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At least 1,063 records · Page 59

Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate–dependent nonheme ferrous enzymes

Determining the requirements for efficient oxygen (O 2 ) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)–dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O 2 ) and a sequential mechanism (cofactor binding and reaction with O 2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Interestingly, spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the Fe II ), αKG binding to Fe II -DAOCS results in ~45% five-coordinate sites that selectively react with O 2 relative to the remaining six-coordinate sites. However, this reaction produces an Fe III species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to Fe II -DAOCS produces five-coordinate sites that rapidly react with O 2 to form an Fe IV =O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Semi-analytical covariance matrices for two-point correlation function for DESI 2024 data

We present an optimized way of producing the fast semi-analytical covariance matrices for the Legendre moments of the two-point correlation function, taking into account survey geometry and mimicking the non-Gaussian effects. We validate the approach on simulated (mock) catalogs for different galaxy types, representative of the Dark Energy Spectroscopic Instrument (DESI) Data Release 1, used in 2024 analyses. We find only a few percent differences between the mock sample covariance matrix and our results, which can be expected given the approximate nature of the mocks, although we do identify discrepancies between the shot-noise properties of the DESI fiber assignment algorithm and the faster approximation (emulator) used in the mocks. Importantly, we find a close agreement (≤ 8% relative differences) in the projected errorbars for distance scale parameters for the baryon acoustic oscillation measurements. This confirms our method as an attractive alternative to simulation-based covariance matrices, especially for non-standard models or galaxy sample selections, making it particularly relevant to the broad current and future analyses of DESI data.

79 ASTRONOMY AND ASTROPHYSICS↗

The Lyman- α forest from LBGs: First 3D correlation measurement with DESI and prospects for cosmology

The Lyman-α (Lyα) forest is a key tracer of large-scale structure at redshifts z > 2, traditionally studied using the spectra of luminous but relatively rare quasars. In this work, we explore the viability of using the fainter yet significantly more abundant Lyman Break Galaxies (LBGs) as alternative background sources for Lyα forest studies. We analyze 4,151 Lyα forest skewers extracted from LBG spectra obtained in the DESI pilot surveys conducted in the COSMOS and XMM-LSS fields. From this dataset, we present the first measurement of the Lyα forest auto-correlation function derived exclusively from LBG spectra, probing comoving separations up to 48 h -1 Mpc at an effective redshift of z eff = 2.70. The measured LBG Lyα forest auto-correlation is consistent with that derived from DESI DR2 quasar Lyα forest spectra at a comparable redshift, validating the use of LBGs as reliable background sources for Lyα forest analyses. In addition, we measure the cross-correlation between the LBG Lyα forest and the positions of 13,362 galaxies, demonstrating that this observable serves as a sensitive diagnostic for assessing the precision and accuracy of galaxy redshift estimates, and for identifying and correcting systematic offsets. Finally, using both synthetic LBG spectra and Fisher matrix forecasts, we show that a future wide-area survey covering ∼5,000 deg 2 , targeting 1,000 LBGs per square degree at signal-to-noise levels comparable to our sample, could enable LBG-based Lyα forest baryon acoustic oscillation (BAO) measurements with expected uncertainties of σ α ISO = 0.4% (isotropic) and σ α AP = 1.3% (Alcock-Paczynski). This performance is further enhanced when combining the BAO analysis with a Lyα forest Full Shape (FS) approach, yielding a predicted uncertainty of σ α ISO FS = 0.6%. These results open a new avenue for precision cosmology at high redshift using the Lyα forest in dense LBG samples.

Lyman alpha forest↗

Gluon Sivers function from forward exclusive χ c 1 photoproduction on unpolarized protons

Exclusive production of a χ c 1 axial vector quarkonia in photon-proton scattering at high energies requires a C -odd t -channel exchange. In the limit of vanishing momentum transfer this occurs either via the exchange of a photon, the Primakoff process, where the spin of the proton does not change. For axial-vector meson production, as a consequence of the Landau-Yang theorem, the Primakoff cross section is finite as t → 0 . Alternatively, a C -odd spin dependent Odderon can be exchanged, which involves a spin flip of the proton. The resulting cross section is related to the square of the collinear trigluon correlator or the k ⊥ -moment of the gluon Sivers function. Using two models for the gluon Sivers function from the literature we compute the ratio of Sivers to Primakoff cross sections and the angular coefficient λ θ governing the angular distribution of the χ c 1 → J / ψ + γ decay as functions of x . We point out that these observables constrain the magnitude of the gluon Sivers function at small x which could be accessed in electron-proton scattering and ultraperipheral proton-proton and nucleus-proton collisions. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Algorithms in Diffraction Profile Analysis

