This paper evaluates the current status of global modeling of the organic aerosol (OA) in the troposphere and analyzes the differences between models as well as between models and observations. Thirty-one global chemistry transport models (CTMs) and general circulation models (GCMs) have participated in this intercomparison, in the framework of AeroCom phase II. The simulation of OA varies greatly between models in terms of the magnitude of primary emissions, secondary OA (SOA) formation, the number of OA species used (2 to 62), the complexity of OA parameterizations (gas-particle partitioning, chemical aging, multiphase chemistry, aerosol microphysics), and the OA physical, chemical and optical properties. The diversity of the global OA simulation results has increased since earlier AeroCom experiments, mainly due to the increasing complexity of the SOA parameterization in models, and the implementation of new, highly uncertain, OA sources. Diversity of over one order of magnitude exists in the modeled vertical distribution of OA concentrations that deserves a dedicated future study. Furthermore, although the OA/OC ratio depends on OA sources and atmospheric processing, and is important for model evaluation against OA and OC observations, it is resolved only by a few global models. The median global primary OA (POA) source strength is 56 Tg a(-1) (range 34-144 Tg a(-1)) and the median SOA source strength (natural and anthropogenic) is 19 Tg a(-1) (range 13-121 Tg a(-1)). Among the models that take into account the semi-volatile SOA nature, the median source is calculated to be 51 Tg a(-1) (range 16-121 Tg a(-1)), much larger than the median value of the models that calculate SOA in a more simplistic way (19 Tg a(-1); range 13-20 Tg a(-1), with one model at 37 Tg a(-1)). The median atmospheric burden of OA is 1.4 Tg (24 models in the range of 0.6-2.0 Tg and 4 between 2.0 and 3.8 Tg), with a median OA lifetime of 5.4 days (range 3.8-9.6 days). In models that reported both OA and sulfate burdens, the median value of the OA/sulfate burden ratio is calculated to be 0.77; 13 models calculate a ratio lower than 1, and 9 models higher than 1. For 26 models that reported OA deposition fluxes, the median wet removal is 70 Tg a(-1) (range 28-209 Tg a(-1)), which is on average 85% of the total OA deposition. Fine aerosol organic carbon (OC) and OA observations from continuous monitoring networks and individual field campaigns have been used for model evaluation. At urban locations, the model-observation comparison indicates missing knowledge on anthropogenic OA sources, both strength and seasonality. The combined model-measurements analysis suggests the existence of increased OA levels during summer due to biogenic SOA formation over large areas of the USA that can be of the same order of magnitude as the POA, even at urban locations, and contribute to the measured urban seasonal pattern. Global models are able to simulate the high secondary character of OA observed in the atmosphere as a result of SOA formation and POA agi...

The subunit interfaces of 122 homodimers of known three-dimensional structure are analyzed and dissected into sets of surface patches by clustering atoms at the interface; 70 interfaces are single-patch, the others have up to six patches, often contributed by different structural domains. The average interface buries 1,940 A2 of the surface of each monomer, contains one or two patches burying 600-1,600 A2, is 65% nonpolar and includes 18 hydrogen bonds. However, the range of size and of hydrophobicity is wide among the 122 interfaces. Each interface has a core made of residues with atoms buried in the dimer, surrounded by a rim of residues with atoms that remain accessible to solvent. The core, which constitutes 77% of the interface on average, has an amino acid composition that resembles the protein interior except for the presence of arginine residues, whereas the rim is more like the protein surface. These properties of the interfaces in homodimers, which are permanent assemblies, are compared to those of protein-protein complexes where the components associate after they have independently folded. On average, subunit interfaces in homodimers are twice larger than in complexes, and much less polar due to the large fraction belonging to the core, although the amino acid compositions of the cores are similar in the two types of interfaces.

Protein-protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein-protein complexes, oligomeric proteins, viral capsids and protein-nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.

