Related papers: On the Iterated Hairpin Completion
Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive…
The hairpin completion is an operation on formal languages which is inspired by the hairpin formation in biochemistry. Hairpin formations occur naturally within DNA-computing. It has been known that the hairpin completion of a regular…
Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and…
The hairpin completion is an operation on formal languages that has been inspired by the hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the hairpin completion of regular languages. It is well known…
Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…
The aim of this paper is to design the polynomial construction of a finite recognizer for hairpin completions of regular languages. This is achieved by considering completions as new expression operators and by applying derivation…
We identify a subclass of the regular commutative languages that is closed under the iterated shuffle, or shuffle closure. In particular, it is regularity-preserving on this subclass. This subclass contains the commutative group languages…
Motivated by work on bio-operations on DNA strings, we consider an outfix-guided insertion operation that can be viewed as a generalization of the overlap assembly operation on strings studied previously. As the main result we construct a…
Indexed languages are a classical notion in formal language theory, which has attracted attention in recent decades due to its role in higher-order model checking: They are precisely the languages accepted by order-2 pushdown automata. The…
We report some further developments regarding the language theory of higher-dimensional automata (HDAs). Regular languages of HDAs are sets of finite interval partially ordered multisets (pomsets) with interfaces. We show a pumping lemma…
Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into…
This thesis investigates three biologically inspired operations: prefix-suffix duplication, bounded prefix-suffix duplication, and prefix-suffix-square completion. Duplication, a common genetic mutation, involves repeating DNA sequences and…
In this article we undertake a study of extension complexity from the perspective of formal languages. We define a natural way to associate a family of polytopes with binary languages. This allows us to define the notion of extension…
We study the fluted fragment of first-order logic which is often viewed as a multi-variable non-guarded extension to various systems of description logics lacking role-inverses. In this paper we show that satisfiable fluted sentences (even…
Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a…
We consider a set of natural operations on languages, and prove that the orbit of any language L under the monoid generated by this set is finite and bounded, independently of L. This generalizes previous results about complement, Kleene…
We study the complexity of basic regular operations on languages represented by incomplete deterministic or nondeterministic automata, in which all states are final. Such languages are known to be prefix-closed. We get tight bounds on both…
We show that the commutative closure combined with the iterated shuffle is a regularity-preserving operation on group languages. In particular, for commutative group languages, the iterated shuffle is a regularity-preserving operation. We…
Let A be a finite alphabet and let L contained in (A*)^n be an n-variable language over A. We say that L is regular if it is the language accepted by a synchronous n-tape finite state automaton, it is quasi-regular if it is accepted by an…
A new technique is presented to prove non-termination of term rewriting. The basic idea is to find a non-empty regular language of terms that is closed under rewriting and does not contain normal forms. It is automated by representing the…