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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Accelerated Sequence Design of Star Block Copolymers: An Unbiased Exploration Strategy via Fusion of Molecular Dynamics Simulations and Machine Learning

Star block copolymers (s-BCPs) have potential applications as novel surfactants or amphiphiles for emulsification, compatibilization, chemical transformations, and separations. s-BCPs have chain architectures where three or more linear diblock copolymer arms comprised of two chemically distinct linear polymers, e.g., solvophobic and solvophilic chains, are covalently joined at one point. The chemical composition of each of the subunit polymer chains comprising the arms, their molecular weights, and the number of arms can be varied to tailor the surface and interfacial activity of these architecturally unique molecules. Further, this makes identification of the optimal s-BCP design nontrivial as the total number of plausible s-BCP architectures is experimentally or computationally intractable. In this work, we use molecular dynamics (MD) simulations coupled with a reinforcement learning-based Monte Carlo tree search (MCTS) to identify s-BCP designs that minimize the interfacial tension between polar and nonpolar solvents. We first validate the MCTS approach for the design of small- and medium-sized s-BCPs and then use it to efficiently identify sequences of copolymer blocks for large-sized s-BCPs. The structural origins of interfacial tension in these systems are also identified by using the configurations obtained from MD simulations. Chemical insights into the arrangement of copolymer blocks that promote lower interfacial tension were mined using machine learning (ML) techniques. Overall, this work provides an efficient approach to solve design problems via fusion of simulations and ML and provides important groundwork for future experimental investigation of s-BCPs for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Molecular Structure and Thermodynamics of CO 2 and Water Adsorption on Mica

The adsorption of CO 2 and water on clay surfaces plays a key role in applications, such as gas storage in saline aquifers and depleted hydrocarbon reservoirs, but is not yet fully understood. Here, we study the adsorption of CO 2 and water vapor using Grand Canonical Monte Carlo and molecular dynamics simulations. At a bulk pressure of 100 bar, pure CO 2 adsorbs strongly on mica and forms extensive layers next to it. CO 2 adsorption is lowered substantially if introducing water vapor above mica and is largely eliminated when the relative humidity (RH) approaches about 60%. When pure water vapor is introduced above a mica surface, a subnanometer thick liquid water film develops on it to form apparent liquid–solid and liquid–vapor interfaces simultaneously. Using the identification of truly interfacial molecules (ITIM) analysis, we delineate how individual water layers develop in this film as RH increases. We highlight that the water film is spatially heterogeneous and the true liquid–vapor interface emerges only at an RH of 60–80%. Introducing 100 bar of CO 2 into the water vapor above the mica surface modulates water adsorption nonlinearly: at RH = 0.01%, the water adsorption is reduced by ∼30%; as RH increases, the reduction is weakened, and eventually, enhancement of water adsorption by about 7% occurs at RH = 90%. These variations are attributed to the interplay of film thinning by high-pressure CO 2 , competition of mica surface sites by CO 2 molecules, and energetic and entropic stabilization of interfacial water by CO 2 molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Why Is Attention Sparse In Particle Transformer?

Transformer-based models have achieved state-of-the-art performance in jet tagging at the CERN Large Hadron Collider (LHC), with the Particle Transformer (ParT) representing a leading example of such models. A striking feature of ParT is its sparse, nearly binary, attention structure, raising questions about the origin of this behavior and whether it encodes physically meaningful correlations. In this work, we investigate the source of ParT's sparse attention by comparing models trained on multiple benchmark datasets and examine the relative contributions of the attention term and the physics-inspired interaction matrix before softmax. We find that binary sparsity arises primarily from the attention mechanism itself, with the interaction matrix playing a secondary role. Moreove, we show that ParT is able to identify key jet substructure elements, such as leptons in semileptonic top decays, even without explicit particle identification inputs. These results provide new insight into the interpretability of transformer-based jet taggers and clarify the conditions under which sparse attention patterns emerge in ParT.

