Tip-sample characterization in the AFM study of a rod-shaped nanostructure

Accurate measurements of line-width standards, sidewalls and non-spherical nanoparticles performed at the nanoscale by means of atomic force microscopy (AFM) suffer from errors due to the tip shape and size. To reduce the uncertainty, the study here presented aims to investigate a bio-plant nanostructure, namely the tobacco mosaic virus (TMV), as a candidate reference tip characterizer. The TMV has a rod-shaped structure with a diameter of about 18 nm, reported earlier from x-ray fibre diffraction, thus representing a reference at the nanoscale. When imaged by AFM, the diameter of the TMV is determined as the top height of the rod from the reconstructed cross-section profile of isolated virions, deposited on a flat substrate like mica. A mean diameter of 16.5 nm, smaller than the nominal value by fibre diffraction measurements, is determined with our metrological AFM. Meanwhile, tip–sample–substrate interactions are discussed with reference to experimental data and models in the literature, in order to determine deformations and the associated uncertainty of corrections, with which the difference between the AFM-reconstructed top-height diameter and the nominal value reduces to about 0.3 nm. Once the virus is fully characterized, a tip profile is estimated by the AFM-reconstructed cross-section profiles of the TMV. The approach is used to evaluate the tip-related enlargement from the nominal circle size, assumed undeformed, of the TMV cross-section profile. A good repeatability of the reconstructed tip shape is achieved from subsequent imaging of virions, while tip degradations are somewhat visible over the working time