassembly to neutralize GII.4 infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Benchmarking large language models for materials synthesis: The case of atomic layer deposition

In this work, we introduce an open-ended question benchmark, ALDbench, to evaluate the performance of large language models (LLMs) in materials synthesis, and, in particular, in the field of atomic layer deposition, a thin film growth technique used in energy applications and microelectronics. Our benchmark comprises questions with a level of difficulty ranging from the graduate level to domain expert current with the state of the art in the field. Human experts reviewed the questions along the criteria of difficulty and specificity, and the model responses along four different criteria: overall quality, specificity, relevance, and accuracy. We ran this benchmark on an instance of OpenAI’s GPT-4o. The responses from the model received a composite quality score of 3.7 on a 1–5 scale, consistent with a passing grade. However, 36% of the questions received at least one below average score. An in-depth analysis of the responses identified at least five instances of suspected hallucination. Finally, we observed statistically significant correlations between the difficulty of the question and the quality of the response, the difficulty of the question and the relevance of the response, the specificity of the question, and the accuracy of the response as graded by the human experts. Furthermore, this emphasizes the need to evaluate LLMs across multiple criteria beyond difficulty or accuracy.

Artificial intelligence↗

DOE OSTI2026

Harnessing evolution: leveraging bacterial isoprenoid pathway diversity toward improved bioengineering strategies

Isoprenoids play vital roles in all domains of life, from beta-carotene in bacteria to heme in humans. Two distinct metabolic pathways have evolved to synthesize the critical precursor of all mature isoprenoids: the mevalonate (MEV) and the methylerythritol phosphate (MEP) pathways. Here, we quantify the extensive inter- and intra-genus heterogeneity in the usage of these two pathways with particular emphasis on rare bacteria that encode both, or neither, pathways. Furthermore, MEP intermediates themselves have non-isoprenogenic roles that may underlie evolutionary pressures driving pathway diversification. Understanding isoprenoid biosynthesis in bacteria offers new avenues toward more sustainable engineering of economically relevant molecules in microbes.

Biotechnology and Synthetic Biology↗

NASA NTRS1991

An autonomous fault detection, isolation, and recovery system for a 20-kHz electric power distribution test bed

Future space explorations will require long term human presence in space. Space environments that provide working and living quarters for manned missions are becoming increasingly larger and more sophisticated. Monitor and control of the space environment subsystems by expert system software, which emulate human reasoning processes, could maintain the health of the subsystems and help reduce the human workload. The autonomous power expert (APEX) system was developed to emulate a human expert's reasoning processes used to diagnose fault conditions in the domain of space power distribution. APEX is a fault detection, isolation, and recovery (FDIR) system, capable of autonomous monitoring and control of the power distribution system. APEX consists of a knowledge base, a data base, an inference engine, and various support and interface software. APEX provides the user with an easy-to-use interactive interface. When a fault is detected, APEX will inform the user of the detection. The user can direct APEX to isolate the probable cause of the fault. Once a fault has been isolated, the user can ask APEX to justify its fault isolation and to recommend actions to correct the fault. APEX implementation and capabilities are discussed.

Quinn, Todd M.↗

DOE OSTI2020

Updates to a Preliminary Probabilistic Performance Assessment Model for Radiological and Chemical Contamination at the West Valley Site, New York - 20420

The New York State Energy Research and Development Authority (NYSERDA) is the owner of the Western New York Nuclear Service Center (WNYNSC), a 1,351-ha site located approximately 48 km south of Buffalo, New York. In 1962, Nuclear Fuel Services, Inc. (NFS) entered into agreements with the Atomic Energy Commission and New York State to construct the first commercial reprocessing plant of nuclear fuel in the United States at the WNYNSC. NFS built and operated the spent fuel reprocessing plant and waste disposal facilities, processing 640 Mg (640 metric tons) of spent nuclear fuel from 1966 to 1972 under an Atomic Energy Commission license. Nuclear fuel reprocessing operations halted in 1972 and never restarted, leaving behind radioactive and chemical wastes. The U.S. Department of Energy (DOE) was required to complete certain waste management activities under the West Valley Demonstration Project (WVDP) Act of 1980 including decommissioning of WVDP facilities. As collaborating agencies, NYSERDA and the DOE are tasked with making decisions about decommissioning and risk reduction for the West Valley Site. Neptune and Company, Inc. (Neptune) was contracted to develop a probabilistic performance assessment (PPA) model to assist the agencies in their decision making process for decommissioning the WVDP and WNYNSC. One important tool that is needed in order to inform the decision-making process is a science-based model of the West Valley Site that evaluates potential future consequences for human health and the environment. This forms the core of the spatial domain of the West Valley PPA Model. The PPA Model, developed using the GoldSim system modeling software, is a tool intended to provide support for decision making that evaluates uncertainty, in a manner that is transparent, defensible, and robust. The PPA Model includes contaminant transport and health effects components, and is organized around geographically-grouped contaminated facilities. These include the waste disposal areas licensed by the U.S. Nuclear Regulatory Commission and the State of New York, a waste tank farm for storage of high level radioactive waste resulting from reprocessing operations, and several areas contaminated with radioactive and chemical constituents. The PPA Model evaluates contaminant transport from these sources to points of exposure across the site and into receiving surface waters and sediments. Hypothetical people and wildlife could be exposed to contamination at these locations, and the effects of these exposures are evaluated. Contaminant transport processes to be evaluated in the PPA Model include groundwater and surface water transport, contaminant translocation by plants and animals, diffusion, and erosion. The evaluation of exposures to people in this preliminary model is limited to a resident farmer scenario, and ecological assessment is performed at the level of a screening analysis. The results of these preliminary evaluations inform future model developments. PPA Model results are subjected to sensitivity analysis in order to determine those pathways and parameters that are most significant in influencing the results. This information allows analysts and decision makers to focus on those aspects of Site behavior and processes. With this information, the decision makers can drive informed, defensible decisions regarding decommissioning of the Site. This paper includes an update of the information presented at WM2019 [1]. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRSDate not supplied

