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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 145 records · Page 8

Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling

Tree growth and survival are dependent on their ability to perceive signals, integrate them, and trigger timely and fitted molecular and growth responses. While ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems, little is known about how and to what extent it helps trees cope with environmental changes. We hypothesized that the presence of Laccaria bicolor influences abiotic cue perception by Populus trichocarpa and the ensuing signaling cascade. We submitted ectomycorrhizal or non-ectomycorrhizal P. trichocarpa cuttings to short-term cessation of watering or ozone fumigation to focus on signaling networks before the onset of any physiological damage. Poplar gene expression, metabolite levels, and hormone levels were measured in several organs (roots, leaves, mycorrhizas) and integrated into networks. We discriminated the signal responses modified or maintained by ectomycorrhization. Ectomycorrhizas buffered hormonal changes in response to short-term environmental variations systemically prepared the root system for further fungal colonization and alleviated part of the root abscisic acid (ABA) signaling. Furthermore, the presence of ectomycorrhizas in the roots also modified the leaf multi-omics landscape and ozone responses, most likely through rewiring of the molecular drivers of photosynthesis and the calcium signaling pathway. In conclusion, P. trichocarpa-L. bicolor symbiosis results in a systemic remodeling of the host's signaling networks in response to abiotic changes. In addition, ectomycorrhizal, hormonal, metabolic, and transcriptomic blueprints are maintained in response to abiotic cues, suggesting that ectomycorrhizas are less responsive than non-mycorrhizal roots to abiotic challenges.

60 APPLIED LIFE SCIENCES↗

Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors. Their rational design, assembly into increasingly complex blueprints, and installation into diverse chassis is an existing frontier that may benefit from emerging technologies to address bottlenecks. Interweaving nature-inspired to fully synthetic parts has already allowed building of fine-tuned regulatory circuits, or new-to-nature metabolic routes insulated from the biological context of the chassis species. Similarly, developments and the evolving need for unifying principles in plant transformation and species-agnostic technologies highlight future opportunities for engineering the next generation of bioenergy plants.

60 APPLIED LIFE SCIENCES↗

Integrated design of aluminum-enriched high-entropy refractory B2 alloys with synergy of high strength and ductility

Refractory high-entropy alloys (RHEAs) are promising high-temperature structural materials. Their large compositional space poses great design challenges for phase control and high strength-ductility synergy. The present research pioneers using integrated high-throughput machine learning with Monte Carlo simulations supplemented by ab initio calculations to effectively navigate phase selection and mechanical property predictions, developing single-phase ordered B2 aluminum-enriched RHEAs (Al-RHEAs) demonstrating high strength and ductility. These Al-RHEAs achieve remarkable mechanical properties, including compressive yield strengths up to 1.7 gigapascals, fracture strains exceeding 50%, and notable high-temperature strength retention. They also demonstrate a tensile yield strength of 1.0 gigapascals with a ductility of 9%, albeit with B2 ordering. Furthermore, we identify valence electron count domains for alloy ductility and brittleness with the explanation from density functional theory and provide crucial insights into elemental influence on atomic ordering and mechanical performance. The work sets forth a strategic blueprint for high-throughput alloy design and reveals fundamental principles governing the mechanical properties of advanced structural alloys.

Science & Technology - Other Topics↗

Structure-based decoupling of the pro- and anti-inflammatory functions of interleukin-10

Interleukin-10 (IL-10) is an immunoregulatory cytokine with both anti-inflammatory and immunostimulatory properties and is frequently dysregulated in disease. We used a structure-based approach to deconvolute IL-10 pleiotropy by determining the structure of the IL-10 receptor (IL-10R) complex by cryo–electron microscopy at a resolution of 3.5 angstroms. The hexameric structure shows how IL-10 and IL-10Rα form a composite surface to engage the shared signaling receptor IL-10Rβ, enabling the design of partial agonists. IL-10 variants with a range of IL-10Rβ binding strengths uncovered substantial differences in response thresholds across immune cell populations, providing a means of manipulating IL-10 cell type selectivity. Some variants displayed myeloid-biased activity by suppressing macrophage activation without stimulating inflammatory CD8 + T cells, thereby uncoupling the major opposing functions of IL-10. These results provide a mechanistic blueprint for tuning the pleiotropic actions of IL-10.

