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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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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

The collection of microbes that live in and on the human body – the human microbiome – can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell–cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology – a systems biology approach.

Xavier, Joao B.↗
DOE OSTI2023

Pseudospectral convex optimization for on-ramp merging control of connected vehicles

It can be a daunting task for human drivers to merge into highways because of the intricate vehicle negotiations and potential risk within limited time and space. Connected vehicle (CV) technologies could be a solution to this problem and offer many benefits to the road safety, traffic mobility, and energy efficiency. However, real-time optimal control of CVs is still an open challenge, due to the nonlinear vehicle dynamics, non-convex fuel consumption model, and highly dynamic uncertain inter-vehicle interactions. To tackle these issues, a novel real-time optimal control approach that balances the computational efficiency and solution optimality is proposed for the purpose of onboard application. To this end, the pseudospectral collocation method is integrated with a sequential convex programming approach to develop two new optimization algorithms, which are implemented within a model predictive control (MPC) framework to allow for real-time generation of optimal merging speed profiles. One algorithm leverages the line search technique to improve convergence, and the other benefits from the trust region method for better computational efficiency. The optimality and convergence process of both proposed algorithms are investigated by comparing their solutions with a popular non-linear solver. Furthermore, simulation results show that the proposed methods outperform the benchmark in terms of computational cost, fuel consumption, and traffic efficiency. In particular, the proposed fuel-economy merging rule can save 57.1% fuel consumption on average on four different traffic volumes. Meanwhile, the proposed optimal control algorithms can reduce 2.2% travel time on average comparing to the “first-in-first-out” merging rule.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2024

Advocating Feedback Control for Human-Earth System Applications

This paper proposes a feedback control perspective for Human-Earth Systems (HESs) which essentially are complex systems that capture the interactions between humans and nature. Recent attention in HES research has been directed towards devising strategies for climate change mitigation and adaptation, aimed at achieving environmental and societal objectives. However, existing approaches heavily rely on HES models, which inherently suffer from inaccuracies due to the complexity of the system. Moreover, overly detailed models often prove impractical for optimization tasks. We propose a framework inheriting from feedback control strategies the robustness against model errors, because inaccuracies are mitigated using measurements retrieved from the field. The framework comprises two nested control loops. The outer loop computes the optimal inputs to the HES, which are then implemented by actuators controlled in the inner loop. Potential fields of applications are also identified and a numerical example is provided.

