Superposition Based on Watson–Crick-Like Complementarity

In this paper we propose a new formal operation on words and languages, called superposition. By this operation, based on a Watson–Crick-like complementarity, we can generate a set of words, starting from a pair of words, in which the contribution of a word to the result need not be one subword only, as happens in classical bio-operations of DNA computing. Specifically, starting from two single stranded molecules x and y such that a suffix of x is complementary to a prefix of y, a prefix of x is complementary to a suffix of y, or x is complementary to a subword of y, a new word z, which is a prolongation of x to the right, to the left, or to both, respectively, is obtained by annealing. If y is complementary to a subword of x, then the result is x. This operation is considered here as an abstract operation on formal languages. We relate it to other operations in formal language theory and we settle the closure properties under this operation of classes in the Chomsky hierarchy. We obtain a useful result by showing that unrestricted iteration of the superposition operation, where the "parents" in a subsequent iteration can be any words produced during any preceding iteration step, is equivalent to restricted iteration, where at each step one parent must be a word from the initial language. This result is used for establishing the closure properties of classes in the Chomsky hierarchy under iterated superposition. Actually, since the results are formulated in terms of AFL theory, they are applicable to more classes of languages. Then we discuss "adult" languages, languages consisting of words that cannot be extended by further superposition, and show that this notion might bring us to the border of recursive languages. Finally, we consider some operations involved in classical DNA algorithms, such as Adleman's, which might be expressed through iterated superposition.     

Relations rationnelles infinitaires

In this paper, we build a theory of infinitary rational relations, which is an extension of the theory of finitary rational relations, i. e. sets ofK-vectors of finite words which are recognized by finite automata withK tapes, and at the same time an extension of the theory of infinitary rational languages, i.e., sets of finite and infinite words which are recognized by finite automata (the condition of recognizability of an infinite word is that its reading by the automaton must go through a state, wich belongs to a designated subset, infinitly time). Our main result is a theorem similar to the Kleene theorem about rational languages of finite words: it is proved that the family of relations recognized by finite automata withK tapes is the family of relations obtained from the finite finitary relations with a finite sequence of operations of: union, product, finite star, and infinite star. Then the closure properties of this family of relations, are studied.      

Two complementary operations inspired by the DNA hairpin formation: Completion and reduction

We consider two complementary operations: Hairpin completion introduced in [D. Cheptea, C. Martin-Vide, V. Mitrana, A new operation on words suggested by DNA biochemistry: Hairpin completion, in: Proc. Transgressive Computing, 2006, pp. 216–228] with motivations coming from DNA biochemistry and hairpin reduction as the inverse operation of the hairpin completion. Both operations are viewed here as formal operations on words and languages. We settle the closure properties of the classes of regular and linear context-free languages under hairpin completion in comparison with hairpin reduction. While the class of linear context-free languages is exactly the weak-code image of the class of the hairpin completion of regular languages, rather surprisingly, the weak-code image of the class of the hairpin completion of linear context-free languages is a class of mildly context-sensitive languages. The closure properties with respect to the hairpin reduction of some time and space complexity classes are also studied. We show that the factors found in the general cases are not necessary for regular and context-free languages. This part of the paper completes the results given in the earlier paper, where a similar investigation was made for hairpin completion. Finally, we briefly discuss the iterated variants of these operations.     

Adherences of languages

This paper studies context-free sets of finite and infinite words. In particular, it gives a natural way of associating to a language a set of infinite words. It then becomes possible to begin a study of families of sets of infinite words rather similar to the classical studies of families of languages.     

Computational ludics

We reformulate the theory of ludics introduced by J.-Y. Girard from a computational point of view. We introduce a handy term syntax for designs, the main objects of ludics. Our syntax also incorporates explicit cuts for attaining computational expressivity. In addition, we consider design generators that allow for finite representation of some infinite designs. A normalization procedure in the style of Krivine’s abstract machine directly works on generators, giving rise to an effective means of computation over infinite designs.The acceptance relation between machines and words, a basic concept in computability theory, is well expressed in ludics by the orthogonality relation between designs. Fundamental properties of ludics are then discussed in this concrete context. We prove three characterization results that clarify the computational powers of three classes of designs. (i) Arbitrary designs may capture arbitrary sets of finite data. (ii) When restricted to finitely generated ones, designs exactly capture the recursively enumerable languages. (iii) When further restricted to cut-free ones as in Girard’s original definition, designs exactly capture the regular languages.We finally describe a way of defining data sets by means of logical connectives, where the internal completeness theorem plays an essential role.     

