Nanowire (NW) arrays form spontaneously after high temperature annealing of a sub monolayer deposition of Pt on a Ge(001) surface. These NWs are a single atom wide, with a length limited only by the underlying beta-terrace to which they are uniquely connected. Using ab-initio density functional theory (DFT) calculations we study possible geometries of the NWs and substrate. Direct comparison to experiment is made via calculated scanning tunneling microscope (STM) images. Based on these images, geometries for the beta-terrace and the NWs are identified, and a formation path for the nanowires as function of increasing local Pt density is presented. We show the beta-terrace to be a dimer row surface reconstruction with a checkerboard pattern of Ge-Ge and Pt-Ge dimers. Most remarkably, comparison of calculated to experimental STM images shows the NWs to consist of germanium atoms embedded in the Pt-lined troughs of the underlying surface, contrary to what was assumed previously in experiments.
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