A robust statistical model for the evaporation of multicomponent-fuel drops containing a multitude of chemical species
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multicomponent-fuel drops↗
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A robust statistical model for the evaporation of multicomponent-fuel drops containing a multitude of chemical species
A statistical formulation is developed describing the composition in an evaporating multicomponent-fuel liquid drop and in the gas phase surrounding it.
Continuous thermo-dynamics CT↗
A multi-temperature TVD algorithm for relaxing hypersonic flows
In this paper, the extension of a multispecies TVD algorithm, second-order accurate for real-gas flows to a multitemperature formulation is described. The convection algorithm is coupled to internal relaxation processes, and the features of the coupling are examined. The first version consists of a three-temperature model, where translational-rotational, vibrational, and electronic energy modes are separately convected. Although several species are present, there is only one vibrational temperature in this model. The second version generalizes to a vibrational temperature for each molecular specie, with additional couplings between species. The algorithms are applied to a generic two-dimensional flow field, and results are compared with experimental observations.
Cambier, Jean-Luc↗
Comparison of mercury (Hg) bioaccumulation with mono- and mixed Lemna minor and Spirodela polyrhiza cultures
Mercury (Hg) is a prevalent and harmful contaminant that persists in the environment. For phytoremediation, it is important to discover which plants can bioaccumulate meaningful amounts of Hg while also tolerating its toxicity. Additionally, increasing biodiversity could create a more resilient and self-sustaining system for remediation. This study explores whether mixed populations of Lemna minor and Spirodela polyrhiza can better bioaccumulate and tolerate Hg than monocultures. Mono- and mixed cultures of L. minor and S. polyrhiza were grown in mesocosms of 0.5 μg/L or 100 μg/L Hg ( HgCl2) spiked water for 96 h. Change in weight of duckweed was used to assess Hg tolerance. Diffusive gradients in thin-films (DGTs) were used as surrogate monitoring devices for bioavailable levels of Hg. For biomass growth, the mixed culture of the L. minor was greater than the monoculture at the high dose. The L. minor accumulated more Hg in the mixed culture at the low dose while the S. polyrhiza was higher in the mixed at the high dose. Hg speciation in water was modeled using Windermere Humic Aqueous Model 7 (WHAM7) to compare the bioavailable species indicated by the DGTs. Potentially due to the controlled conditions, the WHAM7 output of bioavailable Hg was almost 1:1 to that estimated by the DGTs, indicating good predictive capability of geochemical modeling and passive sampler DGT on metal bioavailability. Altogether, the mixed cultures statistically performed as well as or better than the monocultures when tolerating and bioaccumulating Hg. However, there needs to be further work to see if the significant differences translate into practical differences worth the extra resources to maintain multiple species.
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
Tuning plasma parameters to control reactive species fluxes to substrates in the context of plasma catalysis
The key reactive plasma-produced gas phase species responsible for the enhanced conversion of chemicals in plasma catalysis compared to thermal catalysis have to date not been identified. This outstanding question is mainly due to the inherent large variety of plasma-produced species and the challenge of controlling and measuring the flux of each constituent of the cocktail of reactive species to a (catalytic) substrate. In this paper, we explore the possibility to control the dominant reactive species fluxes, relevant for plasma-catalysis, to a substrate in the effluent of an RF driven Ar-O 2 plasma jet. The absolute species densities of the major reactive species (O, O 2 (a 1 Δ g ), O 3 and ions) were quantified by molecular beam mass spectrometry (MBMS) to assess the possibility of using treatment distance, O 2 admixture concentration, plasma dissipated power, RF modulation frequency and duty cycle as well as the feed gas flow rate to alter the dominant species densities. Selected experimental results were also compared with a pseudo-1D plug flow model. The short-lived and long-lived species can be effectively separated by changing the treatment distance and the RF modulation frequency. Furthermore, adjusting the O 2 admixture concentration enables to change the ratio of the O 2 (a 1 Δ g ) and O 3 density. The changes in the trend of ion and O flux were found to be very similar for nearly all investigated parameters. Nonetheless the gas flow rate was able to significantly change the ratio of the O and ion density in the plasma jet effluent. Here, the impact of the surface-dependent loss probability and boundary layer reactions on the species flux to a substrate and how this qualitatively relates to the MBMS density measurements is further addressed.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Runtime performance of a GAMESS quantum chemistry application offloaded to GPUs
