Use of molecular dynamics simulation in interpreting the atomic force microscopy data

Abstract

A new approach to interpreting and refining the atomic force microscopy (AFM) data, based on comparing them with the output of computer-simulated probe scanning, has been tested with lysozyme. Distinct AFM images were obtained experimentally for individual lysozyme monomers adsorbed from a clear aqueous solution onto a mica wafer. Two steps of simulations were performed to reproduce the environment and processes in the AFM experiment. First, we used the molecular dynamics software (NAMD) to model the structure of lysozyme adsorbed from a water solution onto a silicon oxide support (the latter was modeled manually according to its crystal structure). Second, we applied molecular mechanics to reproduce probe tip interactions with the object. As a result, we have obtained the lysozyme surface height as a function of horizontal coordinates. Comparison with the real AFM data gave a fair fit in the shape of lysozyme molecules but a significant difference in size. Analysis of the possible causes of this discrepancy indicated that more detailed simulations of AFM imaging with fuller account of the experimental conditions are needed to reach a better correspondence. The first results of testing our approach provide sufficient information for improving the accuracy in further applications.