Noncalssical multiscale modeling of ssDNA manipulation using a CNT-nanocarrier based on AFM

Abstract

Nanocarriers are useful tools in biological and medical research fields. In nanomanipulation, a nondestructive and successful process can be achieved by using nanocarriers. In this paper, a nonclassical multiscale approach has been presented for modeling a single strand DNA (ssDNA) manipulation based on AFM. To achieve a nondestructive nanomanipulation process, carbon nanotube (CNT) has been used as a nanocarrier. AFM setup has been separated into a Micro field (MF) and a Nano field (NF). The governing equations of the MF have been derived based on Kirchhoff plate model and a modified couple stress theory. The NF has been modeled by molecular dynamics (MD) method. A set of nanomanipulations has been performed for the free ssDNA and the ssDNA inside the nanocarrier (shielded ssDNA) on three types of substrates. The exerted forces on the free ssDNA and the shielded ssDNA have been compared for manipulation on various substrates. The results show that using the nanocarrier reduces the manipulation force considerably. The results of RMSD as a general geometrical criterion have illustrated that the maximum damage occurs on the golden substrate for free ssDNA. Elongation and curvature criteria have been presented to investigate the ssDNA deformation in detail. The elongation and curvature criteria have been shown that using a nanocarrier is a good approach for a successful and nondestructive nanomanipulation. Finally it can be concluded that the manipulation process of free ssDNA on silicon substrate is successful as well as the manipulation process of the shielded ssDNA on all three types of substrates.