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The space-charge spectroscopy, EPR, modeling of inhomogeneous strain field with Keating interatomic potential, hole energy calculation with nearest neighbor tight-binding single-particle Hamiltonian with the sp3 basis and the electronic energy levels calculation with solving three-dimensional effective-mass SchroÂ¿dinger equation were used to study dense array of Ge quantum dots in Si. The enlargement of electron binding energy takes place in multilayer Ge/Si structures with vertical stacking of Ge islands due to accumulation of strain energy from different dot layers in a stack and increase of the potential well depth. In strained dots the change interdot distances causes crossing between the hole energy levels corresponding to bonding and antibonding orbitals. The enhancement of oscillator strength of the optical interband transition in type-II QDs occurs, depending on the interdot separation with peak at 3 nm.