Conformational switching in self-assembling mechanical systems

A study of one-dimensional (1-D) self-assembly of a type of mechanical conformational switches, minus devices is presented where assembly occurs via the sequential mating of a random pair of parts selected from a part bin, referred to as sequential random bin-picking. Parametric design optimization of the minus devices via a genetic algorithm maximizing the yield of a desired assembly, and rate equation analyzes of the resulting designs, reveal that the minus devices facilitate the robust yield of a desired assembly against the variation in the initial fraction of the part types, by specifying a fixed assembly sequence during the self-assembling process. It is also found that while the minus devices can “encode” some assembly sequences, encoding other assembly sequences requires the use of another type of conformational switches, plus devices. To investigate the “encoding power” of these conformational switches, a formal model of selfassembling systems, one-dimensional self-assembling automaton, is introduced, where assembly instructions are written as local rules that specify conformational changes realized by the conformational switches. It is proven that the local rules corresponding to the minus and plus devices, and three conformations per each component, can encode any assembly sequences of a one-dimensional assembly of distinct components with arbitrary length.