Modeling kinetic partitioning of secondary organic aerosol and size distribution dynamics: representing effects of volatility, phase state, and particle-phase reaction

This paper describes and evaluates a new framework for modeling kinetic gas-particle partitioning of secondary organic aerosol (SOA) that takes into account diffusion and chemical reaction within the particle phase. The framework uses a combination of (a) an analytical quasi-steady-state treatment for the diffusion–reaction process within the particle phase for fast-reacting organic solutes, and (b) a two-film theory approach for slow- and nonreacting solutes. The framework is amenable for use in regional and global atmospheric models, although it currently awaits specification of the various gas- and particle-phase chemistries and the related physicochemical properties that are important for SOA formation. Here, the new framework is implemented in the computationally efficient Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) to investigate the competitive growth dynamics of the Aitken and accumulation mode particles. Results show that the timescale of SOA partitioning and the associated size distribution dynamics depend on the complex interplay between organic solute volatility, particle-phase bulk diffusivity, and particle-phase reactivity (as exemplified by a pseudo-first-order reaction rate constant), each of which can vary over several orders of magnitude. In general, the timescale of SOA partitioning increases with increase in volatility and decrease in bulk diffusivity and rate constant. At the same time, the shape of the aerosol size distribution displays appreciable narrowing with decrease in volatility and bulk diffusivity and increase in rate constant. A proper representation of these physicochemical processes and parameters is needed in the next generation models to reliably predict not only the total SOA mass, but also its composition- and number-diameter distributions, all of which together determine the overall optical and cloud-nucleating properties

Global distribution and climate forcing of marine organic aerosol: 1. Model improvements and evaluation

Marine organic aerosol emissions have been implemented and evaluated within the National Center of Atmospheric Research (NCAR)'s Community Atmosphere Model (CAM5) with the Pacific Northwest National Laboratory's 7-mode Modal Aerosol Module (MAM-7). Emissions of marine primary organic aerosols (POA), phytoplankton-produced isoprene- and monoterpenes-derived secondary organic aerosols (SOA) and methane sulfonate (MS<sup>−</sup>) are shown to affect surface concentrations of organic aerosols in remote marine regions. Global emissions of submicron marine POA is estimated to be 7.9 and 9.4 Tg yr<sup>−1</sup>, for the Gantt et al. (2011) and Vignati et al. (2010) emission parameterizations, respectively. Marine sources of SOA and particulate MS<sup>−</sup> (containing both sulfur and carbon atoms) contribute an additional 0.2 and 5.1 Tg yr<sup>−1</sup>, respectively. Widespread areas over productive waters of the Northern Atlantic, Northern Pacific, and the Southern Ocean show marine-source submicron organic aerosol surface concentrations of 100 ng m<sup>−3</sup>, with values up to 400 ng m<sup>−3</sup> over biologically productive areas. Comparison of long-term surface observations of water insoluble organic matter (WIOM) with POA concentrations from the two emission parameterizations shows that despite revealed discrepancies (often more than a factor of 2), both Gantt et al. (2011) and Vignati et al. (2010) formulations are able to capture the magnitude of marine organic aerosol concentrations, with the Gantt et al. (2011) parameterization attaining better seasonality. Model simulations show that the mixing state of the marine POA can impact the surface number concentration of cloud condensation nuclei (CCN). The largest increases (up to 20%) in CCN (at a supersaturation (<i>S</i>) of 0.2%) number concentration are obtained over biologically productive ocean waters when marine organic aerosol is assumed to be externally mixed with sea-salt. Assuming marine organics are internally-mixed with sea-salt provides diverse results with increases and decreases in the concentration of CCN over different parts of the ocean. The sign of the CCN change due to the addition of marine organics to sea-salt aerosol is determined by the relative significance of the increase in mean modal diameter due to addition of mass, and the decrease in particle hygroscopicity due to compositional changes in marine aerosol. Based on emerging evidence for increased CCN concentration over biologically active surface ocean areas/periods, our study suggests that treatment of sea spray in global climate models (GCMs) as an internal mixture of marine organic aerosols and sea-salt will likely lead to an underestimation in CCN number concentration

