New possibilities for nonlinear cooperation between different species of quantum emitters in the process of emission and absorption of photons and phonons was proposed. This nonlinear model of cooperation requires the introduction of new order parameters for induced phase transitions like in the laser emission, in which the square of the field intensity, the square of polarization of the emitter species in interaction, the square of total spin and magnetic moment take into consideration the collective character of the components of each one species. These new order parameters obtain amplitude and a phase well determined and could be used in further study of the structure of biomolecules in the process of interaction of radiation with non-equilibrium systems (which includes cellular tissues). These parameters stay on the basis of the development of modern methods of phase transitions of several species of emitters. The possibilities of cooperation between emitters will be extended both for the collective effects between the photons of the cavity modes or the optical fiber guided light modes and for the vibrations of the amino-acid chains of a series of proteins like rhodopsins, microtubules, hemoglobin. This proposal unites as a whole two types of cooperative effects between the radiators. The first one is related to dipole-active systems of quantum emitters like nuclei, atoms, molecules with dimensions smaller than the emitted or absorbed wavelength (as usual for atoms, nuclei this small parameter is of the order of 1/1000). The second type of coupled quantum emitters can be considered as micro- / nano-resonators, consisting of optical elements with spherical, thyroidal, fibers or other topological structures with geometrical dimensions commensurable with the stationary wavelengths generated in them. These optical coupled elements can form collective structures in the form of photonic molecules or photonic crystals. The elements of these structures being relatively large compared to the atomic (molecular) emitters, allow resonantly be coupled with the first group through the zone of the evanescent field near their surface of each of them. In the laboratory, special attention was drawn to the growth of this contact surface in the evanescent field area when the period of such collective periodical structures was reduced. Thus, at the optical resonance, the atoms, viruses, bacteria placed in this area can be easily manipulated through this interface between the metamaterial and each dipole.

In the present project, new photonic molecules was proposed, which contains a variety of optical elements in contact, which differ in both their size and their topological form. New cooperative effects on the region of the near field of these structures in the optical coupling with radiators like atoms, molecules, biomolecules will be the beginning point of many scientific papers and elaborations with an application character. They will correlate with the pressing needs of molecular biology and medicine in which the manipulation and directing of some molecules under the action of light need the physical explanations. Some situations the selective annihilation of toxic substances or pathogens attracted by the optical tweezers effect proposed by the Nobel laureate in Physics A. Ashkin (2018) was considered. Greater attention was paid to the contact surfaces of the elements of the metamaterials with the contaminated fluid upon its penetration among the elements of the metamaterial. The decontamination equipment developed in the laboratory was modernized both on the basis of the new quasi-periodic structures of composite metamaterials, consisting of balls and quartz fibers of various sizes, as well as by using the laser radiation pulsed by the order of nanoseconds in the UV-C spectral region. For the atoms (molecules) trapped in the above-mentioned structures, new effects was discussed in which the quantum aspect of photon emissions will be taken into account where entanglement, indistinguishability between states and quanta, fidelity, quantum discord will become important properties for scalable quantum flux. New possibilities of excitation, ionization and collective emission of photons by radiators (nuclei, atoms, molecules, biomolecules) trapped in the evanescent field area was highlighted.