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The using of polymeric materials as the basis of photovoltaic cells provides high manufacturability and low cost of production of flexible polymer solar cells (PSC) of a large area. The recent increase in a parameter of the solar energy conversion efficiency (up to 10 %) for materials based on conjugated polymers and fullerenes makes commercialization of plastic solar cell gainful. The peculiarity of the manufacture of PSC leads to the fact that the photoactive layer of photovoltaic cells is formed as a thermodynamically unstable system (with a kinetically frozen state). As a result of constant heating/cooling cycles, a gradual phase separation of the initial components occurs. Thus, searching for key factors helping to increase the long-term stability of organic solar cells is the main challenge for their widespread adoption in everyday practice. Because of the lack of fundamental understanding of the phase behavior of donoracceptor mixtures in the active layers of organic photovoltaic cells, we are carrying out a systematic study of the structural changes that occur after the phase separation of different systems based on a mixture of conjugated polymers with fullerenes. In the report, we discuss our first results on computer simulations of polymer nanocomposites based on conjugated polymers and fullerenes. Specifically, we are interested in the effect of the chemical structure of donor-acceptor copolymers on the morphology of nanocomposites and their thermal stability. Representative systems, that we have chosen to study, are polythiophenes such as poly(3-hexylthiophene-2,5-diyl) (P3HT), poly(3-2-methylbutylthiophene) (P3MBT), poly(3- 2-metilpentilthiophene) (P3MPT), and fullerene [6,6]-phenyl C61 butyric acid methyl ester (PC61BM). We have constructed and parameterized a coarse-grained model of a photoactive layer based on selected polymers and PC61BM. This model is used to study the structure of the photoactive layer. In addition, within the framework of the atomic molecular dynamics method, we carried out a study of the miscibility of selected conjugated polymers with PC61BM. The obtained results make it possible to predict the relationship of the chemical structure of conjugated polymer chains to the morphology of conjugated polymers/fullerenes nanocomposites, their thermophysical properties, the stability of the interface, and to perform the comparison of these data with the optoelectronic properties and functioning of the photocells. The forthcoming experimental studies will allow us to calibrate the design of PSC better. The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University and the resources of the federal collective usage center Complex for Simulation and Data Processing for Megascience Facilities at NRC “Kurchatov Institute” (ministry subvention under agreement RFMEFI62117X0016), http://ckp.nrcki.ru/. The financial support of the Russian Foundation for Basic Research (project № 19-53-52004) and the Ministry of Science and Technology of Taiwan (Project MOST 108-2923-E-002-001-MY3) are highly appreciated.