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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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DOE OSTI2026

Synthetic overlapping genes stabilize genetic systems

Overlapping genes—wherein two different proteins are translated from alternative reading frames of the same DNA sequence—provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapping gene. However, creating overlapping gene pairs is challenging, as it requires redesigning both protein products to accommodate overlap constraints. Here, we present a new “overlapping, alternate-frame insertion” (OAFI) method for creating synthetic overlapping genes by inserting an “inner” gene, encoded in an alternate frame, into a flexible region of an “outer” gene. Using OAFI, we create new overlapping gene pairs of genetic reporters and bacterial toxins within an antibiotic resistance gene. We show that both the inner and outer genes retain function despite redesign, with translation of the inner gene influenced by its overlap position in the outer gene. Importantly, we show that, despite these inner gene sequences not contributing to outer gene function, selection for the outer gene alters the permitted inactivating mutations in the inner gene, and that overlapping toxins can restrict horizontal gene transfer of the antibiotic resistance gene. Overall, OAFI offers a versatile tool for synthetic biology, expanding the applications of overlapping genes in gene stabilization and biocontainment.

Biological and medical sciences↗
DOE OSTI2020

Photoinduced charge transfer in transition metal dichalcogenide heterojunctions – towards next generation energy technologies

Increasing interest in using two-dimensional transition metal dichalcogenides (2D TMDCs) in optical energy conversion technologies creates a demand for improving the yields and lifetimes of photogenerated charge carriers. Despite inherently fast photocarrier decay in neat 2D TMDCs, the unique photophysics in these quantum-confined systems motivates continued effort to control the evolution of photoexcited states and create functional devices. Here, an intriguing strategy to accomplish this goal is to employ TMDCs in heterojunctions with appropriate semiconductors, where energy level offsets drive photoinduced charge transfer (PCT) across material interfaces. PCT in TMDC-based systems can be optimized for many different applications, such as driving free carriers to photocatalytic sites for redox reactions like water splitting, extracting charge to perform work in photovoltaics or photodetectors, and manipulating the spin and momentum valley electronic degrees of freedom for quantum computing systems. Here, we review recent strides in optimizing PCT for such applications through greater fundamental understanding of the photophysics that occurs at TMDC/semiconductor interfaces. After giving an overview of isolated TMDC properties, synthetic methods, and the basics of PCT, we discuss TMDCs in heterojunctions with several classes of materials, including other TMDCs, small molecule semiconductors, polymers, single-walled carbon nanotubes, quantum dots, perovskites, and electrolytes. In addition to highlighting the unique benefits of each materials category, we also identify parallels across common themes, such as the roles of charge-transfer states, spin, electronic coupling, delocalization, interfacial atomic morphology, and the precise design of energy landscapes to direct charge and energy motion. We hope to capture a broad range of the valuable work in this fast-paced field to inspire new research directions for employing PCT in targeted TMDC-based systems.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping

Single-molecule fluorescence spectroscopy allows direct, real-time observation of dynamic photophysical changes in light harvesting complexes. The Anti-Brownian ELectrokinetic (ABEL) trap is one such single-molecule method with useful advantages. This approach is particularly well-suited to make detailed spectroscopic measurements of pigment-protein complexes in solution phase because it enables extended-duration single-molecule observation by counteracting Brownian motion. This Perspective summarizes recent contributions by the authors and others that have utilized the unique capabilities of the ABEL trap to advance our understanding of phycobiliproteins and the phycobilisome complex, the primary light-harvesting apparatus of cyanobacteria. Monitoring the rich spectroscopic data from these measurements, which include brightness, fluorescence lifetime, polarization, and emission spectra, among other measurable parameters, has provided direct characterization of pigments and energy transfer pathways in the phycobilisome, spanning scales from single pigments and monomeric phycobiliproteins to higher order oligomers and protein-protein interactions of the phycobilisome complex. Importantly, new photophysical states and photodynamics were observed to modulate the flow of energy through the phycobilisome and suggest a previously unknown complexity in phycobilisome light harvesting and energy transport with a possible link to photoadaptive or photoprotective functions in cyanobacteria. Here, beyond deepening our collective understanding of natural light-harvesting systems, these and future discoveries may serve as inspiration for engineering improved artificial light-harvesting technologies.

