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At least 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Time-resolved CO 2 , CO, and N 2 vibrational population measurements in Ns pulse discharge plasmas

Abstract Time-resolved CO 2 and N 2 vibrational populations and translational-rotational temperature are measured in a CO 2 –N 2 plasma sustained by a ns pulse discharge burst in plane-to-plane geometry. Time-resolved, absolute number density of CO generated in the plasma is also inferred from the experimental data. CO 2 and CO vibrational populations are measured by mid-IR, tunable quantum cascade laser absorption spectroscopy, and N 2 vibrational populations are measured by the ns broadband vibrational CARS. Transient excitation of N 2 and CO 2 asymmetric stretch vibrational energy modes is detected during the discharge burst. The time-resolved rate of CO generation does not correlate with N 2 or CO 2 ( ν 3 ) vibrational temperatures, indicating that CO 2 dissociation via the vibrational excitation is insignificant at the present conditions. The rate of CO generation decreases gradually during the discharge burst. The estimated specific energy cost of the CO product is close to that of N atoms in pure nitrogen, measured previously at similar operating conditions. Comparison of the experimental data with the kinetic modeling analysis indicates that CO 2 dissociation in collisions with electronically excited N 2 molecules is the dominant channel of CO generation at the present conditions, although the inferred CO yield in these processes is significantly lower than 1. The effect of vibrational energy transfer between N 2 and CO 2 on the plasma chemical processes is insignificant. The kinetic model underpredicts a rapid reduction of the N 2 and CO 2 ( ν 3 ) vibrational temperatures during the later half of the discharge burst and in the afterglow. V–T relaxation of N 2 by N and O atoms generated in the ns pulse discharge plasma does not affect the vibrational relaxation rate in a significant way. However, rapid V–T relaxation of CO 2 by O atoms has a significant effect on the relaxation rate. The difference between the experimental data and the modeling predictions may be due to the unknown scaling of the CO 2 –O V–T rates with the vibrational quantum number.

Physics↗
DOE OSTI2021

Nitrification is a minor source of nitrous oxide (N 2 O) in an agricultural landscape and declines with increasing management intensity

Abstract The long‐term contribution of nitrification to nitrous oxide (N 2 O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N 2 O flux measurements with site‐specific Michaelis–Menten kinetics of nitrification‐derived N 2 O, we test the relative importance of nitrification‐derived N 2 O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N 2 O fluxes was 13%–17% in a conventionally fertilized annual cropping system, 27%–42% in a low‐input cover‐cropped annual cropping system, and 52%–63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N 2 O yields in cultured nitrifiers (typically 0.04%–8% of NH 3 oxidized) and competing sinks for available in situ. Most nitrification‐derived N 2 O was produced by ammonia‐oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification‐derived N 2 O production in all but one ecosystem. Although the proportion of nitrification‐derived N 2 O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification‐derived N 2 O (higher V max ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N 2 O in all ecosystems examined.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarch aeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). In conclusion, our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1996

The Structure and Stability of B(n)H(+) Clusters

The geometries of the B(n)H(+) clusters for n=1-13 have been optimized at the B3LYP level of theory. Excluding B2H(+) all clusters are low-spin coupled. The structures appear to be related to the bare B(+)(n) clusters in two ways: 1) an H atom is added to the B(+)(n) cluster or 2) a BH is added to the B(+)(n-1) cluster. The B(+)(n)-H binding energies are computed at the B3LYP level of theory, and calibrated n using the CCSD(T) level of theory. The computed results tend to fall between the experimental best estimates and the experimental lower bounds. The B(+)(n)-H binding energies show an inverse correspondence with the B+(n-1)-B values) while the B(+)(n-1)-B and B(+)(n-1)-BH results tend to parallel each other.

