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At least 289 records · Page 16

An omnipresent diversity and variability in the chemical composition of atmospheric functionalized organic aerosol

Abstract The atmospheric evolution of organic compounds encompasses many thousands of compounds with varying volatility, polarity, and water solubility. The molecular-level chemical composition of this mixture plays a major, yet uncertain, role in its transformations and impacts. Here we perform a non-targeted molecular-level intercomparison of functionalized organic aerosol from three diverse field sites and a chamber. Despite similar bulk composition, we report large molecular-level variability between multi-hour organic aerosol samples at each site, with 66 ± 13% of functionalized compounds differing between consecutive samples. Single precursor environmental laboratory chamber experiments and fully chemically-explicit modeling confirm this variability is due to changes in emitted precursors, chemical age, and/or oxidation conditions. These molecular-level results demonstrate greater compositional variability than is typically observed in less-speciated measurements, such as bulk elemental composition, which tend to show less daily variability. These observations should inform future field and laboratory studies, including assessments of the effects of variability on aerosol properties and ultimately the development of strategic organic aerosol parameterizations for air quality and climate models.

Ditto, Jenna C.↗

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run microseconds or longer simulations using femtoseconds time steps. While there are several existing methods to overcome this timescale barrier and efficiently sample thermodynamic and/or kinetic properties, problems remain in regard to being able to sample un- known systems, deal with high-dimensional space of collective variables, and focus the computational effort on slow timescales. Hence, in this work, a new sampling method, called the “Concurrent Adaptive Sampling (CAS) algorithm,” has been developed to tackle these three issues and efficiently obtain conformations and pathways. The method is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective vari- ables and uses macrostates (a partition of the collective variable space) to enhance the sampling. The exploration is done by running a large number of short simula- tions, and a clustering technique is used to accelerate the sampling. In this paper, we introduce the new methodology and show results from two-dimensional models and bio-molecules, such as penta-alanine and triazine polymer

59 BASIC BIOLOGICAL SCIENCES↗

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/μl to 0.1 pg/μl (10 –1 to 10 –4 ). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10 –1 (mean Ct value: 20.3) and 10 –2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

59 BASIC BIOLOGICAL SCIENCES↗

Using low volume eDNA methods to sample pelagic marine animal assemblages

Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.

59 BASIC BIOLOGICAL SCIENCES↗

CARBON AND OXYGEN ISOTOPIC RATIOS FOR NEARBY MIRAS

Carbon and oxygen isotopic ratios are reported for a sample of 46 Mira and SRa-type variable asymptotic giant branch (AGB) stars. Vibration–rotation first and second-overtone CO lines in 1.5–2.5 μ m spectra were measured to derive isotopic ratios for {sup 12}C/{sup 13}C, {sup 16}O/{sup 17}O, and {sup 16}O/{sup 18}O. Comparisons with previous measurements for individual stars and with various samples of evolved stars, as available in the extant literature, are discussed. Models for solar composition AGB stars of different initial masses are used to interpret our results. We find that the majority of M-stars have main sequence masses ≤2 M {sub ⊙} and have not experienced sizable third dredge-up (TDU) episodes. The progenitors of the four S-type stars in our sample are slightly more massive. Of the six C-stars in the sample three have clear evidence relating their origin to the occurrence of TDU. Comparisons with O-rich presolar grains from AGB stars that lived before the formation of the solar system reveal variations in the interstellar medium chemical composition. The present generation of low-mass AGB stars, as represented by our sample of long period variables (LPVs), shows a large spread of {sup 16}O/{sup 17}O ratios, similar to that of group 1 presolar grains and in agreement with theoretical expectations for the composition of mass 1.2–2 M {sub ⊙} stars after the first dredge-up. In contrast, the {sup 16}O/{sup 18}O ratios of present-day LPVs are definitely smaller than those of group 1 grains. This is most probably a consequence of the the decrease with time of the {sup 16}O/{sup 18}O ratio in the interstellar medium due to the chemical evolution of the Milky Way. One star in our sample has an O composition similar to that of group 2 presolar grains originating in an AGB star undergoing extra-mixing. This may indicate that the extra-mixing process is hampered at high metallicity, or, equivalently, favored at low metallicity. Similarly to O-rich grains, no star in our sample shows evidence of hot bottom burning, which is expected for massive AGB stars.

