Chemical models of the formation and growth of jovian polar haze particles
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Modeling Chemical Growth Processes in Titan's Atmosphere: 1. Theoretical Rates for Reactions between Benzene and the Ethynyl (C2H) and Cyano (CN) Radicals at Low Temperature and Pressure
Density functional theory calculations at the B3LYP/6-31+G** level were employed to characterize the critical points for adducts, isomers, products, and intervening transition states for the reactions between benzene and the ethynyl (C2H) or cyano (CN) radicals. Both addition reactions were found to have no barriers in their entrance channels, making them efficient at the low temperature and pressure conditions that prevail in the haze-forming region of Titan's atmosphere as well as in the dense interstellar medium (ISM). The dominant products are ethynylbenzene (C6H5C2H) and cyanobenzene (C6H5CN). Hydrogen abstraction reactions were also characterized but found to be non-competitive. Trajectory calculations based on potentials fit to about 600 points calculated at the ROMP2/6-31+G** level for each interaction surface were used to determine reaction rates. The rates incorporated any necessary corrections for back reactions as ascertained from a multiwell treatment used to determine outcome distributions over the range of temperatures and pressures pertinent to Titan and the ISM and are in good agreement with the limited available experimental data.
Woon, David E.↗
Modeling Chemical Reactions in Classical Molecular Dynamics Simulations
An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics (MD) simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed.
Jacob R Gissinger↗
Interiors of the Midsized Moons of Uranus, Degree-Two Gravity Fields, and Electromagnetic Properties from Coupled Physical and Chemical Modeling
No abstract provided
Daswani, Mohit Melwani↗
Tropospheric Ozone Determined from Aura OMI and MLS: Evaluation of Measurements and Comparison with the Global Modeling Initiative's Chemical Transport Model
Ozone measurements from the OMI and MLS instruments on board the Aura satellite are used for deriving global distributions of tropospheric column ozone (TCO). TCO is determined using the tropospheric ozone residual method which involves subtracting measurements of MLS stratospheric column ozone (SCO) from OMI total column ozone after adjusting for intercalibration differences of the two instruments using the convective-cloud differential method. The derived TCO field, which covers one complete year of mostly continuous daily measurements from late August 2004 through August 2005, is used for studying the regional and global pollution on a timescale of a few days to months. The seasonal and zonal characteristics of the observed TCO fields are also compared with TCO fields derived from the Global Modeling Initiative's Chemical Transport Model. The model and observations show interesting similarities with respect to zonal and seasonal variations. However, there are notable differences, particularly over the vast region of the Saharan desert.
Ziemke, J. R.↗
An experimental and chemical kinetic modeling study of 4-butoxyheptane combustion
Here, the combustion kinetics of a novel oxygenated bioblendstock for diesel, 4-butoxyheptane (4-BH), was investigated experimentally using a flow reactor and a heated, high-pressure shock tube. The flow reactor experiments employed oxygen as the oxidizer and helium as the diluent with oxidation conducted at atmospheric pressure and 10 bar for temperatures from 400 to 1000 K at 20-K intervals. The fuel, oxidizer, and diluent flow rates were varied at different temperatures to maintain a constant initial fuel mole fraction of 1000 ppm, with stoichiometric equivalence ratio, and a residence time of 2.0 s. The reacted gas was fed to two separate GC systems that could qualitatively and quantitatively detect product species. Additionally, real fuel-air ignition delay time (IDT) data were collected using a heated, high-pressure shock-tube facility. Fuel lean (φ = 0.5) and stoichiometric (φ = 1.0) mixtures were investigated at 10 atm as well as at 30 atm for the fuel lean case for temperatures between 847 and 1259 K. A detailed chemical kinetics mechanism was developed to model the product distribution from the flow reactor and IDTs from the shock tube. The proposed model was able to predict the double NTC behavior in flow reactor experiments reasonably well. Model predictions at low temperatures were observed to be highly sensitive to the rate constants of ketohydroperoxide (KHP) decomposition in the case of the OOH group in α