Study of Biomolecules Imaging Using Molecular Dynamics Simulations

Abstract

The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip–sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a graphene sheet is used as the substrate. The effects of CNT's geometric parameters such as the CNT height, the diameter, the tilt angle, the flexibility and the number of layers on the image quality have been evaluated.