Legge, Timothy [UC, San Diego]↗
DOE OSTI2023

LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Catalytic Upgrading of Pyrolysis Products for the Production of Sustainable Aviation Fuel

The objective of this project is advance the state-of-technology for a catalytic fast pyrolysis (CFP) + hydrotreating (HT) process to produce sustainable aviation fuel and other biogenic products. Our approach focuses on performing integrated experiments using realistic biomass feedstocks and non-noble metal technical catalyst formulations. CFP is performed in an ex-situ configuration using a fluidized bed reactor without co-fed hydrogen. Research advancements over the past two years include establishing benchmark yield structures and compositional data for each step of the biomass-to-SAF process, demonstrating the ability to produce a cycloalkane-rich SAF product that meets key ASTM 4054 guidelines, generating benchmark characterization data for technical catalyst formulations with an emphasis on determining the unique composition and combustion properties of biogenic coke, and establishing bio-oil critical material attributes to mitigate the risk of plugging during down-stream hydroprocessing. Other impacts from this project include generation of broadly enabling scientific knowledge (12 publications/12 presentations since 2021), engagement with industry partners (Johnson Matthey, ExxonMobil, Phillips 66), and identification of a promising pathway to market that addresses emerging demands for biogenic refinery feedstocks.

biomass↗
DOE OSTI2022

SREMI: Super-resolution electromagnetic imaging with single-channel ground-penetrating radar

High-resolution near-surface imaging has important applications in civil engineering, infrastructure inspection, military threat detection, geological characterization, and lunar and planetary exploration. Zero-offset, singlechannel ground penetrating radar (GPR) imaging is an established technique for near-surface target imaging and sensing but often suffers from low spatial resolution and imaging artifacts, especially of deep structures. In response, we formulate the GPR imaging as a dual-sparsity optimization problem, and develop a super-resolution electromagnetic imaging method based on a fast iterative shrinkage-thresholding algorithm. We develop our GPR imaging method in the framework of electromagnetic exploding-reflectors simulation theory, therefore the imaging method is computationally efficient. In this work, we demonstrate through synthetic and field data examples that our method can produce sharper, more reliable images with fewer artifacts compared with single-pass reverse-time migration GPR method, thus leading to improved near-surface interpretation and object identification.

58 GEOSCIENCES↗
DOE OSTI2022

The discovery of a radio galaxy of at least 5 Mpc

Context. Giant radio galaxies (GRGs, or colloquially ‘giants’) are the Universe’s largest structures generated by individual galaxies. They comprise synchrotron-radiating active galactic nucleus ejecta and attain cosmological (megaparsec-scale) lengths. However, the main mechanisms that drive their exceptional growth remain poorly understood. Aims. To deduce the main mechanisms that drive a phenomenon, it is usually instructive to study extreme examples. If there exist host galaxy characteristics that are an important cause for GRG growth, then the hosts of the largest GRGs are likely to possess them. Similarly, if there exist particular large-scale environments that are highly conducive to GRG growth, then the largest GRGs are likely to reside in them. For these reasons, we aim to perform a case study of the largest GRG available. Methods. We reprocessed the LOFAR Two-Metre Sky Survey DR2 by subtracting compact sources and performing multi-scale CLEAN de-convolutions at 60" and 90" resolution. The resulting images constitute the most sensitive survey yet for radio galaxy lobes, whose diffuse nature and steep synchrotron spectra have allowed them to evade previous detection attempts at higher resolution and shorter wavelengths. We visually searched these images for GRGs. Results. We have discovered Alcyoneus, a low-excitation radio galaxy with a projected proper length l p = 4.99 ± 0.04 Mpc. Both its jets and lobes are detected at very high significance, and the SDSS-based identification of the host, at spectroscopic redshift z spec = 0.24674 ± 6 × 10 -5 , is unambiguous. The total luminosity density at ν = 144 MHz is L ν = 8 ± 1 × 10 25 W Hz -1 , which is below average, though near median (percentile 45 ± 3%) for GRGs. The host is an elliptical galaxy with a stellar mass M* = 2.4 ± 0.4 × 10 11 M ⊙ and a super-massive black hole mass M• = 4 ± 2 × 10 8 M ⊙ , both of which tend towards the lower end of their respective GRG distributions (percentiles 25 ± 9% and 23 ± 11%). The host resides in a filament of the Cosmic Web. Through a new Bayesian model for radio galaxy lobes in three dimensions, we estimate the pressures in the megaparsec-cubed-scale northern and southern lobes to be P min,1 = 4.8 ± 0.3 × 10 -16 Pa and P min,2 = 4.9 ± 0.6 × 10 -16 Pa, respectively. The corresponding magnetic field strengths are B min,1 = 46 ± 1 pT and B min,2 = 46 ± 3 pT. Conclusions. We have discovered what is in projection the largest known structure made by a single galaxy – a GRG with a projected proper length l p = 4.99 ± 0.04 Mpc. The true proper length is at least l min = 5.04 ± 0.05 Mpc. Beyond geometry, Alcyoneus and its host are suspiciously ordinary: the total low-frequency luminosity density, stellar mass, and super-massive black hole mass are all lower than, though similar to, those of the medial GRG. Thus, very massive galaxies or central black holes are not necessary to grow large giants, and, if the observed state is representative of the source over its lifetime, neither is high radio power. A low-density environment remains a possible explanation. The source resides in a filament of the Cosmic Web, with which it might have significant thermodynamic interaction. The pressures in the lobes are the lowest hitherto found, and Alcyoneus therefore represents the most promising radio galaxy yet to probe the warm–hot inter-galactic medium.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Discovery of new isotopes in the fragmentation of 82 Se and insights into their production

