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DOE OSTI2024

Radioisotope Identification with List-Mode Gamma Ray Data: A rigorous assessment on the value of temporal information applied to radioisotope identification.

This work explores the potential of utilizing temporal data from gamma-ray detectors, known as list-mode data, to enhance radioisotope identification. Traditional identification methods, which rely on full gamma-ray spectrum analysis, often require long dwell times and struggle with “confuser” sources, or spectra with similarly spaced spectral peaks. We hypothesize that by leveraging the probabilistic nature of nuclear decay and the time-encoded information from decay sequences and interactions with surrounding materials, we can improve classification accuracy over static spectral analysis. This research rigorously examines the temporal content of list-mode data through exploratory data analysis via correlation discovery and information theory. We further propose a basic classification model that can utilize spectral or temporal data (or both) to determine if the incorporation of temporal information can improve radioisotope identification. The findings suggest that the temporal information present in list-mode gamma-ray data has merit and should be further investigated.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Activity, structure, and diversity of Type II proline-rich antimicrobial peptides from insects

Abstract Apidaecin 1b (Api), the first characterized Type II Proline-rich antimicrobial peptide (PrAMP), is encoded in the honey bee genome. It inhibits bacterial growth by binding in the nascent peptide exit tunnel of the ribosome after the release of the completed protein and trapping the release factors. By genome mining, we have identified 71 PrAMPs encoded in insect genomes as pre-pro-polyproteins. Having chemically synthesized and tested the activity of 26 peptides, we demonstrate that despite significant sequence variation in the N-terminal sequence, the majority of the PrAMPs that retain the conserved C-terminal sequence of Api are able to trap the ribosome at the stop codons and induce stop codon readthrough—all hallmarks of Type II PrAMP mode of action. Some of the characterized PrAMPs exhibit superior antibacterial activity in comparison with Api. The newly solved crystallographic structures of the ribosome complexed with Api and with the more active peptide Fva1 from the stingless bee demonstrate the universal placement of the PrAMPs’ C-terminal pharmacophore in the post-release ribosome despite variations in their N-terminal sequence.

Huang, Weiping (ORCID:0000000273063550)↗

DOE OSTI2021

Tidal Circularization of Binaries by Resonance Locking. I. The Importance of the Pre-main Sequence

Although tidal dissipation in binary stars has been studied for over a century, theoretical predictions have yet to match the observed properties of binary populations. This work quantitatively examines the recent proposal of tidal circularization by resonance locking, where tidal dissipation arises from resonances between the star’s natural oscillation frequencies and harmonics of the orbital frequency, and where resonances are “locked” for an extended period of time due to concurrent stellar evolution. We focus on tidal resonances with axi-symmetric gravity modes, and examine binaries with primary masses from one to two solar masses. We find that orbital evolution via resonance locking occurs primarily during the star’s pre-main-sequence phase, with the main-sequence phase contributing negligibly. Resonance locking, ignoring nonlinearity, can circularize binaries with peri-center distances out to ∼10 stellar radii, corresponding to circular periods of ∼4–6 days. However, we find resonantly excited gravity modes will become nonlinear in stellar cores, which prevents them from reaching their full, linear amplitudes. We estimate that such a “saturated resonance lock” reduces the circularization period by about a third, but resonance locking remains much more effective than the cumulative actions of equilibrium tides. In a companion paper, we examine recent binary data to compare against theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Microstructural evolution of rapidly solidified hypoeutectic Al 10Cu alloy during non-isothermal annealing transients induced by nano-second laser pulses

