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At least 91 records · Page 5

Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites

Poly-N-acetyl-lactosamine (poly-LacNAc) structures are composed of repeating [-Galβ(1,4)-GlcNAcβ(1,3)-]n glycan extensions. They are found on both N- and O-glycoproteins and glycolipids and play an important role in development, immune function, and human disease. The majority of mammalian poly-LacNAc is synthesized by the alternating iterative action of β1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and β1,4-galactosyltransferases. B3GNT2 is in the largest mammalian glycosyltransferase family, GT31, but little is known about the structure, substrate recognition, or catalysis by family members. Here we report the structures of human B3GNT2 in complex with UDP:Mg 2+ and in complex with both UDP:Mg 2+ and a glycan acceptor, lacto-N-neotetraose. The B3GNT2 structure conserves the GT-A fold and the DxD motif that coordinates a Mg 2+ ion for binding the UDP-GlcNAc sugar donor. The acceptor complex shows interactions with only the terminal Galβ(1,4)-GlcNAcβ(1,3)- disaccharide unit, which likely explains the specificity for both N- and O-glycan acceptors. Modeling of the UDP-GlcNAc donor supports a direct displacement inverting catalytic mechanism. Comparative structural analysis indicates that nucleotide sugar donors for GT-A fold glycosyltransferases bind in similar positions and conformations without conserving interacting residues, even for enzymes that use the same donor substrate. In contrast, the B3GNT2 acceptor binding site is consistent with prior models suggesting that the evolution of acceptor specificity involves loops inserted into the stable GT-A fold. These observations support the hypothesis that GT-A fold glycosyltransferases employ coevolving donor, acceptor, and catalytic subsite modules as templates to achieve the complex diversity of glycan linkages in biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Controls Workstation: Algorithms and hardware

The Computational Controls Workstation provides an integrated environment for the modeling, simulation, and analysis of Space Station dynamics and control. Using highly efficient computational algorithms combined with a fast parallel processing architecture, the workstation makes real-time simulation of flexible body models of the Space Station possible. A consistent, user-friendly interface and state-of-the-art post-processing options are combined with powerful analysis tools and model databases to provide users with a complete environment for Space Station dynamics and control analysis. The software tools available include a solid modeler, graphical data entry tool, O(n) algorithm-based multi-flexible body simulation, and 2D/3D post-processors. This paper describes the architecture of the workstation while a companion paper describes performance and user perspectives.

Venugopal, R.↗

Copper availability governs nitrous oxide accumulation in wetland soils and stream sediments

Denitrification is microbially-mediated through enzymes containing metal cofactors. Laboratory studies of pure cultures have highlighted that the availability of Cu, required for the multicopper enzyme nitrous oxide reductase, can limit N2O reduction. However, in natural aquatic systems, such as wetlands and hyporheic zones in stream beds, the role of Cu in controlling denitrification remains incompletely understood. In this study, we collected soils and sediments from three natural environments -- riparian wetlands, marsh wetlands, and a stream -- to investigate their nitrogen species transformation activity at background Cu levels and different supplemented Cu loadings. All of the systems contained solid-phase associated Cu below or around geological levels (40 - 280 nmol g-1) and exhibited low dissolved Cu (3-50 nM), which made them appropriate sites for evaluating the effect of limited Cu availability on denitrification. In laboratory incubation experiments, high concentrations of N2O accumulated in all microcosms lacking Cu amendment except for one stream sediment sample. With Cu added to provide dissolved concentrations at trace levels (10-300 nM), reduction rate of N2O to N 2 in the wetland soils and stream sediments was enhanced. A kinetic model could account for the trends in nitrogen species by combining the reactions for microbial reduction of NO 3 - to NO 2 -/N 2 O/N 2 and abiotic reduction of NO 2 - to N 2 . The model revealed that the rate of N 2 O to N 2 conversion increased significantly in the presence of Cu. For riparian wetland soils and stream sediments, the kinetic model also suggested that overall denitrification is driven by abiotic reduction of NO2- in the presence of inorganic electron donors. This study demonstrated that natural aquatic systems containing Cu at concentrations less than or equal to crustal abundances may display incomplete reduction of N 2 O to N 2 that would cause N 2 O accumulation and release to the atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ionospheric ion composition from satellite measurements made during 1970-1980 - Altitude profiles

