The Aksimentiev Group

Building on the recent technological advances, all atom molecular dynamics (MD) simulationshave become an indispensabletool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, mechanical and electrical properties of DNA origami nanostructures. In this tutorial we describe a method to build all-atom model of lipid spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions.