SAT-assembly: A method for model-driven inverse design of self-assembling 3D lattices, capsids, and polycubes

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 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 design method

“SAT-assembly”, which solves this problem by mapping the design problem in terms of different building block types and interactions between them to Boolean Satisfiability problem (SAT). We then show examples of application of our design pipeline to several highly sought-after self-assembly designs. We first study the design of self-assembled capsids.We next compare different design strategies for finite-size polycube structures built from cube-shaped subunits. Finally, we design colloidal system that self-assemble pyrochlore lattices that are of interest for optical metamaterial construction. For each studied system, we demonstrate its experimental realization by self-assembling DNA origami nanostructures.