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At least 1,117 records · Page 62

Cryo-Ablation Experiments for Omega in FY23 [Slides]

Future HED & Nuclear Survivability platforms will use macroscopic 2PP lattice materials for inter-shell support and as a host for higher-yield DT wetted-lattice ablator targets. Average EOS and shock spatial non-uniformity measurements are needed as a function of lattice properties. The FY23 goal is to understand ablative & shock characteristics of heterogeneous D 2 - filled lattice materials at low drive intensities (~250TW/cm 2 ) in planar geometry.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Investigation of encapsulin nanocompartment systems as ascaffold for biomaterials synthesis in Rhodococcus species (DOE ECRP Annual Report 2023)

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcus species. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., CdS nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcusspecies. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., CdS nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement-induced multipartite-entanglement regimes in collective spin systems

We study the competing effects of collective generalized measurements and interaction-induced scrambling in the dynamics of an ensemble of spin-1/2 particles at the level of quantum trajectories. This setup can be considered as analogous to the one leading to measurement-induced transitions in quantum circuits. We show that the interplay between collective unitary dynamics and measurements leads to three regimes of the average Quantum Fisher Information (QFI), which is a witness of multipartite entanglement, as a function of the monitoring strength. While both weak and strong measurements lead to extensive QFI density (i.e., individual quantum trajectories yield states displaying Heisenberg scaling), an intermediate regime of classical-like states emerges for all system sizes where the measurement effectively competes with the scrambling dynamics and precludes the development of quantum correlations, leading to sub-Heisenberg-limited states. We characterize these regimes and the crossovers between them using numerical and analytical tools, and discuss the connections between our findings, entanglement phases in monitored many-body systems, and the quantum-to-classical transition.

Physics↗

Elevated resistance to insects and plant pathogens without compromising seed production

Described herein are modified plants, plant cells, and plant seeds that have at least one mutant loss-of-function JAZ gene and at least one loss-of-function cdk8 gene. Such plants are highly resistant to pests and environmental stress and have restored growth and increased seed yield compared to plant lines with a jazD genetic background.

Howe, Gregg A.↗

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. - Highlights: • Al foil surface-assisted self-assembly of monomeric structures into larger branched DNA lattice. • FESEM study confirms the uniform distribution of two-dimensional bDNA lattice structures across the surface of Al foil. • Enzyme-free and economic strategy to prepare higher order structures from simpler DNA nanostructures have been confirmed by recovery assay. • Use of well proven sequences for the preparation of pure Y-shaped monomeric DNA nanostructure with high yield.

60 APPLIED LIFE SCIENCES↗

Assessing Structural, Thermal, and Functional Characteristics of Marigold Flower Protein as a Sustainable Food Ingredient

The demand for sustainable and alternative protein sources has been on the rise, driving interest in the valorization of underutilized plants. This study evaluated Calendula officinalis (marigold), a common floral waste, as a sustainable alternative protein source for the food industry. The primary objective of this study was to investigate the physicochemical properties of protein fractions from Calendula officinalis flower to evaluate their potential as a novel protein ingredient. Extraction of the Calendula officinalis flower yielded 92.17% of the crude protein. A sequential extraction of albumin, globulin, glutelin, and prolamin from marigold flower revealed albumin as the dominant fraction (65.47%) and exhibited the highest protein functionality, including water-holding capacity (2.37 g/g), oil-holding capacity (2.49 g/g), and emulsifying capacity (65.22 mL/g). Compared with other protein fractions, glutelin showed a relatively high emulsifying and foaming capacity (EC: 59.13 mL/g; FC: 16.23%). Differential scanning calorimetry revealed high thermal stability for albumin (T p = 105.28 °C) and glutelin (T p = 97.6 °C). Sodium Dodecyl Sulfate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Liquid Chromatography–Mass Spectrometry (LC-MS) confirmed the presence of abundant low-molecular-weight polypeptides (<37 kDa), which enhanced emulsification, while scanning electron microscopy revealed porous structures aligned with hydration properties. Antioxidant activity was higher in albumin and glutelin, linked to surface hydrophobicity. LC-MS/MS identified 33 short-chain proteins, including oxidoreductase proteins and lipid-transfer proteins. Findings highlight marigold flower proteins as a sustainable, functional ingredient for a diverse range of food applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The gallium anomaly