The evolution of characteristic nonequilibrium features presenting in morphologically distinct regions of rapid solidification (RS) microstructures in a hypoeutectic Al—10Cu (atomic %) in response to non-isothermal annealing transients has been studied by transmission electron microscopy (TEM). The capabilities of the Movie-Mode Dynamic TEM (MM-DTEM) instrument were used to expose select regions of the RS microstructure to sequences of rapid heating and cooling transients induced by nanosecond laser pulses while permitting in-situ observation. Partial melting, microstructural scale coarsening, morphological changes of the nonequilibrium features in the multi-phase RS microstructure, and solid-state phase transformation were observed. Heterogeneous nucleation of nanoscale θ-Al 2 Cu phase involved metastable supersaturated α-Al and the θ'-Al 2 Cu phases, establishing different sets of orientation relationships for the stable θ-Al 2 Cu and α-Al phases. Replacement of banded morphology grains that formed under conditions driven farthest from equilibrium by an equiaxed nanocrystalline structure comprised of α-Al phase, the primary solidification product, and an intergranular network of Al 2 Cu crystals has been attributed to local remelting. Here the experimental approach explored, permitted discovery of mechanistic details of location-specific transformation pathways activated in the multi-phase RS microstructure of hypoeutectic Al—Cu during subsequent nonisothermal transients.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine‐Residue Low Complexity Peptide, as Probed by 2 H Solid‐State NMR

Abstract Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid‐state NMR to assess rotameric inter‐conversions and other dynamic modes of the methionine in the context of a nine‐residue random‐coil peptide (RC9) with the low‐complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine‐containing systems, characterized previously. Namely, the M35 of hydrated amyloid‐β 1–40 in the three‐fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)‐methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Vugmeyster, Liliya↗

DOE OSTI2023

Engineering Robust Metallic Zero-Mode States in Olympicene Graphene Nanoribbons

Metallic graphene nanoribbons (GNRs) represent a critical component in the toolbox of low-dimensional functional materials technology serving as 1D interconnects capable of both electronic and quantum information transport. The structural constraints imposed by on-surface bottom-up GNR synthesis protocols along with the limited control over orientation and sequence of asymmetric monomer building blocks during the radical step-growth polymerization have plagued the design and assembly of metallic GNRs. Here, we report the regioregular synthesis of GNRs hosting robust metallic states by embedding a symmetric zero-mode (ZM) superlattice along the backbone of a GNR. Tight-binding electronic structure models predict a strong nearest-neighbor electron hopping interaction between adjacent ZM states, resulting in a dispersive metallic band. First-principles density functional theory-local density approximation calculations confirm this prediction, and the robust, metallic ZM band of olympicene GNRs is experimentally corroborated by scanning tunneling spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A Robust Yule-Walker Method for Online Monitoring of Power System Electromechanical Modes of Oscillation

Reliable power system operation requires that system operators maintain a satisfactory small-signal stability margin at all times. Mode meters allow system operators to continuously monitor the stability margin by analyzing synchrophasor measurements. Experience with mode meters at the Bonneville Power Administration (BPA) has revealed that mode meters sometimes suffer severe bias following transient disturbances. In this paper, a robust version of the Yule-Walker mode meter algorithm is proposed to mitigate this bias. The robust capability is introduced by modifying the estimator of the autocovariance sequence (ACS) on which the algorithm depends. Tests with field-measured data demonstrate that the robust Yule-Walker (RYW) algorithm significantly outperforms its conventional counterpart and is better able to provide system operators with accurate information about the system's stability margin.

Follum, James D.↗

DOE OSTI2020

Advancing reliability assessments of photovoltaic modules and materials using combined-accelerated stress testing

Previously undiscovered failure modes in photovoltaic (PV) modules continue to emerge in field installations despite passing protocols for design qualification and quality assurance. Failure to detect these modes prior to widespread use could be attributed to the limitations of present-day standard accelerated stress tests (ASTs), which are primarily designed to identify known degradation or failure modes at the time of development by applying simultaneous or sequential stress factors (usually two at most). Here, we introduce an accelerated testing method known as the combined-accelerated stress test (C-AST), which simultaneously combines multiple stress factors of the natural environment. Simultaneous combination of multiple stress factors allows for improved identification of failure modes with better ability to detect modes not known a priori. A demonstration experiment was conducted that reproduced the field-observed cracking of polyamide- (PA-) and polyvinylidene fluoride (PVDF)–based backsheet films, a failure mode that was not detected by current design qualification and quality assurance testing requirements. In this work, a two-phase testing protocol was implemented. The first cycle (“Tropical”) is a predominantly high-humidity and high-temperature test designed to replicate harsh tropical climates. The second cycle (“Multi-season”) was designed to replicate drier and more temperate conditions found in continental or desert climates. Testing was conducted on 2 × 2-cell crystalline-silicon cell miniature modules constructed with both ultraviolet (UV)–transmitting and UV-blocking encapsulants. Cracking failures were observed within a cumulative 120 days of the Tropical condition for one of the PA-based backsheets and after 84 days of Tropical cycle followed by 42 days of the Multi-season cycle for the PVDF-based backsheet, which are both consistent with failures seen in fielded modules. In addition to backsheet cracking, degradation modes were observed including solder/interconnect fatigue, various light-induced degradation modes, backsheet delamination, discoloration, corrosion, and cell cracking. The ability to simultaneously apply multiple stress factors may allow many of the test sequences within the standardized design qualification procedure to be performed using a single test setup.

