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Development and validation of urban-scale numerical weather and climate models requires better understanding of three-dimensional structure of urban heat island, including its shape and vertical thickness. An attempt to investigate 3D structure of the urban heat island of Moscow city, which forms the biggest urban agglomeration in Europe, was made during September-October 2014. Three similar MTP-5 microwave temperature profilers, which are available to measure temperature at the heights from 0 to 1000 meters with 50-m resolution, were install at three points in the city and its suburbs. These measurements were joined in single database with weather observations at more than 15 meteorological stations, located in the city and neighborhood, including meteorological observatory of Lomonosov Moscow State University. Observations with MTP-5 profilers were taken one month. During this period, different weather conditions were observed, including periods of calm and clear anticyclonic weather, when urban heat island intensity at ground level reached values up to 8 ⁰C, with mean value about 1.8 ⁰C. Temperature difference between urban territory and suburbs over the surface, according MTP-5 measurements, was also significant (up to 2 ⁰C at several moments) until the height of 1000 m. Measurements of temperature profilers were used for data assimilation in numerical experiments with WRF (Weather Research & Forecasting) model, launched with resolution about 1 km for Moscow region. The effect of data assimilation on forecast quality for rural and urban territories was examined and evaluated. Observations of the MTP-5 temperature profilers and meteorological stations and modelling results were used for investigation of the 3-dimentional structure of urban heat island and It’s dependence on synoptic conditions and wind direction. The study was supported by Russian Scientific Fund (RSF), project №14-27-00134