This chapter introduces several approaches to crystallographic structure refinement from diffraction profile data including the Rietveld method, global optimization methods, and Bayesian modeling. First, the Rietveld method and related nonlinear least squares approaches to analyzing diffraction profiles are briefly discussed. We then review the most common algorithms within global optimization as alternative methods of structure solution: grid search, simulated annealing, and genetic algorithms. As the Rietveld method is the standard tool for analyzing diffraction profile data, we catalogue its challenges and limitations. A Bayesian approach to diffraction profile analysis is presented as an alternative, along with several sampling algorithms including Gibbs sampling, variants of Metropolis sampling, Hamiltonian Monte Carlo, and approximate Bayesian computing. These sampling algorithms are applied to the fitting of a neutron diffraction profile from a National Institute of Standards and Technology silicon standard reference material, and their results are compared.

Singh, Susheela↗

Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation

The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The complex is structurally divided into four modules known as the head, middle, tail and kinase modules, and in Arabidopsis thaliana , comprises 28-34 subunits. Here, we explore the functions of four Arabidopsis Medi-ator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits affect both unique and overlapping sets of genes, providing insight into the functional and structural relationships between them. The mutants pri-marily exhibit changes in the expression of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for MED23, as well as in the production of alternative transcripts. Together, our data help disentangle the individual contributions of these MED subunits to global gene expression and suggest new avenues for future research into their functions.

59 BASIC BIOLOGICAL SCIENCES↗

Superfluids as higher-form anomalies

We recast superfluid hydrodynamics as the hydrodynamic theory of a system with an emergent anomalous higher-form symmetry. The higher-form charge counts the winding planes of the superfluid - its constitutive relation replaces the Josephson relation of conventional superfluid hydrodynamics. This formulation puts all hydrodynamic equations on equal footing. The anomalous Ward identity can be used as an alternative starting point to prove the existence of a Goldstone boson, without reference to spontaneous symmetry breaking. This provides an alternative characterization of Landau phase transitions in terms of higher-form symmetries and their anomalies instead of how the symmetries are realized. This treatment is more general and, in particular, includes the case of BKT transitions. As an application of this formalism we construct the hydrodynamic theories of conventional (0-form) and 1-form superfluids.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Process Model Development and Experimental Investigation for Spent Fuel Disposal in Crystalline Rocks: FY20 Report.

The U.S. Department of Energy Office of Spent Fuel Waste Disposition (SFWD) established in fiscal year 2010 (FY10) the Spent Fuel Waste Science & Technology (SFWST) Program (formerly the Used Fuel Disposition Campaign - UFDC) program to conduct the research and development (R&D) activities related to storage, transportation and disposal of used nuclear fuel and high level nuclear waste. The Mission of the SFWST is: To identify alternatives and conduct scientific research and technology development to enable storage, transportation and disposal of used nuclear fuel and wastes generated by existing and future nuclear fuel cycles. Significant progress has been made in FY20 in both experimental and modeling arenas in evaluation of used fuel disposal in crystalline rocks, especially in model demonstration using field data. The work covers a wide range of research topics identified in the R&D plan.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Evaluation of Spent Fuel Disposition in Crystalline Rocks: FY18 Progress Report

