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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Novel mutation leading to splice donor loss in a conserved site of DMD gene causes Duchenne muscular dystrophy with cryptorchidism

Background As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic aetiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants. Methods In this study, a cohort of 115 Chinese probands with cryptorchidism was analysed using whole-genome sequencing, alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening used to observe the phenotype. Results In 30 of 115 patients (26.1%), we identified four novel genes ( ARSH , DMD , MAGEA4 and SHROOM2 ) affecting at least five unrelated patients and four known genes ( USP9Y , UBA1 , BCORL1 and KDM6A ) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p<2.5×10 −6 ) under the Bonferroni correction. Surprisingly, novel and known genes were mainly found on X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather than de novo origin. CRISPR-Cas9 mouse modelling of a splice donor loss variant in DMD (NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by MRI at 4 and 10 weeks. The movement tests further revealed symptoms of Duchenne muscular dystrophy (DMD) in transgenic mice. Conclusion Our results revealed the role of the DMD gene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.

Chen, Jianhai (ORCID:0000000300932003)↗
DOE OSTI2025

A Comparative Study of Physics‐Informed and Data‐Driven Neural Networks for Compound Flood Simulation at River‐Ocean Interfaces: A Case Study of Hurricane Irene

Simulating compound flooding (CF) at the river-ocean interface within large-scale Earth System Models (ESMs) presents significant challenges due to complex interactions between river discharge, storm surge, and tides. This study assesses the comparative advantages of physics-informed and data-driven machine learning (ML) approaches for enhancing local ESM performance. We systematically compare data-driven neural network models (i.e., CNNs, U-Net, Long Short-Term Memory (LSTM), Gated Recurrent Unit), and physics-informed neural network (PINN) models, including vanilla PINN and a finite-difference-based PINN (FD-PINN). Specifically, FD-PINN is introduced to enhance computational efficiency, accelerating vanilla PINNs by ∼6.5 times while improving accuracy. To enhance data-driven model training, a new data-generation approach is developed to sample historical fluvial and coastal flood events, which ensures a robust data set for extreme event prediction. The models are evaluated using a realistic one-dimensional river domain extracted from an ESM's river mesh and the Hurricane Irene event as an independent test case. Results show that FD-PINN achieves accurate predictions with significantly reduced computational costs relative to vanilla PINNs. Among data-driven models, the best overall performance is achieved by a CNN-LSTM hybrid, which balances accuracy and efficiency. While a fully connected CNN (CNN-FC) provides the best accuracy, it incurs high computational cost. Architectures lacking strong temporal modeling tend to underperform on unseen events. These findings highlight the importance of sequence-aware designs for robust generalization. This study reveals the trade-offs between physics-informed and data-driven models and proposes an adaptive hybrid framework for integrating ML into ESMs to enhance local flood simulations.

Earth Systems Modeling↗
DOE OSTI2025

A VSC-HVDC-Assisted Black-Start Strategy in Bulk Power Systems a Case Study in San Diego

With the worldwide growth in deploying high-voltage direct current (HVDC) transmission systems, their ability to facilitate black-start (BS) restoration has been a research topic of interest. In this context, voltage source converter (VSC)-HVDC is regarded as a BS resource, and this paper proposes a VSC-HVDC-assisted parallel BS restoration strategy in bulk power systems. The proposed strategy consists of two stages: 1) determination of the VSC and generator startup sequence and 2) load restoration simulation. In the first stage, the entire blackout system is sectionalized into multiple subsystems. Each subsystem includes a VSC-HVDC station or traditional BS unit, it independently determines its generator startup timeline and the energization timelines for buses and lines. The second stage involves load restoration, conceptualized as a modified unit commitment problem, with the timelines established in the first stage work as critical inputs. The proposed BS restoration strategy is tested on the San Diego power system to simulate the 2011 Southwest blackout. The simulation results validate the effectiveness of using VSC-HVDC links as a BS resource which not only speeds up the restoration process but also reduces both energy and economic losses.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Mini‐synplastomes for plastid genetic engineering

Summary In the age of synthetic biology, plastid engineering requires a nimble platform to introduce novel synthetic circuits in plants. While effective for integrating relatively small constructs into the plastome, plastid engineering via homologous recombination of transgenes is over 30 years old. Here we show the design–build–test of a novel synthetic genome structure that does not disturb the native plastome: the ‘mini‐synplastome’. The mini‐synplastome was inspired by dinoflagellate plastome organization, which is comprised of numerous minicircles residing in the plastid instead of a single organellar genome molecule. The first mini‐synplastome in plants was developed in vitro to meet the following criteria: (i) episomal replication in plastids; (ii) facile cloning; (iii) predictable transgene expression in plastids; (iv) non‐integration of vector sequences into the endogenous plastome; and (v) autonomous persistence in the plant over generations in the absence of exogenous selection pressure. Mini‐synplastomes are anticipated to revolutionize chloroplast biotechnology, enable facile marker‐free plastid engineering, and provide an unparalleled platform for one‐step metabolic engineering in plants.

