Conformational switching in self-assembling mechanical systems

A study of one-dimensional (1-D) self-assembly of a type of mechanical conf ormational switches, minus devices is presented where assembly occurs via t he sequential mating of a random pair of parts selected from a part bin, re ferred to as sequential random bin-picking. Parametric design optimization of the minus devices via a genetic algorithm maximizing the yield of a desi red assembly, and rate equation analyzes of the resulting designs, reveal t hat the minus devices facilitate the robust yield of a desired assembly aga inst the variation in the initial fraction of the part types, by specifying a fixed assembly sequence during the self-assembling process. It is also f ound that while the minus devices can "encode" some assembly sequences, enc oding other assembly sequences requires the use of another type of con form ational switches, plus devices. To investigate the "encoding power" of thes e conformational switches, a formal model of self-assembling systems, one-d imensional self-assembling automaton, is introduced, where assembly instruc tions are written as local rules that specify conformational changes realiz ed by the conformational switches, It is proven that the local rules corres ponding to the minus and plus devices? and three conformations per each com ponent, can encode any assembly sequences of a one-dimensional assembly of distinct components with arbitrary length.