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This paper presents the development and results of the application of a numerical Lagrangian hydrodynamic model of aerosol particle transport in the urban boundary layer of the atmosphere. The aim of the work is to investigate the influence of air flow parameters and building geometry on the transport of particles of different types: light particles, heavy particles, particles with a limited lifetime, including the example of SARS-CoV-2 virions. The model developed allows to estimate spread and deposition of particles of various genesis taking into account their masses, sizes and lifetimes and also to account for interactions with various surfaces and the effect of turbulence. Simulations can be performed both offline based on input meteorological data, and online as a module coupled to the LES model. The model is verified using idealized analytical solutions for light and heavy particles as well as on the basis of in-situ measurements of dust and sand particle concentrations. Using this model, experiments under realistic atmospheric turbulent flow conditions with different urban development options have been conducted. The influence of urban development is assessed for several typical building geometry configurations for low- and medium-rise buildings. The impact of atmospheric conditions is assessed for several typical stratification, wind speed and wind direction options. The experiments carried out allow conclusions to be drawn not only on the impact of these factors individually, but also on their cumulative impact in various combinations. The work is supported by the Ministry of Education and Science of the Russian Federation, agreements No. 075-15-2021-574, No. 075-15-2022-284, by RSF grants 21-17-00249 and 21-71-30003.