The MESSy aerosol submodel MADE3 (v2.0b): description and a box model test

We introduce MADE3 (Modal Aerosol Dynamics model for Europe, adapted for global applications, 3rd generation; version: MADE3v2.0b), an aerosol dynamics submodel for application within the MESSy framework (Modular Earth Submodel System). MADE3 builds on the predecessor aerosol submodels MADE and MADE-in. Its main new features are the explicit representation of coarse mode particle interactions both with other particles and with condensable gases, and the inclusion of hydrochloric acid (HCl) / chloride (Cl) partitioning between the gas and condensed phases. The aerosol size distribution is represented in the new submodel as a superposition of nine lognormal modes: one for fully soluble particles, one for insoluble particles, and one for mixed particles in each of three size ranges (Aitken, accumulation, and coarse mode size ranges). <br><br> In order to assess the performance of MADE3 we compare it to its predecessor MADE and to the much more detailed particle-resolved aerosol model PartMC-MOSAIC in a box model simulation of an idealised marine boundary layer test case. MADE3 and MADE results are very similar, except in the coarse mode, where the aerosol is dominated by sea spray particles. Cl is reduced in MADE3 with respect to MADE due to the HCl / Cl partitioning that leads to Cl removal from the sea spray aerosol in our test case. Additionally, the aerosol nitrate concentration is higher in MADE3 due to the condensation of nitric acid on coarse mode particles. MADE3 and PartMC-MOSAIC show substantial differences in the fine particle size distributions (sizes &lesssim; 2 μm) that could be relevant when simulating climate effects on a global scale. Nevertheless, the agreement between MADE3 and PartMC-MOSAIC is very good when it comes to coarse particle size distributions (sizes &gtrsim; 2 μm), and also in terms of aerosol composition. Considering these results and the well-established ability of MADE in reproducing observed aerosol loadings and composition, MADE3 seems suitable for application within a global model

Explicit modeling of organic chemistry and secondary organic aerosol partitioning for Mexico City and its outflow plume

The evolution of organic aerosols (OA) in Mexico City and its outflow is investigated with the nearly explicit gas phase photochemistry model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere), wherein precursor hydrocarbons are oxidized to numerous intermediate species for which vapor pressures are computed and used to determine gas/particle partitioning in a chemical box model. Precursor emissions included observed C3-10 alkanes, alkenes, and light aromatics, as well as larger &lt;i&gt;n&lt;/i&gt;-alkanes (up to C25) not directly observed but estimated by scaling to particulate emissions according to their volatility. Conditions were selected for comparison with observations made in March 2006 (MILAGRO). The model successfully reproduces the magnitude and diurnal shape for both primary (POA) and secondary (SOA) organic aerosols, with POA peaking in the early morning at 15–20 μg m&lt;sup&gt;−3&lt;/sup&gt;, and SOA peaking at 10–15 μg m&lt;sup&gt;−3&lt;/sup&gt; during mid-day. The majority (&amp;ge;75%) of the model SOA stems from reaction products of the large &lt;i&gt;n&lt;/i&gt;-alkanes, used here as surrogates for all emitted hydrocarbons of similar volatility, with the remaining SOA originating mostly from the light aromatics. Simulated OA elemental composition reproduces observed H/C and O/C ratios reasonably well, although modeled ratios develop more slowly than observations suggest. SOA chemical composition is initially dominated by &amp;delta;-hydroxy ketones and nitrates from the large alkanes, with contributions from peroxy acyl nitrates and, at later times when NOx is lower, organic hydroperoxides. The simulated plume-integrated OA mass continues to increase for several days downwind despite dilution-induced particle evaporation, since oxidation chemistry leading to SOA formation remains strong. In this model, the plume SOA burden several days downwind exceeds that leaving the city by a factor of &gt;3. These results suggest significant regional radiative impacts of SOA

