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At least 667 records · Page 37

Southeast Atmosphere Studies: Learning from Model-Observation Syntheses

Concentrations of atmospheric trace species in the United States have changed dramatically over the past several decades in response to pollution control strategies, shifts in domestic energy policy and economics, and economic development (and resulting emission changes) elsewhere in the world. Reliable projections of the future atmosphere require models to not only accurately describe current atmospheric concentrations, but to do so by representing chemical, physical and biological processes with conceptual and quantitative fidelity. Only through incorporation of the processes controlling emissions and chemical mechanisms that represent the key transformations among reactive molecules can models reliably project the impacts of future policy, energy and climate scenarios. Efforts to properly identify and implement the fundamental and controlling mechanisms in atmospheric models benefit from intensive observation periods, during which collocated measurements of diverse, speciated chemicals in both the gas and condensed phases are obtained. The Southeast Atmosphere Studies (SAS, including SENEX, SOAS, NOMADSS and SEAC4RS) conducted during the summer of 2013 provided an unprecedented opportunity for the atmospheric modeling community to come together to evaluate, diagnose and improve the representation of fundamental climate and air quality processes in models of varying temporal and spatial scales. This paper is aimed at discussing progress in evaluating, diagnosing and improving air quality and climate modeling using comparisons to SAS observations as a guide to thinking about improvements to mechanisms and parameterizations in models. The effort focused primarily on model representation of fundamental atmospheric processes that are essential to the formation of ozone, secondary organic aerosol (SOA) and other trace species in the troposphere, with the ultimate goal of understanding the radiative impacts of these species in the southeast and elsewhere. Here we address questions surrounding four key themes: gas-phase chemistry, aerosol chemistry, regional climate and chemistry interactions, and natural and anthropogenic emissions. We expect this review to serve as a guidance for future modeling efforts.

atmospheric chemistry↗

Interactions Between Climate and Species Drive Future Forest Carbon and Water Balances

Global change is altering forest carbon and water balances; however, the extent to which tree species shape ecosystem‐scale responses to climate, particularly in biodiverse forests, remains unclear. To address this, we simulated the effects of an envelope of future climate conditions on watershed carbon and water balances and quantified the contributions of tree species based on their xylem anatomy. We accomplished this by incorporating species‐level transpiration calculations into a landscape‐scale ecosystem process model. Our revised model linked the effects of forest succession, species composition, and climate change on water and carbon. Calibration of forest water fluxes using sap flux measurements and catchment water balances captured variability in species transpiration and interannual ET in biodiverse, humid temperate forest catchments in the southern Blue Ridge Mountains, USA. Across wet and dry future climate projections, ET increased, and streamflow and net carbon uptake decreased, particularly under a scenario of increasing drought. Despite accounting for just 30% of current biomass, diffuse‐porous tree species were the main driver of carbon and water flux responses now and in the future, thus intensifying the increase in ET and decline in streamflow. As diffuse‐porous biomass continues to increase, these forests will be increasingly sensitive to drought, amplifying losses of carbon sequestration and freshwater delivery.

54 ENVIRONMENTAL SCIENCES↗

Linking stem rehydration kinetics to hydraulic traits using a novel method and mechanistic model

Background: Despite the recognized importance of hydraulic capacitance as a mechanism used by plants to maintain hydraulic functioning during high transpiration, characterizing the dynamics of capacitance remains a challenge. Methods: For this work, we used a novel ‘two-balance method’ to investigate relationships between stem rehydration kinetics and other hydraulic traits in multiple tree species, and we developed a model to explore stem rehydration kinetics further. Key Results: We found that: (1) rehydration time constants and the amount of water uptake occurring during rehydration differed significantly across species; (2) time constants did not change with declining water potential (Ψ), while water uptake increased at lower Ψ in some species; (3) longer time constants were associated with lower wood density, higher capacitance and less negative stem pressures causing 50 % loss of hydraulic conductivity (P 50 ); (4) greater water uptake occurred in stems with lower wood density and less negative P 50 values; and (5) the model could estimate the total hydraulic resistance of the rehydration path, which cannot be measured directly. Conclusions: Overall, the two-balance method can be used to examine rehydration dynamics quickly and thoroughly in detached woody stems. This method has the potential to improve our understanding of how capacitance functions across tree species, which is an often-overlooked component of whole-plant hydraulics.

