Computed Atomic Force Microscopy Images of Chromosomes by Calculating Forces with Oscillating Probes

Atomic force microscopy (AFM) is a promising tool to visualize biomolecules at the sub-nanometer scale. Experimentally obtained AFM images have been compared with the simulated ones; however, such conventional images of biomolecules were usually computed by calculating equidistance surface from given atomic positions, not by calculating force. Here, we use a polymer model of a chromosome, as a representative biomolecule, and the AFM probe, and computed isoforce surfaces upon the fiber. The oscillation of probes utilized in the dynamic mode of AFM measurements was also implemented in the simulation. The computed isoforce images were clearer than the conventional equidistance ones, and a very similar images to isoforce ones were obtained when the diameter of the probe was reduced to approximately 30% in the equidistance images. Thus, the probe was found to approach very close to samples beyond the estimation of the equidistance surface, contributing clear AFM images.