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At least 1,153 records · Page 64

The Turbulent Life of Phytoplankton

Phytoplankton is a generic name for photosynthesizing microscopic organisms that inhabit the upper sunlit layer (euphotic zone) of almost all oceans and bodies of freshwater. They are agents for "primary production," the incorporation of carbon from the environment into living organisms, a process that, sustains the aquatic food web. It is estimated that phytoplankton contribute about half of the global primary production, the other half being due to terrestrial plants. By sustaining the aquatic food web and controlling the biogeochemical cycles through primary production, phytoplankton exert a dominant influence on life on earth. Turbulence influences this process in three very important ways. First, essential mineral nutrients are transported from the deeper layers to the euphotic zone through turbulence. Second, turbulence helps to suspend phytoplankton in the euphotic zone since in still water, the phytoplankton, especially the larger species, tend to settle out of the sunlit layers. Third, turbulence transports phytoplankton from the surface to the dark sterile waters, and this is an important mechanism of loss. Thus, stable phytoplankton populations are maintained through a delicate dynamic balance between the processes of turbulence, reproduction, and sinking. The first quantitative model for this was introduced by Riley, Stommel and Bumpus in 1949. This is an attempt to extend their efforts through a combination of analysis and computer simulation in order to better understand the principal qualitative aspects of the physical/biological coupling of this natural system.

S Ghosal↗

More-Accurate Model of Flows in Rocket Injectors

An improved computational model for simulating flows in liquid-propellant injectors in rocket engines has been developed. Models like this one are needed for predicting fluxes of heat in, and performances of, the engines. An important part of predicting performance is predicting fluctuations of temperature, fluctuations of concentrations of chemical species, and effects of turbulence on diffusion of heat and chemical species. Customarily, diffusion effects are represented by parameters known in the art as the Prandtl and Schmidt numbers. Prior formulations include ad hoc assumptions of constant values of these parameters, but these assumptions and, hence, the formulations, are inaccurate for complex flows. In the improved model, these parameters are neither constant nor specified in advance: instead, they are variables obtained as part of the solution. Consequently, this model represents the effects of turbulence on diffusion of heat and chemical species more accurately than prior formulations do, and may enable more-accurate prediction of mixing and flows of heat in rocket-engine combustion chambers. The model has been implemented within CRUNCH CFD, a proprietary computational fluid dynamics (CFD) computer program, and has been tested within that program. The model could also be implemented within other CFD programs.

Hosangadi, Ashvin↗

Effects of Intra- and Interchain Interactions on Exciton Dynamics of PTB7 Revealed by Model Oligomers

Recent studies have shown that molecular aggregation structures in precursor solutions of organic photovoltaic (OPV) polymers have substantial influence on polymer film morphology, exciton and charge carrier transport dynamics, and hence, the resultant device performance. To distinguish photophysical impacts due to increasing π-conjugation from chain lengthening and π–π stacking from single/multi chain aggregation in solution and film, we used oligomers of a well-studied charge transfer polymer PTB7 with different lengths as models to reveal intrinsic photophysical properties of a conjugated segment in the absence of inter-segment aggregation. In comparison with previously studied photophysical properties in polymeric PTB7, we found that oligomer dynamics are dominated by a process of planarization of the conjugated backbone into a quinoidal structure that resembles the self-folded polymer and that, when its emission is isolated, this quinoidal excited state resembling the planar polymer chain exhibits substantial charge transfer character via solvent-dependent emission shifts. Furthermore, the oligomers distinctly lack the long-lived charge separated species characteristic of PTB7, suggesting that the progression from charge transfer character in isolated chains to exciton splitting in neat polymer solution is modulated by the interchain interactions enabled by self-folding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Sobering Examination of the Feasibility of Aqueous Aluminum Batteries

Recent reports on aqueous aluminum (Al) batteries boast encouraging metrics including high energy density, nonflammability, and low raw material cost. However, the poorly understood solvation environment around the trivalent aluminum ions (Al3+) raises uncertainty regarding their feasibility. Furthermore, the corrosiveness of the acidic solutions and degree of hydration of aluminum trifluoromethanesulfonate (Al(OTf)3) salt is routinely mischaracterized. This study provides a rigorous examination of aqueous Al electrolytes, with the first compelling evidence for a dynamic octahedral solvation structure around Al3+ dominated by labile water and OH-, without Al-OTf contact ion pairs, at high concentrations. This solvation behavior and the concomitant electrostatic hydrolysis differs greatly from previously reported water-in-salt electrolytes, and occurs due to the high charge density of the Lewis acidic Al3+. Nuclear magnetic resonance spectroscopy and other physicochemical measurements quantitatively reveal how species activity evolves with concentration. The high proton activity observed in transport and electrochemical measurements constitutes a prohibitive barrier to the feasibility of rechargeable aluminum batteries with aqueous electrolyte.

