A question is posed on how a particular subassembly sequence is generated in randomized assembly. An extended design of mechanical conformational switches [16] is proposed that can encode several subassembly sequences. A particular subassembly sequence is generated due to conformational changes of parts during one-dimensional randomized assembly. The optimal subassembly sequence that maximizes the yield of a desired assembly can be found via genetic search over a space of parameterized conformational switch designs, rather than a space of subassembly sequences. The resulting switch design encodes the optimal subassembly sequence so that the desired assemblies are put together only in the optimal sequence. The results of genetic search and rate equation analyses reveal that the optimal subassembly sequence depends on the initial concentration of parts and the defect probabilities during randomized assembly. The results indicate that abundant parts and parts with high defect probabilities should be assembled earlier rather than later.

Bacteriophage viruses spontaneously self-assemble in the presence of their component parts (certain protein molecules). It is believed that conformational switches, interacting chemical bonding sites that allow tentative incorrect bonds, facilitate this randomized assembly process. A one-dimensional conformational switch is proposed and used to study the randomized assembly of mechanical parts. A genetic algorithm is used to search the space of parameterized switch designs to maximize the rate of a desired assembly.