14 SOLAR ENERGY↗

DOE OSTI2023

Insights into ENSO Diversity from an Intermediate Coupled Model. Part II: Role of Nonlinear Dynamics and Stochastic Forcing

Abstract In this study, we investigate how a single leading linear El Niño–Southern Oscillation (ENSO) mode, as studied in Part I, leads to the irregular coexistence of central Pacific (CP) and eastern Pacific (EP) ENSO, a phenomenon known as ENSO spatiotemporal diversity. This diversity is fundamentally generated by deterministic nonlinear pathways to chaos via the period-doubling route and, more prevailingly, the subharmonic resonance route with the presence of a seasonally varying basic state. When residing in the weakly nonlinear regime, the coupled system sustains a weak periodic oscillation with a mixed CP/EP pattern as captured by the linear ENSO mode. With a stronger nonlinearity effect, the ENSO behavior experiences a period-doubling bifurcation. The single ENSO orbit splits into coexisting CP-like and EP-like ENSO orbits. A sequence of period-doubling bifurcation results in an aperiodic oscillation featuring irregular CP and EP ENSO occurrences. The overlapping of subharmonic resonances between ENSO and the seasonal cycle allows this ENSO irregularity and diversity to be more readily excited. In the strongly nonlinear regime, the coupled system is dominated by regular EP ENSO. The deterministic ENSO spatiotemporal diversity is thus confined to a relatively narrow range corresponding to a moderately unstable ENSO mode. Stochastic forcing broadens this range and allows ENSO diversity to occur when the ENSO mode is weakly subcritical. A close relationship among a weakened mean zonal temperature gradient, stronger ENSO activity, and more (fewer) occurrences of EP (CP) ENSO is noted, indicating that ENSO–mean state interaction may yield ENSO regime modulations on the multidecadal time scale.

Geng, Licheng↗

DOE OSTI2024

Discovery of 15 A-F Main Sequence Pulsating Star Candidates

Delta Scuti stars, spanning spectral types A to F with masses between 1.5 and 2.5 solar masses, exhibit a complex mix of radial and non-radial pressure modes. This study focuses on 15 Delta Scuti, Gamma Doradus, and Hybrid candidate stars using TESS satellite photometry data with a time series of exposures ranging from 20 to 600 seconds across different sky regions. Employing the prewhitening technique via fast Fourier transforms, significant frequencies are extracted from light curves. Three approximation methods are used to estimate critical stellar parameters such as density, radius, and mass. This research also verifies the variability of these stars, which are currently not classified as variable in databases like SIMBAD.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a distinctive mode of engaging poly(ADP-ribose)

PARP13/ZAP (zinc-finger antiviral protein) acts against multiple viruses by promoting degradation of viral mRNA. PARP13 has four N-terminal zinc (Zn) fingers that bind CG-rich nucleotide sequences, a C-terminal ADP ribosyltransferase fold, and a central region with a fifth Zn finger and tandem WWE domains. The central PARP13 region, ZnF5-WWE1-WWE2, is implicated in binding poly(ADP-ribose); however, there are limited insights into its structure and function. We present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and in complex with ATP. The crystal structures and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose) chains. The composite ZnF5-WWE1-WWE2 structure forms an extended surface to engage ADP-ribose chains, representing a distinctive mode of recognition that provides a framework for investigating the impact of poly(ADP-ribose) on PARP13 function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Enabling multiple intercavity polariton coherences by adding quantum confinement to cavity molecular polaritons

In this study, the “particle in a box” idea, which was broadly developed in semiconductor quantum dot research, was extended into mid-infrared (IR) cavity modes by applying lateral confinement in an optical cavity. The discrete cavity modes hybridized with molecular vibrational modes, resulting in a quartet of polariton states that can support multiple coherence states in the IR regime. We applied tailored pump pulse sequences to selectively prepare these coherences and verified the multi-coherence existence. The simulation based on Lindblad equation showed that because the quartet of polariton states resided in the same cavity, they were specifically robust toward decoherence caused by fluctuations in space. The multiple robust coherences paved the way for entangled states and coherent interactions between cavity polaritons, which would be critical for advancing polariton-based quantum information technology.