79 ASTRONOMY AND ASTROPHYSICS↗

Cloud, Aerosol and Boundary Layer Structure across the Northeast Pacific Stratocumulus-Cumulus Transition as observed during CSET

During the Cloud System Evolution in the Trades (CSET) field study, 14 research flights of the National Science Foundation G-V sampled the stratocumulus-cumulus transition between Northern California and Hawaii and its synoptic variability. The G-V made vertically resolved measurements of turbulence, cloud microphysics, aerosol characteristics, and trace gases. It also carried dropsondes and a vertically pointing W-band radar and lidar. This paper summarizes these observations with the goals of fostering novel comparisons with theory, models and reanalyses, and satellite-derived products. A longitude-height binning and compositing strategy mitigates limitations of sparse sampling and spatiotemporal variability. Typically, a 1-km-deep decoupled stratocumulus-capped boundary layer near California evolved into 2-km-deep precipitating cumulus clusters surrounded by patches of thin stratus that dissipated toward Hawaii. Low cloud cover was correlated with estimated inversion strength more than with cloud droplet number, even though the thickest clouds were generally precipitating and ultraclean layers indicative of aerosol-cloud-precipitation interaction were common west of 140 degrees W. Accumulation-mode aerosol concentration correlated well with collocated cloud droplet number concentration and was typically largest near the surface. Aitken mode aerosol concentration was typically larger in the free troposphere. Wildfire smoke produced spikes of aerosol and trace gases on some flights. CSET data are compared with space-time collocated output from MERRA-2 reanalysis and from the CAM6 climate model run with winds and temperature nudged toward this reanalysis. The reanalysis compares better with the observed relative humidity than does nudged CAM6. Both vertically diffuse the stratocumulus cloud layer versus observations. MERRA-2 slightly underestimates in situ carbon monoxide measurements and underestimates ozone depletion within the boundary layer.

Bretherton, Christopher S.↗

Comparison of Laboratory Analytical Methods for Uranium Analysis Superior Steel FUSRAP Site - 16606

The Superior Steel Site processed uranium metal in support of the Atomic Energy Commission's fuel-element development program in the 1950's, and was subsequently classified as a Formerly Utilized Sites Remedial Action Program (FUSRAP) Site. Previous investigations at the site identified uranium contamination both inside and outside the buildings associated with historic uranium metalworking activities. The U.S. Army Corps of Engineers (USACE) is currently engaged in the Remedial Investigation (RI) phase in accordance with the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) of 1980, as amended. As part of the RI, gamma spectroscopy analysis of environmental samples was performed on-site using a laboratory-grade, high-purity germanium (HPGe) spectrometer. The gamma spectroscopy analysis included isotopes of uranium and their progeny. As a quality assurance measure, a subset of samples already analyzed on-site were sent to a certified, commercial, off-site laboratory for analysis using a suite of analytical methods including gamma spectroscopy, alpha spectroscopy, and mass spectroscopy. As an element of the quality assurance program implemented for the RI, an assessment of the correlations between the various analytical methods employed by both the on-site and off-site laboratory was performed. This assessment revealed inconsistencies between on-site and off-site gamma spectroscopy analytical results, which raised concerns about the appropriateness and suitability of the analytical data. To resolve the data quality concerns and better understand the source(s) of analytical results variability, the Superior Steel RI team (USACE together with its contractor, Amec Foster Wheeler) developed a quality control test whose design objective was to control or practically eliminate sampling and sample preparation variability in order to focus more clearly on analytical variability. This paper discusses the results of this supplemental quality control test, showing the differences in the various analytical methods (both on-site and off-site). It demonstrates in a practical and real world setting how sample preparation and analytical variability, if not controlled and understood can impact data quality and data defensibility. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

On representation of temporal variability in electricity capacity planning models

