Sharif Digital Repository

This thesis is devoted to the simulation of biomolecules manipulation using Molecular dynamics (MD). In order to investigate the manipulation behavior, we have used the Ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a graphene sample as substrate. Along this line, a lot of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between tip and substrate, initial orientation of protein, and the simulation environment (dry or wet). The results demonstrate that tips with bigger diameters and smaller distances with respect to the substrate increase...