2D IR↗

DOE OSTI2020

Bacterial Origin and Reductive Evolution of the CPR Group

The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO , a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE . The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

On the modes of nanosecond pulsed plasmas for combustion ignition of quiescent CH 4 -air mixtures

The effect of transient plasma modes on ignition kernel development are discussed here for a quiescent CH 4 -air combustion model system. A 10 ns high-voltage pulse was applied to a pin-to-pin electrode in lean fuel-air mixtures at room temperature and atmospheric pressure. High-impedance streamer, transient spark and low-impedance spark discharges were identified based on pulse waveforms of voltage and current. A sustained ignition kernel expansion was observed when the plasma discharge transitioned into a transient spark or spark discharge. The minimum ignition energy was obtained at the transient spark mode, which has less than a third of the energy or Coulomb transfer compared to the low-impedance spark. Employing repetitive 10-pulse sequence at 10 kHz, the lean-fuel limit was extended from an equivalence ratio of 0.6 for the single pulse ignition to 0.5. The use of repetitive pulses also allowed streamer breakdown or spark initiation to occur at a lower voltage.

CH 4↗

DOE OSTI2020

Dynamic Modeling of Sequential Service Restoration in Islanded Single Master Microgrids

This paper presents a methodology for generating restoration sequences in distribution systems and microgrids with emphasis on deriving optimal switching times for remote control switches (RCS). Microgrid architecture considered are assumed to be operating in islanded single master mode. Control methods for handling the unbalance inherent in distribution systems using single-phase controlled PQ inverters were developed and incorporated in the proposed method. The problem of considering simultaneously both energy optimization and dynamic stability of the system, which is lacking in existing methods, was addressed by studying the transient behavior of microgrids based on extended EMTP simulations and then approximate and incorporate these behaviors into the optimization formulation for restoration. The approach is based on multi-objective optimization of final restored load and total restoration time. The methodology was studied on a modified IEEE 123 node test feeder. An EMTP simulation in PSCAD of the formed microgrids was used to validate the accuracy of the dynamic and steady-state characteristics of the resulting systems. By considering the transient behavior of DGs during restoration, a better restoration sequence that does not trigger protection relays could be realized.

42 ENGINEERING↗

DOE OSTI2025

Sequential Stress Identifies Processing Defects in Bifacial Photovoltaic Modules That Limit Durability

Here, we use sequential stress to investigate hurdles to bifacial photovoltaic (PV) module durability from lamination defects. We test mini-modules with glass/glass (G/G) and glass/transparent-backsheet (G/TB) constructions using either ethylene vinyl acetate or polyolefin elastomer (POE) based encapsulants under a modified IEC 63209-2 sequential stress. This sequence includes multiple iterations of damp heat (DH200), full spectrum light exposure (A3), thermal cycling (TC50), and humidity/freeze (HF10). We compare indoor stress with outdoor exposure. Results show similar relative trends in degradation after a year outdoors compared to our first stress cycle. Subsequent stress cycles impart more severe damage than outdoor exposure for the short outdoor duration used here. Edge-pinch lamination defects in G/G mini-modules limit durability causing delamination and cell cracks. Conversely, we observe greater degradation in G/TB mini-modules compared to G/G in the later stages of the stress sequence when the backsheets are directly exposed to UV-containing light. Our results highlight: 1) the utility of sequential stress testing to uncover degradation modes in bifacial PV, 2) implications of using mini-modules for testing PV quality, and 3) the importance of lamination defects that must be avoided to ensure durability as the industry adopts G/G or G/TB packaging.

14 SOLAR ENERGY↗