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The theory behind scanning tunneling microscopy and spectroscopy is presented and the basic manipulation
techniques are described. Construction details of a low-temperature scanning tunneling
microscope for single atom manipulation experiments are given. Single crystal copper (111) and (211)
surfaces are studied. Single atom extraction, followed by lateral manipulation procedures is demonstrated.
Cobalt adatoms are deposited onto copper samples at room- and at low- temperatures. Cobalt
nanoislands are observed and the Kondo effect on single cobalt adatoms is measured by means of scanning
tunneling spectroscopy. A detailed study of the surface diffusion of cobalt adatoms as a function
of temperature is presented. Embedded defects in the copper (111) surfaces are studied and their
influence on the stability and properties of cobalt adatoms. It is shown by density functional theory
calculations and proved by a deposition experiment that the embedded defects are substitutional silver
atoms. The structure of cobalt pairs is studied into detail using a combination of manipulation and
imaging techniques.