14 SOLAR ENERGY↗
DOE OSTI2025

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Spinodal enhancement of fluctuations in nucleus-nucleus collisions

Subensemble Acceptance Method (SAM) [1, 2] is an essential link between measured event-by-event fluctuations and their grand canonical theoretical predictions such as lattice QCD. The method allows quantifying the global conservation law effects in fluctuations. In its basic formulation, SAM requires a sufficiently large system such as created in central nucleus-nucleus collisions and sufficient space-momentum correlations. Directly in the spinodal region of the First Order Phase Transition (FOPT) different approximations should be used that account for finite size effects. Thus, we present the generalization of SAM applicable in both the pure phases, metastable and unstable regions of the phase diagram [3]. Obtained analytic formulas indicate the enhancement of fluctuations due to crossing the spinodal region of FOPT and are tested using molecular dynamics simulations. A rather good agreement is observed. Using transport model calculations with interaction potential we show that the spinodal enhancement of fluctuations survives till the later stages of collision via the memory effect [4]. However, at low collision energies the space-momentum correlation is not strong enough for this signal to be transferred to second and third order cumulants measured in momentum subspace. This result agrees well with recent HADES data on proton number fluctuations at $\sqrt{S_{NN}}$ = 2.4 GeV which are found to be consistent with the binomial momentum space acceptance [5].

Poberezhnyuk, Roman↗
DOE OSTI2021

Persistent Homology Metrics Reveal Quantum Fluctuations and Reactive Atoms in Path Integral Dynamics

Nuclear quantum effects (NQEs) are known to impact a number of features associated with chemical reactivity and physicochemical properties, particularly for light atoms and at low temperatures. In the imaginary time path integral formalism, each atom is mapped onto a “ring polymer” whose spread is related to the quantum mechanical uncertainty in the particle’s position, i.e., its thermal wavelength. A number of metrics have previously been used to investigate and characterize this spread and explain effects arising from quantum delocalization, zero-point energy, and tunneling. Many of these shape metrics consider just the instantaneous structure of the ring polymers. However, given the significant interest in methods such as centroid molecular dynamics and ring polymer molecular dynamics that link the molecular dynamics of these ring polymers to real time properties, there exists significant opportunity to exploit metrics that also allow for the study of the fluctuations of the atom delocalization in time. Here we consider the ring polymer delocalization from the perspective of computational topology, specifically persistent homology, which describes the 3-dimensional arrangement of point cloud data, (i.e. atomic positions). We employ the Betti sequence probability distribution to define the ensemble of shapes adopted by the ring polymer. The Wasserstein distances of Betti sequences adjacent in time are used to characterize fluctuations in shape, where the Fourier transform and associated principal components provides added information differentiating atoms with different NQEs based on their dynamic properties. We demonstrate this methodology on two representative systems, a glassy system consisting of two atom types with dramatically different de Broglie thermal wavelengths, and ab initio molecular dynamics simulation of an aqueous 4 M HCl solution where the H-atoms are differentiated based on their participation in proton transfer reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks

Abstract Background Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study’s aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds. Methods Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison. Results All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (–2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%–49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness. Conclusions The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.

Tedim, Ana P.↗
DOE OSTI2025

Control Oriented Models for Co-Design: Technical Overview of MT HVDC, MVDC, and Solid State Transformer Building Blocks

