Abstract. We introduce the Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS). CATT-BRAMS is an on-line transport model fully consistent with the simulated atmospheric dynamics. Emission sources from biomass burning and urban-industrial-vehicular activities for trace gases and from biomass burning aerosol particles are obtained from several published datasets and remote sensing information. The tracer and aerosol mass concentration prognostics include the effects of sub-grid scale turbulence in the planetary boundary layer, convective transport by shallow and deep moist convection, wet and dry deposition, and plume rise associated with vegetation fires in addition to the grid scale transport. The radiation parameterization takes into account the interaction between the simulated biomass burning aerosol particles and short and long wave radiation. The atmospheric model BRAMS is based on the Regional Atmospheric Modeling System (RAMS), with several improvements associated with cumulus convection representation, soil moisture initialization and surface scheme tuned for the tropics, among others. In this paper the CATT-BRAMS model is used to simulate carbon monoxide and particulate material (PM2.5) surface fluxes and atmospheric transport during the 2002 LBA field campaigns, conducted during the transition from the dry to wet season in the southwest Amazon Basin. Model evaluation is addressed with comparisons between model results and near surface, radiosondes and airborne measurements performed during the field campaign, as well as remote sensing derived products. We show the matching of emissions strengths to observed carbon monoxide in the LBA campaign. A relatively good comparison to the MOPITT data, in spite of the fact that MOPITT a priori assumptions imply several difficulties, is also obtained.

Abstract. We present a new version of the Brazilian developments on the Regional Atmospheric Modeling System (BRAMS), in which different previous versions for weather, chemistry, and carbon cycle were unified in a single integrated modeling system software. This new version also has a new set of state-of-the-art physical parameterizations and greater computational parallel and memory usage efficiency. The description of the main model features includes several examples illustrating the quality of the transport scheme for scalars, radiative fluxes on surface, and model simulation of rainfall systems over South America at different spatial resolutions using a scale aware convective parameterization. Additionally, the simulation of the diurnal cycle of the convection and carbon dioxide concentration over the Amazon Basin, as well as carbon dioxide fluxes from biogenic processes over a large portion of South America, are shown. Atmospheric chemistry examples show the model performance in simulating near-surface carbon monoxide and ozone in the Amazon Basin and the megacity of Rio de Janeiro. For tracer transport and dispersion, the model capabilities to simulate the volcanic ash 3-D redistribution associated with the eruption of a Chilean volcano are demonstrated. The gain of computational efficiency is described in some detail. BRAMS has been applied for research and operational forecasting mainly in South America. Model results from the operational weather forecast of BRAMS on 5 km grid spacing in the Center for Weather Forecasting and Climate Studies, INPE/Brazil, since 2013 are used to quantify the model skill of near-surface variables and rainfall. The scores show the reliability of BRAMS for the tropical and subtropical areas of South America. Requirements for keeping this modeling system competitive regarding both its functionalities and skills are discussed. Finally, we highlight the relevant contribution of this work to building a South American community of model developers.

Abstract. Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS, version 4.5) is an on-line regional chemical transport model designed for local and regional studies of atmospheric chemistry from the surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT-BRAMS model takes advantage of BRAMS-specific development for the tropics/subtropics as well as the recent availability of preprocessing tools for chemical mechanisms and fast codes for photolysis rates. BRAMS includes stateof-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations down to the meter. This on-line coupling of meteorology and chemistry allows the system to be used for simultaneous weather and chemical composition forecasts as well as potential feedback between the two. The entire system is made of three preprocessing software tools for user-defined chemical mechanisms, aerosol and trace gas emissions fields and the interpolation of initial and boundary conditions for meteorology and chemistry. In this paper, the model description is provided along with the evaluations performed by using observational data obtained from ground-based stations, instruments aboard aircrafts and retrieval from space remote sensing. The evaluation accounts for model applications at different scales from megacities and the Amazon Basin up to the intercontinental region of the Southern Hemisphere.

Network motif algorithms have been a topic of research mainly after the 2002-seminal paper from Milo et al. [1], which provided motifs as a way to uncover the basic building blocks of most networks. Motifs have been mainly applied in Bioinformatics, regarding gene regulation networks. Motif detection is based on induced subgraph counting. This paper proposes an algorithm to count subgraphs of size k + 2 based on the set of induced subgraphs of size k. The general technique was applied to detect 3, 4 and 5-sized motifs in directed graphs. Such algorithms have time complexity O(a(G)m), O(m(2)) and O(nm(2)), respectively, where a(G) is the arboricity of G(V, E). The computational experiments in public data sets show that the proposed technique was one order of magnitude faster than Kavosh and FANMOD. When compared to NetMODE, acc-Motif had a slightly improved performance.