This study systematically investigates how to represent intra-annual temporal variability in models of optimum electricity capacity investment. Inappropriate aggregation of temporal resolution can introduce substantial error into model outputs and associated economic insight. The mechanisms underlying the introduction of this error are shown. How many representative periods are needed to fully capture the variability is then investigated. For a sample dataset, a scenario-robust aggregation of hourly (8760) resolution is possible in the order of 10 representative hours when electricity demand is the only source of variability. The inclusion of wind and solar supply variability increases the resolution of the robust aggregation to the order of 1000. A similar scale of expansion is shown for representative days and weeks. These concepts can be applied to any such temporal dataset, providing, at the least, a benchmark that any other aggregation method can aim to emulate. Finally, how prior information about peak pricing hours can potentially reduce resolution further is also discussed.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

An independent analysis of bias sources and variability in wind plant pre-construction energy yield estimation methods

The wind resource assessment community has long had the goal of reducing the bias between wind plant pre-construction energy yield assessment (EYA) and the observed annual energy production (AEP). This comparison is typically made between the 50% probability of exceedance (P50) value of the EYA and the long-term corrected operational AEP (hereafter OA P50), and is known as the P50 bias. The industry has critically lacked an independent analysis of bias reduction investigated across multiple consultants to identify the greatest sources of uncertainty and variance in the EYA process and the best opportunities for uncertainty reduction. The present study addresses this gap by benchmarking consultant methodologies against each other and against operational data at a scale not seen before in industry collaborations. We consider data from 10 wind plants and evaluate discrepancies between eight consultancies in the steps taken from estimates of gross to net energy. Consultants tend to overestimate the gross energy produced at the turbines and then compensate by further overestimating downstream losses, leading to a mean P50 bias near zero, still with significant variability among the individual wind plants. Within our data sample, we find that consultant estimates of all loss categories, except environmental losses, tend to reduce the project-to-project variability of the P50 bias. The disagreement between consultants, however, remains flat throughout the addition of losses. Finally, we find that differences in consultants’ estimates of project performance can lead to differences up to $10/MWh in the levelized cost of energy for a wind plant.

Todd, Austin C.↗

Improved Infrared Optical Constants from Pressed Pellets: II. Ellipsometric n and k Values for Ammonium Sulfate with Variability Analysis

Infrared spectral imaging is facilitated via the comparison of spectra recorded in situ to a databank of actual or synthetic infrared reflectance spectra. It has recently been shown that reference spectra corresponding to the many different morphological forms of the same chemical can be generated synthetically using the imaginary, k, and real, n, components of the complex refractive index, n~ = n + ik. One method to obtain the n and k vectors is infrared ellipsometry, which measures the changes in amplitude, tan ?, and phase, ?, of polarized light reflected from the sample both as a function of wavenumber and angle of incidence. The method requires specularly reflected light so best results are usually obtained with polished planar samples of large surface area. Due to the difficulties of obtaining such samples, however, we investigate the possibility of pressing powders of neat materials and obtaining the corresponding optical constants from the pellets. In this paper, variability in the sample pellet and preparation method is investigated, as is variability in the fitting procedure for the derived optical constants. The n/k vectors are derived from the measured ellipsometric parameters, tan ? and ?, as they are fit by an oscillator model which yield n(?) and k(?) vectors as a function of wavenumber, ?. Construction of the oscillator model is not automatic and depends on significant input from the analyst as well as the sample’s physical characteristics. For the pellet pressing, the experimental variability was found to be minimized for size-selected powdered samples as gauged by the minimal variance in ? and ? for three different pellets; similarly, the analytical precision for multiple measurements of the same pellet was also quite good, suggesting that a pressed pellet is a viable sample preparation method. The greatest variability came in the analytic fitting procedure with differences up to 20% arising from four different fits to the same data set. The final ellipsometric n/k data are compared to literature values obtained from crystalline (NH4)2SO4 samples as well as single-angle reflectance measurements that also used pressed pellets. Comparison with the previous literature values shows generally good agreement although higher k-values are observed for the independent sets of data derived from pressed pellets. These data are suggested as an improved set of optical constants for (NH4)2SO4.

optical constants, ellipsometry, ammonium sulfate,↗

Establishing ZIF‐8 as a reference material for hydrogen cryoadsorption: An interlaboratory study