In order to test the end-to-end operations of gallium solar neutrino experiments, intense electron-capture sources were fabricated to measure the responses of the radiochemical SAGE and GALLEX/GNO detectors to known fluxes of low-energy neutrinos. Such tests were viewed at the time as a cross-check, given the many tests of 71 Ge recovery and counting that had been routinely performed, with excellent results. However, the four 51 Cr and 37 Ar source experiments yielded rates below expectations, a result commonly known as the Ga anomaly. As the intensity of the electron-capture sources can be measured to high precision, the neutrino lines they produce are fixed by known atomic and nuclear rates, and the neutrino absorption cross section on 71 Ga is tightly constrained by the lifetime of 71 Ge, no simple explanation for the anomaly has been found. To check these calibration experiments, a dedicated experiment BEST was performed, utilizing a neutrino source of unprecedented intensity and a detector optimized to increase statistics while providing some information on counting rate as a function of distance from the source. The results BEST obtained are consistent with the earlier solar neutrino calibration experiments, and when combined with those measurements, yield a Ga anomaly with a significance of approximately 4𝜎, under conservative assumptions. But BEST found no evidence of distance dependence and thus no explicit indication of new physics. In this review we describe the extensive campaigns carried out by SAGE, GALLEX/GNO, and BEST to demonstrate the reliability and precision of their experimental procedures, including 71 Ge recovery, counting, and analysis. We also describe efforts to define uncertainties in the neutrino capture cross section, which now include estimates of effects at the ≲ 0.5% level such as radiative corrections and weak magnetism. With the results from BEST, an anomaly remains even if one retains only the transition to the 71 Ge ground state, whose strength is fixed by the known lifetime of 71 Ge. We then consider the new-physics solution most commonly suggested to resolve the Ga anomaly, oscillations into a sterile fourth neutrino, 𝜈 𝑒 → 𝜈 𝑠 . We find such a solution generates substantial tension with several null experiments, owing to the large mixing angle required. While this does not exclude such solutions – the sterile sector might include multiple neutrinos as well as new interactions – it shows the need for more experimental constraints, if we are to make progress in resolving the Ga and other low-energy neutrino anomalies. We conclude by consider the role future low-energy electron-capture sources could play in this effort.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1

The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in the fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure–function relationships within the ADCSF in general.

59 BASIC BIOLOGICAL SCIENCES↗

Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases

While density functional theory (DFT) is often an accurate and efficient methodology for evaluating molecular properties such as energies and multipole moments, this approach often yields larger errors for response properties such as the dipole polarizability (α), which describes the tendency of a molecule to form an induced dipole moment in the presence of an electric field. In this work, we provide static α tensors (and other molecular properties such as total energy components, dipole and quadrupole moments, etc.) computed using quantum chemical (QC) and DFT methodologies for all 7,211 molecules in the QM7b database. We also provide the same quantities for the 52 molecules in the AlphaML showcase database, which includes the DNA/RNA nucleobases, uncharged amino acids, several open-chain and cyclic carbohydrates, five popular pharmaceutical molecules, and 23 isomers of C 8 H n . All QC calculations were performed using linear-response coupled-cluster theory including single and double excitations (LR-CCSD), a sophisticated approach for electron correlation, and the d-aug-cc-pVDZ basis set to mitigate basis set incompleteness error. DFT calculations employed the B3LYP and SCAN0 hybrid functionals, in conjunction with d-aug-cc-pVDZ (B3LYP and SCAN0) and d-aug-cc-pVTZ (B3LYP).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a non-model bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in non-model organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T 7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool’s utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. In conclusion, our CRISPRi tool will be useful to facilitate functional studies of this non-model organism and engineer this promising microbial chassis for lignin valorization.