Ricca, Alessandra↗
DOE OSTI2020

Snowmelt Periods as Hot Moments for Soil N Dynamics: a Case Study in Maine, USA

We examined patterns of soil N availability during the vernal transition and how warming winter and ecosystem N status (N-enriched vs. N-limited) altered these patterns. Soils were sampled at the Bear Brook Watershed in Maine during 2015 and 2016. 2016 was a warmer winter with less snowfall than 2015, and therefore had earlier snowmelt and a longer vernal transition. Across both years, thaw periods consistently showed signs of being transition periods, especially evident in the N-enriched watershed — ammonium concentrations were highest during this period due to microbial community turnover and cell lysis, whereas nitrate concentrations were lowest due to flushing by meltwater. The N-enriched soils had 4–5-times more ammonium than the N-limited soils overall, although this difference was magnified during melt periods (10–14-fold). This indicates that the altered microbial community in the chronically N-manipulated soils might be more susceptible to community turnover and lysis during snowmelt. Our results indicate that ecosystem N status influences the response of forest soil N dynamics to a changing vernal transition in a time of accelerating climate change.

vernal transition, forest soils, nitrogen, N-enric↗
DOE OSTI2021

Long-term leaf C:N ratio change under elevated CO 2 and nitrogen deposition in China: Evidence from observations and process-based modeling

Climate change, elevating atmosphere CO 2 (eCO 2 ) and increased nitrogen deposition (iNDEP) are altering the biogeochemical interactions between plants, microbes and soils, which further modify plant leaf carbon-nitrogen (C:N) stoichiometry and their carbon assimilation capability. Many field experiments have observed large sensitivity of leaf C:N ratio to eCO 2 and iNDEP. However, the large-scale pattern of this sensitivity is still unclear, because eCO 2 and iNDEP drive leaf C:N ratio toward opposite directions, which are further compounded by the complex processes of nitrogen acquisition and plant-and-microbial nitrogen competition. Here, we attempt to map the leaf C:N ratio spatial variation in the past 5 decades in China with a combination of data-driven model and process-based modeling. These two approaches showed consistent results. Over different regions, we found that leaf C:N ratio had significant but uneven changes between 2 time periods (1960-1989 and 1990-2015): a 5% ± 8% increase for temperate grasslands in northern China, a 3% ± 6% increase for boreal grasslands in western China, and by contrast, a 7% ± 6% decrease for temperate forests in southern China, and a 3% ± 5% decrease for boreal forests in northeastern China. Additionally, the structural equation models indicated that the leaf C:N change was sensitive to ΔNDEP, ΔCO 2 and ΔMAT rather than ΔMAP and ecosystem types. In this work, process-based modeling suggested that iNDEP was the main source of soil mineral nitrogen change, dominating leaf C:N ratio change in most areas in China, while eCO 2 led to leaf C:N ratio increase in low iNDEP area. This study also indicates that the long-term leaf C:N ratio acclimation was dominated by climate constraint, especially temperature, but was constrained by soil N availability over decade scale.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1992

Progress in p(+)n InP solar cells fabricated by thermal diffusion

In SPRAT XI, we proposed that p(sup +)n diffused junction InP solar cells should exhibit a higher conversion efficiency than their n(sup +)p counterparts. This was mainly due to the fact that our p(sup +)n (Cd,S) cell structures consistently showed higher V (sub OC) values than our n(sup +)p (S,Cd) structures. The highest V(sub OC) obtained with the p(sup +)n (Cd,S) cell configuration was 860 mV, as compared to the highest V(sub OC) 840 mV obtained with the n(sup +)p (S,Cd) configuration (AMO, 25 C). In this work, we present the performance results of our most recent thermally diffused cells using the p(sup +)n (Cd,S) structure. We have been able to fabricate cells with V(sub OC) values approaching 880 mV. Our best cell with an unoptimized front contact grid design (GS greater than or equal to 10%) showed a conversion efficiency of 13.4% (AMO, 25 C) without an AR coating layer. The emitter surface was passivated by a -50A P rich oxide. Achievement of such high V(sub OC) values was primarily due to the fabrication of emitter surfaces, having EPD densities as low as 2E2 cm(sup -2) and N(sub a)N(sub d) of about 3E18 cm (sup -3). In addition, our preliminary investigation of p(sup +)n structures seem to suggest that Cd-doped emitter cells are more radiation resistant than Zn-doped emitter cells against both high energy electron and proton irradiation.

