We have developed our original DFT (density-functional theory) calculation code “RSDFT” using real-space schemes. The code is FFT-free, leading to high-performance computing in massively-parallel supercomputers. The code allows us to deal with systems including huge numbers of atoms from first-principles. We have applied our schemes to clarify atomic and electronic structures of two relevant nano-scale systems: twisted bilayer graphene and silicene on Ag substrate.