Summary Computational chemistry is at the forefront of solving urgent societal problems, such as polymer upcycling and carbon capture. The complexity of modeling these processes at appropriate length and time scales is mainly manifested in the number and types of chemical species involved in the reactions and may require models of several thousand atoms and large basis sets to accurately capture the chemical complexity and heterogeneity in the physical and chemical processes. The quantum chemistry package General Atomic and Molecular Electronic Structure System (GAMESS) has a wide array of methods that can efficiently and accurately treat complex chemical systems. In this work, we have used the GAMESS Effective Fragment Molecule Orbital (EFMO) method for electronic structure calculation of a challenging mesoporous silica nanoparticle (MSN) model surrounded by about 4700 water molecules to investigate the strong scaling and GPU offloading on hybrid CPU‐GPU nodes. Experiments were performed on the Perlmutter platform at the National Energy Research Scientific Computing Center. Good strong scaling and load balancing have been observed on up to 88 hybrid nodes for different settings of the execution parameters for the calculation considered here. When GPUs are oversubscribed by offloading work from multiple CPU processes, using the NVIDIA multi‐process service (MPS) has consistently reduced time to solution and energy consumed. Additionally, for some configuration parameter settings, oversubscription with MPS improved performance by up to 5.8% over the case without oversubscription.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modeling the Effects of Global Change on Ecosystem Processes in a Tropical Rainforest
Ongoing land-use change and climate change in wet tropical forests can potentially drive shifts in tree species composition, representing a change in individual species within a functional group, tropical evergreen trees. The impacts on the global carbon cycle are potentially large, but unclear. We explored the differential effects of species within this functional group, in comparison with the effects of climate change, using the Century model as a research tool. Simulating effects of individual tree species on biome-level biogeochemical cycles constituted a novel application for Century. Background and Objectives: A unique, long-term, replicated field experiment containing five evergreen tree species in monodominant stands under similar environmental conditions in a Costa Rican wet forest provided data for model evaluation. Our objectives were to gain insights about this forest’s biogeochemical cycles and effects of tree species within this functional group, in comparison with climate change. Materials and Methods: We calibrated Century, using long-term meteorological, soil, and plant data from the field-based experiment. In modeling experiments, we evaluated effects on forest biogeochemistry of eight plant traits that were both observed and modeled. Climate-change simulation experiments represented two climate-change aspects observed in this region. Results: Model calibration revealed that unmodeled soil processes would be required to sustain observed P budgets. In species-traits experiments, three separate plant traits (leaf death rate, leaf C:N, and allocation to fine roots) resulted in modeled biomass C stock changes of >50%, compared with a maximum 21% change in the climate-change experiments. Conclusions: Modeled ecosystem properties and processes in Century were sensitive to changes in plant traits and nutrient limitations to productivity. Realistic model output was attainable for some species, but unusual plant traits thwarted predictions for one species. Including more plant traits and soil processes could increase realism, but less-complex models provide an accessible means for exploring plant-soil-atmosphere interactions.
54 ENVIRONMENTAL SCIENCES↗
CNO isotope production in nova outbursts
A current model of novae is presented which explains their outbursts assuming that the progenitor of a common nova is a carbon-oxygen dwarf. This white dwarf accretes H-rich material from its companion which produces strong shock waves at its surface; as the amount of accreted material increases later, its bottom ignites. The nova outburst is then triggered by CNO-Ne reactions which favor the formation of rare isotopes with proton-rich radioactive parents such as C-13, N-15, O-17, and Ne-21. The production of such nuclear species is examined in different nova models, and conclusions are drawn concerning the importance of novae in models of chemical evolution of the galaxy.
Audouze, J.↗
Informing Dionaea muscipula (Venus Flytrap) Conservation Through Habitat Modeling and Forecasted Land Cover Change
The carnivorous Dionaea muscipula (Venus flytrap, Droseraceae) is threatened by habitat loss, fire suppression, and poaching. For rare plant species like D. muscipula with specialized habitat requirements and fragmented distribution, habitat suitability modeling is an important method for guiding conservation efforts. To support the D. muscipula conservation, this study: 1) modeled suitable habitat across the extent of the species’ known range and 2) forecasted land cover change due to development in the study area to the year 2050. Habitat modeling was conducted by overlaying high-confidence presence data observed since 1980 (n=292) with environmental predictor variables (n=23). Suitable habitats were then compared with land cover change to identify areas at risk of habitat loss due to human development. According to those models, nearly half (107.1km2) of modeled highly suitable D. muscipula habitat outside of protected lands are likely to face development pressure. On the other hand, 39.4% (139.9km2) of highly suitable habitats overlap with protected lands and may serve as lasting D. muscipula habitat. Results from this study can inform D. muscipula conservation, including targeted seed banking of populations at risk of extirpation, prioritization of habitats for protection and management, and reintroduction to suitable habitats within protected areas.