Faur, Mircea↗
DOE OSTI2020

N-jettiness beam functions at N3LO

We present the first complete calculation for the quark and gluon N -jettiness ( $$ {\mathcal{T}}_N $$ T N ) beam functions at next-to-next-to-next-to-leading order (N 3 LO) in perturbative QCD. Our calculation is based on an expansion of the differential Higgs boson and Drell-Yan production cross sections about their collinear limit. This method allows us to employ cutting edge techniques for the computation of cross sections to extract the universal building blocks in question. The class of functions appearing in the matching coefficents for all channels includes iterated integrals with non-rational kernels, thus going beyond the one of harmonic polylogarithms. Our results are a key step in extending the $$ {\mathcal{T}}_N $$ T N subtraction methods to N 3 LO, and to resum $$ {\mathcal{T}}_N $$ T N distributions at N 3 LL' accuracy both for quark as well as for gluon initiated processes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Plasma-Assisted Epitaxy of Piezoelectric Sc x Al 1-x N Films on Sapphire for Use in Harsh-Environment Microwave Acoustic Sensors

The Sc x Al 1-x N wurtzite structure has been shown theoretically and experimentally to exhibit significantly higher piezoelectric coupling compared to pure AlN. In this work, a plasma-assisted epitaxial growth method has been used to synthesize epitaxial (0002) Sc x Al 1-x N films on c-sapphire substrates from x = 0.07 to 0.30 by co-evaporating high-purity Sc and Al sources in the presence of a nitrogen plasma generated by an RF plasma source. Epitaxial Sc x Al 1-x N films with highly oriented (0002) grains and in-plane registry were produced on c-sapphire substrates that were pre-exposed to the nitrogen plasma to form an oxynitride seed layer. Growth of Sc x Al 1-x N films was carried out at 930°C under both metal-rich and N-rich conditions using precisely controlled Sc, Al, and N-plasma fluxes. Metal-rich depositions yielded non-(0002)-oriented Sc x Al 1-x N grains and intermetallic ScAl grains. Nitrogen-rich growth with a Sc/Al flux ratio of 1/3 produced the best (0002) epitaxy as determined by x-ray diffraction analysis. Surface acoustic wave resonator (SAWR) devices were fabricated from 500-nm-thick Sc x Al 1-x N and AlN films to extract their electromechanical coupling coefficients, k 2 . As the Sc concentration in the films increases, the degree of (0002) epitaxy is reduced, yet the value of k 2 increases becasue there is more Sc in the wurzite lattice despite the decreased level of (0002) grain alignment. As a result, the use of a 10-nm-thick Si x N y capping layer on top of the Sc x Al 1-x N films aids in preventing etching during SAWR device photolithography and also helps hinder film oxidation up to 800°C.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Synergistic double-atom catalysts of metal-boron anchored on g-C 2 N for electrochemical nitrogen reduction: Mechanistic insight and catalyst screening

The rational design of a novel catalytic center with a sound basis remains both challenging and rewarding for the electrochemical reduction of N 2 (eNRR), which has provided a feasible route for achieving clean and sustainable NH 3 production under ambient conditions. Herein, using density functional theory calculations, we demonstrate that hybrid metal (M)-boron (B) double-atom catalysts (DACs) embedded in g-C 2 N substrate (M-B@C 2 N, M = 3d, 4d and 5d transition metals) can achieve both high catalytic activity and high selectivity in eNRR. The proposed M-B@C 2 N DACs have exhibited impressive feasibility and stability thanks to the resilient and robust C 2 N substrate with abundant pyridinic N atoms distributed among right-sized pore structures. Our results reveal that like the metal center, the embedded B atom can actively involve in Ntriple bondN bond activation via π*-backdonation mechanism concomitant with the substantial charge transfer to adsorbed *N 2 , leading to sizable Nsingle bondN bond elongation. Accordingly, both adsorption energy and Nsingle bondN bond length of *N 2 can be employed as catalytic descriptors for predicting eNRR activity in terms of the limiting potentials (UL). Using high-throughput screening method, we found that six M-B@C 2 N candidates have stood out as the outstanding electrocatalysts for driving eNRR, namely, M = Ti (U L = 0 V), Mo (U L = 0 V), Nb (U L = -0.04 V), W (U L = -0.23 V), Zr (U L = -0.26 V), V (U L = -0.28 V). The underlying origin is attributed to the balanced and constrained N-affinity of M-B dual site working in synergy, which can thus be used as one important guide of catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Higher than expected N 2 O emissions from soybean crops in the Pampas Region of Argentina: Estimates from DayCent simulations and field measurements