Ion-mass spectrometers were carried by a number of satellites in the 1970s. The ion-composition measurements from two of these missions, the Orbiting Geophysical Observatory-6 and the Atmosphere Explorer-C, are collected into an ion composition data base to evaluate several widely used empirical and theoretical models for the species H(+), He(+), N(+), O(+), NO(+), N2(+), and O2(+). The data base covers all latitudes and local times, and the altitude range from 150 km to 1200 km, but here altitude plots are presented of the ion densities at noon and at dip latitudes of 20-40 deg N. The satellite data are compared with an early ion-density profile, with the Koehnlein and IRI-90 empirical models, and with the Utah State University theoretical ionosphere model. These comparisons serve to verify some aspects of the models, but they also reveal some outstanding differences. The solar activity dependence of H(+), He(+), N(+), and O(+) is demonstrated, although this has not been possible for the molecular ions because low altitude measurements have not been made near solar maximum.

Hoegy, W. R.↗

Carbon-Nitrogen Coupling Under Three Schemes of Model Representation: A Traceability Analysis

The interaction between terrestrial carbon (C) and nitrogen (N) cycles has been incorporated into more and more land surface models. However, the scheme of C-N coupling differs greatly among models, and how these diverse representations of C-N interactions will affect C-cycle modeling remains unclear. In this study, we explored how the simulated ecosystem C storage capacity in the terrestrial ecosystem (TECO) model varied with three different commonly used schemes of C-N coupling. The three schemes (SM1, SM2, and SM3) have been used in three different coupled C-N models (i.e., TECO-CN, CLM 4.5, and O-CN, respectively). They differ mainly in the stoichiometry of C and N in vegetation and soils, plant N uptake strategies, down regulation of photosynthesis, and the pathways of N import. We incorporated the three C-N coupling schemes into the C-only version of the TECO model and evaluated their impacts on the C cycle with a traceability framework. Our results showed that all three of the C-N schemes caused significant reductions in steady-state C storage capacity compared with the C-only version with magnitudes of −23%, −30%, and −54% for SM1, SM2, and SM3, respectively. This reduced C storage capacity was mainly derived from the combined effects of decreases in net primary productivity (NPP; −29%, −15%, and −45%) and changes in mean C residence time (MRT; 9%, −17%, and −17%) for SM1, SM2, and SM3, respectively. The differences in NPP are mainly attributed to the different assumptions on plant N uptake, plant tissue C : N ratio, down regulation of photosynthesis, and biological N fixation. In comparison, the alternative representations of the plant vs. microbe competition strategy and the plant N uptake, combined with the flexible C : N ratio in vegetation and soils, led to a notable spread in MRT. These results highlight the fact that the diverse assumptions on N processes represented by different C-N coupled models could cause additional uncertainty for land surface models. Understanding their difference can help us improve the capability of models to predict future biogeochemical cycles of terrestrial ecosystems.

Du, Zhenggang↗

On the origin and evolution of isotopes of carbon, nitrogen, and oxygen

Calculations of CNO processing in stellar envelopes, based on theoretical nucleosynthesis rather than empirical abundances in evolving stars, are presented and used in two models for the chemical evolution of the solar neighborhood. Seven stable isotopes are considered: C-12, C-13, N-14, N-15, O-16, O-17, and O-18. The two models ('infall' and 'initial-burst') represent extremes of types consistent with general constraints and include theoretical estimates of other nucleosynthesis sites and yields for CNO isotopes. The results obtained are found to predict that all CNO isotopes are produced mainly by stars with lifetimes much less than the age of the Galaxy (even at the present time when low-mass stars have the greatest death rate), so that isotopic ratios evolve very slowly after the first few billion years. Consequences of these slow changes are that the isotopic ratios cannot be employed to test between alternative hypotheses and that galactic evolution does not seem to be able to account for the apparent difference between the C-13/C-12 ratio in the solar system and in molecular clouds. The predicted envelope processing is shown to lead to approximately the solar-system values for the C-13/C-12 and O-17/O-16 abundance ratios but to a N-14/C-12 ratio that is too small by at least a factor of 2.

