26:T468,

The concept of hairpin structures in formal languages is motivated from the biocomputing and bioinformatics fields. Hairpin (-free) DNA structures have numerous applications to DNA computing and molecular genetics in general. A word is called hairpin-free if it cannot be written in the form xuyθ(u)z, with certain additional conditions, for an involution θ (a function θ with the property that θ ^2 equals the identity function). A particular involution, the so-called Watson-Crick involution, can characterize binding of two DNA strands.

We study algebraic and decision properties, finiteness and descriptional complexity of hairpin (-free) languages. We show an existence of polynomial-time algorithms deciding hairpin-freeness of regular and context-free sets. Two related DNA secondary structures are considered, taking into the account imperfect bonds (bulges, mismatches) and multiple hairpins. Finally, effective methods for design of long hairpin-free DNA words are given.

27:T507,

Subtyping is a basic concept in object-oriented languages. It supports subsumption but, unfortunately, it does not support inheritance of binary methods, i.e., methods taking another argument of type Self? – the same type as the object itself. For this reason, a relation, called matching, on recursive object types has been proposed. This relation does not support subsumption but it allows to inherit binary methods. Two different definitions of matching, called F-bounded and higher-order subtyping, have been proposed and discussed. It was shown that the higher-order interpretation has better theoretical properties, i.e., it leads to a reflexive and transitive matching relation. In this paper we concentrate on two problems in languages with self types and matching based on the higher-order interpretation. We show that the flexibility of self types may not allow the programmer to define certain classes and/or methods which are based on constant values. Furthermore, the higher-order interpretation, especially in the context of bounded quantification, is too restrictive. We argue that a language should be based on both versions of matching and a notion of a type This distinguished from the type Self.

28:T4a0,Fundamenta Informaticae is an international journal publishing original research results in all areas of theoretical computer science. Papers are encouraged contributing: - solutions by mathematical methods of problems emerging in computer science - solutions of mathematical problems inspired by computer science. Topics of interest include (but are not restricted to): theory of computing, complexity theory, algorithms and data structures, computational aspects of combinatorics and graph theory, programming language theory, theoretical aspects of programming languages, computer-aided verification, computer science logic, database theory, logic programming, automated deduction, formal languages and automata theory, concurrency and distributed computing, cryptography and security, theoretical issues in artificial intelligence, machine learning, pattern recognition, algorithmic game theory, bioinformatics and computational biology, quantum computing, probabilistic methods, & algebraic and categorical methods.