Different forms of silicon nanotubes and their interactions with DNA nucleotides: A molecular dynamics study

Abstract

The interaction between different forms of silicon nanotubes (SiNTs) and DNA nucleotides is investigated using molecular dynamics simulations. The optimized geometries of infinite single-walled SiNTs made of hexagonal and tetragonal lattices are assessed at the classical level based on Tersoff and Stillinger-Weber potentials. Properties such as Si–Si bond length, diameters as well as formation energy per Si atom are calculated for different SiNTs. Our results for the armchair and zigzag structures show relatively good agreements with other classical and quantum level studies. Therefore, the same method is applied to the less investigated tetragonal type nanotubes. In the next step, the interaction between different DNA nucleotides and stable SiNTs is investigated. The results indicate that the van der Waals dispersion forces are mainly responsible for the nucleotide-SiNT interaction. A unique interaction feature of each nucleotide with SiNTs provides general guidelines for the design of SiNTs-based biosensors.