Abstract Hydrogen storage by cryoadsorption on porous materials has the advantages of low material cost, safety, fast kinetics, and high cyclic stability. The further development of this technology requires reliable data on the H 2 uptake of the adsorbents, however, even for activated carbons the values between different laboratories show sometimes large discrepancies. So far no reference material for hydrogen cryoadsorption is available. The metal‐organic framework ZIF‐8 is an ideal material possessing high thermal, chemical, and mechanical stability that reduces degradation during handling and activation. Here, we distributed ZIF‐8 pellets synthesized by extrusion to 9 laboratories equipped with 15 different experimental setups including gravimetric and volumetric analyzers. The gravimetric H 2 uptake of the pellets was measured at 77 K and up to 100 bar showing a high reproducibility between the different laboratories, with a small relative standard deviation of 3–4 % between pressures of 10–100 bar. The effect of operating variables like the amount of sample or analysis temperature was evaluated, remarking the calibration of devices and other correction procedures as the most significant deviation sources. Overall, the reproducible hydrogen cryoadsorption measurements indicate the robustness of the ZIF‐8 pellets, which we want to propose as a reference material.

08 HYDROGEN↗

Soil organic carbon is not just for soil scientists: measurement recommendations for diverse practitioners

Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. Here, we advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.

54 ENVIRONMENTAL SCIENCES↗

Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis

Immunoprecipitation is one of the most effective methods for enrichment of lysine-acetylated peptides for comprehensive acetylome analysis using mass spectrometry. Manual acetyl peptide enrichment method using non-conjugated antibodies and agarose beads has been developed and applied in various studies. However, it is time consuming, and can introduce contaminants and variability that leads to potential sample loss and decreased sensitivity and robustness of the analysis. Here we describe a fast, automated enrichment protocol that enables reproducible and comprehensive acetylome analysis using a magnetic bead-based immunoprecipitation reagent.

Lysine acetylation, Acetylome, Acetyl peptide enri↗

Indexing habitat opportunity for juvenile anadromous fishes in tidal-fluvial wetland systems

In intertidal wetlands, annual habitat use by migrating juvenile salmon is limited by both physical and biological constraints. Physical limits are set by inundation patterns and water quality parameters, while biological bounds are determined by species specific migration timing and seasonal residency behaviors. We developed a new metric called the fish habitat opportunity index (FHOI) to quantify the total time per calendar year that salmon could access intertidal sites, based on periods of inundation and juvenile salmon seasonal migration. The index was applied using data collected at a recently reconnected tidal freshwater wetland area during 2006-2009. We found the wetland to be accessible to different salmon species for different lengths of time and periods of the year. On average, chum salmon (Oncorhynchus keta) had remarkably consistent opportunities to use marsh habitat over the 4 years sampled, while opportunities were more variable for Chinook (O. tshawytscha), and coho salmon (O. kisutch). Inundation varied nonlinearly with tidal height, and fish had access to the productive marsh edge for approximately 40-50% of the time during periods of access. The FHOI is widely applicable to wetland systems throughout the tidal fluvial continuum, and provides a metric for assessing fish habitat opportunity that is more realistic than simple wetted area calculations. Finally, the FHOI affords a method of a priori comparison among potential restoration sites to help resource managers predict the likely relative benefit to juvenile salmon.

wetland restoration, estuary, habitat opportunity,↗

Field-to-farm gate greenhouse gas emissions from corn stover production in the Midwestern U.S.

