Related papers: Iterated Hairpin Completions of Non-crossing Words
The (bounded) hairpin completion and its iterated versions are operations on formal lan- guages which have been inspired by the hairpin formation in DNA-biochemistry. The paper answers two questions asked in the literature about the…
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…
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…
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 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…
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…
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…
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…
Often, when analyzing the behaviour of systems modelled as context-free languages, we wish to know if two languages overlap. To this end, we present an effective semi-decision procedure for regular separability of context-free languages,…
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…
In a consistent text, many words and phrases are repeatedly used in more than one sentence. When an identical phrase (a set of consecutive words) is repeated in different sentences, the constituent words of those sentences tend to be…
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…
Extracting frequent words from a collection of texts is commonly performed in many subjects. However, as useful as it is to obtain a collection of commonly occurring words from texts, there is a need for more specific information to be…
It is well-known that: (i) every context-free language over a singleton terminal alphabet is regular, and (ii) the class of languages that satisfy the Pumping Lemma is a proper super-class of the context-free languages. We show that any…
The paper demonstrates the non-closure of the family of unambiguous linear languages (that is, those defined by unambiguous linear context-free grammars) under complementation. To be precise, a particular unambiguous linear grammar is…
The avoidability, or unavoidability of patterns in words over finite alphabets has been studied extensively. A word (pattern) over a finite set is said to be unavoidable if, for all but finitely many words, there exists a morphism mapping…
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…
A tree automatic structure is a structure whose domain can be encoded by a regular tree language such that each relation is recognisable by a finite automaton processing tuples of trees synchronously. Words can be regarded as specific…
Partial words are sequences over a finite alphabet that may contain wildcard symbols, called holes, which match or are compatible with all letters; partial words without holes are said to be full words (or simply words). Given an infinite…