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At least 1,081 records · Page 60

Cost function for low-dimensional manifold topology assessment

Abstract In reduced-order modeling, complex systems that exhibit high state-space dimensionality are described and evolved using a small number of parameters. These parameters can be obtained in a data-driven way, where a high-dimensional dataset is projected onto a lower-dimensional basis. A complex system is then restricted to states on a low-dimensional manifold where it can be efficiently modeled. While this approach brings computational benefits, obtaining a good quality of the manifold topology becomes a crucial aspect when models, such as nonlinear regression, are built on top of the manifold. Here, we present a quantitative metric for characterizing manifold topologies. Our metric pays attention to non-uniqueness and spatial gradients in physical quantities of interest, and can be applied to manifolds of arbitrary dimensionality. Using the metric as a cost function in optimization algorithms, we show that optimized low-dimensional projections can be found. We delineate a few applications of the cost function to datasets representing argon plasma, reacting flows and atmospheric pollutant dispersion. We demonstrate how the cost function can assess various dimensionality reduction and manifold learning techniques as well as data preprocessing strategies in their capacity to yield quality low-dimensional projections. We show that improved manifold topologies can facilitate building nonlinear regression models.

42 ENGINEERING↗

Highly efficient and very robust blue-excitable yellow phosphors built on multiple-stranded one-dimensional inorganic–organic hybrid chains

Inorganic–organic hybrid semiconductors are promising candidates for energy-related applications. Here, we have developed a unique class of multiple-stranded one-dimensional (1D) structures as very robust and efficient lighting phosphors. Following a systematic ligand design strategy, these structures are constructed by forming multiple coordination bonds between adjacent copper iodide inorganic building units Cu m I m (m = 2, 4, 6) (e.g. dimer, tetramer and hexamer clusters) and strong-binding bidentate organic ligands with low LUMO energies which give rise to infinite 1D chains of high stability and low bandgaps. The significantly enhanced thermal/photostability of these multiple-stranded chain structures is largely attributed to the multi-dentate nature and enhanced Cu–N bonding, and their excellent blue excitability is a result of using benzotriazole based ligands with low-lying LUMO energies. These facts are confirmed by Density Functional Theory (DFT) calculations. The luminescence mechanism of these compounds is studied by temperature dependent photoluminescence experiments. High internal quantum yields (IQYs) are achieved under blue excitation, marking the highest value reported so far for crystalline inorganic–organic hybrid yellow phosphors. Excellent thermal- and photo-stability, coupled with high luminescence efficiency, make this class of materials promising candidates for use as rare-earth element (REE) free phosphors in energy efficient general lighting devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancements in Laser-Direct-Drive Nuclear Performance with Target Radius

Inertial confinement fusion is likely to require significant improvements in technology and design for large targets to implode at high driver energies. Here, to assess the potential for benefits, we report on nuclear performance as a function of target radius 𝑅 t in direct-drive cryogenic implosions as performed on the OMEGA laser. The neutron yield and areal density are found to increase as 𝑅 5.0±0.2 t and 𝑅 1.8±0.2 t , respectively, and exhibit a much stronger dependence on target radius than previous studies have assumed. As this paper demonstrates, these types of sensitivities should be expected when implosions are unstable, and have been degraded by a range of multidimensional effects in 3D. If the imperfections in a target and laser system are fixed in magnitude, it follows that larger implosions have higher relative quality, and approach criteria to ignite much more quickly than commonly appreciated.

inertial confinement fusion↗

Adaptive Power Flow Approximations With Second-Order Sensitivity Insights

The power flow equations are fundamental to power system planning, analysis, and control. However, the inherent non-linearity and non-convexity of these equations present formidable obstacles in problem-solving processes. To mitigate these challenges, recent research has proposed adaptive power flow linearizations that aim to achieve accuracy over wide operating ranges. The accuracy of these approximations inherently depends on the curvature of the power flow equations within these ranges, which necessitates considering second-order sensitivities. In this paper, we leverage second-order sensitivities to both analyze and improve power flow approximations. We evaluate the curvature across broad operational ranges and subsequently utilize this information to inform the computation of various sample-based power flow approximation techniques. Additionally, we leverage second-order sensitivities to guide the development of rational approximations that yield linear constraints in optimization problems. In conclusion, this approach is extended to enhance accuracy beyond the limitations of linear functions across varied operational scenarios.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Strain shift measured from stress-controlled oscillatory shear: Evidence for a continuous yielding transition and new techniques to determine recovery rheology measures

Understanding the yielding of complex fluids is an important rheological challenge that affects our ability to engineer and process materials for a wide variety of applications. Common theoretical understandings of yield stress fluids follow the Oldroyd–Prager formalism in which the material behavior below the yield stress is treated as solidlike, and above the yield stress as liquidlike, with an instantaneous transition between the two states. This formalism was built on a quasi-static approach to the yield stress, while most applications, ranging from material processing to end user applications, involve a transient approach to yielding over a finite timescale. Using stress-controlled oscillatory shear experiments, we show that yield stress fluids flow below their yield stresses. This is quantified through measuring the strain shift, which is the value about which the strain oscillates during a stress-controlled test and is a function of only the unrecoverable strain. Measurements of the strain shift are, therefore, measurements of flow having taken place. These experimental results are compared to the Herschel–Bulkley form of the Saramito model, which utilizes the Oldroyd–Prager formalism, and the recently published Kamani–Donley–Rogers (KDR) model, in which one constitutive equation represents the entire range of material responses. Scaling relationships are derived, which allow us to show why yield stress fluids will flow across all stresses, above and below their yield stress. Finally, derivations are presented that show strain shift can be used to determine average metrics previously attainable only through recovery rheology, and these are experimentally verified.

Mechanics↗

$\Sigma (1385)^{\pm }$ resonance production in Pb–Pb collisions at $\sqrt{s_{\textrm{NN}}} = 5.02$ TeV

Hadronic resonances are used to probe the hadron gas produced in the late stage of heavy-ion collisions since they decay on the same timescale, of the order of 1–10 fm/c, as the decoupling time of the system. In the hadron gas, (pseudo)elastic scatterings among the products of resonances that decayed before the kinetic freeze-out and regeneration processes counteract each other, the net effect depending on the resonance lifetime, the duration of the hadronic phase, and the hadronic cross sections at play. In this context, the Σ(1385) ± particle is of particular interest as models predict that regeneration dominates over rescattering despite its relatively short lifetime of about 5.5 fm/c. The first measurement of the Σ(1385) ± resonance production at midrapidity in Pb–Pb collisions at $\sqrt{s_{NN}}$=5.02 TeV with the ALICE detector is presented in this Letter. The resonances are reconstructed via their hadronic decay channel, Λπ, as a function of the transverse momentum (p T ) and the collision centrality. The results are discussed in comparison with the measured yield of pions and with expectations from the statistical hadronization model as well as commonly employed event generators, including PYTHIA8/Angantyr and EPOS3 coupled to the UrQMD hadronic cascade afterburner. None of the models can describe the data. For Σ(1385) ± , a similar behaviour as K*(892) 0 is observed in data unlike the predictions of EPOS3 with afterburner.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

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↗