Pastel, Glenn R.↗

Experimental and computational investigations of ethane and ethylene kinetics with copper oxide particles for Chemical Looping Combustion

In this work, reaction pathways for the oxidation of methane, ethane, and ethylene with CuO was obtained by ReaxFF Molecular Dynamics (MD) simulations between temperatures of 1000 K and 2000 K. Experiments in a fixed-bed flow reactor were preformed with methane, ethane, and ethylene at temperatures ranging from 500 K to 1000 K with time-dependent species measurements from an Electron-Ionization Molecular Beam Mass Spectrometer (MBMS), and species validation with Gas Chromatography (GC) for detection of complete and intermediate combustion products. The MBMS and GC allow for the detection of oxygenated species and larger species produced from radical reformation. The simulation and experiment agree on the production of such species as CH 3 CHO, CH 2 O, CO, and H 2 O, which allow for the creation of simple C1 and C2 reaction pathways, which can be used in kinetic models of C2 species and larger fuels such as biofuels, which inherently depend on C1 and C2 kinetics and reaction pathway. The simulation and experiment disagree on the formation of C 2 H 2 , CH 3 OH, and CO 2 with large amounts of C 2 H 2 being measured in the ethylene oxidation simulations and CH 3 OH being formed in methane oxidation simulations, while neither species were experimentally found. In the case of CO 2 large amounts of CO 2 are rapidly produced in experiments with C2 fuels at 800 K, while little-to-no CO 2 was observed in simulations. This is believed to be resulting from the extremely short timescale of the simulations, preventing total oxidation of the fuel. Here, the differences in products produced between simulation and experiment allow for the potential to modify the ReaxFF potential functions to more accurately model the experimental products of Cu–H–O–C reaction kinetics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dynamic interactions at the mineral–organic matter interface

Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.

54 ENVIRONMENTAL SCIENCES↗

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Significance Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially adapted to local climates, leading to changes in their composition. Furthermore, we detected strain-level evolution, providing direct evidence that both ecological and evolutionary processes operate on annual timescales. The consideration of eco-evolutionary dynamics may therefore be important to understand the response of soil microbiomes to future environmental change.

54 ENVIRONMENTAL SCIENCES↗

An ascomycete H4 variant with an unknown function

Histone variants leading to altered nucleosome structure, dynamics and DNA accessibility occur frequently, albeit rarely for H4. We carried out a comprehensive in silico scrutiny of fungal genomes, which revealed the presence of a novel H4 variant (H4E) in the ascomycetes, throughout the Pezizomycotina, in basal species of the Taphrinomycotina and also in the Glomeromycota. The coding cognate genes show a specific intron/exon organization, different from H4 canonical genes. H4Es diverge from canonical H4s mainly in the N- and C-terminal extensions, showing marked differences in the distribution and number of Lys and Arg residues, which may result in novel post-translational modifications. In Aspergillus nidulans (Pezizomycotina, Eurotiomycetes) the H4E variant protein level is low in mycelia. However, the encoding gene is well expressed at 37°C under nitrogen starvation. H4E localizes to the nucleus and interacts with H3, but its absence or overexpression does not result in any detectable phenotype. Deletion of only one of the of the two canonical H4 genes results in a strikingly impaired growth phenotype, which indicates that H4E cannot replace this canonical histone. Thus, an H4 variant is present throughout a whole subphylum of the ascomycetes, but with hitherto no experimentally detectable function.