The electric power system is shifting toward a power electronics–enabled grid, where converter based “building blocks” (e.g., high voltage direct current (HVDC) links, multi terminal HVDC (MT HVDC) networks, medium voltage DC (MVDC) links, and solid state transformers (SSTs)) provide fast, precise control of power flows, voltage, and frequency. This report develops and applies publicly shareable electromagnetic transient (EMT) and phasor models to examine how such building blocks can be composed and coordinated to support offshore wind integration, inter area transfers, feeder support, and resilience. Section 2 documents a modular multilevel converter (MMC)–based MT HVDC modeling framework and two use cases: a compact WSCC/IEEE 9 bus test system and a 240 bus “mini WECC” case with five offshore wind plants (OWFs). Phasor to EMT transfer, initialization, and sanity checks are summarized, and neutral demonstrations of normal and contingency operation are reported. Section 3 frames the problem of wind plant inertial frequency response (IFR): shaping energy release and recovery to improve nadir while avoiding aerodynamic stall; representative simulations illustrate the issues without disclosing proprietary control. Section 4 develops MVDC concepts through an IEEE 16 bus loop and an Olympic Peninsula case study that compares AC vs. MVDC corridors and shows how feeder headroom can be pooled via DC couplers. Section 5 surveys SST architectures and identifies a gap: scalable, communication free coordination of multiple SSTs for islanded feeder networks. Across the report, novel methods and configurations under separate publication and IP review are not disclosed; only topic oriented, replicable setups and non proprietary results are shown. These models and use cases are intended as foundations for future publications and co design studies on architecture, control, and coordination of PE enabled grids.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Nanosecond Structure of Radical Pair Intermediates from High-Frequency Quantum Oscillations: Insight into the Q A •– to Q B Electron Transfer Step in Purple Bacterial Photosynthesis

We demonstrate the validity of our approach to deduce, from the anisotropy of quantum oscillations, the geometry of short-lived radical pair intermediates in photosynthesis. A global fit of a two-dimensional W-band (94 GHz) electron paramagnetic resonance (EPR) experiment provides the same global minimum values for the geometry of the A-side radical pair P 700 •+ A 1A •− in photosystem I (PSI) as observed in a previous Q-band (34 GHz) EPR study, yet with a significantly increased convergence rate of 62%. This demonstrates that the global fit yields the correct radical pair geometry even at Q-band frequencies. With this information, we revisit our previous Q-band study of the cofactor arrangement of P 865 •+ Q A •− , the stabilized charge-separated state in purple bacterial reaction centers (RCs). Analysis of calculated two-dimensional data sets of P 865 •+ Q A •− reveals that the quantum oscillation technique is unaffected by a mirror ambiguity in disordered solids and thus can provide unambiguous solutions for all five Euler angles of the radical pair geometry. This enables us to elucidate the Q A •− to Q B electron transfer step in purple bacterial photosynthesis, the subject of controversial discussions for more than 25 years. Our results show that this electron transfer step involves a gating mechanism requiring a 60° rotation of the headgroup of Q A •− in its binding pocket.

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

Process-dependent anisotropic thermal conductivity of laser powder bed fusion AlSi10Mg: impact of microstructure and aluminum-silicon interfaces

Purpose AlSi10Mg alloy is commonly used in laser powder bed fusion due to its printability, relatively high thermal conductivity, low density and good mechanical properties. However, the thermal conductivity of as-built materials as a function of processing (energy density, laser power, laser scanning speed, support structure) and build orientation, are not well explored in the literature. This study aims to elucidate the relationship between processing, microstructure, and thermal conductivity. Design/methodology/approach The thermal conductivity of laser powder bed fusion (L-PBF) AlSi10Mg samples are investigated by the flash diffusivity and frequency domain thermoreflectance (FDTR) techniques. Thermal conductivities are linked to the microstructure of L-PBF AlSi10Mg, which changes with processing conditions. The through-plane exceeded the in-plane thermal conductivity for all energy densities. A co-located thermal conductivity map by frequency domain thermoreflectance (FDTR) and crystallographic grain orientation map by electron backscattered diffraction (EBSD) was used to investigate the effect of microstructure on thermal conductivity. Findings The highest through-plane thermal conductivity (136 ± 2 W/m-K) was achieved at 59 J/mm 3 and exceeded the values reported previously. The in-plane thermal conductivity peaked at 117 ± 2 W/m-K at 50 J/mm 3 . The trend of thermal conductivity reducing with energy density at similar porosity was primarily due to the reduced grain size producing more Al-Si interfaces that pose thermal resistance. At these interfaces, thermal energy must convert from electrons in the aluminum to phonons in the silicon. The co-located thermal conductivity and crystallographic grain orientation maps confirmed that larger colonies of columnar grains have higher thermal conductivity compared to smaller columnar grains. Practical implications The thermal properties of AlSi10Mg are crucial to heat transfer applications including additively manufactured heatsinks, cold plates, vapor chambers, heat pipes, enclosures and heat exchangers. Additionally, thermal-based nondestructive testing methods require these properties for applications such as defect detection and simulation of L-PBF processes. Industrial standards for L-PBF processes and components can use the data for thermal applications. Originality/value To the best of the authors’ knowledge, this paper is the first to make coupled thermal conductivity maps that were matched to microstructure for L-PBF AlSi10Mg aluminum alloy. This was achieved by a unique in-house thermal conductivity mapping setup and relating the data to local SEM EBSD maps. This provides the first conclusive proof that larger grain sizes can achieve higher thermal conductivity for this processing method and material system. This study also shows that control of the solidification can result in higher thermal conductivity. It was also the first to find that the build substrate (with or without support) has a large effect on thermal conductivity.

