We demonstrate that the sub-atomically focused beam of a scanning transmission electron microscope (STEM) can be used to controllably manipulate individual dopant atoms in a 2D graphene lattice. We demonstrate the manipulation of adsorbed source materials and the graphene lattice with the electron beam such that individual vacancy defects can be controllably passivated by Si substitutional atoms. We further demonstrate that these Si defects may be directed through the lattice via e-beam control or modified (as yet, uncontrollably) to form new defects which can incorporate new atoms into the graphene lattice. These studies demonstrate the potential of STEM for atom-by-atom nanofabrication and fundamental studies of chemical reactions in 2D materials on the atomic level.

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