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The work focuses on the investigation of single Co-implanted ZnO nanowires using X-ray fluorescence (XRF), X-ray absorption spectroscopy (XAS), and X-ray diffraction (XRD) techniques with a nanometer resolution. The ZnO nanowires (NWs) were grown on Si substrates using VLS mechanism. The synthesized ZnO NWs were doped with Co via an ion implantation process. For the first time, the combined use of these techniques allows us to study the dopant homogeneity, composition, short- and large-range structural order of single NWs. The nano-XRF results indicate the successful and homogeneous Co doping with the desired concentrations in the ZnO NWs by an ion implantation process. The nano-XAS and XRD data analyses provide new insights into the lattice distortions produced by the structural defect formation generated by the ion implantation process. These findings highlight the importance of the post-implantation thermal annealing to recover the structure of single ZnO NWs at the nanometer length scale. In general, the methodologies used in this work open new avenues for the application of synchrotron based multi-techniques for detailed study of single semiconductor NWs at the nanoscale.