biological system modeling↗
DOE OSTI2021

NO 2 Interactions with MoO 3 and CuO at Atmospherically Relevant Pressures

NO x concentrations in some geographic regions are harmful to human health. Gas filters to trap NO x and other toxic chemicals contain metal oxides, including MoO 3 and CuO. These materials are also being investigated for NO x gas sensors. In a step to understand the fundamental adsorption mechanism in sensors and the effect on binding site availability in gas filters, ambient-pressure X-ray photoelectron spectroscopy (APXPS) was used to study the interaction of NO 2 with polycrystalline MoO 3 and CuO surfaces under pressures up to 0.01 Torr (14 parts per million volume (ppmv)). Density functional theory-based computational modeling was performed to reveal the mechanisms of NO 2 interactions with the MoO 3 (010) and CuO(111) surfaces to aid interpretation of the experimental results. With pressure dependence, NO 2 interacts with reduced Mo 5+ atoms generated by oxygen vacancies and abstracts hydrogen atoms from hydroxyl groups on MoO 3 without accumulating N-containing species on the surface; vacancy-induced electronic states in the band gap are also removed, hinting toward an increase in the resistivity of the material. N-containing species begin accumulating on the CuO surface at atmospherically relevant pressures of 140 ppbv. NO 2 only decomposes at oxygen vacancy sites of CuO. The nitrogen species leave the CuO surface upon evacuation, highlighting the importance of in situ surface characterization when studying gas sensing and adsorption mechanisms. Finally, these results imply that NO 2 removes hydroxyl and O vac binding sties on these materials when used in gas filtration and sensing applications. Furthermore, the results show the key role of O vac sites in the gas sensing mechanism of MoO 3 and highlight the potential of APXPS for further studies of gas sensors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Understanding the spatial interactions between the elements of the tumor microenvironment -i.e. tumor cells. fibroblasts, immune cells- and how these interactions relate to the diagnosis or prognosis of a tumor is one of the goals of computational pathology. We present NaroNet, a deep learning framework that models the multi-scale tumor microenvironment from multiplex-stained cancer tissue images and provides patient-level interpretable predictions using a seamless end-to-end learning pipeline. Trained only with multiplex-stained tissue images and their corresponding patient-level clinical labels, NaroNet unsupervisedly learns which cell phenotypes, cell neighborhoods, and neighborhood interactions have the highest influence to predict the correct label. To this end, NaroNet incorporates several novel and state-of-the-art deep learning techniques, such as patch-level contrastive learning, multi-level graph embeddings, a novel max-sum pooling operation, or a metric that quantifies the relevance that each microenvironment element has in the individual predictions. We validate NaroNet using synthetic data simulating multiplex-immunostained images where a patient label is artificially associated to the -adjustable- probabilistic incidence of different microenvironment elements. We then apply our model to two sets of images of human cancer tissues: 336 seven-color multiplex-immunostained images from 12 high-grade endometrial cancer patients; and 382 35-plex mass cytometry images from 215 breast cancer patients. In both synthetic and real datasets, NaroNet provides outstanding predictions of relevant clinical information while associating those predictions to the presence of specific microenvironment elements.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts↗
DOE OSTI2023

LDRD23-0730: Invoking Multilayer Networks to Develop a Paradigm for Security Science—Summary Report

Current approaches to securing high consequence facilities (HCF) and critical assets are linear and static and therefore struggle to adapt to emerging threats (e.g., unmanned aerial systems) and changing environmental conditions (e.g., decreasing operational control). The pace of change in technological, organizational, societal, and political dynamics necessitates a move toward codifying underlying scientific principles to better characterize the rich interactions observed between HCF security technology, infrastructure, digital assets, and human or organizational components. The promising results of Laboratory Directed Research and Development (LDRD) 20-0373—“Developing a Resilient, Adaptive, and Systematic Paradigm for Security Analysis”—suggest that when compared to traditional security analysis, invoking multilayer network (MLN) modeling for HCF security system components captures unexpected failure cases and unanticipated interactions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

MiNAA: Microbiome Network Alignment Algorithm

A microbial network is a mathematical representation of a microbial community where nodes represent microbes and edges represent interactions. It is well-recognized that microbes are among the main drivers of biological phenotypes in soil, plants, and animals alike, and thus, their study has vast implications for soil, plant and human health. In particular, recognizing the microbial, environmental, and agricultural factors that drive plant and soil phenotypes is crucial to comprehend processes connected to plant and soil health, to identify global practices of sustainable agriculture, as well as to predict plant and soil responses to environmental perturbations such as climate change. The adaptability of microbes to thrive in every environment poses challenges for scientists who try to understand their communities. Indeed, two microbial communities with the exact same players can interact differently depending on the environmental conditions. It is thus desirable to identify commonalities and differences on two microbial networks, hence the need for computational tools that can match (or align) them.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Abstract Host‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Q-VR: System-Level Design for Future Mobile Collaborative Virtual Reality

High Quality Mobile Virtual Reality (VR) is what the incoming graphics technology era demands: users around the world, regardless of their hardware and network conditions, can all enjoy the immersive virtual experience. However, the state-of-the-art software-based mobile VR designs cannot fully satisfy the realtime performance requirements due to the highly interactive nature of user's actions and complex environmental constraints during VR execution. Inspired by the unique human visual system effects and the strong correlation between VR motion features and realtime hardware-level information, we propose Q-VR, a novel dynamic collaborative rendering solution via software-hardware co-design for enabling future low-latency high-quality mobile VR. At software-level, Q-VR provides flexible high-level tuning interface to reduce network latency while maintaining user perception. At hardware-level, Q-VR accommodates a wide spectrum of hardware and network conditions across users by effectively leveraging the computing capability of the increasingly powerful VR hardware. Extensive evaluation on real-world games demonstrates that Q-VR can achieve an average end-to-end performance speedup of 3.4x (up to 6.7x) over the traditional local rendering design in commercial VR devices, and a 4.1x frame rate improvement over the state-of-the-art static collaborative rendering.