Engineering↗
DOE OSTI2024

Heterogenous catalysis for oxygen tolerant photoredox atom transfer radical polymerization and small-molecule dehalogenation

Heterogeneous photocatalysts (PCs) have garnered attention for their sustainability and cost-effectiveness. Despite the existence of various types of these PCs, their synthesis often involves complex, multi-step procedures and laborious purification. Herein, we propose a simple method for attaching small-molecule photocatalytic species onto crosslinked 3-D polymer networks as insoluble scaffolds to create robust heterogeneous PCs. The highly swellable poly(ethylene glycol)-based ChemMatrix (CM) resin, known for its amphiphilic properties and high functional group loading, facilitated the covalent immobilization of the photoredox dye Eosin Y (EY), but also streamlined functionalization with Ir( III ) complexes. The resulting heterogeneous CM-EY demonstrated efficient photocatalytic performance in open-to-air dual photoredox catalysis of atom transfer radical polymerization (photo-ATRP) under green light. This was confirmed by the well-controlled synthesis of polymers with molecular masses ranging from 20 kDa to 300 kDa and low dispersities. Furthermore, CM-EY exhibited excellent photostability and recyclability over multiple cycles of ATRP. The heterogeneous catalysis of photo-ATRP provided high temporal control and enabled benign conditions for synthesizing protein-polymer hybrids (PPH). When combined with the initiator-modified CM (CM-BIB), CM-EY facilitated the solid-phase synthesis of homopolymers and block copolymers with recyclable performance. However, the coordinatively bound Ir@CM showed decreased catalytic activity and efficiency toward photoredox dehalogenation due to the leaching of active species during recycling. This study highlights the advantages of the covalent linking of catalysts to solid supports over non-covalent interactions, underscoring the potential of functionalized polymer resin as a promising scaffold. Such an approach offers customization and tunability, presenting opportunities for innovation in green chemistry.

Kapil, Kriti↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
DOE OSTI2025

Product ion distributions using H 3 O + proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS): mechanisms, transmission effects, and instrument-to-instrument variability

Abstract. Proton-transfer-reaction mass spectrometry (PTR-MS) using hydronium ion (H3O+) ionization is widely used for the measurement of volatile organic compounds (VOCs) both indoors and outdoors. H3O+ ionization, as well as the associated chemistry in an ion–molecule reactor, is known to generate product ion distributions (PIDs) that include other product ions besides the proton-transfer product. We present a method, using gas-chromatography pre-separation, for quantifying PIDs from PTR-MS measurements of nearly 100 VOCs of different functional types including alcohols, ketones, aldehydes, acids, aromatics, organohalides, and alkenes. We characterize instrument configuration effects on PIDs and find that reactor reduced electric field strength (E/N), ion optic voltage gradients, and quadrupole settings have the strongest impact on measured PIDs. Through an interlaboratory comparison of PIDs measured from calibration cylinders, we characterized the variability of PID production from the same model of PTR-MS across seven participating laboratories. Product ion variability was generally smaller (e.g., < 20 %) for ions with larger contributions to the PIDs (e.g., > 0.30) but less predictable for product ions formed through O2+ and NO+ reactions. We present a publicly available library of H3O+ PTR-MS PIDs that will be updated periodically with user-provided data for the continued investigation into instrument-to-instrument variability of PIDs.

