Inside cells, protein nanopores regulate the permeability of molecules across lipid membranes. The design of functional devices that resemble such biological nanopores has the potential not only to expand our understanding of how nanopores function in vivo but also aid the construction of responsive nanomachines for sensing applications. Artificial nanopores can now be assembled using the DNA origami technique. This technique exploits the specificity of DNA base-pairing to fold a long single-stranded DNA into complex shapes aided by hundreds of short single DNA strands. By combining a DNA origami nanopore with a long double-stranded DNA leash and glass nanocapillaries, the Keyser group has successfully produced nanopores that respond to applied voltages. In this project, the student will work under the supervision of Dr. Collepardo and in close contact with experimentalists at the Keyser group to develop a new coarse-grained model and computer simulation code to represent and assess the responsive nanopore experimental system. The aim of this project is to extend the current capabilities of the experimental measurements by providing structural views and mechanistic information of the structural changes that the
nanopore undergoes as a function of the applied voltage. The results of this project will be exploited to inform the design of new sensing nanodevices.