09 BIOMASS FUELS↗

Non-monotonic magnetic anisotropy behavior as a function of adsorbate coverage in Fe ultrathin films near the spin reorientation transition

Carbon monoxide (CO) adsorption on ultrathin fcc Fe films is known to result in the rotation of magnetization from out-of-plane to in-plane. By imaging in real time the magnetic domain structure of perpendicularly magnetized Fe/(2 ML)Ni/Cu(100) films during exposure to CO, we demonstrate that the effect of adsorption on the magnetic properties occurs in two distinct stages. Initially, when CO bonds preferentially on bridge sites, perpendicular magnetic anisotropy is enhanced. Later, when on-top adsorption dominates, magnetization rotates towards in-plane in agreement with previous studies. This CO-induced spin reorientation transition (SRT) is not reversible by annealing, as CO desorption would require high temperature cycles which yield permanent structural changes in the metal films. This study demonstrates the existence of a novel non-monotonic behavior of the magnetic anisotropy as a function of adsorbate coverage. The influence of CO on ultrathin film magnetism in real time near critical points, where the anisotropy balance is extremely sensitive to small variations, reveals the previously elusive complexity of this adsorbate induced SRT.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase-based velocity extraction method for photonic Doppler velocimetry with potential higher time resolution

We present an extension of the [Takeda et al., J. Opt. Soc. Am. 72, 156 (1982)] phase extraction method to heterodyne photonic Doppler velocimetry applications. The method yields results equivalent to those obtained by the short-time Fourier transform (STFT), while offering potential improvements in time resolution. Unlike STFT, which relies on window functions, such as the Hamming window, that emphasize central data points and diminish the influence of edges, the extended Takeda method utilizes all data uniformly. This uniform treatment allows for the derivation of empirical equations that directly relate velocity error to the actual time resolution rather than to the local analysis duration. The established equation provides a useful metric for both optimizing hardware configuration and guiding data analysis. Simulation and experimental results confirm that, for a given dataset, specifying a target time resolution yields consistent velocity errors for both methods. These findings underscore the Takeda method’s advantages, particularly its potential higher time resolution and reduced computational burden, making it a valuable tool for high-throughput applications such as laser dynamic compression experiments.

Computer simulation↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of CELF Pretreatment Severity on Lignin Structure and the Lignin-Based Polyurethane Properties

Conversion of technical lignin into performance biopolymers such as polyurethane offers environmental and economic advantages when combined with production of biofuels from biomass sugars, presenting significant interest toward studying the role of pretreatment on lignin structure and functionality. Co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment, employing acidic aqueous tetrahydrofuran (THF) mixtures, was developed to effectively break down the lignin-carbohydrate matrix and promote extraction of lignin from lignocellulosic biomass with desirable purity and yield. In this study, we report the effects of CELF pretreatment reaction severity on the molecular structure of CELF-extracted lignin and its impact toward the mechanical properties of the resulting lignin-based polyurethanes. Reaction temperature was found to play the most significant role, compared to reaction time and acidity, in manipulating structural features such as molecular weight, functionality and intra-polymer structure. At the severe reaction conditions at 180&#x00B0;C, the order of reactivity for primary lignin interlinkages characterized by semiquantitative HSQC NMR analysis were found to be &#x03B2;-ether &#x003E; phenylcoumaran (&#x03B2;&#x2212;5&#x2032;) &#x003E; resinol (&#x03B2;&#x2212;&#x03B2;&#x2032;) facilitating a high degree of depolymerization and yielding a high frequency of free phenolics and reduced aliphatic hydroxyl groups. All side-chain interlinkages were depleted converting guaiacyl subunits into condensed forms, while still retaining uncondensed syringyl subunits. Under the mild 150&#x00B0;C temperature reaction, CELF lignin had higher molecular weight and retained more &#x03B2;-ether interlinkages. The results from CELF lignin-based polyurethane synthesis indicated that the tensile properties depended on the miscibility of CELF lignin with other components and low molecular weight cuts improved the dispersion of lignin in the polyurethane network. Pre-mixing of CELF with poly(ethylene glycol) (PEG) reduced the brittleness and improved the ductility of the CELF lignin-PEG polyurethanes.

