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The improvement of the resolution of DNA sequencing by nanopore technology is very important for its real-life application. In this paper, we report our work on using molecular dynamics simulation to study the dependence of DNA sequencing on the translocation time of DNA through a graphene nanopore, using the single-strand DNA fragment translocation through graphene nanopores with diameters down to ∼2 nm as examples. We found that A, T, C, and G could be identified by the difference in the translocation time between different types of nucleotides through 2 nm graphene nanopores. In particular, the recognition of the graphene nanopore for different nucleotides can be greatly enhanced in a low electric field. Our study suggests that the recognition of a graphene nanopore by different nucleotides is the key factor for sequencing DNA by translocation time. Our study also indicates that the surface of a graphene nanopore can be modified to increase the recognition of nucleotides and to improve the resolution of DNA sequencing based on the DNA translocation time with a suitable electric field.

Understanding the mechanism and pathway of anti-cancer drugs to be pumped out by P-glycoprotein (P-gp) in cancer cell is very important for the successful chemotherapy. P-gp is a member of ATP-binding cassette (ABC) transporters. In this study, random accelerated molecular dynamics (RAMD) simulation was used to explore the potential egress pathway of ligands from the binding pocket. This could be considered as a reverse process of drug binding. The most possible portal of drugs to dissociate is TM4/TM6, which is almost the same for different drugs, such as paclitaxel and doxorubicin. The interactions in the binding site are found to be remarkably stronger than that outside of the binding site. The results were suggested by the free energy calculation between P-gp and different drugs from metadynamics simulation. All the results indicate that the flexibility of inner residues, especially the residue Phe339, is very important for the drugs to access the binding site.

Understanding of the mechanism and dynamics of DNA loading into carbon nanotubes (CNTs) is very important for the promising applications of CNTs in DNA sequencing, drug delivery and gene delivery systems etc. In this work, the loading mechanism and dynamics of different ssDNA oligomers into single-walled carbon nanotubes (SWNTs) was investigated through molecular dynamics simulations, steered molecular dynamics simulation and binding free energy calculations. Our simulation results showed that the loading of different ssDNA oligomers into the zigzag SWNT is much easier than for the armchair SWNT. Confined in both zigzag and armchair type SWNTs, ssDNA oligomers have a helical structure and their bases adapt the orientation parallel to the interior wall. From detailed analysis of the interaction energy, potential of mean force (PMF) of the unloading process and nucleotide binding free energy, our results show that the chirality of SWNTs has a large effect on the binding strength of nucleotides, and hence affects the loading dynamics of ssDNA into SWNTs.