Black carbon (BC) is functionally defined as the absorbing component of atmospheric total carbonaceous aerosols (TC) and is typically dominated by soot-like elemental carbon (EC). However, organic carbon (OC) has also been shown to absorb strongly at visible to UV wavelengths and the absorbing organics are referred to as brown carbon (BrC), which is typically not represented in climate models. We propose an observationally based analytical method for rigorously partitioning measured absorption aerosol optical depths (AAOD) and single scattering albedo (SSA) among EC and BrC, using multiwavelength measurements of total (EC, OC, and dust) absorption. EC is found to be strongly absorbing (SSA of 0.38) whereas the BrC SSA varies globally between 0.77 and 0.85. The method is applied to the California region. We find TC (EC + BrC) contributes 81% of the total absorption at 675 nm and 84% at 440 nm. The BrC absorption at 440 nm is about 40% of the EC, whereas at 675 nm it is less than 10% of EC. We find an enhanced absorption due to OC in the summer months and in southern California (related to forest fires and secondary OC). The fractions and trends are broadly consistent with aerosol chemical-transport models as well as with regional emission inventories, implying that we have obtained a representative estimate for BrC absorption. The results demonstrate that current climate models that treat OC as nonabsorbing are underestimating the total warming effect of carbonaceous aerosols by neglecting part of the atmospheric heating, particularly over biomass-burning regions that emit BrC.short lived climate pollutants | aerosol forcing B lack carbon (BC) emitted from combustion sources such as automobile exhaust and biomass burning (1-3) absorbs solar radiation in both the visible and the near-infrared spectra and is estimated to be a principal contributor to global atmospheric warming (4). The short atmospheric lifetime of BC aerosol particles, typically of the order of 1 wk (5, 6), compared with greenhouse gases (which have atmospheric lifetimes of several years or decades) results in BC being not well mixed in the atmosphere but instead geographically and temporally correlated to emission sources. For this reason, reducing BC emissions is an attractive control strategy for climate change that is expected to have a more immediate and regional impact (4,7,8). The state of California appears to be a successful example where aggressive control policies for vehicular diesel emissions and domestic wood burning have produced a near 50% decrease in BC concentrations (9). This decline in conjunction with the near-static concentrations of primarily scattering aerosol particles (such as sulfates) may have led to a large negative change in the direct radiative forcing (9).A simplification in such model estimates of aerosol forcing is that BC is considered to be equivalent to elemental carbon (EC), and the organic fraction of carbonaceous aerosols [organic carbon (OC)] is treated as scattering and is therefore found to have a cooling...

Measurements of submicron particles by Fourier transform infrared spectroscopy in 14 campaigns in North America, Asia, South America, and Europe were used to identify characteristic organic functional group compositions of fuel combustion, terrestrial vegetation, and ocean bubble bursting sources, each of which often accounts for more than a third of organic mass (OM), and some of which is secondary organic aerosol (SOA) from gas-phase precursors. The majority of the OM consists of alkane, carboxylic acid, hydroxyl, and carbonyl groups. The organic functional groups formed from combustion and vegetation emissions are similar to the secondary products identified in chamber studies. The near absence of carbonyl groups in the observed SOA associated with combustion is consistent with alkane rather than aromatic precursors, and the absence of organonitrate groups can be explained by their hydrolysis in humid ambient conditions. The remote forest observations have ratios of carboxylic acid, organic hydroxyl, and nonacid carbonyl groups similar to those observed for isoprene and monoterpene chamber studies, but in biogenic aerosols transported downwind of urban areas the formation of esters replaces the acid and hydroxyl groups and leaves only nonacid carbonyl groups. The carbonyl groups in SOA associated with vegetation emissions provides striking evidence for the mechanism of esterification as the pathway for possible oligomerization reactions in the atmosphere. Forest fires include biogenic emissions that produce SOA with organic components similar to isoprene and monoterpene chamber studies, also resulting in nonacid carbonyl groups in SOA.atmospheric aerosol | organic particles | smog chamber aerosol | alkane oxidation products | photochemical reactions R ecent literature reviews have highlighted significant advances in identifying compounds formed as "secondary" organic aerosol (SOA) in a wide range of laboratory-simulated atmospheric conditions, and field studies have identified several individual products from chamber studies (1-3). Paulot et al. have used global modeling to show that extrapolating these laboratory results for modeled global oxidant distributions helps explain biogenic SOA (4). However, the observations needed to confirm the proposed sources of organic aerosols (OAs) in global modelsnamely, quantitative field measurements of the proposed products to compare with the model predictions-remain elusive (5). Without such confirmation, it is difficult to identify which of the mechanisms proposed to explain controlled laboratory studies of simple volatile organic compound (VOC)-oxidant systems would satisfactorily capture those aspects of the chemistry that determine SOA formation in the more complex atmosphere.There has been significant progress in quantifying organic mass (OM, the particle-phase components of OA) from the fragments produced by online mass spectrometry of particles, with recent promulgation of techniques to quantify the resulting mixtures by two to four fragment-based positive matri...

