The Aksimentiev Group

Using nanopores to sequence DNA rapidly and at a low cost has the potential to radicallytransforms the field of genomic research. However, despite all the exciting developments inthe field, sequencing DNA using a nanopore has yet to be demonstrated. Among the manyproblems that hinder development of the nanopore sequencing methods is the inability of currentexperimental techniques to visualize DNA conformations in a nanopore and directly relate themicroscopic state of the system to the measured signal. We have recently shown that such taskscould be accomplished through computation. This chapter provides step-by-step instructionsof how to build atomic scale models of biological and solid-state nanopore systems, use themolecular dynamics method to simulate the electric field-driven transport of ions and DNAthrough the nanopores, and analyze the results of such computational experiments.Tutorial is designed for use on Unix/Linux platforms, but will work on any system with working installations of VMD and NAMD.