position which were modeled based on existing literature studies on ethers. It was noted that in the absence of theoretical or experimental studies, the rate constants for KHP decomposition used in the literature were empirically set. Additional studies are required to address the gap in model prediction obtained in this study and to reduce the uncertainty in kinetics models for ether oxidation. Predicted product concentrations and IDTs showed some quantitative agreement with experimental data, but the overall reactivity of the IDTs is underpredicted. Additionally, significant deviation is observed for the IDT results at 10 atm for the stoichiometric case with minor deviations for the other cases. The reaction pathways to the missing products were then further analyzed theoretically through quantum-mechanical calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Io - Thermal models and chemical evolution
A combined thermal and chemical evolution model of Io is presented, outlining limits on the possible starting materials, heating history, chemical history, and present state of Io. Our best scenario starts with Io being accreted from material in a proto-Jovian nebula which condensed between 400-600 K. Radionuclides and tidal heating would lead to large-scale convection within Io and chemical reactions leading to the outgassing of water and methane. Reactions between Fe(0)-FeS and water, at least near the surface, go to completion, resulting in all Fe being oxidized with elemental sulfur producing a low-conductivity crust. In the deep interior, these reactions may not completely exhaust Fe metal, and an FeS-rich core may be formed.
Consolmagno, G. J.↗
Implementation of a vibrationally linked chemical reaction model for DSMC
A new procedure closely linking dissociation and exchange reactions in air to the vibrational levels of the diatomic molecules has been implemented in both one- and two-dimensional versions of Direct Simulation Monte Carlo (DSMC) programs. The previous modeling of chemical reactions with DSMC was based on the continuum reaction rates for the various possible reactions. The new method is more closely related to the actual physics of dissociation and is more appropriate to the particle nature of DSMC. Two cases are presented: the relaxation to equilibrium of undissociated air initially at 10,000 K, and the axisymmetric calculation of shuttle forebody heating during reentry at 92.35 km and 7500 m/s. Although reaction rates are not used in determining the dissociations or exchange reactions, the new method produces rates which agree astonishingly well with the published rates derived from experiment. The results for gas properties and surface properties also agree well with the results produced by earlier DSMC models, equilibrium air calculations, and experiment.
Carlson, A. B.↗
Assessment and Applications of NASA Ozone Data Products Derived from Aura OMI-MLS Satellite Measurements in Context of the GMI Chemical Transport Model
Measurements from the Ozone Monitoring Instrument (OMI) and Microwave Limb Sounder (MLS), both onboard the Aura spacecraft, have been used to produce daily global maps of column and profile ozone since August 2004. Here we compare and evaluate three strategies to obtain daily maps of tropospheric and stratospheric ozone from OMI and MLS measurements: trajectory mapping, direct profile retrieval, and data assimilation. Evaluation is based upon an assessment that includes validation using ozonesondes and comparisons with the Global Modeling Initiative (GMI) chemical transport model (CTM). We investigate applications of the three ozone data products from near-decadal and inter-annual timescales to day-to-day case studies. Zonally averaged inter-annual changes in tropospheric ozone from all of the products in any latitude range are of the order 1-2 Dobson Units while changes (increases) over the 8-year Aura record investigated http://eospso.gsfc.nasa.gov/atbd-category/49 vary approximately 2-4 Dobson Units. It is demonstrated that all of the ozone products can measure and monitor exceptional tropospheric ozone events including major forest fire and pollution transport events. Stratospheric ozone during the Aura record has several anomalous inter-annual events including stratospheric warming split events in the Northern Hemisphere extra-tropics that are well captured using the data assimilation ozone profile product. Data assimilation with continuous daily global coverage and vertical ozone profile information is the best of the three strategies at generating a global tropospheric and stratospheric ozone product for science applications.