59 BASIC BIOLOGICAL SCIENCES↗

Beneath the Bark: Assessing Woody Stem Water and Carbon Fluxes and Its Prevalence Across Climates and the Woody Plant Phylogeny

While woody stems are known to influence carbon and water dynamics, direct exchange with the atmosphere is seldom quantified, limiting our understanding of how these processes influence the exchange of mass and energy. The presence of woody stem chlorophyll in a diversity of climates and across a range of species suggests an evolutionary advantage to sustaining carbon assimilation and water relations through permeable stem tissue. However, no formal evaluation of this hypothesis has been performed. In this mini-review, we explore the interactions between woody stems and the atmosphere by examining woody stem photosynthesis and bark-atmosphere water exchange. Specifically, we address the following questions: (1) How do water and carbon move between the atmosphere and woody stems? (2) In what climate space is woody stem photosynthesis and bark water uptake advantageous? (3) How ubiquitous across plant families is woody stem photosynthesis and bark-atmosphere water exchange? In the literature, only seven species have been identified as exhibiting bark water uptake while over 300 species are thought to conduct woody stem photosynthesis. The carbon dioxide and water gained from these processes can offset respiration costs and improve plant water balance. These species span diverse biomes suggesting a broad prevalence of bark-atmosphere permeability. Finally, our results demonstrate that there may be an evolutionary component as demonstrated by a high Pagel’s lambda for the presence of stem photosynthesis. We end with recommendations for future research that explores how bark water and carbon interactions may impact plant function and mass flow in a changing climate.

54 ENVIRONMENTAL SCIENCES↗

Diffusion and Solvation Dynamics of Ions in Water: Beyond the Brownian Approximation

The coupled dynamics of ions and water molecules in their first hydration shell impact a variety of processes including ion diffusion, selective ion transport in water-filled nanopores, and the kinetics of ion-pairing, ion adsorption, and metal-ligand binding reactions. In this work, we study these coupled dynamics for alkali metals (Li, Na, K, Rb, Cs), alkaline Earth metals (Mg, Ca, Sr, Ba), and chloride through the lens of their dependence on ion isotopic mass. Results are validated against previous measurements of the isotopic mass-dependence of ion diffusion coefficients in water and previous ab initio calculations of ion high-frequency dynamics in water. We find that the vibrational power spectra of ions in water consistently exhibit either two or three peaks, i.e., ions have several rattling frequencies within their solvations shells as previously reported for a subset of the species examined here. These frequencies have different sensititivies to isotopic mass that may serve as signatures of ion solvation processes (such as the tendency of ions to orient their first-shell water molecules) and that also may relate to Hofmeister-like effects including the relative affinity of different metals for ribonucleic acid (RNA).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vegetation Warming Experiment: Chamber and ambient plot digital camera imagery for vegetation phenology, Utqiagvik (Barrow), Alaska, 2019

Time lapse photography of experimental plots within five warming chambers (ZPWs) and paired control plots located on the Barrow Environmental Observatory (BEO), Utqiagvik, Alaska. Images were recorded from 21 June to 25 September, 2019 to capture vegetation dynamics during the growing season. Vegetation phenology, including green up and senescence were captured. Images were recorded daily at 30 minute intervals, from 09:00 - 16:30 Alaska daylight time (AKDT, UTC-8), using Wingscapes TimelapseCam cameras. The target species was Eriophorum angustifolium. Image files (.jpg) captured by Wingscapes TimelapseCams, compressed as zip files. Additional information in *.pdf and *.csv files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Vegetation Warming Experiment: Chamber and ambient plot digital camera imagery for vegetation phenology, Utqiagvik (Barrow), Alaska, 2017

Time lapse photography (*.jpg) of experimental plots within five warming chambers (ZPWs) and paired control plots located on the Barrow Environmental Observatory (BEO), Barrow (now Utqiagvik), Alaska. Images were recorded from 21 June to 18 September, 2017 to capture vegetation dynamics during the growing season. Vegetation phenology, including green up and senescence were captured. Images were recorded daily at 30 minute intervals, from 11:00-14:30 Alaska daylight time (AKDT, UTC-8), using Wingscapes TimelapseCam cameras. The target species was Petasites frigidus. Also included multiple metadata files including reporting formats as *.pdf and *.csv files. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Utilization of STRAT Data