59 BASIC BIOLOGICAL SCIENCES↗

Exact solution of burst pressure for thick-walled pipes using the flow theory of plasticity

This paper develops an exact solution of burst pressure for defect-free, thick-walled pipes using the flow theory of plasticity in terms of the average shear stress yield criterion (or Zhu-Leis yield criterion). The pipe steel is assumed to obey the power-law strain hardening rule, and large plastic deformation is described by the finite strain theory. On this basis, internal pressure is obtained as a power series function of the effective strains on the inside and outside surfaces of the thick-walled pipe with use of the second Bernoulli numbers. At burst failure, the Zhu-Leis flow solution of burst pressure is determined as a power series solution, and the burst effective strains, the burst effective stresses, and the burst pressure are functions of the diameter ratio (D o / D i ), strain hardening exponent (n), and ultimate tensile strength (UTS). Similarly, the Tresca and von Mises flow solutions of burst pressure are also determined as a power series solution in terms of the Tresca and von Mises yield criteria. A general closed-from exact solution of burst pressure is then proposed for the three yield criteria, and the results showed that the proposed exact solution matches well with the power series solution for each yield criterion. Moreover, the von Mises flow solution is an upper bound prediction, the Tresca flow solution is a lower bound prediction, and the Zhu-Leis flow solution is an intermediate prediction that agrees well with the finite element analysis results of burst pressure for thick-walled pipes. Furthermore, two datasets of full-scale burst tests are then utilized to evaluate and validate the proposed flow solutions of burst pressure for both thin and thick-walled pipes.

42 ENGINEERING↗

Comparative DFT Computational Studies with Experimental Investigations for Novel Synthesized Fluorescent Pyrazoline Derivatives

A novel series of pyrazoline derivatives were synthesized and their spectral properties were characterized via FT-IR, {sup 1}H, and {sup 13}C NMR. The electronic transitions and fluorescence properties were tracked via UV-Vis and emission spectrometry. The density functional theory (DFT) calculations have been also computed to get spot onto the geometry, electronic transitions and spectroscopic properties theoretically that has been compared with the encountered experimental ones. Moreover, the dipole moment, optimized energy, HOMO - LUMO energies and band gaps were calculated for novel candidates pyrazoline derivatives with highly fluorescence quantum yield.

74 ATOMIC AND MOLECULAR PHYSICS↗

Participant and spectator scaling of spectator fragments in Au + Au and Cu + Cu collisions at s N N = 19.6 and 22.4 GeV

Spectator fragments resulting from relativistic heavy ion collisions, consisting of single protons and neutrons along with groups of stable nuclear fragments up to nitrogen (Z = 7), are measured in PHOBOS. These fragments are observed in Au+Au ( s N N = 19.6 GeV) and Cu+Cu (22.4 GeV) collisions at high pseudorapidity (η). The dominant multiply-charged fragment is the tightly bound helium (α), with lithium, beryllium, and boron all clearly seen as a function of collision centrality and pseudorapidity. In this paper, we observe that in Cu+Cu collisions, it becomes much more favorable for the α fragments to be released than lithium. The yields of fragments approximately scale with the number of spectator nucleons, independent of the colliding ion. The shapes of the pseudorapidity distributions of fragments indicate that the average deflection of the fragments away from the beam direction increases for more central collisions. Finally, a detailed comparison of the shapes for α and lithium fragments indicates that the centrality dependence of the deflections favors a scaling with the number of participants in the collision.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