60 APPLIED LIFE SCIENCES↗

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

We present Microbe-seq, a high-throughput single-microbe method that yields strain-resolved genomes from complex microbial communities. We encapsulate individual microbes into droplets with microfluidics and liberate their DNA, which we amplify, tag with droplet-specific barcodes, and sequence. We use Microbe-seq to explore the human gut microbiome; we collect stool samples from a single individual, sequence over 20,000 microbes, and reconstruct nearly-complete genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe genomic signatures of microbial interactions: we reconstruct the horizontal gene transfer (HGT) network within the individual and observe far greater exchange within the same bacterial phylum than between different phyla. We probe bacteria-virus interactions; unexpectedly, we identify a significant in vivo association between crAssphage, an abundant bacteriophage, and a single strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo–electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.

60 APPLIED LIFE SCIENCES↗

Broadening a SARS-CoV-1–neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing antibody that neutralizes one virus but not a related virus. Through a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1–neutralizing antibody, to bind to the receptor binding domain of SARS-CoV-2 with >1000-fold increased affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of engineered CR3022 elucidated the molecular mechanisms by which the antibody can accommodate sequence differences in the epitopes between SARS-CoV-1 and SARS-CoV-2. This workflow provides a blueprint for the rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.

Biochemistry & Molecular Biology↗

Quantum Algorithm Implementations for Beginners

As quantum computers become available to the general public, the need has arisen to train a cohort of quantum programmers, many of whom have been developing classical computer programs for most of their careers. While currently available quantum computers have less than 100 qubits, quantum computing hardware is widely expected to grow in terms of qubit count, quality, and connectivity. This review aims at explaining the principles of quantum programming, which are quite different from classical programming, with straightforward algebra that makes understanding of the underlying fascinating quantum mechanical principles optional. We give an introduction to quantum computing algorithms and their implementation on real quantum hardware. We survey 20 different quantum algorithms, attempting to describe each in a succinct and self-contained fashion. We show how these algorithms can be implemented on IBM’s quantum computer, and in each case, we discuss the results of the implementation with respect to differences between the simulator and the actual hardware runs. This article introduces computer scientists, physicists, and engineers to quantum algorithms and provides a blueprint for their implementations.

97 MATHEMATICS AND COMPUTING↗

The (R)evolution of Scientific Workflows in the Agentic AI Era: Towards Autonomous Science

Modern scientific discovery increasingly requires coordinating distributed facilities and heterogeneous resources, forcing researchers to act as manual workflow coordinators rather than scientists. Advances in AI leading to AI agents show exciting new opportunities that can accelerate scientific discovery by providing intelligence as a component in the ecosystem. However, it is unclear how this new capability would materialize and integrate in the real world. To address this, we propose a conceptual framework where workflows evolve along two dimensions which are intelligence (from static to intelligent) and composition (from single to swarm) to chart an evolutionary path from current workflow management systems to fully autonomous scientific laboratories. With these trajectories in mind, we present an architectural blueprint that can help the community take the next steps towards harnessing the opportunities in autonomous science with the potential for 100x discovery acceleration and transformational scientific workflows.

Shin, Woong [ORNL] (ORCID:0000000172077814)↗

cis -Regulatory Elements in Plant Development, Adaptation, and Evolution

cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗

Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates

The COVID-19 pandemic represents a global challenge that has impacted and is expected to continue to impact the lives and health of people across the world for the foreseeable future. The rollout of vaccines has provided highly anticipated relief, but effective therapeutics are required to further reduce the risk and severity of infections. Monoclonal antibodies have been shown to be effective as therapeutics for SARS-CoV-2, but as new variants of concern (VoC) continue to emerge, their utility and use have waned due to limited or no efficacy against these variants. Furthermore, cumbersome systemic administration limits easy and broad access to such drugs. As well, concentrations of systemically administered antibodies in the mucosal epithelium, a primary site of initial infection, are dependent on neonatal Fc receptor mediated transport and require high drug concentrations. To reduce the viral load more effectively in the lung, we developed an inhalable formulation of a SARS-CoV-2 neutralizing antibody binding to a conserved epitope on the Spike protein, ensuring pan-neutralizing properties. Administration of this antibody via a vibrating mesh nebulization device retained antibody integrity and resulted in effective distribution of the antibody in the upper and lower respiratory tract of non-human primates (NHP). In comparison with intravenous administration, significantly higher antibody concentrations can be obtained in the lung, resulting in highly effective reduction in viral load post SARS-CoV-2 challenge. This approach may reduce the barriers of access and uptake of antibody therapeutics in real-world clinical settings and provide a more effective blueprint for targeting existing and potentially emerging respiratory tract viruses.