GMI↗
Determination of the density and chemical profiles of government-furnished charred elastomeric ablator models
Chemical analysis of ablative materials
Source record↗
Chemically reacting Couette flow with hydrogen injection for two diffusion models
Chemically reacting Couette flow with variable transport properties and hydrogen injection for two diffusion models
Graves, R. A., Jr.↗
A Single-Point Modeling Approach for the Intercomparison and Evaluation of Ozone Dry Deposition Across Chemical Transport Models (Activity 2 of AQMEII4)
A primary sink of air pollutants and their precursors is dry deposition. Dry deposition estimates differ across chemical transport models, yet an understanding of the model spread is incomplete. Here, we introduce Activity 2 of the Air Quality Model Evaluation International Initiative Phase 4 (AQMEII4). We examine 18 dry deposition schemes from regional and global chemical transport models as well as standalone models used for impact assessments or process understanding. We configure the schemes as single-point models at eight Northern Hemisphere locations with observed ozone fluxes. Single-point models are driven by a common set of site-specific meteorological and environmental conditions. Five of eight sites have at least 3 years and up to 12 years of ozone fluxes. The interquartile range across models in multiyear mean ozone deposition velocities ranges from a factor of 1.2 to 1.9 annually across sites and tends to be highest during winter compared with summer. No model is within 50 % of observed multiyear averages across all sites and seasons, but some models perform well for some sites and seasons. For the first time, we demonstrate how contributions from depositional pathways vary across models. Models can disagree with respect to relative contributions from the pathways, even when they predict similar deposition velocities, or agree with respect to the relative contributions but predict different deposition velocities. Both stomatal and nonstomatal uptake contribute to the large model spread across sites. Our findings are the beginning of results from AQMEII4 Activity 2, which brings scientists who model air quality and dry deposition together with scientists who measure ozone fluxes to evaluate and improve dry deposition schemes in the chemical transport models used for research, planning, and regulatory purposes.
Dry deposition↗
An investigation of sulfate production in clouds using a flow-through chemical reactor model approach
A flow-through chemical reactor model is developed to describe the mass transfer and chemical processes that atmospheric gases undergo in clouds. The model includes the simultaneous absorption of SO2, NH3, O3, NO(x), HNO3, CO2 and H2O2, the accompanying dissociation and oxidation reactions in cloud water, considers electrical neutrality, and includes qualitative parameterization of cloud microphysics. The model is used to assess the importance of the oxidation reactions H2O2-S(IV), O3-S(IV), and S(IV)-Mn(2+) catalysis, and the effects of cloud parameters such as drop size, rain intensity, liquid water content, and updraft velocity. Both precipitating and nonprecipitating clouds are studied. Model results predict sulfate production rates varying from 3 percent/hr to 230 percent/hr. The actual rate is highly dependent on the chemical composition of the uptake air and the physical conditions of the cloud. Model results also show that both the H2O2 and the O3 oxidation reactions can be significant.
Hong, M. S.↗
Production of Lightning NO(x) and its Vertical Distribution Calculated from 3-D Cloud-scale Chemical Transport Model Simulations
A 3-D cloud scale chemical transport model that includes a parameterized source of lightning NO(x), based on observed flash rates has been used to simulate six midlatitude and subtropical thunderstorms observed during four field projects. Production per intracloud (P(sub IC) and cloud-to-ground (P(sub CG)) flash is estimated by assuming various values of P(sub IC) and P(sub CG) for each storm and determining which production scenario yields NO(x) mixing ratios that compare most favorably with in-cloud aircraft observations. We obtain a mean P(sub CG) value of 500 moles NO (7 kg N) per flash. The results of this analysis also suggest that on average, P(sub IC) may be nearly equal to P(sub CG), which is contrary to the common assumption that intracloud flashes are significantly less productive of NO than are cloud-to-ground flashes. This study also presents vertical profiles of the mass of lightning NO(x), after convection based on 3-D cloud-scale model simulations. The results suggest that following convection, a large percentage of lightning NO(x), remains in the middle and upper troposphere where it originated, while only a small percentage is found near the surface. The results of this work differ from profiles calculated from 2-D cloud-scale model simulations with a simpler lightning parameterization that were peaked near the surface and in the upper troposphere (referred to as a "C-shaped" profile). The new model results (a backward C-shaped profile) suggest that chemical transport models that assume a C-shaped vertical profile of lightning NO(x) mass may place too much mass neat the surface and too little in the middle troposphere.