One of the goals of the STRAT mission was to improve our understanding of transport in the stratosphere. We have used our coupled 2-D model to analyse transport between the tropics and midlatitudes using aircraft measurements of (CO2) and (N2O) made during the SPADE and ASHOE/MAESA campaigns (Boering et al. 1994) for model validation. We have further used the model to estimate errors in the experimental determination of the age of stratospheric air that arise from nonlinear increases of real tracers such as (CO2) and (SF6). The interpretation of measurements made during STRAT is still in progress. Most of the work performed under this contract has been described in the second year progress report, submitted in April of 1996. In the following, the research is summarized and some additional work that has become relevant in the meantime is described. We have developed an interactive model of the dynamics, chemistry and radiation of the stratosphere with partial support from this contract. The dynamics module integrates the primitive equations on a sphere. Lower boundary zonal winds and eddy geopotential heights are specified from observations. Chemistry and tracer transport are done in two dimensions. The chemistry model is a family model. Long lived species are transported and short lived species are determined in intervals of 5 to 10 days by assuming photochemical steady state. Full diurnal integrations with the fast species are performed periodically and diurnal coefficients, derived from the explicit integration are used to determine the steady state solution. Heating rates in the stratosphere are calculated from model ozone and the model temperatures and circulation fields are used in the chemistry transport module.

Source record↗

Model Assessment of the Impact on Ozone of Subsonic and Supersonic Aircraft

This is the final report for work performed between June 1999 through May 2000. The work represents continuation of the previous contract which encompasses five areas: (1) continued refinements and applications of the 2-D chemistry-transport model (CTM) to assess the ozone effects from aircraft operation in the stratosphere; (2) studying the mechanisms that determine the evolution of the sulfur species in the aircraft plume and how such mechanisms affect the way aircraft sulfur emissions should be introduced into global models; (3) the development of diagnostics in the AER 3-wave interactive model to assess the importance of the dynamics feedback and zonal asymmetry in model prediction of ozone response to aircraft operation; (4) the development of a chemistry parameterization scheme in support of the global modeling initiative (GMI); and (5) providing assessment results for preparation of national and international reports which include the "Aviation and the Global Atmosphere" prepared by the Intergovernmental Panel on Climate Change, "Assessment of the effects of high-speed aircraft in the stratosphere: 1998" by NASA, and the "Model and Measurements Intercomparison II" by NASA. Part of the work was reported in the final report. We participated in the SAGE III Ozone Loss and Validation Experiment (SOLVE) campaign and we continue with our analyses of the data.

Ko, Malcolm↗

Hybrid MD-Nernst Planck Model of Alpha-hemolysin Conductance Properties

Motivated by experiments in which an applied electric field translocates polynucleotides through an alpha-hemolysin protein channel causing ionic current transient blockade, a hybrid simulation model is proposed to predict the conductance properties of the open channel. Time scales corresponding to ion permeation processes are reached using the Poisson-Nemst-Planck (PNP) electro-diffusion model in which both solvent and local ion concentrations are represented as a continuum. The diffusion coefficients of the ions (K(+) and Cl(-)) input in the PNP model are, however, calculated from all-atom molecular dynamics (MD). In the MD simulations, a reduced representation of the channel is used. The channel is solvated in a 1 M KCI solution, and an external electric field is applied. The pore specific diffusion coefficients for both ionic species are reduced 5-7 times in comparison to bulk values. Significant statistical variations (17-45%) of the pore-ions diffusivities are observed. Within the statistics, the ionic diffusivities remain invariable for a range of external applied voltages between 30 and 240mV. In the 2D-PNP calculations, the pore stem is approximated by a smooth cylinder of radius approx. 9A with two constriction blocks where the radius is reduced to approx. 6A. The electrostatic potential includes the contribution from the atomistic charges. The MD-PNP model shows that the atomic charges are responsible for the rectifying behaviour and for the slight anion selectivity of the a-hemolysin pore. Independent of the hierarchy between the anion and cation diffusivities, the anionic contribution to the total ionic current will dominate. The predictions of the MD-PNP model are in good agreement with experimental data and give confidence in the present approach of bridging time scales by combining a microscopic and macroscopic model.