Cytoplasmic-Genic Male-Sterility in Interspecific Matings of Cajanus

The discovery of two stable male-sterile genes and the prevalence of adequate insect-aided cross-pollination led to the development and release of the first pigeonpea [Cajanus cajan (L.) Millsp.] hybrid in India. Commercialization of this hybrid is constrained because of the labor intensiveness of seed production and concerns about seed purity. Cytoplasmic male-steriles would effectively circumvent these constraints and revolutionize the hybrid seed industry. This paper reports the development of cytoplasmically determined male-sterility, which was accomplished by two methods: wide hybridization involving conventional backcrossing of Cajanus sericeus van der Maesen and Cajanus cajan and multiple cross genome transfer. In these matings, two forms of reversion to fertility were noticed, one influenced by low temperature and high humidity, and the other probably determined by genetic factors alone. The influence of temperature on fertility restoration as reported for Viciafaba L. is different from that seen in species crosses of Cajanus. The multiple cross genome transfer method resulted in stable cytoplasmic-genic male sterility maintainable by the pigeonpea genotypes ICPL 85030 and ICPL 90035. These male-sterile lines are in agronomically desirable backgrounds

Spectro-microscopic measurements of carbonaceous aerosol aging in Central California

Carbonaceous aerosols are responsible for large uncertainties in climate models, degraded visibility, and adverse health effects. The Carbonaceous Aerosols and Radiative Effects Study (CARES) was designed to study carbonaceous aerosols in the natural environment of the Central Valley, California, and learn more about their atmospheric formation and aging. This paper presents results from spectro-microscopic measurements of carbonaceous particles collected during CARES at the time of a pollution accumulation event (27&ndash;29 June 2010), when in situ measurements indicated an increase in the organic carbon content of aerosols as the Sacramento urban plume aged. Computer-controlled scanning electron microscopy coupled with an energy dispersive X-ray detector (CCSEM/EDX) and scanning transmission X-ray microscopy coupled with near-edge X-ray absorption spectroscopy (STXM/NEXAFS) were used to probe the chemical composition and morphology of individual particles. It was found that the mass of organic carbon on individual particles increased through condensation of secondary organic aerosol. STXM/NEXAFS indicated that the number fraction of homogenous organic particles lacking inorganic inclusions (greater than ~50 nm equivalent circular diameter) increased with plume age, as did the organic mass per particle. Comparison of the CARES spectro-microscopic dataset with a similar dataset obtained in Mexico City during the MILAGRO campaign showed that fresh particles in Mexico City contained three times as much carbon as those sampled during CARES. The number fraction of soot particles at the Mexico City urban site (ranging from 16.6 to 47.3%) was larger than at the CARES urban site (13.4&ndash;15.7%), and the most aged samples from CARES contained fewer carbon–carbon double bonds. Differences between carbonaceous particles in Mexico City and California result from different sources, photochemical conditions, gas phase reactants, and secondary organic aerosol precursors. The detailed results provided by these spectro-microscopic measurements will allow for a comprehensive evaluation of aerosol process models used in climate research

Modeling regional aerosol variability over California and its sensitivity to emissions and long-range transport during the 2010 CalNex and CARES campaigns

Abstract. The performance of the Weather Research and Forecasting regional model with chemistry (WRF-Chem) in simulating the spatial and temporal variations in aerosol mass, composition, and size over California is quantified using measurements collected during the California Nexus of Air Quality and Climate Experiment (CalNex) and the Carbonaceous Aerosol and Radiative Effects Study (CARES) conducted during May and June of 2010. The extensive meteorological, trace gas, and aerosol measurements collected at surface sites and along aircraft and ship transects during CalNex and CARES were combined with operational monitoring network measurements to create a single dataset that was used to evaluate the one configuration of the model. Simulations were performed that examined the sensitivity of regional variations in aerosol concentrations to anthropogenic emissions and to long-range transport of aerosols into the domain obtained from a global model. The configuration of WRF-Chem used in this study is shown to reproduce the overall synoptic conditions, thermally-driven circulations, and boundary layer structure observed in region that controls the transport and mixing of trace gases and aerosols. However, sub-grid scale variability in the meteorology and emissions as well as uncertainties in the treatment of secondary organic aerosol chemistry likely contribute to errors at a primary surface sampling site located at the edge of the Los Angeles basin. Differences among the sensitivity simulations demonstrate that the aerosol layers over the central valley detected by lidar measurements likely resulted from lofting and recirculation of local anthropogenic emissions along the Sierra Nevada. Reducing the default emissions inventory by 50% led to an overall improvement in many simulated trace gases and black carbon aerosol at most sites and along most aircraft flight paths; however, simulated organic aerosol was closer to observed when there were no adjustments to the primary organic aerosol emissions. The model performance for some aerosol species was not uniform over the region, and we found that sulfate was better simulated over northern California whereas nitrate was better simulated over southern California. While the overall spatial and temporal variability of aerosols and their precursors were simulated reasonably well, we show cases where the local transport of some aerosol plumes were either too slow or too fast, which adversely affects the statistics regarding the differences between observed and simulated quantities. Comparisons with lidar and in-situ measurements indicate that long-range transport of aerosols from the global model was likely too high in the free troposphere even though their concentrations were relatively low. This bias led to an over-prediction in aerosol optical depth by as much as a factor of two that offset the under-predictions of boundary-layer extinction resulting primarily from local emissions. Lowering the boundary conditions of aerosol concentrations by 50% greatly reduced the bias in simulated aerosol optical depth for all regions of California. This study shows that quantifying regional-scale variations in aerosol radiative forcing and determining the relative role of emissions from local and distant sources is challenging during "clean" conditions and that a wide array of measurements are needed to ensure model predictions are correct for the right reasons. In this regard, the combined CalNex and CARES datasets are an ideal testbed that can be used to evaluate aerosol models in great detail and develop improved treatments for aerosol processes