Kathryn Caruso↗
Atmospheric Research 2014 Technical Highlights
Atmospheric research in the Earth Sciences Division (610) consists of research and technology development programs dedicated to advancing knowledge and understanding of the atmosphere and its interaction with the climate of Earth. The Division's goals are to improve understanding of the dynamics and physical properties of precipitation, clouds, and aerosols; atmospheric chemistry, including the role of natural and anthropogenic trace species on the ozone balance in the stratosphere and the troposphere; and radiative properties of Earth's atmosphere and the influence of solar variability on the Earth's climate. Major research activities are carried out in the Mesoscale Atmospheric Processes Laboratory, the Climate and Radiation Laboratory, the Atmospheric Chemistry and Dynamics Laboratory, and the Wallops Field Support Office. The overall scope of the research covers an end-to-end process, starting with the identification of scientific problems, leading to observation requirements for remote-sensing platforms, technology and retrieval algorithm development; followed by flight projects and satellite missions; and eventually, resulting in data processing, analyses of measurements, and dissemination from flight projects and missions. Instrument scientists conceive, design, develop, and implement ultraviolet, infrared, optical, radar, laser, and lidar technology to remotely sense the atmosphere. Members of the various Laboratories conduct field measurements for satellite sensor calibration and data validation, and carry out numerous modeling activities. These modeling activities include climate model simulations, modeling the chemistry and transport of trace species on regional-to-global scales, cloud resolving models, and developing the next-generation Earth system models. Satellite missions, field campaigns, peer-reviewed publications, and successful proposals are essential at every stage of the research process to meeting our goals and maintaining leadership of the Earth Sciences Division in atmospheric science research. Figure 1.1 shows the 20-year record of peer-reviewed publications and proposals among the various Laboratories. This data shows that the scientific work being conducted in the Laboratories is competitive with the work being done elsewhere in universities and other government agencies. The office of Deputy Director for Atmospheric Research will strive to maintain this record by rigorously monitoring and promoting quality while emphasizing coordination and integration among atmospheric disciplines. Also, an appropriate balance will be maintained between the scientists' responsibility for large collaborative projects and missions and their need to carry out active science research as a principal investigator. This balance allows members of the Laboratories to improve their scientific credentials, and develop leadership potentials. Interdisciplinary research is carried out in collaboration with other laboratories and research groups within the Earth Sciences Division, across the Sciences and Exploration Directorate, and with partners in universities and other government agencies. Members of the Laboratories interact with the general public to support a wide range of interests in the atmospheric sciences. Among other activities, the Laboratories raise the public's awareness of atmospheric science by presenting public lectures and demonstrations, by making scientific data available to wide audiences, by teaching, and by mentoring students and teachers. The Atmosphere Laboratories make substantial efforts to attract and recruit new scientists to the various areas of atmospheric research. We strongly encourage the establishment of partnerships with Federal and state agencies that have operational responsibilities to promote the societal application of our science products. This report describes our role in NASA's mission, provides highlights of our research scope and activities, and summarizes our scientists' major accomplishments during calendar year 2014. The composition of the organization is shown in Figure 1.2 for each code. This report is published in a printed version with an electronic version on our atmospheres Web site, http://atmospheres.gsfc.nasa.gov/.