Dearborn, D.↗

Global electroweak symmetric vacuum

Although the Higgs potential in the Standard Model (SM) contains only a simple electroweak symmetry breaking vacuum in the small field region, additional metastable or global vacua could exist in models beyond the SM. In this paper, we study one intriguing scenario with an additional electroweak symmetric vacuum that could be the global one. For the thermal universe ending at the current metastable vacuum, the electroweak symmetry should stay non-restored at high temperatures. We realize the scenario in a model with Higgs-portal couplings to SM singlet scalars with approximately global O(N) symmetries with a large N. For a large portion of model parameter space, both the quantum and thermal tunneling rates are suppressed such that our current metastable vacuum is long-lived enough. Our scenario predicts order-one changes for the Higgs self-couplings and a large contribution to the signal of the off-shell Higgs invisible decay. It can be partly probed at the LHC Run 3 and well tested at the high luminosity LHC. We also discuss the subcritical (anti-de Sitter) bubbles from the thermal tunneling that could have a large population and interesting cosmological implications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Assessing Nutrient and Carbon Responses to Agricultural Conservation Practices in Two Midwest Watersheds

The United States is undertaking efforts to transition to a low-carbon economy in response to the heightened impacts of climate change, which are largely attributed to decades of carbon-intensive development. A concerted effort by the energy sector to achieve net-zero carbon emissions is aimed at strategically reducing the carbon footprint of the energy supply chain, particularly in the production of feedstocks for biofuels. The production of biofuels relies heavily on land use and management practices in biomass cultivation. Among other factors, soil organic carbon (SOC) plays a crucial role in the biofuel carbon cycle, impacting land productivity, greenhouse gas emissions, and water quality. The process of carbon drawdown during plant growth and storage helps to mitigate the release of carbon dioxide (CO 2 ) into the atmosphere. Another key parameter is the release of nitrous oxide (N 2 O) — a potent greenhouse gas with a global warming potential 273 times that of CO 2 — from soil. While prioritizing low-carbon production, sustainable bioenergy also necessitates improved water quality and ecosystem services. Agricultural conservation practices can contribute to enhanced soil health and reduce nutrient and sediment loss into streams. However, studies that explore the broader impact of these practices on soil carbon storage and N 2 O emissions at a watershed scale are limited. Specifically, our understanding of how low-carbon feedstock production and management affect nutrient cycle dynamics is incomplete. This study assesses watershed responses to land management practices in two agriculturally dominant watersheds: the Raccoon River watershed and the Southfork of Iowa River watershed. The study focuses on carbon and nutrient dynamics, characterizing spatial and temporal variations in SOC, N 2 O, and nutrient loadings to examine the relationship between nutrient and carbon responses and agricultural conservation practices. The study employs the newly developed Soil Water Analysis Tool for Carbon (SWAT-C) model, calibrated using 20 years’ of climate and water monitoring data, to simulate and evaluate two agricultural conservation practices: no-till and crop residue harvest with cover crop planting. We compared the calibrated SWAT-C model with a historical baseline model, which allowed us to analyze various aspects of the watershed, including stream flow, suspended sediments, nitrogen, phosphorus, organic carbon, SOC at different depths, and N 2 O emissions from topsoil. Our SWAT-C modeling results indicate that, compared with results from the historical baseline model, no-till practices are positively correlated with SOC accumulation, reduced N 2 O emissions, and decreased soil loss. We also observed no change or slightly increased nitrogen and phosphorus loss to water bodies in the watersheds compared with the baseline. Conversely, crop residue harvest with cover crop planting improved water quality by reducing nutrient and soil losses but also increased N 2 O emissions. This SWAT-C modeling study establishes the groundwork for further smaller-scale and/or sub-basin-level assessments of nitrogen, phosphorus, and carbon cycles. It provides valuable science-based insights to inform policy decisions — particularly in the context of transitioning to biofuel feedstock production in these watersheds — by addressing concerns about nutrient exports to local water bodies and, ultimately, the Mississippi River.

