Self-assembling automata: a model of conformational self-assembly.

An abstract model of self-assembling systems is presented where assembly instructions are written as conformational switches-local rules that specify conformational changes of a component. The model, the self-assembling automaton, is defined as a sequential rule-based machine that operates on one-dimensional strings of symbols. Classes of self-assembling automata are defined based on classes of subassembly sequences in which the components self-assemble. The minimum number of conformations is provided which are necessary to encode subassembly sequences in the each class. It is shown that three conformations for each component are enough to encode any subassembly sequences of a string with arbitrary length.