## 2 Site Description and Techniques for Data Analyses
### Numerical Modelling
#### 2.4.2 Models Description and Set-Up  
BOLCHEM is an on-line atmospheric composition model, which comprises the hydrostatic meteorological model BOLAM [44], an algorithm for airborne transport and diffusion of pollutants, the photochemical mechanisms SAPRC90 [45] extended to describe the formation of condensable organic products and the oxidation in aqueous [46] and the aerosol dynamic model AERO3 [47]. The aerosol model is coupled with the inorganic thermodynamic equilibrium model ISORROPIA [48] and with the partitioning model SORGAM [49] for secondary organic aerosol. A full description of the model and its performance over European and Italian domain can be found in [PERSON] et al. [32], and a model application of estimation and inclusion of emissions from specific source is shown in [PERSON] et al. [50]. In the present study, the model has been used in a one-way nested grid configuration [51], with a parent domain covering Italy with horizontal resolution of 0.25\({}^{\circ}\)\(\times\) 0.25\({}^{\circ}\) and a nested domain covering Apulia region at 0.06\({}^{\circ}\)\(\times\) 0.06\({}^{\circ}\) horizontal resolution. Both parent and nested simulations used 50 vertical levels for the meteorology and 25 for the chemistry. We recall that the vertical coordinate is based on a hybrid, pressure-based coordinate system, in which the pure terrain-following coordinate at the model surface, gradually tends to a pure pressure coordinate with increasing height above the ground. In the adopted set up, the first vertical level height was about 20 m. The parent run was driven by initial and boundary conditions for meteorology provided by ECMWF. The simulations were re-initialised every 24 h with the ECMWF fields and lateral boundary conditions were updated every 6 h. Climatological boundary conditions provided by INERIS in the frame of the CityZen project were used for chemistry [52]. The anthropogenic emission data were based on TNO inventory for the 2010 year [53]. For the nested run, the initial and boundary conditions, both meteorological and chemical, were provided by the output of the parent simulation. The anthropogenic emissions field, developed within the CESAPO project, was based on the 2007 regional emission inventory INEMAR (INventarioEMissioni in Aria), the emission inventory ISPRA 2005 (focused on 2007 and with the addition of PM by road re-suspension and agriculture) and the emission inventory EMEP 2007. Only ship emissions from the port of Brindisi refer to the year 2010 and were calculated following the methodology described in Section 2.4.1 in order to take into account the European Directive concerning the sulphur content of maritime fuels. In both simulations, biogenic emissions, calculated run time by the model, were based on an inventory providing potential emissions and generated by NKUA (National and Kapodistrian University of Athens) in the frame of the GEMS project [54]. Two runs were performed with BOLCHEM over the inner domain: the base simulation including anthropogenic emissions from all sources, the other one switching off the ship emissions from the Brindisi port. Following the zero-out method, the difference between the concentration fields produced by the two runs then represented the contribution of ship emissions. Figure 2a shows the simulation domain. ADMS-Urban simulations were then performed over a grid of 100 \(\times\) 100 cells covering an area of 13 km \(\times\) 7 km. ADMS-Urban is a multiple-source advanced Gaussian dispersion model which can simulate urban air pollution arising from industrial, domestic, and road traffic sources in urban areas using point, line, area, volume, and grid-source types. Concentration distributions are Gaussian in stable and neutral conditions, but the vertical distribution is non-Gaussian in convective conditions to take account of the skewed structure of the vertical component of the turbulence.