54 ENVIRONMENTAL SCIENCES↗

Quantum-Accelerated Distributed Algorithms for Approximate Steiner Trees and Directed Minimum Spanning Trees

We present two algorithms in the Quantum CONGEST-CLIQUE model of distributed computation that succeed with high probability; one for producing an approximately optimal Steiner Tree, and one for producing an exact spanning arborescence of minimum weight, the analog of a Minimum Spanning Tree in a directed graph, each of which uses O~(n^(1/4)) rounds of communication and O~(n^(9/4)) messages, achieving a lower round and message complexity than any known algorithms in the classical CONGEST-CLIQUE model. The CONGEST distributed computational model allows limited-sized messages to be transmitted within a network described by a communication graph of size n in a series of rounds to address a computational problem. The size limitation for such messages isO(log(n)) bits at each edge of the communication graph per round. The communication graph in the CONGEST-CLIQUE model is fully connected. In the Quantum CONGEST-CLIQUE model, at most O(log(n)) classical and quantum bits (qubits) can be communicated across each edge of the communication graph per round. At a high level, we achieve these results by combining classical algorithms with fast quantum subroutines. These speedups further contribute to understanding what problems can be solved more efficiently when we allow quantum communication in this CONGEST-CLIQUE model of distributed computation.

quantum distributed algorithms↗

First direct measurement of the 13 $\mathrm{N(α, ρ)}$ 16 $\mathrm{O}$ reaction relevant for core-collapse supernovae nucleosynthesis

We report that understanding the explosion mechanism of a core-collapse supernova (CCSN) is important to accurately model CCSN scenarios for different progenitor stars using model-observation comparisons. The uncertainties of various nuclear reaction rates relevant for CCSN scenarios strongly affect the accuracy of these stellar models. Out of these reactions, the 13 N(α, p) 16 O reaction has been found to affect various stages of a CCSN at varying temperatures. This work presents the first direct measurement of the 13 N(α, p) 16 O reaction performed using a 34.6 MeV beam of radioactive 13 N ions and the active-target detector MUSIC (MUlti-Sampling Ionization Chamber) at Argonne National Laboratory. The resulting total 13 N(α, p) 16 O reaction cross sections from this measurement in the center-of-mass energy range of 3.26 - 6.02 MeV are presented and compared with calculations using the Hauser-Feshbach formalism. Uncertainties in the reaction rate have been dramatically reduced at CCSN temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

KGML-ag: a modeling framework of knowledge-guided machine learning to simulate agroecosystems: a case study of estimating N<sub>2</sub>O emission using data from mesocosm experiments

Abstract. Agricultural nitrous oxide (N2O) emission accounts for a non-trivial fraction of global greenhouse gas (GHG) budget. To date, estimating N2O fluxes from cropland remains a challenging task because the related microbial processes (e.g., nitrification and denitrification) are controlled by complex interactions among climate, soil, plant and human activities. Existing approaches such as process-based (PB) models have well-known limitations due to insufficient representations of the processes or uncertainties of model parameters, and due to leverage recent advances in machine learning (ML) a new method is needed to unlock the “black box” to overcome its limitations such as low interpretability, out-of-sample failure and massive data demand. In this study, we developed a first-of-its-kind knowledge-guided machine learning model for agroecosystems (KGML-ag) by incorporating biogeophysical and chemical domain knowledge from an advanced PB model, ecosys, and tested it by comparing simulating daily N2O fluxes with real observed data from mesocosm experiments. The gated recurrent unit (GRU) was used as the basis to build the model structure. To optimize the model performance, we have investigated a range of ideas, including (1) using initial values of intermediate variables (IMVs) instead of time series as model input to reduce data demand; (2) building hierarchical structures to explicitly estimate IMVs for further N2O prediction; (3) using multi-task learning to balance the simultaneous training on multiple variables; and (4) pre-training with millions of synthetic data generated from ecosys and fine-tuning with mesocosm observations. Six other pure ML models were developed using the same mesocosm data to serve as the benchmark for the KGML-ag model. Results show that KGML-ag did an excellent job in reproducing the mesocosm N2O fluxes (overall r2=0.81, and RMSE=3.6 mgNm-2d-1 from cross validation). Importantly, KGML-ag always outperforms the PB model and ML models in predicting N2O fluxes, especially for complex temporal dynamics and emission peaks. Besides, KGML-ag goes beyond the pure ML models by providing more interpretable predictions as well as pinpointing desired new knowledge and data to further empower the current KGML-ag. We believe the KGML-ag development in this study will stimulate a new body of research on interpretable ML for biogeochemistry and other related geoscience processes.