Occhialini, Alessandro↗
DOE OSTI2023

Advanced Drying Cycle Simulator Thermal Response to Commercial Drying Conditions

The purpose of this report is to document updates on testing of the apparatus built to simulate commercial drying procedures for spent nuclear fuel at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention that incorporate relevant physics and well-controlled boundary conditions. This report documents testing updates for the Advanced Drying Cycle Simulator (ADCS). This apparatus was built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. These waterproof heaters are the next generation design to heater rods developed and tested at Sandia National Laboratories in FY20. This report describes preliminary testing of the ADCS through measurement and analysis of the thermal response of the system to a subset of commercial drying conditions that exclude the introduction of water, namely simulated decay heats and pressures relevant to commercial drying. This test series, referred to as a “dry” test series in this report, spans three uniform waterproof heater rod powers (representing spent fuel decay heats), four helium fill pressures, and six vacuum levels. This test series was conducted to cover the range of expected ADCS testing conditions for upcoming “wet” testing, where water will be introduced and a simulated commercial drying cycle will be performed. The dry test conditions were derived from the commercial drying conditions seen in the High Burnup Demonstration and the vacuum drying conditions chosen for a smaller scale Dashpot Drying Apparatus tested at Sandia National Laboratories in FY22. For a given uniform power and pressure/vacuum level, the ADCS was operated at constant power and pressure and allowed to reach steady state conditions. The thermal data obtained from these tests were analyzed, and the results can inform computational models built to simulate commercial drying processes by providing baseline thermal data prior to the introduction of water. Following the preliminary dry tests, a test plan for the ADCS will be developed to implement a drying procedure that begins with the introduction of water to the system and is based on measurements from the drying process used for the High Burnup Demonstration Project. While applying power to the simulated fuel rods, this procedure is expected to consist of filling the ADCS vessel with water, draining the water with applied pressure and multiple helium blowdowns, evacuating additional water with a vacuum drying sequence at successively lower pressures, and backfilling the vessel with helium. Additional investigations are expected to feature failed fuel rod simulators with engineered cladding defects and guide tubes with obstructed dashpots to challenge the drying system with multiple water retention sites. The data from these investigations is expected to inform the efficacy of commercial drying operations through the quantification of residual water in a prototypic-length dry storage canister.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile

Abstract Aim The objective of the work was to assess the effect of biostimulation with selected plant growth-promoting bacteria on growth and metabolite profile of Salicornia europaea. Methods and results Salicornia europaea seeds were inoculated with different combinations of plant growth-promoting bacteria Brevibacterium casei EB3, Pseudomonas oryzihabitans RL18, and Bacillus aryabhattai SP20. Plants germinated from inoculated seeds were grown either in laboratory conditions or in a saline crop field. Fresh and dry weight were determined at the end of the experiment, for biomass quantification. The microbiological quality of fresh shoots for human consumption as salad greens was assessed, and the persistence of the inoculated strains in the plant rhizosphere was confirmed by next-generation sequencing (Illumina) of the 16S rDNA gene. The primary metabolite profile of biostimulated plants was characterized by GC–TOF-MS. In laboratory conditions, inoculation with the two strains Br. casei EB3 and Ps. oryzihabitans RL18 caused the most significant increase in biomass production (fresh and dry weight), and caused a shift in the central metabolic pathways of inoculated plants toward amino acid biosynthesis. In the field experiment, no significant biostimulation effect was detected with any of the tested inoculants. Seed inoculation had no significant effect on the microbiological quality of the edible parts. The persistence of inoculants was confirmed in both experiments. Conclusions Manipulation of the plant microbiome can trigger primary metabolic reconfiguration and modulate the plant metabolism while promoting plant growth.