The production cross sections of neutron-rich nuclei for elements just above 60 Ca were measured at the Facility for Rare Isotope Beams (FRIB). Four previously unobserved isotopes ( 63 Sc, 65,66 Ti, and 68 V) were produced, separated, and identified for the first time using the Advanced Rare Isotope Separator (ARIS). One event was found to be consistent with 61 Ca . The new isotopes were created through the interaction of an 82 Se beam with a carbon target at an energy of 228 MeV/𝑢 and a primary beam current of 1.07 p⁢µ⁢A. The event-by-event particle identification of the mass number (𝐴), atomic number (𝑍), and ionic charge state (𝑞) for the reaction products was achieved by combining measurements of energy loss, time of flight, magnetic rigidity, and total kinetic energy. This successful search for new isotopes, conducted at the beginning of FRIB's third year of operation, highlights the facility's discovery potential, which will continue to grow as the beam current increases. The production cross sections were analyzed in the context of the newly developed Δ⁢𝐵⁢𝐸 systematics that provides trends in neutron-rich regions and increased sensitivity to nuclear binding, an important nuclear structure observable. Furthermore, the new systematics addresses gaps in 𝑄 𝑔 -based methods commonly used to interpret the production cross sections of light neutron-rich elements, and provides an efficient empirical approach to describe cross-section trends across isotopic chains. Good agreement with the measured data was obtained when the Δ⁢𝐵⁢𝐸 systematics and abrasion-ablation calculations were performed using the Hartree-Fock-Bogoliubov (HFB-22) mass table.