Ott, Lesley↗
Improving Lightning NO(x) Parameterizations for Global Chemical Transport Models
Parameterization of lightning NO(x) in global chemical transport models requires a method to specify the temporal and geographic distribution of flash rates, an estimate of NO production per flash, and a method to specify the effective vertical distribution of NO production. Flash rate parameterizations using the upward convective cloud mass flux have been developed and tested for several GCM and assimilated meteorological data sets. This parameterization and others involving the cloud-top height and convective precipitation provide a generally acceptable climatological distribution of flashes after normalization with satellite data. However, considerable improvement in terms of geographic and temporal variability may be achieved in the future using cloud microphysics data available from next-generation GCMs. Cloud-resolving case-study simulations of convective transport and lightning NO production have yielded results which are directly applicable to the NO production per flash and the vertical NO distribution portions of the global model lightning parameterizations. In this work we have used cloud-resolving models (the Goddard Cumulus Ensemble Model (GCE) and MM5) to drive an off-line cloud-scale chemical transport model (CSCTM). The CSCTM, in conjunction with aircraft measurements of NO(x) in thunderstorms and ground-based lightning observations, has been used to constrain the amount of NO produced per flash. Observed lightning flash rates have been incorporated into the CSCTM, and several scenarios of NO production per intracloud (IC) and per cloud-to-ground (CG) flash have been tested in each of several case study storms. The resulting NO(x) mixing ratios are compared with aircraft measurements taken within the storm (typically the anvil region) to determine the most likely NO production scenario. The range of values of NO production per flash (or per meter of lightning channel length) that have been deduced from the model will be shown and compared with values of production in the literature that have been deduced from observed NO spikes and from anvil flux calculations. Results show that on a per flash basis, IC flashes are nearly as productive of NO as CG flashes. Estimates of mean NO production per flash vary by a factor of three from one simulated storm to another. Vertical profiles of lightning NOx mass at the end of the 3-D storm simulations have been summarized to yield suggested profiles for use in global models. These profiles show a larger percentage of the total lightning NO(x) mass in the free troposphere than those suggested by Pickering et al. (1998).
Pickering, Kenneth E.↗
Secondary metallicity in analytic models of chemical evolution of galaxies
Analytic models of the chemical evolution of galactic regions that grow in mass owing to the continuous infall of matter are characterized, emphasizing the solutions for secondary nuclei (defined as those nuclei whose stellar yields are proportional to the abundance of a primary seed nucleus) in the families of models described by Clayton (1984 and 1985). Wide variations in time dependence of both primary and secondary nuclei as well as in the ratio of secondary to primary are displayed by these model families, confirming again the usefulness of these families as interpretive guides if galaxies do in fact evolve with substantial infall. Additionally, analytic solutions are presented for two other possible interesting systems: the evolution of abundances if the primary metallicity in the infall is increasing in time, and the evolution of abundances if the primary yield changes linearly with time owing to continuous changes in the stellar mass function, the opacity, or other astrophysical agents. Finally, test evaluations of the instantaneous recycling approximation on which these analytic models rely are presented.
Clayton, D. D.↗
Development of a Grid-Independent Geos-Chem Chemical Transport Model (v9-02) as an Atmospheric Chemistry Module for Earth System Models
The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.
CTM↗
Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