Using molecular simulations to guide realization of bionanotechnology devices: from metamaterials to nanomotors

The control over the self-assembly of complex structures is a long-standing challenge of material science, especially at the colloidal scale, as the desired assembly pathway is often kinetically derailed by the formation of competing alternative structures or amorphous aggregates. The goal of the inverse design problem in nanotechnology is hence to find a set of blocks that reliably self-assemble in high yield into a target structure while avoiding kinetic traps and alternative competing states. We present here a new design pipeline, called SAT-Assembly, that uses multiscale molecular simulations of DNA, RNA and proteins to design nanostructures and devices that can be successfully realized in the lab. We show applications of our modeling pipeline to design particles that are shown to experimentally self-assemble pyrochlore lattice, a highly coveted 3D lattice with promising applications in metamaterial designs. We further show examples of designing self-assembled finite-size polycube nanostructures and capsids, along with preliminary experimental results of successful assembly of these designs using DNA nanostructures. We further discuss examples of other recent applications of our modeling pipeline tools: a chemically powered oscillating nanoengine, and multivalent protein-DNA hybrid nanostructures that inhibit SARS-CoV-2 spike protein binding.