59 ≤ A ≤ 89↗
DOE OSTI2022

Restoration Hydro: A Watershed Approach to Standard Modular New Hydropower

The objectives of FOA DE- FOA-0001836- “Standard Modular Hydropower” included designing a standardized, modular, and environmentally compatible hydropower schematic for implementation in greenfield sites that generate up to 10 MW of capacity. Utilizing funds competitively awarded under DOE’s Water Power Technologies Office, the Natel Energy team developed a concept for modular new stream reach (NSR) hydropower that incorporates multi species upstream and downstream fish passage, improved river channel connectivity, and recreational modules. The in-stream design of the collective modules minimized site specific design and maximized the opportunities for modularity. Financial data was also presented using actual costs from regional suppliers, with figures provided in 2022 dollars. While the project team did not address potential permitting process improvements, the site selection criteria did consider established barriers to hydropower development such as tribal and preserved lands, interconnection proximity, and endangered species to exclude or deprioritize. The project’s design schematic met the objectives of the FOA, and presented a unique solution that targets alluvial pockets as natural features for sustainable development. Natel’s concept also incorporated the company's fish-safe Restoration Hydro Turbine for safe downstream passage, while featuring a rock arch that integrates fish passage, water, recreation, and grade control modules (including sediment). Alignment with the Department of Energy Office of Energy Efficiency and Renewable Energy (EERE) “Innovative Design Concepts for Standard Modular Hydropower and Pumped-Storage Hydropower” Program: According to the Hydropower Vision (DOE, 2016), approximately 16 GW of hydropower growth is possible with the development of technology solutions that balance efficiency, economics, and environmental sustainability. The desired outcome of the SMH program is transformational innovation specifically in the site identification, conceptual, and detailed design phases of technology development lifecycles (DOE, 2018). In developing the SMH design schematic, the team aimed to address the opportunities outlined in the Vision through an inverted design philosophy; rather than singularly prioritizing efficiency and power production, the team focused on integrating hydropower with restoration of degraded streams to optimal ecosystem function and provision of exceptional recreation value as design criteria. To achieve this, Restoration Hydro incorporates the principles of nature-based engineering (WWAP, 2018) and biomimicry (Biomimicry NL.) to strategically deploy complementary combinations of permanent, semi-permanent, and ephemeral low-head structures - such as natural and engineered log jams - that harness geomorphological and hydrological processes at the landscape-scale. Primary applications of Restoration Hydro include: 1) restoration of degraded watersheds’ natural ecological function and enhancement of hydrological connectivity; and 2) creation of associated co-benefits to hydro production, including increased groundwater recharge, improved sediment transport and management, improved water security and water quality. Restoration Hydro projects build upon proven watershed restoration engineering techniques by integrating hydropower turbines into low-head structures using innovative and evolving civil works concepts that facilitate fish and sediment passage, and in some cases create additional revenue-generating recreational opportunities. Powering low-head structures creates a directly monetizable layer of economic value in the form of flexible, reliable, renewable energy on top of the already high-value water, environmental and recreational benefits of watershed and river restoration. The approach aims to create a virtuous, self-reinforcing cycle whereby Restoration Hydro projects support the scaling of ecosystem restoration activities, creating a water-energy-carbon multiplier effect that, through the principles of adaptive change management: 1) improves the resilience of landscapes and downstream population centers for changing hydrological cycles; 2) creates a reliable energy resource that facilitates the integration of intermittent renewable power sources into grids; and 3) supports climate change mitigation through grid decarbonization and enhanced ecosystem carbon capture and retention.

13 HYDRO ENERGY↗
DOE OSTI2024

Genomic analysis and identification of a novel superantigen, SargEY, in Staphylococcus argenteus isolated from atopic dermatitis lesions

During surveillance of Staphylococcus aureus in lesions from patients with atopic dermatitis (AD), we isolated Staphylococcus argenteus, a species registered in 2011 as a new member of the genus Staphylococcus and previously considered a lineage of S. aureus. Genome sequence comparisons between S. argenteus isolates and representative S. aureus clinical isolates from various origins revealed that the S. argenteus genome from AD patients closely resembles that of S. aureus causing skin infections. We previously reported that 17%–22% of S. aureus isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of S. argenteus isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of S. argenteus revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among S. argenteus. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4 + and CD8 + T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. S arg EY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. S arg EY and SEY may play roles in exacerbating the respective toxin-producing strains in AD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Time calibration and synchronization of the scintillation light detection system in ICARUS-T600

The ICARUS-T600 Liquid Argon (LAr) Time Projection Chamber (TPC) is presently taking data in the Short Baseline Neutrino (SBN) program at Fermilab (U.S.A.) to search for a possible LSND-like sterile neutrino signal at Δm 2 ≈ 1 eV 2 with the Booster Neutrino Beam (BNB). A light detection system, based on 360 large area Photo-Multiplier Tubes (PMTs), has been realized for ICARUS-T600 to detect VUV photons produced by the passage of ionizing particles in LAr. This system is fundamental for the TPC operation, providing an efficient trigger and contributing to the 3D reconstruction of events. Moreover, since the detector is exposed to a huge flux of cosmic rays due to its shallow depths installation, the light detection system allows for the time reconstruction of events, contributing to the identification and to the selection of genuine neutrino interactions. The correct time reconstruction of events requires the precise knowledge of the delay of each PMT channel and a good synchronization of recording electronics, this last based on fast sampling digitizers. To achieve a time resolution better than 1 ns, we perform three consecutive timing corrections deployed at different stages of the optical data flow. Results demonstrate the capability of the ICARUS-T600 light detection system to allow a precise reconstruction of the temporal evolution of each event occurring in the detector and the association of neutrino events with the bunched structure of BNB.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, operating independently from the host metabolism with reduced engineering complexity and improved theoretical yields. However, a major bottleneck was identified as the suboptimal kinetics of the core C1–C1 condensation enzyme, 2-hydroxyacyl-CoA synthase (HACS), catalyzing the acyloin condensation reaction between formaldehyde and formyl-CoA. Furthermore, we used a combinatorial approach of bioprospecting and rational protein engineering to identify multiple HACS variants with significantly improved activities toward C1 substrates. Sequence and structure alignment of the active variants elucidated the key regions for the catalytic function, which were targeted for mutagenesis, leading to improved catalytic efficiency. In parallel, a consecutive round of bioprospecting for homologs with high similarity with active variants revealed a highly active HACS variant exhibiting up to 7-fold improvement in catalytic efficiency (k cat /K M ) and 14-fold improvement in the FORCE pathway flux in vivo compared to the previous reports. Upon further optimization of the downstream pathway, the orthogonal C1-to-product bioconversion system showed a metabolic flux of up to 700 μM glycolate OD –1 h –1 (2.1 mmol gDCW –1 h –1 ) and an industrially relevant glycolate titer, rate, and yield of 5.2 g L –1 (67.8 mM), 0.22 g L –1 h –1 , and 94% carbon yield, respectively.

2-hydroxyacyl-CoA synthase↗
DOE OSTI2021

D-Band EPR and ENDOR Spectroscopy of 15 N-Labeled Photosystem I

For billions of years, nature has optimized the photosynthetic machinery that converts light energy into chemical energy. Key primary reactions of photosynthesis occur in large membrane protein-cofactor complexes. The light-induced sequential electron transfer reactions occur through a chain of donor/acceptor cofactors embedded in the protein matrix resulting in a long-lived transmembrane charge-separated state. EPR is the method of choice to study electron transfer and the interaction of protein environment with redox-active cofactors. However, the spectra of organic cofactor radicals typically are not fully resolved and severely overlap at conventional X-band EPR. Even at Q-band EPR, this overlap is present and often a serious problem. As a result, there is a large variation of the reported EPR data and limited understanding of electronic structures of several redox-active cofactors. These serious problems can often be overcome by the excellent spectral resolution provided by high-frequency EPR (HF EPR). In this work, we study the electronic structure of the primary electron donor P 700 and the secondary electron acceptor A 1 of Photosystem I (PSI) using 130 GHz (D-band) EPR and Electron-Nuclear-Double-Resonance (ENDOR) spectroscopy. PSI was isotopically labeled with 15 N (I = $\frac{1/2}$) to avoid quadrupolar interactions in the most abundant nitrogen isotope 14 N (I = 1) and simplify the ENDOR spectra. ENDOR spectroscopy is central for determining the hyperfine coupling of nitrogen atoms of the two chlorophyll molecules comprising oxidized P 700 and the involvement of protein nitrogen atoms with reduced A 1 . While HF ENDOR of A 1 - allows identification of two nitrogen atoms, HF ENDOR of P 700 + still does not permit unique assignment of the recorded hyperfine couplings.

15N↗
DOE OSTI2025

Atomic-resolution imaging as a mechanistic tool for studying single-site heterogeneous catalysis

Heterogeneous catalysts dominate the chemical industry but typically feature diverse, incompletely defined active sites. Thus, describing structure-activity relationships, unlike homogeneous catalysts, remains challenging. In contrast, molecularly defined single-site heterogeneous catalysts (SSHCs), using appropriate tools, are poised to address these challenges and provide new avenues for catalysis research and development. The present study explores eco-friendly H 2 production mediated by discrete MoO 2 sites supported on carbon nanohorns (CNHs) and active for alcohol dehydrogenation. While informative, detailed ensemble EXAFS/XANES/XPS, kinetic measurements, and DFT analysis alone cannot provide a full molecular picture of the reaction pathway. Here, using single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), we propose the identification of four key catalytic intermediates anchored to CNHs and uncover a new reaction pathway involving alkoxide/hemiacetal equilibration and acetal oligomerization. Furthermore, these intermediates are inferred through a combination of theory and SMART-EM, showcasing the potential of SMART-EM as a complementary tool for exploring mechanistic hypotheses in catalysis.

36 MATERIALS SCIENCE↗
DOE OSTI2022

EstG is a novel esterase required for cell envelope integrity in Caulobacter

Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the α-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. Further, this molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

EI_MS_ML

The unambiguous identification of compounds from their electron ionization mass (EI-MS) spectra remains a significant unsolved problem in the field of metabolomics and analytical chemistry as a whole. Typically EI-MS spectra are compared using various mathematical operations that convert the spectral similarity or differences into a distance-like metric that roughly approximates the similarity of any two spectra. A commonly used metric for this is the cosine similarity metric which has values close to one for very similar spectra and a value of zero for very dissimilar spectra; however, no metric is perfect. Due to the prevalence of structurally-similar compounds such as isomers and the prevalence of certain fragmentation patterns across structurally-dissimilar compounds, the unambiguous assignment of EI-MS spectra compounds remains difficult. Frequently, querying an observed EI-MS spectrum against a large database such as the NIST17 library yields multiple possible assignments requiring the end user to distinguish between multiple high scoring hits, or multiple low scoring hits while keeping in mind that the correct hit may not be in the database at all. Although techniques such as orthogonal information from techniques such as chromatography can greatly aid in unambiguous assignment, this also requires more complicated experimental designs and access to more complicated analytical instrumentation. Substructures can be trivially detected and represented as strings using a previously published technique called node coloring from a known chemical structure. However, for experimentally-derived EI-MS spectra this information must be derived from the spectra itself (i.e., because we do not know what compound it represents). To achieve this, the software uses techniques from the field of machine learning and a large training dataset of EI-MS spectra corresponding to known structures annotated with substructure strings, to build models that can predict the presence of a given chemical substructure from an EI-MS spectrum directly.If these predictions are of high-quality (i.e., are unlikely to be false positives), the presence of one or more predicted substructures can be used to constrain the number of possible hits for a query spectrum. Mathematically, this restriction could be expressed in many forms, but the most straight-forward implementation is to weight the cosine similarity of a query spectrum and a plausible database match with a Tanimoto-like coefficient based on the ratio of the number of substructures predicted to the number of substructures present in the potential database hit. Determining which combination of models best reduces assignment ambiguity will be achieved using a combination of manual curation and optimization techniques such as genetic algorithms. This software will perform all the steps necessary to construct said models from a training dataset and evaluate them using a holdout dataset. Various statistical analyses can be performed to determine if this approach does decrease assignment ambiguity. For example, if this approach works, on average, the rank-order of the correct assignment for the holdout set of EI-MS spectra should decrease and the weighted cosine similarities for most of the possible matches in the database should be better than the unweighted cosine similarities. Furthermore, this same pipeline can be used on real experimental data to generate less ambiguous assignments.

Mitchell, Joshua↗
DOE OSTI2022

Autonomous Wireless Technology Detection in Seamless IoT Applications

The ever-increasing use of Internet of Things (IoT) devices results in the implementation of multiple wireless technologies that would not only cater their data rate requirements but also support various applications. To optimize the energy efficiency and security of the wireless transmission, it is imperative to identify the wireless technologies in various IoT implementations. Many of the existing approaches are based on measuring only the receiving signal strength indicator (RSSI). However, such approaches may not work well because of transmit power control and complex channel variations among different wireless technologies. In this article, we propose an autonomous wireless detection scheme that considers multiple distinguishable physical (PHY)-layer settings for real-time identification of wireless technologies for real-time applications. Specifically, the proposed scheme relies on the PHY-layer measurements of the targeted spectrum. Transmission settings, such as bandwidth, carrier frequency, and RSSI are estimated from the raw in-phase and quadrature-phase (I/Q) measurements. In addition, a symbol-level extraction scheme is implemented to extract unique features of modulation settings. These aforementioned features are applied to a machine learning process to identify the received wireless technologies. Compared with raw I/Q measurements, the extracted features are much simplified and, thus, the machine learning classifier can be designed with a simple structure for fast processing on IoT nodes. Finally, the proposed schemes are primarily evaluated theoretically, followed by implementing them on a USRP software-defined radio (SDR)-based hardware testbed. The evaluation results demonstrate high accuracy in the real-time detection of different wireless technologies for seamless IoT applications.