Link, Michael F. (ORCID:0000000218412455)↗
DOE OSTI2020

Robust Online Sequential RVFLNs for Data Modeling of Dynamic Time-Varying Systems with Application of an Ironmaking Blast Furnace

In a world where the increasing complexity of modern industrial processes brings difficulties for accurate mathematical modeling, taking advantage of data has become an efficient solution to complex dynamic process modeling issue. In this paper, we develop a novel robust online sequential version of random vector functional-link networks (RVFLNs) for data-driven modeling of dynamic time-varying system and applied it in a blast furnace (BF) ironmaking process. First, to overcome the time-varying dynamics of process and to enable the RVFLNs to learn online with avoiding data saturation, an improved online sequential version of RVFLNs (OS-RFVLNs) is first presented by online sequential learning with forgetting factor. This improved OS-RVFLNs algorithm is not only suitable for the real-time and large data transfer situation, but also can adjust the sensitivity of the algorithm to different samples with the help of the introduced forgetting factor. Second, since the output weights of the improved OS-RVFLNs as well as other RVFLNs algorithms are obtained by the least squares approach, a robustness problem may occur when the training dataset is contaminated with various outliers. To solve this problem, a Cauchy distribution weighted M-estimator is introduced to improve the robustness of the improved OS- RVFLNs. For this proposed robust OS-RVFLNs (R-OS- RVFLNs), since the weights of different outlier data are properly determined by the Cauchy distribution function, their corresponding contribution on modeling can be properly distinguished. Thus robust and better modeling results can be achieved. Experiments using actual industrial data of BF ironmaking process and comparative studies have demonstrated that the proposed method produces a better estimation accuracy and stronger robustness than other methods.

Blast furnace (BF), Modelling, Dynamic systems↗
DOE OSTI2021

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Anion exchange and extraction chromatography tandem column isolation of zirconium-89 ( 89 Zr) from cyclotron bombarded targets using an automated fluidic platform

The long-lived positron emitter 89 Zr is a highly promising nuclide employed in diagnostic Positron Emission Tomography (PET) imaging. Methods of radiochemical processing to obtain 89 Zr for clinical use are traditionally performed with a single hydroxamate resin column. In this work, we present a tandem column purification method for the preparation of high-purity 89 Zr from cyclotron bombarded Y metal foils. The primary column is a macroporous, strongly basic anion exchange resin on styrene divinylbenzene co-polymer. The secondary microcolumn, with an internal volume of 33 µL, is packed with an extraction chromatography resin (ExCR) loaded with HDEHP. A condition of “inverted selectivity” is presented, wherein the 89 Zr elution from the primary column is synonymous with the load condition on the secondary column. The ability to transfer 89 Zr from one column to the next allows two sequential column clean-up methods to be performed prior to the final elution of the 89 Zr product. This approach assures delivery of very high purity 89 Zr . The tandem column purification process has been implemented into a prototype automated fluidic system. Optimization of the method is presented, followed by evaluation of the process using seven cyclotron bombarded Y metal foil targets. Once optimized, we found that 93.7±2.3% of the 89 Zr present in the foils was recovered in the secondary column elution fraction (0.8 M oxalic acid). Radiochromatograms of the product elution peaks enabled determination of full width at half-maximum (FWHM) and 89 Zr collection yields as a function of volume. Because of the small size of the secondary microcolumn, a 89 Zr product volume of ~0.28 mL is reported, which provides a substantially increased nuclide concentration over traditional methods. Finally, we evaluated the transchelation of the resulting 89 Zr oxalate product to deferoxamine mesylate (DFOM) salt. We observed effective specific activities (ESA) and bindable metals concentrations ([M B ]) that exceed those reported by the traditional single hydroxamate column method.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Near-field radiative heat transfer between irregularly shaped dielectric particles modeled with the discrete system Green's function method