Fundamental properties of infinite trees

Infinite trees naturally arise in the formalization and the study of the semantics of programming languages. This paper investigates some of their combinatorial and algebraic properties that are especially relevant to semantics.This paper is concerned in particular with regular and algebraic infinite trees, not with regular or algebraic sets of infinite trees. For this reason most of the properties stated in this work become trivial when restricted either to finite trees or to infinite words.It presents a synthesis of various aspects of infinite trees, investigated by different authors in different contexts and hopes to be a unifying step towards a theory of infinite trees that could take place near the theory of formal languages and the combinatorics of thefree monoid.     

Topology on words

We investigate properties of topologies on sets of finite and infinite words over a finite alphabet. The guiding example is the topology generated by the prefix relation on the set of finite words, considered as a partial order. This partial order extends naturally to the set of infinite words; hence it generates a topology on the union of the sets of finite and infinite words. We consider several partial orders which have similar properties and identify general principles according to which the transition from finite to infinite words is natural. We provide a uniform topological framework for the set of finite and infinite words to handle limits in a general fashion.     

Palindrome words and reverse closed languages

A word which is equal to its mirror image is called a palindrome word. Any language consisting of palindrome words is called a palindrome language. In this paper we investigate properties of palindrome words and languages. We show that there is no dense regular language consisting of palindrome words. A language contains all the mirror images of its elements is called a reverse closed language. Clearly, every palindrome language is reverse closed. We show that whether a given regular or context-free language is reverse closed is decidable. We study certain properties concerning reverse closed finite maximal prefix codes in this paper. Properties of languages that commute with reverse closed languages are investigated too.     

Pseudo-inversion: closure properties and decidability

We consider a pseudo-inversion operation inspired by biological events, such as DNA sequence transformations, where only parts of a string are reversed. We define the pseudo-inversion of a string \(w = uxv\) to be the set of all strings \(v^Rxu^R\), where \(uv \ne \lambda \) and consider the operation from a formal language theoretic viewpoint. We show that regular languages are closed under the pseudo-inversion operation whereas context-free languages are not. Furthermore, we study the iterated pseudo-inversion operation and show that the iterated pseudo-inversion of a context-free language is recognized by a nondeterministic reversal-bounded multicounter machine. Finally, we introduce the notion of pseudo-inversion-freeness and examine closure properties and decidability problems for regular and context-free languages. We demonstrate that pseudo-inversion-freeness is decidable in polynomial time for regular languages and undecidable for context-free languages.     

Accepting Zeno words: a way toward timed refinements

Timed models were introduced to describe the behaviors of real-time systems and they were usually required to produce only executions with divergent sequences of times. However, when some physical phenomena are represented by convergent executions, Zeno words appear in a natural way. Moreover, time can progress if such an infinite execution can be followed by other ones. Therefore, in a first part, we extend the definition of timed automata, allowing to generate sequences of infinite convergent executions, while keeping good properties for the verification of systems: emptiness is still decidable. In a second part, we define a new notion of refinement for timed systems, in which actions are replaced by recognizable Zeno (timed) languages. We study the properties of these timed refinements and we prove that the class of transfinite timed languages is the closure of the usual one (languages accepted by Muller or Büchi timed automata) under refinement. Received: 16 October 1998 / 8 March 2000     

Regular Languages of Thin Trees

An infinite tree is called thin if it contains only countably many infinite branches. Thin trees can be seen as intermediate structures between infinite words and infinite trees. In this work we investigate properties of regular languages of thin trees. Our main tool is an algebra suitable for thin trees. Using this framework we characterize various classes of regular languages: commutative, open in the standard topology, and definable in weak MSO logic among all trees. We also show that in various meanings thin trees are not as rich as all infinite trees. In particular we observe a collapse of the parity index to the level (1, 3) and a collapse of the topological complexity to co-analytic sets. Moreover, a gap property is shown: a regular language of thin trees is either weak MSO-definable among all trees or co-analytic-complete.     

Schützenberger and Eilenberg theorems for words on linear orderings

This paper contains extensions to words on countable scattered linear orderings of two well-known results of characterization of languages of finite words. We first extend a theorem of Schützenberger establishing that the star-free sets of finite words are exactly the languages recognized by finite aperiodic semigroups. This gives an algebraic characterization of star-free sets of words over countable scattered linear orderings. Contrarily to the case of finite words, first-order definable languages are strictly included into the star-free languages when countable scattered linear orderings are considered. Second, we extend the variety theorem of Eilenberg for finite words: there is a one-to-one correspondence between varieties of languages of words on countable scattered linear orderings and pseudo-varieties of algebras. The star-free sets are an example of such a variety of languages.     