Cozmuta, Ioana↗

NASA GEOS Composition Forecast Modeling System GEOS-CF v1.0: Stratospheric Composition

The NASA Goddard Earth Observing System (GEOS) Composition Forecast (GEOS-29CF) provides recent estimates and five-day forecasts of atmospheric composition to the public in near-real time. To do this, the GEOS Earth system model is coupled with the GEOS-Chem tropospheric-stratospheric unified chemistry extension (UCX) to represent composition from the surface to the top of the GEOS atmosphere (0.01 hPa). The GEOS-CF system is described, including updates made to the GEOS-Chem UCX mechanism within GEOS-CF for improved representation of stratospheric chemistry. Comparisons are made against balloon, lidar and satellite observations for stratospheric composition, including measurements of ozone (O3) and important nitrogen and chlorine species related to stratospheric O3recovery. The GEOS-CF nudges the stratospheric O3towards the GEOS Forward Processing (GEOS FP) assimilated O3product; as a result the stratospheric O3in the GEOS-CF historical estimate agrees well with observations. During abnormal dynamical and chemical environments such as the 2020 polar vortexes, the GEOS-CF O3forecasts are more realistic than GEOS FP O3forecasts because of the inclusion of the complex GEOS-Chem UCX stratospheric chemistry. Overall, the spatial patterns of the GEOS-CF simulated concentrations of stratospheric composition agree well with satellite observations. However, there are notable biases – such as low NOx and HNO3 in the polar regions and generally low HCl throughout the stratosphere – and future improvements to the chemistry mechanism and emissions are discussed. GEOS-CF is a new tool for the research community and instrument teams observing trace gases in the stratosphere and troposphere, providing near-real-time three-dimensional gridded information on atmospheric composition.

GEOS-CF↗

Photon–photon chemical thermodynamics of frequency conversion processes in highly multimode systems

Abstract Frequency generation in highly multimode nonlinear optical systems is inherently a complex process, giving rise to an exceedingly convoluted landscape of evolution dynamics. While predicting and controlling the global conversion efficiencies in such nonlinear environments has long been considered impossible, here, we formally address this challenge even in scenarios involving a very large number of spatial modes. By utilizing fundamental notions from optical statistical mechanics, we develop a universal theoretical framework that effectively treats all frequency components as chemical reactants/products, capable of undergoing optical thermodynamic reactions facilitated by a variety of multi-wave mixing effects. These photon–photon reactions are governed by conservation laws that directly determine the optical temperatures and chemical potentials of the ensued chemical equilibria for each frequency species. In this context, we develop a comprehensive stoichiometric model and formally derive an expression that relates the chemical potentials to the optical stoichiometric coefficients, in a manner akin to atomic/molecular chemical reactions. This advancement unlocks new predictive capabilities that can facilitate the optimization of frequency generation in highly multimode photonic arrangements, surpassing the limitations of conventional schemes that rely exclusively on nonlinear optical dynamics. Notably, we identify a universal regime of Rayleigh–Jeans thermalization where an optical reaction at near-zero optical temperatures can promote the complete and entropically irreversible conversion of light to the fundamental mode at a target frequency. Our theoretical results are corroborated by numerical simulations in settings where second-harmonic generation, sum-frequency generation and four-wave mixing processes can manifest.

Optics↗

The influence of particle size on the fluid dynamics of a laser-induced plasma

The interaction of a laser-induced shock wave with nanoparticles and microparticles of aluminum oxide is investigated through experiments and modeling. The chemistry and physics of the interaction between the particles and plasma generated from laser ablation shows similarities and discrete differences for the two particle sizes. For both particle sizes, early stage (< 10 μs) ionization was dominant and evidenced by higher concentrations of Al II. While both sizes exhibit ionization over the same duration, the intensity of emission was greater for nanoparticles indicating greater concentrations of ionized species. Moreover, the dispersion of species was notably more elongated for microparticles while radial dispersion was more pronounced for nanoparticles with elevated drag forces. At later stages (i.e., > 10 μs), oxidation reactions were dominant for both particle sizes, but the same distinctions in flow field were observed and attributed to particle drag. In all stages of interaction, microparticles expand axially with less drag that suppresses their radial expansion. As a result, the dispersion of reactive species was mapped over an up to 80% larger area for nanoparticles relative to microparticles. Results shown here can be applied toward advancing experimental diagnostics and particle-shock wave modeling and simulation efforts for energetic materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