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We present results of design, preparation and characterization of new nanocomposite nanofilm biocompatible magnetic capsules based on the complexes of lipids, functional amphiphiles, nanoparticles and polymers which can be perspective for development of novel efficient means for capsulation, targeted transport, controlled spatial localization, remote activation and stimuli-addressed delivery of various compounds in aqueous media for biomedical controlled drug delivery and other applications. The developed nanofilm structures are based on the planar complexes of biogenic lipids, synthetic cationic amphiphilic compounds, biogenic and synthetic polyelectrolytes, and functional inorganic nanoparticles (magnetic iron oxide nanoparticles and plasmonic Au nanoparticles). The features of interactions of colloid inorganic nanoparticles and polyelectrolytes of aqueous phase with liposomes formed by phosphatidylcholine and synthetic cationic amphiphiles have been studied. Nanocomposite capsules were prepared by sequential adsorption of colloid inorganic nanoparticles and polyanions onto the cationic hybrid liposomes preliminarily formed using conventional ultrasound method. The obtained vesicles were characterized by transmission electron microscopy, scanning probe microscopy, electron magnetic resonance technique, laser light scattering, electrophoresis, conductometry, etc. The suspensions of model nanocomposite vesicles and capsules containing NaCl solution in the internal volume were obtained. The study of the effect of short high strength electromagnetic pulses on those capsules have been carried out. The non-thermal decapsulation effect and efficient delivery of capsulated compound was demonstrated. Theoretical analysis of electromagnetic pulses effect on the nanocomposite vesicular structures with surface-bound inorganic conductive nanoparticles have been carried out. It was experimentally demonstarted and theoretically proved that the presence of conducting nanoparticles can decrease substantially the applied voltage necessary for electrical breakdown of the lipid vesicle membrane resulting in membrane structural changes and vesicle "opening". TEM data showed that the structure of vesicles was destroyed substantially due to the electromagnetic treatment. Polymeric layers formed on the surface of nanocomposite liposomes can change substantially the physical-chemical characteristics of such liposomes and their stability and resistivity against external factors as electromagnetic fields. This work was supported by Russian Scientific Fund (grant 14-12-01379).