Near-field radiative heat transfer (NFRHT) between irregularly shaped dielectric particles made of SiO 2 and morphology characterized by Gaussian random spheres is studied. Particles are modeled using the discrete system Green's function (DSGF) approach, which is a volume integral numerical method based on fluctuational electrodynamics. This method is applicable to finite, three-dimensional objects, and all system interactions are defined independent of thermal excitation by a generalized system Green's function. The DSGF method is deemed suitable to model NFRHT between irregularly shaped particles after verification against the analytical solution for chains of two and three SiO 2 spheres. The NFRHT results reveal that geometric irregularity in particles leads to a reduction of the total conductance from that of comparable perfect spheres at vacuum separation distances smaller than the particle size, a regime in which NFRHT is a surface phenomenon. At vacuum separation distances larger than the particle size, NFRHT becomes a volumetric process, and the total conductance between irregularly shaped particles converges to that of comparable perfect spheres. Spectral analysis reveals, however, that particle irregularity leads to damping and broadening of resonances at all separation distances, thereby highlighting the importance of the DSGF method for spectral engineering in the near field. The reduced spectral coherence when particle size is larger than the vacuum separation distance is attributed to coupling of surface phonon-polaritons within the randomly generated, distorted particle features. For particle size smaller than the vacuum separation distance, resonance broadening and damping are linked with the multiple localized surface phonon modes supported by the composite spherical harmonic morphologies of the Gaussian random spheres. In conclusion, this paper has direct implications for thermal management of packed particle systems, with applications in radiative property control, electronics, energy conversion, and nanomanufacturing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

In situ catalyst activation and regeneration enable energy-efficient high-current CO 2 reduction to ethanol-rich C 2+ mixtures

Electrochemical conversion of dissolved CO 2 in bicarbonate electrolytes, i.e., bicarbonate electrolysis, offers distinct advantages over gas diffusion electrode systems by enabling direct utilization of the CO 2 capture electrolyte while bypassing the energy-intensive CO 2 release step. However, bicarbonate electrolysis faces challenges such as CO 2 mass-transfer limitation, local pH-driven CO 2 depletion, and high cathodic potentials. The higher potential often causes catalyst surface reorganization, leading to a gradual loss of active sites and variations in selectivity during CO 2 reduction. Here, we report a directed, in situ activation and regeneration method that allows precatalysts to equilibrate under dynamic (pulsed) electrolysis conditions. We demonstrate in situ activation of a scalable Cu 2 O/Cu mesh that, under short-width (t = 4 s) pulsed electrolysis, provides stable mixed oxidation states of Cu, favoring the formation of an ethanol-rich crude mixture. The pulsed electrolysis waveform, consisting of six distinct segments, is tuned to form Cu + oxides, which are then reduced to generate local alkaline conditions favoring C–C coupling. This synergistic effect results in FEs of 73% for C2+ products and 39% for ethanol at an applied current density of −150 mA cm −2 and a cathodic potential of −1.45 V (vs. RHE). The overall half-cell energy efficiency is ∼30% for C 2+ products. The in situ Raman experiments confirm the role of pCO 2 R in dynamically regenerating Cu+-containing surface species during pulsed operation, thereby steering selectivity towards C 2+ products. A comprehensive multiscale, multiphysics model is developed to investigate the dynamic behavior of copper surface species (Cu, Cu + , and Cu 2+ ) and local microenvironmental conditions during the pCO 2 R. The results reveal that the coexistence of different copper oxidation states, especially the Cu+ intermediate, is critical in steering selectivity towards multicarbon (C 2+ ) products. The dynamic modulation of surface redox states via tailored pulsing strategies favors C–C coupling pathways by inducing localized alkaline conditions and stabilizing reactive intermediates. This work establishes a predictive modeling platform that links pulse waveform design with mechanistic insights into catalyst state evolution and product selectivity. Overall, this study provides valuable insights into the synergistic effect of in situ activation of pre-catalysts and pulsed electrolysis for higher selectivity towards C 2+ products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