Black carbon over Mexico: the effect of atmospheric transport on mixing state, mass absorption cross-section, and BC/CO ratios

A single particle soot photometer (SP2) was operated on the NCAR C-130 during the MIRAGE campaign (part of MILAGRO), sampling black carbon (BC) over Mexico. The highest BC concentrations were measured over Mexico City (sometimes as much as 2 μg/m&lt;sup&gt;3&lt;/sup&gt;) and over hill-fires to the south of the city. The age of plumes outside of Mexico City was determined using a combination of HYSPLIT trajectories, WRF-FLEXPART modeling and CMET balloon tracks. As expected, older, diluted air masses had lower BC concentrations. A comparison of carbon monoxide (CO) and BC suggests a CO background of around 65 ppbv, and a background-corrected BC/CO&lt;sub&gt;net&lt;/sub&gt; ratio of 2.89&amp;plusmn;0.89 (ng/m&lt;sup&gt;3&lt;/sup&gt;-STP)/ppbv (average &amp;plusmn; standard deviation). This ratio is similar for fresh emissions over Mexico City, as well as for aged airmasses. Comparison of light absorption measured with a particle soot absorption photometer (PSAP) and the SP2 BC suggests a BC mass-normalized absorption cross-section (MAC) of 10.9&amp;plusmn;2.1 m&lt;sup&gt;2&lt;/sup&gt;/g at 660 nm (or 13.1 m&lt;sup&gt;2&lt;/sup&gt;/g @ 550 nm, assuming MAC is inversely dependent on wavelength). This appears independent of aging and similar to the expected absorption cross-section for aged BC, but values, particularly in fresh emissions, could be biased high due to instrument artifacts. SP2-derived BC coating indicators show a prominent thinly-coated BC mode over the Mexico City Metropolitan Area (MCMA), while older air masses show both thinly-coated and thickly-coated BC. Some 2-day-old plumes do not show a prominent thickly-coated BC mode, possibly due to preferential wet scavenging of the likely-hydrophilic thickly-coated BC

Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

BACKGROUND: Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described for identifying conditionally essential genes whose tolerance for insertions varies between two conditions. However, for large-scale experiments involving many conditions, a method is needed for identifying genes that exhibit significant variability in insertions across multiple conditions. RESULTS: In this paper, we introduce a novel statistical method for identifying genes with significant variability of insertion counts across multiple conditions based on Zero-Inflated Negative Binomial (ZINB) regression. Using likelihood ratio tests, we show that the ZINB distribution fits TnSeq data better than either ANOVA or a Negative Binomial (in a generalized linear model). We use ZINB regression to identify genes required for infection of M. tuberculosis H37Rv in C57BL/6 mice. We also use ZINB to perform a analysis of genes conditionally essential in H37Rv cultures exposed to multiple antibiotics. CONCLUSIONS: Our results show that, not only does ZINB generally identify most of the genes found by pairwise resampling (and vastly out-performs ANOVA), but it also identifies additional genes where variability is detectable only when the magnitudes of insertion counts are treated separately from local differences in saturation, as in the ZINB model