State Complexity of Overlap Assembly

Abstract

The state complexity of a regular language [Formula: see text] is the number [Formula: see text] of states in a minimal deterministic finite automaton (DFA) accepting [Formula: see text]. The state complexity of a regularity-preserving binary operation on regular languages is defined as the maximal state complexity of the result of the operation where the two operands range over all languages of state complexities [Formula: see text] and [Formula: see text], respectively. We determine, for [Formula: see text], [Formula: see text], the exact value of the state complexity of the binary operation overlap assembly on regular languages. This operation was introduced by Csuhaj-Varjú, Petre, and Vaszil to model the process of self-assembly of two linear DNA strands into a longer DNA strand, provided that their ends “overlap”. We prove that the state complexity of the overlap assembly of languages [Formula: see text] and [Formula: see text], where [Formula: see text] and [Formula: see text], is at most [Formula: see text]. Moreover, for [Formula: see text] and [Formula: see text] there exist languages [Formula: see text] and [Formula: see text] over an alphabet of size [Formula: see text] whose overlap assembly meets the upper bound and this bound cannot be met with smaller alphabets. Finally, we prove that [Formula: see text] is the state complexity of the overlap assembly in the case of unary languages and that there are binary languages whose overlap assembly has exponential state complexity at least [Formula: see text].