Technical↗
Atmospheric Research 2016 Technical Highlights
Atmospheric research in the Earth Sciences Division (610) consists of research and technology development programs dedicated to advancing knowledge and understanding of the atmosphere and its interaction with the climate of Earth. The Divisions goals are to improve understanding of the dynamics and physical properties of precipitation, clouds, and aerosols; atmospheric chemistry, including the role of natural and anthropogenic trace species on the ozone balance in the stratosphere and the troposphere; and radiative properties of Earth's atmosphere and the influence of solar variability on the Earth's climate. Major research activities are carried out in the Mesoscale Atmospheric Processes Laboratory, the Climate and Radiation Laboratory, the Atmospheric Chemistry and Dynamics Laboratory, and the Wallops Field Support Office. The overall scope of the research covers an end-to-end process, starting with the identification of scientific problems, leading to observation requirements for remote-sensing platforms, technology and retrieval algorithm development; followed by flight projects and satellite missions; and eventually, resulting in data processing, analyses of measurements, and dissemination from flight projects and missions. Instrument scientists conceive, design, develop, and implement ultraviolet, infrared, optical, radar, laser, and lidar technology to remotely sense the atmosphere. Members of the various laboratories conduct field measurements for satellite sensor calibration and data validation, and carry out numerous modeling activities. These modeling activities include climate model simulations, modeling the chemistry and transport of trace species on regional-to-global scales, cloud resolving models, and developing the next-generation Earth system models. Satellite missions, field campaigns, peer-reviewed publications, and successful proposals are essential at every stage of the research process to meeting our goals and maintaining leadership of the Earth Sciences Division in atmospheric science research. Figure 1.1 shows the 22-year record of peer-reviewed publications and proposals among the various laboratories.
Atmospheric↗
Unraveling the Molecular Origin of Prey-Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR
Prey wrapping spider silk's unique mechanical properties are investigated confirming the silk's high degree of extensibility and superior toughness compared to other types of spider silk. For the first time, the pre-spinning dope phase is studied in isotope-enriched intact aciniform (AC) silk glands using solution NMR that reveals a combination of α-helical domains linked by disordered random coil chains consistent with previously proposed “beads-on-a-string” models. The model is further refined through the AlphaFold2 protein structure prediction tool. Finally, extensive magic angle spinning (MAS) solid-state (SS) NMR data for isotopically-enriched fibers is used to refine the structural model for AC silk from two species, A. aurantia and A. argentata. The SSNMR data shows that the AC silk fibers are highly α-helical, coiled-coil in structure but, also exhibit significant β-sheet components that can be traced back to the Gly-rich disordered linker regions in the pre-spinning dope phase that are converted to β-sheet structures during fiber formation. This combination of mechanical and structural characterization enhances the understanding of AC silk's liquid-to-solid transition and structure-mechanics relationship. In conclusion, these prey wrap silk results and models will provide the basis for the design of biomimetic materials inspired by the AC spider silk system.
36 MATERIALS SCIENCE↗
Global and Regional Temperature-change Potentials for Near-term Climate Forcers
The emissions of reactive gases and aerosols can affect climate through the burdens of ozone, methane and aerosols, having both cooling and warming effects. These species are generally referred to near-term climate forcers (NTCFs) or short-lived climate pollutants (SLCPs), because of their short atmospheric residence time. The mitigation of these would be attractive for both air quality and climate on a 30-year timescale, provided it is not at the expense of CO2 mitigation. In this study we examine the climate effects of the emissions of NTCFs from 4 continental regions (East Asia, Europe, North America and South Asia) using results from the Task Force on Hemispheric Transport of Air Pollution Source-Receptor global chemical transport model simulations. We address 3 aerosol species (sulphate, particulate organic matter and black carbon - BC) and 4 ozone precursors (methane, reactive nitrogen oxides - NOx, volatile organic compounds VOC, and carbon monoxide - CO). For the aerosols the global warming potentials (GWPs) and global temperature change potentials (GTPs) are simply time-dependent scaling of the equilibrium radiative forcing, with the GTPs decreasing more rapidly with time than the GWPs. While the aerosol climate metrics have only a modest dependence on emission region, emissions of NOx and VOCs from South Asia have GWPs and GTPs of higher magnitude than from the other northern hemisphere regions. On regional basis, the northern mid-latitude temperature response to northern mid-latitude emissions is approximately twice as large as the global average response for aerosol emission, and about 20-30% larger than the global average for methane, VOC and CO emissions. We also found that temperatures in the Arctic latitudes appear to be particularly sensitive to black carbon emissions from South Asia.