Advancements in Frequency Domain Analysis of Dual Centerline Propellant Tanks for Space Vehicle Stability and Design

This paper presents advancements in the frequency domain stability analysis for landing and ascent vehicle configurations with dual centerline propellant tanks, developed in support of Guidance, Navigation, and Control (GNC) insight activities for the Human Landing System project. The study focuses on the impact of axial thrust on the dual tank slosh danger zone solution. The frequency domain stability analysis tool is developed within the GeneraLized Aerospace Simulation in Simulink® (GLASS) framework at NASA Marshall Space Flight Center. The frequency domain stability analysis tool is used to determine slosh damping and control systems design requirements. The accuracy of the tool’s instability predictions is validated against time-domain outcomes within the GLASS simulation environment, showing consistent and anticipated results. Additionally, the method is validated by comparing its results with Frequency Domain Analysis and Comparison Tool Assuming Linearity (FRACTAL), a frequency domain analysis tool with extensive heritage and rigorous verification and validation using NASA Ares I-X and SLS flight data. The findings of this paper contribute to a better understanding of dual-tank slosh instability and support improved design and operation margins of space vehicles.

Han Woong (Brian) Bae↗

NASA NTRSDate not supplied

Advancements in Frequency Domain Analysis of Dual Centerline Propellant Tanks for Space Vehicle Stability and Design

Han Woong (Brian) Bae↗

DOE OSTI2025

Exploring Domain-Wall Pinning in Ferroelectrics via Automated High-Throughput Atomic Force Microscopy

Domain-wall dynamics in ferroelectric materials are strongly position-dependent, since each polar interface is locked into a unique local microstructure. This necessitates spatially resolved studies of wall pinning using scanning-probe microscopy techniques. The pinning centers and pre-existing domain walls are usually sparse within the image plane, precluding the use of dense hyperspectral imaging modes and requiring time-consuming human experimentation. Here, a large-area epitaxial PbTiO 3 film on cubic KTaO 3 was investigated to quantify the electric-field-driven dynamics of the polar–strain domain structures using ML-controlled automated piezoresponse force microscopy. Analysis of 1500 switching events reveals that domain-wall displacement depends not only on field parameters but also on the local ferroelectric–ferroelastic configuration. For example, twin boundaries in polydomains regions, like a 1 – /c+ ∥ a 2 – /c – , stay pinned up to a certain level of bias magnitude and change only marginally as the bias increases from 20 to 30 V, whereas single-variant boundaries, like the a 2 + /c + ∥ a 2 – /c – stack, are already activated at 20 V. These statistics on the possible ferroelectric and ferroelastic wall orientations, together with the automated high-throughput AFM workflow, can be distilled into a predictive map that links domain configurations to pulse parameters. Here, this microstructure-specific rule set forms the foundation for the design of ferroelectric memories.

automated scanning probe microscopy↗

DOE OSTI2023

Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery

G-protein metallochaperone MeaB in bacteria [methylmalonic aciduria type A (MMAA) in humans] is responsible for facilitating the delivery of adenosylcobalamin (AdoCbl) to methylmalonyl-CoA mutase (MCM), the only AdoCbl-dependent enzyme in humans. Genetic defects in the switch III region of MMAA lead to the genetic disorder methylmalonic aciduria in which the body is unable to process certain lipids. Here, we present a crystal structure of Methylobacterium extorquens MeaB bound to a nonhydrolyzable guanosine triphosphate (GTP) analog guanosine-5'-[(β,γ)-methyleno]triphosphate (GMPPCP) with the Cbl-binding domain of its target mutase enzyme (MeMCM cbl ). This structure provides an explanation for the stimulation of the GTP hydrolyase activity of MeaB afforded by target protein binding. We find that upon MCM cbl association, one protomer of the MeaB dimer rotates ~180°, such that the inactive state of MeaB is converted to an active state in which the nucleotide substrate is now surrounded by catalytic residues. Importantly, it is the switch III region that undergoes the largest change, rearranging to make direct contacts with the terminal phosphate of GMPPCP. These structural data additionally provide insights into the molecular basis by which this metallochaperone contributes to AdoCbl delivery without directly binding the cofactor. Our data suggest a model in which GTP-bound MeaB stabilizes a conformation of MCM that is open for AdoCbl insertion, and GTP hydrolysis, as signaled by switch III residues, allows MCM to close and trap its cofactor. Substitutions of switch III residues destabilize the active state of MeaB through loss of protein:nucleotide and protein:protein interactions at the dimer interface, thus uncoupling GTP hydrolysis from AdoCbl delivery.

59 BASIC BIOLOGICAL SCIENCES↗