Xie, Chenhao↗
DOE OSTI2021

Interactive Mesh Generation and Comparison Tools for Nuclear Energy Advanced Modeling & Simulation Phase I. Final Report

The promise of computer simulations for nuclear reactor designs is the opportunity to speed up the design process while also improving safety, providing more detail and higher fidelity, reducing cost, minimizing schedule risk, and avoiding many other potential problems; because simulations have the potential to be much less expensive and time-consuming than traditional development – where scale models and physical tests require construction and long lead times – it is possible to consider more alternatives and complete more comprehensive assessments before the design is finalized and constructed. As more design scenarios are studied by simulation, the speed that simulations promise is only available as long as bottlenecks are addressed for these scenarios. A frequent bottleneck is the amount of human labor required to describe the shape of the objects being designed and decompose the shape into simple elements, such as hexahedra, that are small enough to capture the physical phenomena of interest without being so small that even fast computers cannot perform the simulation in a reasonable amount of time. Recently, techniques for creating all-hexahedral decompositions have been developed, but they require some human input. Many simulation codes prefer all-hexahedral decompositions, so we proposed to evaluate the feasibility of these techniques on nuclear reactor geometries to see whether they required too much human input to be commercially viable. Our study concluded that they can be made viable with some additional software tools to reduce the amount of user input required.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Fluorescent Detection of Carbon Disulfide by a Highly Emissive and Robust Isoreticular Series of Zr-Based Luminescent Metal Organic Frameworks (LMOFs)

Carbon disulfide (CS 2 ) is a highly volatile neurotoxic species. It is known to cause atherosclerosis and coronary artery disease and contributes significantly to sulfur-based pollutants. Therefore, effective detection and capture of carbon disulfide represents an important aspect of research efforts for the protection of human and environmental health. In this study, we report the synthesis and characterization of two strongly luminescent and robust isoreticular metal organic frameworks (MOFs) Zr 6 (µ 3- O) 4 (OH) 8 (tcbpe) 2 (H 2 O) 4 (here termed 1) and Zr 6 (µ 3- O) 4 (OH) 8 (tcbpe-f) 2 (H 2 O) 4 (here termed 2) and their use as fluorescent sensors for the detection of carbon disulfide. Both MOFs demonstrate a calorimetric bathochromic shift in the optical bandgap and strong luminescence quenching upon exposure to carbon disulfide. The interactions between carbon disulfide and the frameworks are analyzed by in-situ infrared spectroscopy and computational modelling by density functional theory. These results reveal that both the Zr metal node and organic ligand act as the preferential binding sites and interact strongly with carbon disulfide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Considerations for Introducing Artificial Intelligence into Nuclear Power Plants