In developing countries, agriculture generally represents a large fraction of GHG emissions reported in National Inventories, and emissions are typically estimated using Tier 1 IPCC guidelines. However, field data and locally adapted simulation models can improve the accuracy of IPCC estimations. In this report we aimed to quantify anthropogenic N2O emissions from croplands of Argentina through field measurements, model simulations and IPCC guidelines. Here we measured N 2 O emissions and their controlling factors in 62 plots of the Pampas Region with corn, soybean and wheat/soybean crops and in unmanaged grasslands. We accounted for gross emissions from crops and background emissions from unmanaged grasslands to calculate net anthropogenic emissions from crops as the difference between them. We calibrated and evaluated the DayCent model and then simulated different weather and management scenarios. Finally, we applied IPCC guidelines to estimate anthropogenic N 2 O emissions at the same plots. The DayCent model accurately simulated annual N 2 O emission for all crops as compared to measured data (RMSE = 1.4 g N ha -1 day -1 ). Measured and simulated emissions in soybean crops were higher than in corn and wheat/soybean crops. Gross N 2 O emissions ranged from 1.4 to 5.1 kg N ha -1 yr -1 for current environmental (soil and weather) and management (crops and fertilizer doses) conditions. Background emissions ranged between 1.1 and 1.3 kg N ha -1 yr -1 , and therefore net anthropogenic emissions ranged from 0.3 to 4.0 kg N ha-1 yr -1 . IPCC Tier 1 emission factors underestimated N2O releases from soybean, that were on average 4.87 times greater when estimated with DayCent and observations (0.53 vs 2.47 and 2.69 kg N ha -1 yr -1 , respectively). On the contrary, IPCC estimates for corn and wheat/soybean crops were similar to modeled and measured values. Our results suggest that N 2 O emissions from the vast 15 million ha of soybean croplands in the Pampas Region may be substantially underestimated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

NO Coupling at Copper to cis -Hyponitrite: N 2 O Formation via Protonation and H-Atom Transfer

Copper nitrite reductases (CuNIRs) convert NO 2 – to NO as well as NO to N 2 O under high NO flux at a mononuclear type 2 Cu center. While model complexes illustrate N–N coupling from NO that results in symmetric trans-hyponitrite [Cu II ]– ONNO–[Cu II ] complexes, in this work we report NO assembly at a single Cu site in the presence of an external reductant Cp* 2 M (M = Co, Fe) to give the first copper cis-hyponitrites [Cp* 2 M]{[Cu II ](κ 2 - O 2 N 2 )[Cu I ]}. Importantly, the κ 1 –N-bound [Cu I ] fragment may be easily removed by the addition of mild Lewis bases such as CNAr or pyridine to form the spectroscopically similar anion {[Cu II ](κ 2 -O 2 N 2 )} – . The addition of electrophiles such as H + to these anionic copper(II) cis-hyponitrites leads to N 2 O generation with the formation of the dicopper(II)-bis-μ-hydroxide [Cu II ] 2 (μ- OH) 2 . One-electron oxidation of the {[Cu II ](κ 2 -O 2 N 2 )} – core turns on H-atom transfer reactivity, enabling the oxidation of 9,10- dihydroanthracene to anthracene with concomitant formation of N 2 O and [Cu II ] 2 (μ-OH) 2 . These studies illustrate both the reductive coupling of NO at a single copper center and a way to harness the strong oxidizing power of nitric oxide via the neutral cis- hyponitrite [Cu](κ 2 -O 2 N 2 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Sustained bacterial N 2 O reduction at acidic pH

Nitrous oxide (N 2 O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N 2 O to dinitrogen (N 2 ) is the major consumption process but microbial N 2 O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N 2 O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N 2 O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N 2 O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N 2 O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N 2 O reduction between pH 4.5 and 6, highlighting microbial N 2 O reduction potential in acidic soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Aliovalent gallium dopants remove Ti 3+ defects and improve photocatalytic and photoelectrochemical water oxidation properties of LaTiO 2 N