A strongly primitive word of arbitrary length and its application †

It is known that both the class of all (n,k)-languages and the class of all time-variant languages over a finite alphabet contain the class of all regular languages. In this paper we show that in general neither one of these two classes of languages contains the other by constructing an infinite sequence of strongly primitive words over an alphabet with four letters.     

On iterated hairpin completion

(Bounded) hairpin completion and its iterated versions are operations on formal languages which have been inspired by hairpin formation in DNA biochemistry. The paper answers two questions asked in the literature about iterated hairpin completion.The first question is whether the class of regular languages is closed under iterated bounded hairpin completion. Here we show that this is true by providing a more general result which applies to all classes of languages which are closed under finite union, intersection with regular sets, and concatenation with regular sets. In particular, all Chomsky classes and all standard complexity classes are closed under iterated bounded hairpin completion.In the second part of the paper we address the question whether the iterated hairpin completion of a singleton is always regular. In contrast to the first question, this one has a negative answer. We exhibit an example of a singleton language whose iterated hairpin completion is not regular: actually, it is not context-free, but context-sensitive.     

Decision procedures for term algebras with integer constraints

Term algebras can model recursive data structures which are widely used in programming languages. To verify programs we must be able to reason about these structures. However, as programming languages often involve multiple data domains, in program verification decision procedures for a single theory are usually not applicable. An important class of mixed constraints consists of combinations of data structures with integer constraints on the size of data structures. Such constraints can express memory safety properties such as absence of memory overflow and out-of-bound array access, which are crucial for program correctness. In this paper we extend the theory of term algebras with the length function which maps a term to its size, resulting in a combined theory of term algebras and Presburger arithmetic. This arithmetic extension provides a natural but tight coupling between the two theories, and hence the general purpose combination methods like Nelson-Oppen combination are not applicable. We present decision procedures for quantifier-free theories in structures with an infinite constant domain and with a finite constant domain. We also present a quantifier elimination procedure for the extended first-order theory that can remove a block of existential quantifiers in one step.     

Strategical languages of infinite words

We deal in this paper with strategical languages of infinite words, that is those generated by a nondeterministic strategy in the sense of game theory. We first show the existence of a minimal strategy for such languages, for which we give an explicit expression. Then we characterize the family of strategical languages as that of closed ones, in the topological space of infinite words. Finally, we give a definition of a Nash equilibrium for such languages, that we illustrate with a famous example.     

Periodic and Sturmian languages

Counting the number of distinct factors in the words of a language gives a measure of complexity for that language similar to the factor-complexity of infinite words. Similarly as for infinite words, we prove that this complexity function f(n) is either bounded or f(n)?n+1. We call languages with bounded complexity periodic and languages with complexity f(n)=n+1Sturmian. We describe the structure of periodic languages and characterize the Sturmian languages as the sets of factors of (one- or two-way) infinite Sturmian words.     

Sequences of languages in forbidding–enforcing families

 Forbidding-enforcing systems were introduced as a model of molecular processes, with DNA computing as one of the intended application areas. A number of results concerning fe systems deal with the fact that for an infinite ascending sequence of languages satisfying certain properties, their union satisfies the same, or closely related, properties. We generalize these results, mainly by lifting them to converging (in the topological sense) sequences of languages. Furthermore, we discuss in detail the importance of (sequences of) finite languages in forbidding and enforcing families.     

Formes de langages et de grammaires

Summary This paper is devoted to the study of context-free languages over infinite alphabets. This work can be viewed as a new attempt to study families of grammars, replacing the usual grammar forms and giving a new point of view on these questions. A language over an infinite alphabet or I-language appears as being a model for a family of usual languages; an interpretation is an homomorphism from the infinite alphabet to any finite alphabet. Using this notion of interpretation we can associate to each family of I-languages an image, called its shadow, which is a family of usual languages.The closure properties of families, generalizing to infinite alphabets the family of context-free languages, lead to define rational transductions between infinite alphabets or I-transductions, and then, families of I-languages closed under I-transductions, or I-cones. We study here relations between the closure properties of a family of I-languages and these of its shadow. As a result, we obtain that any union closed rational cone of context-free languages, principal or not, is the shadow of a principal I-cone.This work leads to new results about the classical theory of context-free languages. For instance, we prove that any principal rational cone of context-free languages can be generated by a context-free language, whose grammar has only 6 variables. This work also leads to more general considerations about the adequacy of some generating devices to the generated languages. It appears that the context-free grammars are fair, in a sense that we define, for generating context-free languages but that non-expansive context-free grammars are not for generating non-expansive context-free languages. This point of view raises a number of questions.