The U.S. Department of Energy Office of Spent Fuel Waste Disposition (SFWD) established in fiscal year 2010 (FY10) the Spent Fuel Waste Science & Technology (SFWST) Program (formerly the Used Fuel Disposition Campaign - UFDC) program to conduct the research and development (R&D) activities related to storage, transportation and disposal of used nuclear fuel and high level nuclear waste. The Mission of the SFWST is: To identify alternatives and conduct scientific research and technology development to enable storage, transportation and disposal of used nuclear fuel and wastes generated by existing and future nuclear fuel cycles. The work package of Crystalline Disposal R&D directly supports the following SFWST objectives: Develop a fundamental understanding of disposal system performance in a range of environments for potential wastes that could arise from future nuclear fuel cycle alternatives through theory, simulation, testing, and experimentation. ; Develop a computational modeling capability for the performance of storage and disposal options for a range of fuel cycle alternatives, evolving from generic models to more robust models of performance assessment. The objective of the Crystalline Disposal R&D control account is to advance our understanding of long-term disposal of used fuel in crystalline rocks and to develop necessary experimental and computational capabilities to evaluate various disposal concepts in such media. Significant progress has been made in FY18 in both experimental and modeling arenas in evaluation of used fuel disposal in crystalline rocks, especially in model demonstration using field data. The work covers a wide range of research topics identified in the R&D plan. The major accomplishments are summarized.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Energetic considerations for engineering novel biochemistries in photosynthetic organisms

Humans have been harnessing biology to make valuable compounds for generations. From beer and biofuels to pharmaceuticals, biology provides an efficient alternative to industrial processes. With the continuing advancement of molecular tools to genetically modify organisms, biotechnology is poised to solve urgent global problems related to environment, increasing population, and public health. However, the light dependent reactions of photosynthesis are constrained to produce a fixed stoichiometry of ATP and reducing equivalents that may not match the newly introduced synthetic metabolism, leading to inefficiency or damage. While photosynthetic organisms have evolved several ways to modify the ATP/NADPH output from their thylakoid electron transport chain, it is unknown if the native energy balancing mechanisms grant enough flexibility to match the demands of the synthetic metabolism. In this review we discuss the role of photosynthesis in the biotech industry, and the energetic considerations of using photosynthesis to power synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

Midfidelity model verification for a point-absorbing wave energy converter with linear power take-off

In the preliminary design stage of a wave energy converter (WEC), researchers need fast and reliable simulation tools. High-fidelity numerical models are usually employed to study the wave-structure interaction, but the computational cost is demanding. As an alternative, midfidelity models can provide simulations in the order of real time. In this study, we operate Uppsala University’s WEC in a relatively mild sea state and model it using WEC-Sim. The model is verified based on OpenFOAM simulations. To analyze the ability of the midfidelity model to capture WEC dynamics, we investigate the system separately with 1, 2, and 3 degrees of freedom. We examine the contribution of viscous phenomena, and study both linear and weakly nonlinear solutions provided by WEC-Sim. Our results indicate that the viscous effects can be neglected in heave and surge motion, but not for pitch. We also find that the weakly nonlinear WEC-Sim solution successfully agrees with the computational fluid dynamics, whereas the linear solution could suggest misleading results.

16 TIDAL AND WAVE POWER↗

Status of NO sub x control for coal-fired power plants

The status of technologies for controlling emissions of oxides of nitrogen (NOx) from coal-fired power plants is reviewed. A discussion of current technology as well as future NOx control approaches is presented. Advanced combustion approaches are included as well as post-combustion alternatives such as catalytic and noncatalytic ammonia-bases systems and wet scrubbing. Special emphasis is given to unresolved development issues as they relate to practical applications on coal-fired power plants.

Teixeira, D. P.↗

Origin of the coronal line emission from novae

It is proposed that the coronal line emission from V1500 Cyg and other fast novae originates in gas shocked to about 10 to the 6th power K as a result of supersonic random motions within the principal ejecta. This model simultaneously explains the similar widths of the coronal and nebular lines, the temperature and luminosity of the coronal line region, the gradual decrease in ionization, the variability of the coronal line profiles, and the progressive sharpening of velocity structure in the nebular line profiles. The ejecta are characterized by approximately 10 to the 3rd power clouds with a relative velocity dispersion of about 10 to the 2.2 power km/s, compared with an expansion velocity about 10 to the 3.2 power km/s. Alternative models for the coronal lines involving photoionization or interaction of the principal shell with circumstellar gas or with a fast wind from the central object are considered and rejected.