54 ENVIRONMENTAL SCIENCES↗

The Significance of Aggregation Methods in Functional Group Modeling

The growth of forests and the feedbacks between forests and environmental changes are central issues in the planetary carbon cycle, global climate change, and basic plant ecology. A challenge to understanding both growth and feedbacks from local to global scales is that many critical metabolic processes vary among species. An innovation in solving this challenge is the recognition that species can be lumped into “functional groups” based on metabolic similarity, and these functional groups can then be studied in computational models that simulate ecosystem function. Despite the vast resources devoted to functional group studies and the progress made by them, an important logical and biological question has not been formally addressed, “How do the groupings alter the results of modeling studies?” To what extent do modeling results depend on the choices made in aggregating taxa into functional groups. Here, we consider the effects of using different aggregation strategies in simulating the carbon dynamics of a deciduous forest. Understanding the impacts that aggregation strategy has on efforts to simulate regional-to-global-scale forest dynamics offers insights into both ecosystem regulation and model function and addresses this central problem in the study of carbon dynamics.

54 ENVIRONMENTAL SCIENCES↗

Dusty Gas Model for Solid Oxide Fuel Cell Fuel Electrode

This model applies the Dusty Gas Model simulate multi-component species transport in SOFC (solid oxide fuel cell) anodes which considers the pressure gradient across the fuel electrode. This studyhas been verified with the analytical solution for different fuel electrode thicknesses and with literature values. The model was developed using the VoronoiFVM platform in Julia which is a built in implicit and semi implicit solver that integrates electrochemical behavior, microstructural effects, and transient analysis for accurate prediction of species transport under varying conditions.

dusty gas model (DGM)↗

Coupled Thermal-Hydraulic Analysis and Species Mass Transport in a Versatile Experimental Salt Irradiation Loop (VESIL) using COBRA-TF

With the resurgence of interest in Molten Salt Reactor (MSR) technology among commercial and governmental agencies, there is a need for new experiments and new modelling capabilities to characterize the unique phenomena present in this fluid fuel system. A Versatile Experimental Salt Irradiation Loop (VESIL) is currently under investigation at Idaho National Laboratory. It is designed to be a dynamic fuel-bearing salt loop placed in the Advanced Test Reactor. One of the key phenomena this proposed experiment plans to elucidate is fission product speciation in the fuel-salt and the subsequent effects this can have on fuel-salt properties, fission product transport and interactions, source term generation, corrosion and redox potential control. Specifically, noble gases (Xe & Kr) will bubble out to a plenum or off-gas system and noble metals (Mo, Tc, Te etc.) will precipitate and deposit in specific zones in the loop. This work extends the mass transfer and species interaction models in the general species transport capability of COBRA-TF (CTF) and applies these models to give a preliminary estimation of fission product behavior in the proposed VESIL design.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Two-Species, 3D, MHD Simulation of Europa's Interaction with Jupiter's Magnetosphere

The interaction of Europa with the Jovian a magnetosphere has been studied by using a two species in ideal magnetohydrodynamic (MHD) numerical model. This model considers the upstream plasma in the Jovian magnetosphere and the molecular oxygen ions in the ionosphere of Europa, separately. We present results a from simulation studies, which take into account impact ionization, recombination, and the effect of a possible induced dipole magnetic field of Europa. The total mass loading of the magnetospheric flow and the ionization frequency used in the model are consistent with the estimates of Europa's ionosphere and atmosphere. The multi-species MHD equations are solved by using a finite volume, high-order, Godunov-type method on an adoptively refined unstructured grid, which allows a detailed modeling of the region near Europa's surface, while still resolving both the upstream region and the satellite's wake. We have paid special attention to the wake of Europa, in order to be able to make comparisons with the Galileo's E4 flyby observations, as well as other model calculations. The calculated escape flux of a O2+ down the tail was found to be about 5.6 x 10(exp 25) s(sup -1).

Liu, Yifan↗

Modeling aqueous association constants and mineral solubilities at subcritical and supercritical temperatures

The need for sustainable power generation has increased interest in the use of hydrothermal fluids for industrial applications. New high-enthalpy geothermal systems and biowaste-to-fuel processes are two relevant examples that employ supercritical fluids which require an in-depth understanding of complex chemical reactions occurring near the supercritical temperature of water (374 °C). As these processes operate in thermodynamic regimes that are not currently covered by a standard molar Gibbs energy of formation model, only empirical fits for single reaction systems are available which limit the use of multi-component phase equilibria calculations that are standard practice for less extreme environments. Here, in this paper, we advance a standard molar Gibbs energy of formation model able to operate in these otherwise inaccessible thermodynamic states to include species needed for key mineral solubility systems and ion association reactions. This work extends a model based on molecular statistical thermodynamics (MST) into four new systems (Na 3 PO 4 -H 2 O, LiOH-H 2 O, KOH-H 2 O, and BaSO 4 -H 2 O) by extending the model to cover 10 new species. For each of these systems, model predictions were consistently within the experimental uncertainties for the new systems covered. A breakdown of MST contributions to the model revealed that electrostatic and hard sphere contributions were key to reproducing density dependencies of standard molar Gibbs energy of formation values around the critical point of water.