60 APPLIED LIFE SCIENCES↗

Co-catabolism of arginine and succinate drives symbiotic nitrogen fixation

Biological nitrogen fixation emerging from the symbiosis between bacteria and crop plants holds promise to increase the sustainability of agriculture. One of the biggest hurdles for the engineering of nitrogen-fixing organisms is an incomplete knowledge of metabolic interactions between microbe and plant. In contrast to the previously assumed supply of only succinate, we describe here the CATCH-N cycle as a novel metabolic pathway that co-catabolizes plant provided arginine and succinate to drive the energy-demanding process of symbiotic nitrogen fixation in endosymbiotic rhizobia. Using systems biology, isotope labeling studies and transposon sequencing in conjunction with biochemical characterization, we uncovered highly redundant network components of the CATCH-N cycle including transaminases that interlink the co-catabolism of arginine and succinate. The CATCH-N cycle uses N2 as an additional sink for reductant and therefore delivers up to 25% higher yields of nitrogen than classical arginine catabolism—two alanines and three ammonium ions are secreted for each input of arginine and succinate. We argue that the CATCH-N cycle has evolved as part of a synergistic interaction to sustain bacterial metabolism in the microoxic and highly acid environment of symbiosomes. Thus, the CATCHN cycle entangles the metabolism of both partners to promote symbiosis. Our results provide a theoretical framework and metabolic blueprint for the rational design of plants and plant-associated organisms with new properties to improve nitrogen fixation.

59 BASIC BIOLOGICAL SCIENCES↗

Moly 99 Reactor Case Study

Molybdenum-99 (Moly 99) is a critical raw material for Technetium (Tc) 99m, a radioactive isotope most widely used in nuclear medicine procedures. Moly 99 has a short half-life of about six hours, which means it cannot be stockpiled. When Moly 99 decays, it turns into Tc 99m, which has a half-life of 214,000 years. The photon energy emitted from the decay of Moly 99 is used in a variety of nuclear imaging technologies such as gamma cameras. Furthermore, radiopharmaceutical manufacturers use the photon energy emitted from the decay of Moly 99 to produce generators for hospitals, clinics, and radiopharmacies. Once Moly 99 decays to Tc 99m, it is used to make individual patient doses for a variety of diagnostic imaging procedures. The Moly 99 Reactor Design is a conceptual blueprint for Moly 99 production that does not use weapon-grade uranium; instead, the reactor has a target core of low-enriched uranium. The reactor design is small, reaching a foot-and-a-half in height and diameter and consumes less than two megawatts of power. The reactor's only purpose is for medical isotope production and with every fission, Moly 99 is produced.

07 ISOTOPE AND RADIATION SOURCES↗

Innovations in Building Energy Modeling: Research and Development Opportunities for Emerging Technologies

Building energy modeling (BEM) is a multipurpose tool for building energy efficiency (EE). The U.S. Department of Energy Building Technologies Office (BTO) seeks to expand the use and effectiveness of BEM in the design and operation of commercial and residential buildings with the goal of achieving lasting reductions in total and peak energy use. This report identifies gaps and outlines recommended initiatives to achieve this goal, based on a combination of technical analysis and stakeholder input. In addition to BTO, this report can benefit BEM professionals (architects, mechanical engineers, energy consultants, building auditors, equipment manufacturers, and BEM software vendors) and BEM clients (building owners and operators, EE program administrators, EE service providers, policymakers, and policy and code jurisdictions such as states and cities). This report was developed in two phases. In the first, BTO worked with a team from Navigant Consulting (now Guidehouse) to characterize objectives, opportunities, and current activities; identify gaps and barriers; and define initiatives. To collect input, Navigant conducted telephone interviews and workshops with industry experts. The initial phase produced a draft report, which was released for public review in 2016 and yielded over 400 comments. Based on these comments, BTO compiled a second draft report that addressed many of those comments while acknowledging changes that had occurred both at BTO and in the industry. Unlike the first draft report, the second focused much more heavily on BTO’s own role, portfolio, and activities. BTO is a direct player in the BEM field - it funds the development of several significant software packages that are embedded in commercial products - and transparency about its goals and future plans is requisite. BTO recognizes that a great number of other public and private organizations contribute to the BEM enterprise. With the second draft report, BTO did not attempt to produce a blueprint for the industry as a whole, but rather a working document BTO can use to iteratively solicit stakeholder input and synthesize it into a program. BTO released the second draft report for public review in 2019. The second round of review generated 83 pages of feedback and comments - almost exactly the length of the draft report itself - a significant portion of which was collected and synthesized by IBPSA-USA Advocacy Committee. This final report incorporates this feedback. This report does not address the use of BEM in support of building-based grid services, a recent BTO initiative called Grid-interactive Efficient Buildings (GEB). In 2019, BTO published a report that specifically addresses the role of BEM - and other “integration” technologies - in GEB.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Land Surface Modeling 2.0 for agricultural climate change impact assessments