Ferreira, Maria J.↗
DOE OSTI2024

A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain

Abstract SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5′-TCGGAT-3′) of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Heating events in the nascent solar system recorded by rare earth element isotopic fractionation in refractory inclusions

Equilibrium condensation of solar gas is often invoked to explain the abundance of refractory elements in planets and meteorites. This is partly motivated, by the observation that the depletions in both the least and most refractory rare earth elements (REEs) in meteoritic group II calcium-aluminum–rich inclusions (CAIs) can be reproduced by thermodynamic models of solar nebula condensation. We measured the isotopic compositions of Ce, Nd, Sm, Eu, Gd, Dy, Er, and Yb in eight CAIs to test this scenario. Contrary to expectation for equilibrium condensation, we find light isotope enrichment for the most refractory REEs and more subdued isotopic variations for the least refractory REEs. This suggests that group II CAIs formed by a two-stage process involving fast evaporation of preexisting materials, followed by near-equilibrium recondensation. The calculated time scales are consistent with heating in events akin to FU Orionis– or EX Lupi–type outbursts of eruptive pre–main-sequence stars.

58 GEOSCIENCES↗
DOE OSTI2020

High‐order cubature rules for tetrahedra

Summary In this paper, we construct new high‐order numerical integration schemes for tetrahedra, with positive weights and integration points that are in the interior of the domain. The construction of cubature rules is a challenging problem, which requires the solution of strongly nonlinear algebraic (moment) equations with side conditions given by affine inequality constraints. We present a robust algorithm based on a sequence of three modified Newton procedures to solve the constrained minimization problem. In the literature, numerical integration rules for the tetrahedron are available up to order p =15. We obtain integration rules for the tetrahedron from p =2 to p =20, which are computed using multiprecision arithmetic. For p ≤15, our approach provides integration rules that have the same or fewer number of integration points than existing rules; for p =16 to p =20, our rules are new. Numerical tests are presented that verify the polynomial‐precision of the cubature rules. Convergence studies are performed for the integration of exponential, rational, weakly singular and trigonometric test functions over tetrahedra with flat and curved faces. In all tests, improvements in accuracy is realized as p is increased, though in some cases nonmonotonic convergence is observed.

Jaśkowiec, Jan↗
DOE OSTI2020

Universal interferometric signatures of a black hole’s photon ring

The Event Horizon Telescope image of the supermassive black hole in the galaxy M87 is dominated by a bright, unresolved ring. General relativity predicts that embedded within this image lies a thin “photon ring,” which is composed of an infinite sequence of self-similar subrings that are indexed by the number of photon orbits around the black hole. The subrings approach the edge of the black hole “shadow,” becoming exponentially narrower but weaker with increasing orbit number, with seemingly negligible contributions from high-order subrings. Here, we show that these subrings produce strong and universal signatures on long interferometric baselines. These signatures offer the possibility of precise measurements of black hole mass and spin, as well as tests of general relativity, using only a sparse interferometric array.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Case Study: NREL Campus Chilled Water Storage Potential: Benchmark Datasets Development and Applications, Task 4 - Use Case Demonstration

The Benchmark Datasets Development and Applications project is a three-year collaboration between the National Renewable Energy Laboratory (NREL), Oak Ridge National Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory. The project seeks to collect and curate high-resolution, well-calibrated time series of building operational and indoor/outdoor environmental data, which are crucial to understanding and optimizing building energy efficiency performance and demand flexibility capabilities as well as benchmarking energy algorithms. Project outcomes include approximately twelve high-fidelity building datasets, enhanced data representation tools, and four case studies to illustrate example applications. The goal of these case studies is to define and execute analyses that demonstrate how one or more datasets collected through this project can address a data gap or challenge historically faced by building stakeholders. This technical paper summarizes the findings of one of these case studies, in which we studied the operational efficiencies of the central cooling system at NREL. We looked at three years of data from the three chillers in the Field Test Laboratory Building (FTLB), from 2019 to 2021, to compare equipment operation and demand throughout the time period. Our analysis indicates that all three chillers are operating at or below the optimal loading conditions for most of the operation time, and thus there was no efficiency drop due to loading of the chillers at full capacity. Our recommendation is that no chiller capacity increase is needed; instead, the central plant could benefit from adopting advanced control logics for optimal sequencing of chillers during part load operations. Analysis of adding chilled water thermal storage to the central plant indicated 34% savings in demand cost and 24.5% savings in total cost (energy consumption and demand charge cost). The payback period is estimated to be 11-22 years with an assumed TES cost of $\$$100-$200 per ton. This case study shows how a selected dataset is used to solve a practical building problem - learning the operational status of its components, analyzing the effectiveness of a proposed new technique, and aiding decision-making for the building operations and maintenance team.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water

Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.