climate forcer↗
Understanding the influence of solvents on the Pt-catalyzed hydrodeoxygenation of guaiacol
Bio-oil derived from fast pyrolysis of lignocellulosic biomass needs to be deoxygenated to become a substitute for petroleum fuels. Here, we study the hydrodeoxygenation mechanism of guaiacol, a bio-oil model compound derived from the lignin fraction of biomass, on Pt(1 1 1) terrace sites in the presence of water, diethyl ether, 1-butanol, and n-hexane as solvent. Using first-principles periodic density functional theory (DFT) calculations and mean-field microkinetic reactor modeling, a detailed reaction mechanism is investigated targeting various products such as catechol, phenol, anisole, benzene, cyclohexanone, and cyclohexanol. Solvent phase DFT outcomes are mostly similar to that of the vapor phase; however, microkinetic modeling results suggest that rate controlling species and transition states differ somewhat in the various reaction environments. Catechol was found to be the major aromatic product across all reaction environments. Over Pt(1 1 1), unsaturated monooxygenate production from catechol is unlikely.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation
Enhancers are important non-coding elements, but they have traditionally been hard to characterize experimentally. The development of massively parallel assays allows the characterization of large numbers of enhancers for the first time. Here, we developed a framework using Drosophila STARR-seq to create shape-matching filters based on meta-profiles of epigenetic features. We integrated these features with supervised machine-learning algorithms to predict enhancers. We further demonstrated that our model could be transferred to predict enhancers in mammals. We comprehensively validated the predictions using a combination of in vivo and in vitro approaches, involving transgenic assays in mice and transduction-based reporter assays in human cell lines (153 enhancers in total). The results confirmed that our model can accurately predict enhancers in different species without re-parameterization. Finally, we examined the transcription factor binding patterns at predicted enhancers versus promoters. Here, we demonstrated that these patterns enable the construction of a secondary model that effectively distinguishes enhancers and promoters.
59 BASIC BIOLOGICAL SCIENCES↗
Future directions for H sub x O sub y detection, executive summary
New methods for the measurement of OH radicals were assessed as were currently available and possible future methods for the other H sub x O sub y species, HO2 and H2O2. The workshop participants were invited from different groups: modelers of atmospheric photochemistry, experimentalists measuring H sub x O y species with laser and nonlaser methods, and chemists and physicists familiar with such experiments but not involved in atmospheric monitoring. There were three major conclusions from the workshop concerning the OH radical. First, it was felt that local measurements made by laser techniques would be ready within 2 or 3 years to furnish reliable measurements at the level of 1,000,000 cu. cm. Second, measurements at this level of sensitivity and with attainable levels of precision could indeed be used to make useful and interesting tests of the fast photochemistry of the troposphere. It is important, however, that the measurements be carefully designed, with respect to spatial and temporal averaging, if there is to be a meaningful comparison between results from two experimental methods or a measurement and a model. Third, nonlocal measurements using released reactants and tracers would also be very useful. These could be made on a regional or global basis, although they still require experimental design including choice of compounds.
Source record↗
Classification of animal sounds in a hyperdiverse rainforest using convolutional neural networks with data augmentation
To protect tropical forest biodiversity, we need to be able to detect it reliably, cheaply, and at scale. Automated detection of sound producing animals from passively recorded soundscapes via machine-learning approaches is a promising technique towards this goal, but it is constrained by the necessity of large training data sets. Using soundscapes from a tropical forest in Borneo and a Convolutional Neural Network model (CNN), we investigate i) the minimum viable training data set size for accurate prediction of call types (‘sonotypes’), and ii) the extent to which data augmentation and transfer learning can overcome the issue of small and imbalanced training data sets. We found that even relatively high sample sizes (>80 per sonotype) lead to mediocre accuracy, which however improved significantly with data augmentation and transfer learning, including at extremely small sample sizes (3 per sonotype), regardless of taxonomic group or call characteristics. Neither transfer learning nor data augmentation alone achieved high accuracy. Our results suggest that transfer learning and data augmentation could make the use of CNNs to classify species’ vocalizations feasible even for small soundscape-based projects with many rare species. Retraining our open-source model requires only basic programming skills which makes it possible for individual conservation initiatives to match their local context, in order to enable more evidence-informed management of biodiversity.
54 ENVIRONMENTAL SCIENCES↗
Chromosome-Level Genome Assembly of Mentha longifolia L. Reveals Gene Organization Underlying Disease Resistance and Essential Oil Traits
Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat (NBS-LRR) plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. Here, the bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.
59 BASIC BIOLOGICAL SCIENCES↗