Astrophysical neutrinos measured by ICECUBE challenge existing models of multi-messenger sources. Goal of thesis is modeling of sources of cosmic rays, gamma rays and neutrinos taking into account all experimental constraints from direct measurements, KASCADE-Grande and Pierre Auger Observatory for cosmic rays, HESS, Fermi and CTA for gamma-rays and ICECUBE/km3 for neutrinos, study propagation of cosmic rays and gamma-rays in the Galaxy and intergalactic space, search for the imprints of such sources in the experimental data. First model of Galactic sources which explain all data from TeV to 100 PeV energies was found by our group. Part of thesis will be development of this model. Possible discovery of cosmic ray sources would solve 100 years old puzzle of their origin.