نسيم رجبي

Fast, low-cost and reliable DNA sequencing is one of the most desirable innovations in recent years, which can pave the way for high quality and low-cost genome sequencing. The process of reading the order of nucleotides in DNA molecule is called DNA sequencing. In this thesis, we demonstrate by molecular dynamics simulation that the single-base resolution detection can be realized by pulling a single-strand DNA through graphene nanopores with ~1/2nm diameter.By translocation of four homogeneous DNA strands (poly(A)9, poly(T)9, poly(G)9, poly(C)9) Using Steered molecular dynamic (SMD), through the graphene nanopore, by simply monitoring and analyzing the peak values of the pulling force profile verses time, each nucleotide in the DNA strand can be identified and characterized, except for cytosine and thymine which remain indistinguishable. Actually, the graphene nanopore is easily oxidized during preparation process, thus it is great necessary to develop other new and simple method for DNA sequencing. One of these methods is functionalization of the nanopore by hydrogen and the hydroxyl group. In this thesis in order to achieve a more efficient way for DNA sequencing, we decorate the edge of the nanopore with the same charge as hydrogen and oxygen. an‎d investigate the effect of charged nanopore on accuracy of detection of nucleotides. It was found that when passing through a positive charged nanopore the accuracy of the detection of nucleotides from each other increase significantly compared to the uncharged or even with negative charged nanopore, which is related to the difference electrostatic interactions between the base and pore. Keywords: Graphene Nanopore, DNA sequencing, Steered Molecular simulation (SMD), ssDNA (single strand DNA), functionalized graphene nanopore