The paper develops the application of a mathematical model describing the physical vacuum and matter by two-component systems. In contrast to Newtonian physics, when describing the energy of a body, its volume is taken into account. The model allows representing matter as a middle state between "black" holes and space. Using examples of matter energy changes, the appearance of electric charge and magnetic fields is shown. The interconnection of matter with the processes of the Universe evolution is shown. The conclusion that the motion of time is impossible without a change in the rate of time is substantiated. The dependence of the change in the rate of time motion, on the interval of time, distorts the data on the rate of expansion of the Universe. It is concluded that the movement of time is a transformation of the future into the past. The spiral motion of photons is explained. The justification of the description of the physical essence of phenomena using rectangular coordinates is considered.