42 ENGINEERING↗

Remote Sensing of Coastal Wetlands Biomass Using Thematic Mapper Wavebands

Spectral data, simulating thematic mapper bands 3, 4 and 5 were gathered in salt and brackish marshes using a hand-held radiometer. Simple regression models were developed equating spectral radiance indicies with total live biomass for S. alterniflora in a salt marsh and for a variety of plant species in a brackish marsh. Models were then tested and compared to harvest estimates of biomass. In the salt marsh, biomass estimates from spectral data were similar to harvest biomass estimates during most of the growing season. Estimates of annual net aerial primary productivity calculated from spectral data were within 21% of production estimated from harvest data. During August, biomass estimates from spectral data in the brackish marsh were similar to biomass estimated by harvesting techniques but not always comparable at other times in the growing season.

Hardisky, M. A.↗

Remote sensing of coastal wetlands biomass using Thematic Mapper wavebands

Spectral data, simulating thematic mapper bands 3, 4 and 5 are gathered in salt and brackish marshes using a hand-held radiometer. Simple regression models are developed equating spectral radiance indices with total live biomass for S. alterniflora in a salt marsh and for a variety of plant species in a brackish marsh. Models are then tested using an independent set of data and compared to harvest estimates of biomass. In the salt marsh, biomass estimates from spectral data are similar to harvest biomass estimates during most of the growing season. Estimates of annual net aerial primary productivity calculated from spectral data are within 21% of production estimated from harvest data. During August, biomass estimates from spectral data in the brackish marsh are similar to biomass estimated by harvesting techniques. At other times during the growing season, spectral data estimates of biomass are not always comparable to harvest biomass estimates. Reasonable estimates of wetlands biomass are possible during the peak of the growing season (August) using spectral data similar to thematic mapper bands 3, 4 and 5 gathered with hand-held radiometers.

Hardisky, M. A.↗

Association‐based activity coefficient model for electrolyte solutions

Abstract This work presents an association‐based activity coefficient model that explicitly considers the solution nonideality due to associations among ions and solvent species. Built upon the electrolyte nonrandom two‐liquid (eNRTL) model, the model greatly improves the accuracy of eNRTL model for strongly associating electrolyte solutions due to presence of ionic species with high surface charge density. The model successfully correlates mean ionic activity coefficients of 46 aqueous single‐salt systems from 10 cations and 5 anions at 298.15 K up to their solubility limits. With the ion‐specific association parameters identified, the model accurately predicts activity and osmotic coefficients for aqueous mixed‐salt systems at 298.15 K. The temperature dependence of the model results has also been examined at 273–373 K. With superior accuracy over a wide range of concentration and temperature, the model represents a major advancement over eNRTL model and has a great potential to be a next‐generation model for electrolyte solutions.

Lin, Yu‐Jeng↗

Uncertainty propagation in a stratospheric model. I - Development of a concise stratospheric model. II - Monte Carlo analysis of imprecisions due to reaction rates

The paper discusses the development of a concise stratospheric model which uses iteration to obtain coupling between interacting species. The one-dimensional, steady-state, diurnally-averaged model generates diffusion equations with appropriate sources and sinks for species odd oxygen, H2O, H2, CO, N2O, odd nitrogen, CH4, CH3Cl, CCl4, CF2Cl2, CFCl3, and odd chlorine. The model evaluates steady-state perturbations caused by injections of chlorine and NO(x) and may be used to predict ozone depletion. The model is used in a Monte Carlo study of the propagation of reaction-rate imprecisions by calculating an ozone perturbation caused by the addition of chlorine. Since the model is sensitive to only 10 of the more than 50 reaction rates considered, only about 1000 Monte Carlo cases are required to span the space of possible results.

