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State complexity of overlap assembly. (English) Zbl 1458.68091

Summary: The state complexity of a regular language \(L_m\) is the number \(m\) of states in a minimal deterministic finite automaton (DFA) accepting \(L_m\). 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 \(\leq m\) and \(\leq n \), respectively. We determine, for \(m\geq2\), \(n\geq3\), 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 \(L_m\) and \(L_n\), where \(m\geq2\) and \(n\geq1\), is at most \(2(m-1) 3^{n - 1}+ 2^n\). Moreover, for \(m\geq2\) and \(n\geq3\) there exist languages \(L_m\) and \(L_n\) over an alphabet of size \(n\) whose overlap assembly meets the upper bound and this bound cannot be met with smaller alphabets. Finally, we prove that \(m+n\) 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 \(m( 2^{n - 1}-2)+2\).

MSC:

68Q45 Formal languages and automata
92D20 Protein sequences, DNA sequences
Full Text: DOI

References:

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