42 ENGINEERING↗
DOE OSTI2023

TRACER-Coastal Urban Boundary-Layer Interactions with Convection (TRACER-CUBIC) Field Campaign Report

To better understand the complicated web of processes governing convective cloud life cycle and aerosol-convection interactions, the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) user facility supported deployment of a variety of advanced atmospheric measurement systems to the greater Houston, Texas, area from 1 October 2021 to 30 September 2022 as part of the Tracking Aerosol Convection Interactions Experiment (TRACER). Houston was selected as a study area because isolated convection and a variety of aerosol conditions are common in this region. This one-year ARM Mobile Facility (AMF) deployment featured a four-month intensive operational period (IOP) during summer 2022 (1 June–30 September). The ARM instrumentation was deployed at three sites along an east-west transect from La Porte, Texas to an ancillary site in a less-polluted rural region southwest of downtown Houston (Figure 1). At the La Porte Site, which is located near the Houston ship channel in an area that experiences significant pollution, the first ARM Mobile Facility (AMF1) was deployed. During the IOP, the ARM tethered balloon system (TBS) operated at the ancillary site. The second-generation C-Band Scanning ARM Precipitation Radar (CSAPR) operated near Pearland, Texas, roughly halfway between the Laporte and ancillary sites. As part of the TRACER- Coastal Urban Boundary-Layer Interactions with Convection (CUBIC) project, three boundary-layer profiling systems) were deployed along a north-south transect spanning from the University of Houston Coastal Center to the Aldine site north of downtown Houston (also blue dot in Figure 1) during the TRACER IOP. These systems included the National Oceanic and Atmospheric Administration (NOAA) National Severe Storms Laboratory CLAMPS2 (C2), which was deployed at the UHCC, the University of Wisconsin SPARC, which was deployed at the ARM CSAPR site near Pearland (orange diamond in middle of map in Figure 1), and the University of Oklahoma CLAMPS1 (C1), which was deployed at Aldine. These three systems have been successfully operated in various field campaigns, providing data sets that collectively offer new insights into atmospheric-boundary-layer (ABL) processes, sea-breeze (SB) circulations, and convection initiation (CI). For the TRACER IOP window, these systems ran continuously between 1 June and 26 September, 2022. Due to commitments to NOAA projects, the Doppler lidar at the UHCC site was not available until 24 June 2022. The CLAMPS and SPARC profiling systems are self-contained platforms that have benefited from several years of development and deployment. Instruments and data processing were maintained remotely, which made the 4-month deployment for the TRACER-CUBIC IOP period possible. The same basic instrument configuration comprises each system: a scanning Doppler wind lidar for flow characterization and passive profiler(s) for characterizing planetary-boundary-layer (PBL) thermodynamic properties. Each platform includes a Halo Streamline Doppler wind lidar, an Atmospheric Emitted Radiance Interferometer (AERI), and a surface meteorology station. CLAMPS1 and CLAMPS2 each also include a microwave radiometer (MWR, Figure 1d). The TRACER-CUBIC hypotheses included (i) Interactions of SB and urban circulations and how they affect the PBL structure in the Houston environment, causing spatially (horizontally and vertically) and temporally highly variable flow patterns, (ii) heat, moisture, and aerosol transport and mixing depend on these flow dynamics, and (iii) an improved understanding of the flow patterns and PBL structure are critical for investigating the processes leading to CI. To test these hypotheses, the project aimed at (i) characterizing SB circulations and their impacts on the diurnal evolution of the structure of the ABL, (ii) studying the evolution of Houston’s complex urban boundary layer, and (iii) identifying effects of urban-induced circulations on pre-convective environments. TRACER-CUBIC observations generally provide good coverage during the summer IOP. Initial screening of the data indicates a good number of cases with bay-breeze (BB) and/or SB signatures, local CI, and interesting boundary-layer features such as strong nocturnal low-level jets (LLJs, Table 1). The numbers listed in rows 3-5 in this table will be further updated as part of ongoing in-depth analyses and systematic identification of local circulations and CI events. More detailed information about the data availability and quality for each instrument is provided in the “readme” files that were submitted to the ARM Data Center along with each archived data sets. These “readme” files also provide instrument descriptions, information about the data collection and processing procedures, data formats, and any additional information relevant for further data analysis.

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