Rundel, R. D.↗

Interaction of Inner Heliosheath Ions with Electromagnetic Ion Cyclotron Waves

Abstract Inner heliosheath (IHS) ions are expected to be exposed to various waves, shocks, and turbulence, which can affect ion distributions and thus their charge-exchange rates with interstellar neutral atoms. This work addresses the potential significance of electromagnetic ion cyclotron (EMIC) waves under expected IHS conditions. From a kinetic dispersion relation, we find the possibility of frequent triggering of EMIC instability in the IHS. The threshold anisotropy of proton temperatures required for the instability is small, ( T ⊥ – T ∣∣ )/ T ∣∣ ≈ 0.1 or less, mainly due to high plasma β (ratio of the plasma to magnetic pressures). Numerical calculations on the scattering of ions (protons, He + , and He 2+ with energy of 0.01–50 keV) based on two models for EMIC waves with a moderate intensity indicate significant scattering in the pitch angle (mostly a few tens of degrees) and energy (mostly a few tens of percent) although details depend on the energy and pitch angle of each species and adopted EMIC wave models. This occurs on a short timescale (<100 times the gyro-period of each ion species). Resonant scattering in a few to a few tens of keV (corresponding to the expected pickup ion energy in the IHS) is easily expected unless the wavenumber is too large. The scattering effect is distinguished among different species such that for lower gyrofrequency ions (He + versus He 2+ and He 2+ versus protons), the main scattering effect moves toward a lower energy domain. All these results imply continuous disturbance of ion distributions by possibly prevailing EMIC waves in the IHS.

79 ASTRONOMY AND ASTROPHYSICS↗

An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F 1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

Chung, Henri C.↗

Advances in genome-scale metabolic models of industrially important fungi

Many fungal species have been used in industrial production for biofuels and bioproducts. Developing strains with better performance in biomanufacturing requires systematic understanding of cellular metabolism. Genome-scale metabolic models (GEMs) offer a comprehensive view of interconnected pathways and a mathematical framework for downstream analysis. Recently, GEMs have been developed or updated in several industrially important fungi. Some of them incorporate enzyme constraints, enabling improved predictions of cell states and proteome allocation. In this report we provide an overview of these newly developed GEMs and computational methods that facilitate construction of enzyme-constrained GEMs and utilize flux predictions from GEMs. Furthermore, we highlight the pivotal roles of these GEMs in iterative design-build-test- learn cycles, ultimately advancing the field of fungal biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

Thermodynamically consistent incorporation of the Langmuir adsorption model into compressible fluctuating hydrodynamics

For a gas–solid interfacial system where chemical species undergo reversible adsorption, we develop a mesoscopic stochastic modeling method that simulates both gas-phase hydrodynamics and surface coverage dynamics by coupling the Langmuir adsorption model with compressible fluctuating hydrodynamics. To this end, we derive a thermodynamically consistent mass–energy update scheme that accounts for how the mass and energy variables in the gas and surface subsystems should be updated according to the changes in the number of molecules of each species in each subsystem due to adsorption and desorption events. By performing a stochastic analysis for the ideal Langmuir model and the full hydrodynamic system, we analytically confirm that our mass–energy update scheme captures thermodynamic equilibrium predicted by equilibrium statistical mechanics. We find that an internal energy correction term is needed, which is attributed to the difference in the mean kinetic energy of gas molecules colliding with the surface from that computed from the Maxwell–Boltzmann distribution. By performing an equilibrium simulation study for an ideal gas mixture of CO and Ar, with CO undergoing reversible adsorption, we validate our overall simulation method and implementation.

Adsorption↗

Effects of multiple scattering and surface albedo on the photochemistry of the troposphere

The effect of treatment of incoming solar radiation on the photochemistry of the troposphere is discussed. A one dimensional photochemical model of the troposphere containing the species of the nitrogen, oxygen, carbon, hydrogen, and sulfur families was developed. The vertical flux is simulated by use of the parameterized eddy diffusion coefficients. The photochemical model is coupled to a radiative transfer model that calculates the radiation field due to the incoming solar radiation which initiates much of the photochemistry of the troposphere. Vertical profiles of tropospheric species were compared with the Leighton approximation, radiative transfer, matrix inversion model. The radiative transfer code includes the effects of multiple scattering due to molecules and aerosols, pure absorption, and surface albedo on the transfer of incoming solar radiation. It is indicated that significant differences exist for several key photolysis frequencies and species number density profiles between the Leighton approximation and the profiles generated with, radiative transfer, matrix inversion technique. Most species show enhanced vertical profiles when the more realistic treatment of the incoming solar radiation field is included

Augustsson, T. R.↗