LaTiO 2 N is a promising semiconductor for the water splitting reaction due to its 2.1 eV band gap and stability against corrosion. However, its solar energy conversion is limited by Ti 3+ recombination defects introduced during ammonolysis. Here we show for the first time that Ti 3+ defects in LaTiO 2 N can be suppressed with incorporation of 2, 5, and 10% aliovalent gallium (Ga 3+ ) dopants during synthesis via the layered La 2 Ti 2 O 7 intermediate. Electron paramagnetic resonance (EPR) spectroscopy on the solid powders confirms a reduction in the Ti 3+ donor density from 2.97 × 10 17 cm −3 for the non-doped material to ∼6.24 × 10 16 cm −3 for 5% Ga-doped LaTiO 2 N. The remaining Ti 3+ defects are concentrated near the LaTiO 2 N surface, according to X-ray photoelectron spectroscopy. The defect reduction shifts the optical absorption edge from 2.02 to 2.09 eV and eliminates a broad absorption band at 1050 nm from the optical absorption spectra. It also removes a 1.0–1.7 eV sub-band gap photovoltage signal from surface photovoltage spectra. This suggests that empty Ti 3+ d-orbitals are located 1.0–1.7 eV above the LaTiO 2 N valence band edge. Removing these recombination states with increasing Ga 3+ content enhances the photoconversion efficiency of LaTiO 2 N during water oxidation. The optimized 2 wt% CoO x -loaded 5% Ga-doped LaTi O2 N material has a 16% AQE (400 nm) for O 2 production from aqueous silver nitrate solution and a ∼2.1 mA cm −2 water oxidation photocurrent at 1.23 V under 100 mW cm −2 Xe arc lamp illumination. The water oxidation photocurrent is stable during a 50 min test, and the Faraday efficiency for O 2 generation is 97%, confirming short-term corrosion stability of LaTiO 2 N. Altogether, these results provide a better understanding of the distribution, concentration, and impact of Ti 3+ defects on the optical, photovoltage, and photoelectrochemical properties of LaTiO 2 N. In combination with other defect control strategies, aliovalent Ga 3+ doping can help bring the solar energy conversion efficiency of LaTiO 2 N closer to the theoretical limit.

Wang, Li [University of California, Davis, CA (Uni↗
DOE OSTI2022

Improving the damage tolerance of Si 3 N 4 by forming laminate composites with refractory metals

The objective of this research was to demonstrate that the damage tolerance of Si 3 N 4 could be significantly improved by forming laminate composites with refractory metals, providing materials that undergo graceful failure, rather than the fast-fracture mechanism exhibited by monolithic Si 3 N 4 . A damage tolerant Si 3 N 4 could be used as a ring material in an all-ceramic bearing, decreasing the chance for catastrophic failure if the ring is stressed in tension during operation. The technical approach formed a laminate composite material using alternating Si 3 N 4 -metallic layers, with both outer layers being Si 3 N 4 to take advantage of its greater wear resistance, chemical stability, and thermal stability. The metallic layers are designed to arrest any cracks in the outer layers, thus producing a toughened Si 3 N 4 and avoiding the catastrophic failure behavior exhibited by monolithic ceramics. The laminate composites were fabricated using a combination of tape-casting Si 3 N 4 and metals from slurries, as well as metal foils, followed by hot pressing at 1500°C. The metallic materials employed were chromium, titanium, and tantalum. Analysis confirmed that the interfaces were well formed, and the laminates with chromium and titanium formed intermetallic compounds more readily than the composites with tantalum. The Si 3 N 4 -Ta laminates demonstrated crack deflection and bridging behavior during failure and flexural strength of 800–900 MPa. The hardness and elastic modulus of Si 3 N 4 -Ta laminates measured by nanoindentation were similar to those reported in literature. The hardness across the interface of the Si 3 N 4 -Ta composite varied according to the composition of the interface, which displayed a profile indicative of a diffusion bond.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation

All lineages of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, contain mutations between amino acids 199 and 205 in the nucleocapsid (N) protein that are associated with increased infectivity. The effects of these mutations have been difficult to determine because N protein contributes to both viral replication and viral particle assembly during infection. Here, we used single-cycle infection and virus-like particle assays to show that N protein phosphorylation has opposing effects on viral assembly and genome replication. Ancestral SARS-CoV-2 N protein is densely phosphorylated, leading to higher levels of genome replication but 10-fold lower particle assembly compared to evolved variants with low N protein phosphorylation, such as Delta (N:R203M), Iota (N:S202R), and B.1.2 (N:P199L). A new open reading frame encoding a truncated N protein called N*, which occurs in the B.1.1 lineage and subsequent lineages of the Alpha, Gamma, and Omicron variants, supports high levels of both assembly and replication. Our findings help explain the enhanced fitness of viral variants of concern and a potential avenue for continued viral selection.

Microbiology↗
DOE OSTI2024

Protein N -Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

Diabetes is expected to directly affect renal glycosylation; yet to date, there has not been a comprehensive evaluation of alterations in N-glycan composition in the glomeruli of patients with diabetic kidney disease (DKD). Here, we used untargeted mass spectrometry imaging to identify N-glycan structures in healthy and sclerotic glomeruli in formalin-fixed paraffin-embedded sections from needle biopsies of five patients with DKD and three healthy kidney samples. Regional proteomics was performed on glomeruli from additional biopsies from the same patients to compare the abundances of enzymes involved in glycosylation. Secondary analysis of single-nucleus RNA sequencing (snRNAseq) data were used to inform on transcript levels of glycosylation machinery in different cell types and states. We detected 120 N-glycans, and among them, we identified 12 of these protein post-translated modifications that were significantly increased in glomeruli. All glomeruli-specific N-glycans contained an N-acetyllactosamine epitope. Five N-glycan structures were highly discriminant between sclerotic and healthy glomeruli. Sclerotic glomeruli had an additional set of glycans lacking fucose linked to their core, and they did not show tetra-antennary structures that were common in healthy glomeruli. Orthogonal omics analyses revealed lower protein abundance and lower gene expression involved in synthesizing fucosylated and branched N-glycans in sclerotic podocytes. In snRNAseq and regional proteomics analyses, we observed that genes and/or proteins involved in sialylation and N-acetyllactosamine synthesis were also downregulated in DKD glomeruli, but this alteration remained undetectable by our spatial N-glycomics assay. Integrative spatial glycomics, proteomics, and transcriptomics revealed protein N-glycosylation characteristic of sclerotic glomeruli in DKD.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Similarity Downselection: Finding the n Most Dissimilar Molecular Conformers for Reference-Free Metabolomics

Computational methods for creating in silico libraries of molecular descriptors (e.g., collision cross sections) are becoming increasingly prevalent due to the limited number of authentic reference materials available for traditional library building. These so-called “reference-free metabolomics” methods require sampling sets of molecular conformers in order to produce high accuracy property predictions. Due to the computational cost of the subsequent calculations for each conformer, there is a need to sample the most relevant subset and avoid repeating calculations on conformers that are nearly identical. The goal of this study is to introduce a heuristic method of finding the most dissimilar conformers from a larger population in order to help speed up reference-free calculation methods and maintain a high property prediction accuracy. Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population size grows large. Because there exists a pairwise relationship between each item and all other items in the population, finding the set of the n most dissimilar items is different than simply sorting an array of numbers. For instance, if you have a set of the most dissimilar n = 4 items, one or more of the items from n = 4 might not be in the set n = 5. An exact solution would have to search all possible combinations of size n in the population exhaustively. We present an open-source software called similarity downselection (SDS), written in Python and freely available on GitHub. SDS implements a heuristic algorithm for quickly finding the approximate set(s) of the n most dissimilar items. We benchmark SDS against a Monte Carlo method, which attempts to find the exact solution through repeated random sampling. We show that for SDS to find the set of n most dissimilar conformers, our method is not only orders of magnitude faster, but it is also more accurate than running Monte Carlo for 1,000,000 iterations, each searching for set sizes n = 3–7 out of a population of 50,000. We also benchmark SDS against the exact solution for example small populations, showing that SDS produces a solution close to the exact solution in these instances. Using theoretical approaches, we also demonstrate the constraints of the greedy algorithm and its efficacy as a ratio to the exact solution.

97 MATHEMATICS AND COMPUTING↗