Measured field data were used to compare two allocation methods on life cycle greenhouse gas emissions from corn (Zea mays L.) stover production in the Midwest U.S. We used publicly-available crop yield, nitrogen fertilizer, and direct soil nitrous oxide emissions data from the USDA-ARS Resilient Economic Agricultural Practices research program. Field data were aggregated from 9 locations across 26 site-years for 3 stover harvest rates (no removal; moderate removal – 3.1 Mg ha –1 ; high removal – 7.2 Mg ha –1 ) and 2 tillage practices (conventional; reduced/no-till). Net carbon uptake by crops was computed from measured plant carbon content. Monte Carlo simulations sampled input distributions to assess variability in farm-to-gate GHG emissions. The base analysis assumed no change in soil organic carbon stocks. In all cases, net CO 2 uptake during crop growth and soil-respired CO 2 dominated system emissions. Emissions were most sensitive to co-product accounting method, with system expansion emissions ~15% lower than mass allocation. Regardless of accounting method, lowest emissions occurred for a moderate removal rate under reduced/no-till management. The absence of correlations between N fertilization rate and stover removal rate or soil N 2 O emissions in this study challenges the use of such assumptions typically employed in life cycle assessments Storage of all carbon retained on the field as SOC could reduce emissions by an additional 15%. Furthermore, our results highlight how variability in GHG emissions due to location and weather can overshadow the impact of farm management practices on field-to-farm gate emissions. Graphical abstract

54 ENVIRONMENTAL SCIENCES↗

Interfacial Hydrophilicity Controls Mineral Transformation Outcomes for Enstatite and Amorphous MgSiO 3

Subsurface injection of carbon dioxide (CO 2 ) into mafic-ultramafic rocks for permanent storage via mineralization is being studied to reduce emissions. Here, we investigated the carbonation products of enstatite (MgSiO 3 ) to assess its efficiency in sequestering CO 2 for safe and permanent storage as carbonate minerals. This was accomplished by conducting variable temperature carbonation reactions with samples of differing crystallinities and surface chemistries. Reaction progress was monitored utilizing in situ X-ray diffraction, and the presence of carbonate products was confirmed using additional techniques, such as thermogravimetric analysis coupled with mass spectrometry and scanning electron microscopy with energy dispersive spectrometry. Our results show that crystalline enstatite produces small amounts of the anhydrous form of MgCO 3 (magnesite), while amorphous MgSiO 3 , which was used to simulate mafic glass, more readily converts to the hydrated/hydroxylated hydromagnesite [Mg 5 (CO 3 ) 4 (OH) 2 ·4H 2 O]. These results, supplemented with dynamic vapor sorption experiments, suggest that surface properties play a significant role in the pathway and degree of carbonation. These developments concerning the reactivity of CO 2 with reactive mafic phases will help further our understanding of the reactivity of these mafic-ultramafic minerals with implications for permanent carbon storage and other subsurface engineering scenarios involving reactive reservoirs.

basalt↗

Parameterization Strategies for Intermolecular Potentials for Predicting Trajectory-Based Collision Parameters

The accuracy of separable strategies for constructing full-dimensional potential energy surfaces for collisional energy transfer and collision rate calculations is studied systematically for three alcohols (A = methanol, ethanol, and butanol) and three bath gases (M = Ar, N 2 , and H 2 O). The fitting efficiency (defined as the number of ab initio data required to achieve parametrizations of a desired accuracy) is quantified for both pairwise (Buckingham or "exp6") and nonpairwise (permutationally invariant polynomials, PIPs, of Morse variables) functional forms, for four sampling strategies, and as a function of the complexity and anisotropy of the interaction potential. We find that convergence with respect to the number of sampled ab initio data is largely independent of the choice of functional form but instead varies nearly linearly with the number of adjustable parameters and depends strongly on the sampling strategy. Specifically, the use of biased Sobol quasirandom sampling is similar to 7X more efficient than using unbiased pseudorandom sampling, on average, requiring just similar to 3 computed ab initio energies per adjustable fitting parameter. The pairwise exp6 functional form is shown to provide accurate and transferable parametrizations for M = Ar but is unable to accurately describe alcohol interactions with M = N 2 and H 2 O. The nonpairwise PIP functional form, which is systematically improvable, can produce separable parametrizations with arbitrarily small fitting errors. However, these can suffer from overfitting, which is demonstrated using dynamics calculations of collision parameters for a large number of exp6 and PIP parametrizations. The tests described here validate a robust strategy for automatically generating A + M potential energy surfaces with minimal human intervention, including a quantifiable out of sample metric for judging the accuracy of the fitted surface. We further analyze this set of automatically generated potential energy surfaces to identify areas where more sophisticated fitting strategies may be desired, including pruning of the PIP expansions for large systems and improved sampling strategies more closely coupled with the description of the functional form.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