Molecular dynamics study of bio-manipulation in aqueous media

Nano-manipulation is one of the most important aspects of nano-robotics and nano-assembly. The positioning process is considered by many researches to be one of the most important parts of nano-assembly, but has been poorly investigated, particularly for biologic samples. This Letter is devoted to modelling the process of positioning a biomolecule with atomic force microscopy (AFM) in an aqueous media using molecular dynamics simulations. Carbon nanotube (CNT) and graphite sheet are selected as AFM tip and substrate, respectively. To consider the effects of the medium on the manipulation, several models for decreasing the calculations including implicit, coarse grained, and all-atom methods have been investigated. They examined several parameters which may affect the quality of the manipulation process such as the CNT initial position with respect to the sample and substrate, its diameter and positioning strategies (pushing or pulling). The results demonstrate that despite of the implicit solvent methods, coarse-grained model can simulate the aqueous media accurately with lower computational cost. Furthermore, pulling method with a CNT which has a larger diameter and a smaller gap with respect to the substrate is the most appropriate setting for manipulation.