Molecular Dynamics Study Of Confined Fluid In Nanopores And Gene Sequencing

With the miniaturization of the NEMS/MEMS, the size effect becomes significant in the nanochannels/nanopores through which fluid flows as well as the interface effect. By all-atom molecular dynamics (MD) simulations, the ion transportation is investigated in nanopores as well as the physical properties at solid-liquid interface. To describe the anion and cation distributions of NaCl solution in vicinity of graphene nanopores, a new MD model was developed, taking thermal vibration of wall atoms, the structure of solvent molecules and ion sizes into consideration. The main peak locations of ion distributions stayed unchanged by changing the nanopore size, the solution concentration and the electric field strength. The ionic currents increased linearly with the diameter and the electric field strength, while it increased non-linearly with the solution concentration. All-atom steered molecular dynamics (SMD) simulations provide the means to study the single-stranded DNA (ssDNA) translocation through graphene nanopores at a controllable speed. The ssDNA is pulled by an elastic force similar to the manipulation by an AFM tip. At the same time, an electric field is applied across the reservoir along the direction of the pulling force, in order to hold the ssDNA strand taut and drive the ions in the solutions through the nanopore. By monitoring and analyzing the average ionic current blockage of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10, it is found that one can indeed discriminate the different DNA bases from each other by holding each nucleotide in the pore for sufficiently long time. Tt is obtained the average blocked ionic currents can be listed, in a increasing order, as IG<IA<IT, which is almost in agreement with the order of sizes of the four nucleotides (VG>VA>VT>VC), apart from C. The results indicate that physical occupancy of the nucleotide plays the major role in affecting average blocked ionic current when the DNA translocation speed is effectively slowed down. This work provides a clue for the further investigation to realize the discrimination of the four nucleotides by the method of actively controlling DNA molecule translocation speed through the nanopores.