Acharya, Shwetha M↗
DOE OSTI2026

Overview of IMPACT Data Acquisition System and Data Reduction Process

This report documents the development of the data acquisition system (DAS) and data reduction methodologies for the Irradiated Material Property Accelerated Characterization Test (IMPACT) experiment at the Advanced Test Reactor (ATR). The IMPACT experiment is designed to enable in-pile measurement of thermal conductivity in metallic nuclear fuels, specifically U-10Zr, using an instrumented thermal conductivity probe. The DAS supports both passive temperature monitoring and active thermal interrogation of the probe through controlled AC and DC excitation. Significant modifications to laboratory-scale systems were required to accommodate the higher resistance paths associated with the in-pile application. Custom electronics and relay-controlled measurement sequencing were developed to enable the measurement and sufficient power delivery to the sensing region. A reduced-order, axisymmetric thermal model based on the thermal quadrupoles method is presented to support data interpretation. This model enables efficient evaluation of transient heat transfer behavior and facilitates solution of the inverse problem required to extract thermal properties from measured signals. Multiple boundary condition formulations are discussed to address varying experimental time scales and geometries. Additionally, machine learning techniques are introduced to support data reduction and improve confidence in inverse solutions. Convolutional neural networks are applied to identify the presence of gas gaps and other evolving geometric features that significantly impact thermal response during irradiation. These efforts contribute to the broader integration of digital twin frameworks and real-time modeling capabilities within the Advanced Fuels Campaign.

46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
DOE OSTI2024

Deformation and Delamination of Dynamically Bulging Bilayered Films

We employ finite element simulations to study the dynamic bulging of films under shock tube conditions and compare these responses with quasi-static bulging. Both scenarios subject the film to time-varying pressure. Two film types are considered: uniform material films and bilayers with a relatively soft interior layer and a hard exterior layer. The interface between the materials in the bilayer cases is modeled as a cohesive zone that follows a bilinear normal traction-separation cohesive law. Additionally, bilayer films with preexisting cracks in the interior layer are analyzed. Parametric studies are also conducted to explore the effects of loading rate and specimen size. The mechanical response of all materials is assumed to be strain-rate independent, focusing solely on the inertial effects in the response of the films under dynamic loading, and the absence of such effects under quasi-static loading. The results indicate that quasi-static bulging exhibits a predictable plate bending like deformation. In contrast, depending on the loading rate and specimen size, dynamic bulging can give rise to elastic waves, and a sequence of deformation processes including initial uniform acceleration, followed by bending-like deformation, and finally through-thickness biaxial stretching. Dynamic loading also leads to larger bulge formation and greater deformation than quasi-static loading. A key finding is the role of preexisting cracks in driving delamination under dynamic loading, which is absent in quasi-static loading. This work enhances our understanding of dynamic bulging and motivates further research on characterizing delamination in layered films using dynamic bulge tests.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Tuning Shinkarev’s Bicycle: Separating the Parallel Cycles of Photosystem II Using Empirical Wavelet Transform

The oxygen-evolving complex (OEC) of Photosystem II (PSII) catalyzes light-driven water oxidation, a process necessary to sustain Earth’s atmospheric oxygen. Oxygen yields measured during single-turnover flash sequences exhibit period-four oscillations, which form the basis of the Joliot–Kok (S-state) model. However, when the oscillations of other processes contribute to the measured oxygen yield, fitting methods can conflate these signals and distort estimates of inefficiencies and initial S-state populations. To address this, we applied the empirical wavelet transform (EWT) as a model-independent method to separate overlapping oscillators and capture damping dynamics that are not well represented in Fourier analysis. We tested this framework on polarographic flash-oxygen traces from both our Synechocystis sp. PCC 6803 thylakoid membrane preparations and archival datasets on Chlorella and isolated chloroplasts. EWT consistently resolves the expected period-four component alongside a distinct binary oscillation. Simulations suggest that fitting this isolated period-four signal recovers VZAD parameters more accurately than analysis of raw traces, yielding different estimates for S-state distributions and transition probabilities. Notably, this binary oscillation aligns closely with semiquinone dynamics predicted solely from period-four fit parameters. These findings indicate that EWT can effectively distinguish complex signals in oxygen evolution, offering a framework potentially applicable to other spectroscopic probes of the S-state cycle.

Ferrari, Nicholas [Louisiana State Univ., Baton Ro↗