Petr Šulc, "DNA and RNA nanotechnology: molecular computing, therapeutics, and the quest for the holy grail of self-assembly"

Thursday 20 Mar 2025, 14:15 → 15:30 Europe/Ljubljana

A/1-106 - Seminarska soba fizike (F5) (Jamova)

The control over the self-assembly of complex structures is a long-standing challenge of biomimetic nanotechnology, as the desired assembly pathway is often kinetically derailed by the formation of competing alternative structures or amorphous aggregates. The goal of inverse design problem is hence to find a set of blocks that reliably assemble in high yield into a target structure while avoiding kinetic traps and alternative competing states. We present here a framework called SAT-assembly, which solves this problem by combination of multiscale molecular simulation, graph theory, and constrained optimization methods. While the general approach is abstract, the proposed designs can be realized experimentally e.g. with building blocks made out of DNA or RNA strands. We then show how our models are used to guide experimental realization of highly coveted nanostructure shapes with applications ranging from therapeutic delivery to nanoscale templating, including designs such as capsids, diamond lattices, 3D polycube assemblies, and dynamic reconfigurable multifarious structures, which can switch between multiple possible stable folds.