54 ENVIRONMENTAL SCIENCES↗

Ionospheric hot spot at high latitudes

Schunk and Raitt (1980) and Sojka et al. (1981) have developed a model of the convecting high-latitude ionosphere in order to determine the extent to which various chemical and transport processes affect the ion composition and electron density at F-region altitudes. The numerical model produces time-dependent, three-dimensional ion density distributions for the ions NO(+), O2(+), N2(+), O(+), N(+), and He(+). Recently, the high-latitude ionospheric model has been improved by including thermal conduction and diffusion-thermal heat flow terms. Schunk and Sojka (1982) have studied the ion temperature variations in the daytime high-latitude F-region. In the present study, a time-dependent three-dimensional ion temperature distribution is obtained for the high-latitude ionosphere for an asymmetric convection electric field pattern with enhanced flow in the dusk sector of the polar region. It is shown that such a convection pattern produces a hot spot in the ion temperature distribution which coincides with the location of the strong convection cell.

Schunk, R. W.↗

Importance of aggregation and small ice crystals in cirrus clouds, based on observations and an ice particle growth model

The 1 November 1986 FIRE I case study was used to test an ice particle growth model which predicts bimodal size spectra in cirrus clouds. The model was developed from an analytically based model which predicts the height evolution of monomodal ice particle size spectra from the measured ice water content (IWC). Size spectra from the monomodal model are represented by a gamma distribution, N(D) = N(sub o)D(exp nu)exp(-lambda D), where D = ice particle maximum dimension. The slope parameter, lambda, and the parameter N(sub o) are predicted from the IWC through the growth processes of vapor diffusion and aggregation. The model formulation is analytical, computationally efficient, and well suited for incorporation into larger models. The monomodal model has been validated against two other cirrus cloud case studies. From the monomodal size spectra, the size distributions which determine concentrations of ice particles less than about 150 mu m are predicted.

Mitchell, David L.↗

Potential surfaces for O atom-polymer reactions

Ab initio quantum chemistry methods are used to study the energetics of interactions of O atoms with organic compounds. Polyethylene (CH2)n has been chosen as the model system to study the interactions of O(3P) and O(1D) atoms with polymers. In particular, H abstraction is investigated and polyethylene is represented by a C3 (propane) oligomeric model. The gradient method, as implemented in the GRADSCF package of programs, is used to determine the geometries and energies of products and reactants. The saddle point, barrier geometry is determined by minimizing the squares of the gradients of the potential with respect to the internal coordinates. To correctly describe the change in bonding during the reaction at least a two configuration MCSCF (multiconfiguration self consistent field) or GVB (generalized valence bond) wave function has to be used. Basis sets include standard Pople and Dunning sets, however, increased with polarization functions and diffuse p functions on both the C and O atoms. The latter is important due to the O(-) character of the wave function at the saddle point and products. Normal modes and vibrational energy levels are given for the reactants, saddle points and products. Finally, quantitative energetics are obtained by implementing a small CAS (complete active space) approach followed by limited configuration interaction (CI) calculations. Comparisons are made with available experimental data.

Laskowski, B. C.↗

First discovery of the organic materials in deep-sea iron cosmic spherule

The dust impact mass analyzer (PUMA) carried by the spacecraft Vega 1, Vega 2 and Giotto has provided the first direct measurements of the physical and chemical properties of cometary dust. The results indicate that most of the cometary dust particles are rich in light elements such as H, C, N, and O, suggesting the validity of models that describe the cometary dust as including organic material. Up to now, there were none found with the organic material from the deep-sea cosmic spherules. We have determined this from the deep-sea iron cosmic spherules collected from the North Pacific. An iron cosmic spherule (382 microns in diameter) was determined by the Laser Raman Microprobe.

Hanchang, Peng↗

Observations of the far ultraviolet airflow by the Ultraviolet Limb Imaging experiment on STS-39

The Ultraviolet Limb Imaging (UVLIM) experiment flew on STS-39 in the spring of 1991 to observe the Earth's thermospheric airglow and included a far ultraviolet (1080-1800 A) spectrometer. We present first results from this spectrometer, including a spectroscopic analysis at 6-A resolution of H, O, N, and N2 dayglow emissions and modeling of the observed limb-scan profiles of dayglow emissions. The observed N2 Lyman-Birge-Hopfield (LBH) emission reflects a vibrational population distribution in the a(1 Pi)(sub g) state that differs significantly from those predicted for direct electron excitation and excitation with cascade from the a('1 Sigma)(sub u)(-) and w(1 Delta)(sub u) states. The vibrational population distribution and LBH brightness suggest a total cascade rate 45% that of direct excitation, in contrast to laboratory measurements. For the first time, pronounced limb brightening is observed in both the N I lambda 1200 limb emission profiles, as expected for emissions excited by N2 dissociation which produces kinetically fast N fragments; however, optically thick components of these features are also observed. Preliminary modeling of the OI lambda 1356, HI lambda 1216, and OI lambda 1304 and OI lambda 1641 emissions agrees to within roughly 10% of the observed limb-scan profiles, but the models underestimate the N2 LBH profiles by a factor of 1.4-1.6, consistent with the inferred cascade effect. Other findings include: an OI lambda 1152/lambda 1356 intensity ratio that is inconsistent with the large cascade contribution to OI lambda 1356 from np 5P states required by laboratory and nightglow observations; nightglow observations of the tropical ultraviolet arcs exhibit a wide range of OI lambda 1356/lambda 1304 intensity ratios and illustrate the complicated observing geometry and radiative transfer effects that must be modeled; and we find a 3-sigma upper limit of 8.5 R to the total LBH vehicle glow emission.

Budzien, S. A.↗

Dissociative Recombination (DR) and Associative Ionization (AI) Cross Section Calculations for the NO+ + e yields N + O (2D+3P, 2P+3P, and 2D+1D) Reaction for Atmospheric Entry Modeling

During entry of a space craft into Earth atmosphere, the flow surrounding the vehicle becomes partially ionized leading to significant cation and free-electron production. Subsequently, electron impact excitation and dissociation form radiating excited state species that contribute to the heat load on the vehicle. While experimental data on selected total cross sections are available, few experiments address the need for accurate AI cross sections for metastable atomic states at the high temperatures realized in atmospheric re-entry. In order to maintain desired safety margins during atmospheric entry of a space vehicle, chemical reaction models need to accurately account for this process. For the present study, we have computed vibrationally resolved cross sections for the DR of NO+ for electron energies between 0.01 to 10 eV and apply microscopic reversibility to obtain the AI cross sections and rate coefficients. For the DR cross section calculations, we use state-of-the-art MRCI potential energy curves. The resulting adiabatic potential curves are transformed to a diabatic representation, which is used in time-dependent wave packet calculations to describe the nuclear motion of the dissociating cation upon collision with an electron. Based on the wave function evolution in time, these calculations provide T-matrix and cross sections for the DR including recombination into the low energy metastable atomic states. The DR and AI rate coefficients are compared with the available experimental data.

Ewa Papajak↗