Shields, G. A.↗

Retrofit energy conservation in residential buildings in southern California

The common energy conservation techniques (ECTs) that can be retrofit-installed into residential buildings are surveyed. The quantity of saved energy for heating and cooling attributable to each ECT is evaluated for three common modes of heating: natural gas heating at 60/therm; heating via heat pump at $1.20/therm; and electric resistance heating at $2.40/therm. In every case, a life cycle cost comparison is made between the long term revenue due to energy conservation and a safe and conventional alternative investment that might be available to the prudent homeowner. The comparison between investment in an ECT and the alternative investment is brought into perspective using the life cycle payback period and an economic Figure of Merit (FOM). The FOM allows for relative ranking between candidate ECTs. Because the entire spectrum of winter heating climates in California is surveyed, the decision maker can determine whether or not a considered ECT is recommended in a given climate, and under what conditions an ECT investment becomes attractive.

Turner, R. H.↗

Dark Halo Craters and the Thickness of Grooved Terrain on Ganymede

Dark halo craters on grooved terrain on Ganymede represent potential probes of the subsurface geology. These craters are surrounded by a broad, diffuse low albedo annulus, or halo and have apparently lost the bright rim and ray deposits associated with very young craters. The recognition of dark halo craters, almost all greater than 12 km in diameter, indicates that material darker and redder than grooved terrain material forms a stratigraphy horizon at about 1 km depth the present surface of grooved terrain in Uruk Sulcus. This material is most likely downdropped cratered terrain material, which only larger craters have excavated into. This is most consistent with extensional tectonic models for grooved terrain formation whereby the lithosphere is stretched and blocks of ancient cratered terrain are downdropped along bounding faults, and subsequently resurfaced by a shallow layer of relatively clean icy material. Evidence for the preservation of cratered terrain material at shallow depth beneath grooved terrain material poses great difficulties for alternative grooved and smoothed terrain formation mechanisms.

Schenk, P. M.↗

Evolution of the sun's polar fields during sunspot cycle 21 - Poleward surges and long-term behavior

Longitudinally averaged observations of the photospheric field during 1976-1986 are analyzed using a flux transport model. The way in which source eruptions, supergranular diffusion, and meridional flow collaborate to produce strong, highly concentrated polar fields near sunspot minimum is clarified as follows: (1) widespread eruptions of individual bipolar magnetic regions, with their leading polarity flux equatorward of their trailing polarity flux, collectively establish a large-scale separation of polarities in latitude; (2) the low-latitude, leading polarity flux diffuses across the equator and merges with its opposite hemisphere counterpart; and (3) meridional flow carries the resulting surplus of trailing polarity flux to the poles, and concentrates it there against the spreading effect of diffusion. Episodic 'surges' of flux to the poles are induced by fluctuations in the source eruption rate. Simulations indicate that relatively weak, trailing polarity surges may occur even in a steady flow field. However, in order to account for the giant surges of alternating polarity and the resulting oscillations in the polar field strength observed during 1980-1982, both accelerated flow and enhanced eruption rates are required.

Wang, Y.-M.↗

No-net-rotation model of current plate velocities incorporating plate motion model NUVEL-1

NNR-NUVEL1 is presented which is a model of plate velocities relative to the unique reference frame defined by requiring no-net-rotation of the lithosphere while constraining relative plate velocities to equal those in global plate motion model NUVEL-1 (DeMets et al., 1990). In NNR-NUVEL1, the Pacific plate rotates in a right-handed sense relative to the no-net-rotation reference frame at 0.67 deg/m.y. about 63 deg S, 107 deg E. At Hawaii the Pacific plate moves relative to the no-net-rotation reference frame at 70 mm/yr, which is 25 mm/yr slower than the Pacific plate moves relative to the hotspots. Differences between NNR-NUVEL1 and HS2-NUVEL1 are described. The no-net-rotation reference frame differs significantly from the hotspot reference frame. If the difference between reference frames is caused by motion of the hotspots relative to a mean-mantle reference frame, then hotspots beneath the Pacific plate move with coherent motion towards the east-southeast. Alternatively, the difference between reference frames can show that the uniform drag, no-net-torque reference frame, which is kinematically equivalent to the no-net-rotation reference frame, is based on a dynamically incorrect premise.

Argus, Donald F.↗