Advanced computational tools and techniques such as artificial intelligence and machine learning (AI/ML) can transform the nuclear power industry. This is necessary given that the economic viability of the existing fleet is in jeopardy and its labor-centric approach to operations and maintenance. Currently, AI/ML research is being undertaken for reactor system design and analysis including fault and accident prognosis, nuclear risk analysis such as plant safety and security evaluation, and plant operations and maintenance including predictive maintenance. Applications include both existing and advanced reactor technologies with the aim of improving operational and business efficiencies. Most every aspect of the organization can benefit, from instrumentation and control, to work planning, to human-machine interactions and business management. AI/ML in nuclear can simplify complex problems and produce more effective decision-making. Nonetheless, careful consideration must be given to the implementation of an AI/ML initiative. The aims of this research are to 1) review barriers to AI/ML adoption within the nuclear power industry, and 2) suggest potential solutions. These barriers are organized along five distinct categories (Figure 1) that are interconnected. The first are historical barriers that track the industry’s development over the decades including worldwide nuclear events that shaped public perceptions. The resulting federal scrutiny and intense safety culture that emerged are discussed. Technical barriers to AI/ML adoption are considerable, and include data privacy concerns, data governance, and the current lack of AI/ML expert knowledge at the plants. The main business case barrier remains cost, but an absence of an industry-wide vision and wide-scale adoption also produces reluctance. Stakeholder readiness is reviewed with special attention given to regulatory readiness. The 5-year strategic plan for AI readiness recently published by the U.S. Nuclear Regulatory Commission is highlighted. Last, adoption barriers at the user level are addressed including the importance of user experience and explainable AI. The AI adoption barriers described here are inter-related and ideally should be addressed in a holistic fashion.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Measuring Cities with Software-Defined Sensors

The Chicago Array of Things (AoT) project, funded by the US National Science Foundation, created an experimental, urban-scale measurement capability to support diverse scientific studies. Initially conceived as a traditional sensor network, collaborations with many science communities guided the project to design a system that is remotely programmable to implement Artificial Intelligence (AI) within the devices-at the “edge” of the network-as a means for measuring urban factors that heretofore had only been possible with human observers, such as human behavior including social interaction. The concept of “software-defined sensors” emerged from these design discussions, opening new possibilities, such as stronger privacy protections and autonomous, adaptive measurements triggered by events or conditions. We provide examples of current and planned social and behavioral science investigations uniquely enabled by software-defined sensors as part of the SAGE project, an expanded follow-on effort that includes AoT.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

AI-Based Protein Interaction Screening and Identification (AISID)

In this study, we presented an AISID method extending AlphaFold-Multimer’s success in structure prediction towards identifying specific protein interactions with an optimized AISIDscore. The method was tested to identify the binding proteins in 18 human TNFSF (Tumor Necrosis Factor superfamily) members for each of 27 human TNFRSF (TNF receptor superfamily) members. For each TNFRSF member, we ranked the AISIDscore among the 18 TNFSF members. The correct pairing resulted in the highest AISIDscore for 13 out of 24 TNFRSF members which have known interactions with TNFSF members. Out of the 33 correct pairing between TNFSF and TNFRSF members, 28 pairs could be found in the top five (including 25 pairs in the top three) seats in the AISIDscore ranking. Surprisingly, the specific interactions between TNFSF10 (TNF-related apoptosis-inducing ligand, TRAIL) and its decoy receptors DcR1 and DcR2 gave the highest AISIDscore in the list, while the structures of DcR1 and DcR2 are unknown. The data strongly suggests that AlphaFold-Multimer might be a useful computational screening tool to find novel specific protein bindings. This AISID method may have broad applications in protein biochemistry, extending the application of AlphaFold far beyond structure predictions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Brain Connectivity Workshop Series Report

The National Institutes of Health (NIH) BRAIN Initiative aims to accelerate development and application of technologies that show how individual brain cells in complex neural circuits interact at the speed of thought and action. Complete wiring diagrams of the mammalian brain will revolutionize the capabilities of researchers to formulate and test models of how activity within brain circuits drives coordinated function and behavior. A top priority for the BRAIN Initiative, motivated by the strategic guidance of the BRAIN 2.0 Working Group report, is to muster the resources and foster the collaborations needed to generate these wiring diagrams at the level of long-range projections (“projectomes”) and synapses (“connectomes”) in whole mammalian brains, including those from rodents, humans, and other large-brained mammals. Achieving the scale and resolution necessary to characterize and use these projectomes and connectomes will not only push the boundaries of current imaging and computational capabilities to generate faster, cheaper, and more scalable technologies, but also drive broad innovation in data science, artificial intelligence, and machine learning.

42 ENGINEERING↗