We present an analysis of the water molecules immobilized at the protein-protein interfaces of 115 homodimeric proteins and 46 protein-protein complexes, and compare them with 173 large crystal packing interfaces representing nonspecific interactions. With an average of 15 waters per 1000 A2 of interface area, the crystal packing interfaces are more hydrated than the specific interfaces of homodimers and complexes, which have 10-11 waters per 1000 A2, reflecting the more hydrophilic composition of crystal packing interfaces. Very different patterns of hydration are observed: Water molecules may form a ring around interfaces that remain "dry," or they may permeate "wet" interfaces. A majority of the specific interfaces are dry and most of the crystal packing interfaces are wet, but counterexamples exist in both categories. Water molecules at interfaces form hydrogen bonds with protein groups, with a preference for the main-chain carbonyl and the charged side-chains of Glu, Asp, and Arg. These interactions are essentially the same in specific and nonspecific interfaces, and very similar to those observed elsewhere on the protein surface. Water-mediated polar interactions are as abundant at the interfaces as direct protein-protein hydrogen bonds, and they may contribute to the stability of the assembly.

We analyze the protein–RNA interfaces in 81 transient binary complexes taken from the Protein Data Bank. Those with tRNA or duplex RNA are larger than with single-stranded RNA, and comparable in size to protein–DNA interfaces. The protein side bears a strong positive electrostatic potential and resembles protein–DNA interfaces in its amino acid composition. On the RNA side, the phosphate contributes less, and the sugar much more, to the interaction than in protein–DNA complexes. On average, protein–RNA interfaces contain 20 hydrogen bonds, 7 that involve the phosphates, 5 the sugar 2′OH, and 6 the bases, and 32 water molecules. The average H-bond density per unit buried surface area is less with tRNA or single-stranded RNA than with duplex RNA. The atomic packing is also less compact in interfaces with tRNA. On the protein side, the main chain NH and Arg/Lys side chains account for nearly half of all H-bonds to RNA; the main chain CO and side chain acceptor groups, for a quarter. The 2′OH is a major player in protein–RNA recognition, and shape complementarity an important determinant, whereas electrostatics and direct base–protein interactions play a lesser part than in protein–DNA recognition.

Estimating the aerosol contribution to the global or regional radiative forcing can take advantage of the relationship between the spectral aerosol optical properties and the size and chemical composition of aerosol. Long term global optical measurements from observational networks or satellites can be used in such studies. Using in-situ chemical mixing state measurements can help us to constrain the limitations of such estimates.

In this study, the Absorption Ångström Exponent (AAE) and the Scattering Ångström Exponent (SAE) derived from 10 operational AERONET sites in California are combined for deducing chemical speciation based on wavelength dependence of the optical properties. In addition, in-situ optical properties and single particle chemical composition measured during three aircraft field campaigns in California between 2010 and 2011 are combined in order to validate the methodology used for the estimates of aerosol chemistry using spectral optical properties.

Results from this study indicate a dominance of mixed types in the classification leading to an underestimation of the primary sources, however secondary sources are better classified. The distinction between carbonaceous aerosols from fossil fuel and biomass burning origins is not clear, since their optical properties are similar. On the other hand, knowledge of the aerosol sources in California from chemical studies help to identify other misclassification such as the dust contribution