Focus Area: This white paper addresses DOE AI4ESP focus area #2 by providing a sketch blueprint for a next generation, hybrid AI/process-based global Land Surface Modeling (LSM) framework to improve projections of climate change impacts on the land surface system including agriculture and the hydrological cycle. Science Challenge: Climate change impacts on agriculture are highly uncertain: -50% to +150% global production changes for major grains under high-end climate change, for example. The core challenge in land surface system predictability is the large gap between the scale at which the relevant biological processes act and the scale at which the risks need to be assessed. Conventional empirical and process-based modeling approaches are insufficient. A new multi-scale modeling paradigm which employs AI/ML to learn from new streams of remote sensing data and targeted ’gene-to-global’ simulations is needed.

54 ENVIRONMENTAL SCIENCES↗

INTERSECT Architecture Specification: System-of-systems Architecture (Version 0.5)

Oak Ridge National Laboratory (ORNL)’s Self-driven Experiments for Science / Interconnected ScienceEcosystem (INTERSECT) architecture project, titled “An Open Federated Architecture for the Laboratory of the Future”, creates an open federated hardware/software architecture for the laboratory of the future using a novel system of systems (SoS) and microservice architecture approach, connecting scientific instruments, robot-controlled laboratories and edge/center computing/data resources to enable autonomous experiments, “self-driving” laboratories, smart manufacturing, and artificial intelligence (AI)-driven design, discovery and evaluation. The architecture project is divided into three focus areas: design patterns; SoS architecture; and microservices architecture. The design patterns area focuses on describing science use cases as design patterns that identify and abstract the involved hardware/software components and their interactions interms of control, work and data flow. The SoS architecture area focuses on an open architecture specification for the federated ecosystem that clarifies terms, architectural elements, the interactions between them and compliance. The microservices architecture describes blueprints for loosely coupled microservices, standardized interfaces, and multi-programming language support. This document is the SoS Architecture specification only, and captures the system of systems architecture design for the INTERSECT Initiative and its components. It is intended to provide a deep analysis and specification of how the INTERSECT platform will be designed, and to link the scientific needs identified across disciplines with the technical needs involved in the support, development, and evolution of a science ecosystem. PLEASE NOTE: This is a working document and reflects current discussions and design activity among the authors. There may be inconsistencies within the document as different parts evolve at a different pace. We invite comments and thoughts from the public on this and following working drafts. The first finished version of this document is scheduled for release in September 2023.

97 MATHEMATICS AND COMPUTING↗

FY23 Status Report of the Activated Materials Laboratory at the Advanced Photon Source

The Activated Materials Laboratory (AML) is a new radiological facility located at the Advanced Photon Source (APS) in Argonne National Laboratory (ANL), adjacent to the high-energy x-ray microscopy (HEXM) beamline in the long beamline building (LBB) constructed under the APS-upgrade (APS-U) project. The AML is a centralized facility to facilitate the safe conduct of experiments on activated materials at the APS. This report provides an overview of the status of the AML as a Nuclear Science User Facilities (NSUF) partner user facility in preparation for the general user access in 2024 upon the commissioning of the APS-U beamlines. Specifically, details are provided regarding the laboratory's scope, functionality, components, operational blueprint, and data management approach. The plans on augmenting the instrumentation, refining operational procedures and developing a robust data management strategy for FY24 and beyond are also discussed.

43 PARTICLE ACCELERATORS↗