Theoretical Computer Science

We introduce a model that describes rearrangement pathways of DNA recombination events. The recombination processes may happen in a succession, possibly with some recombination events performed simultaneously, but others in a prescribed order. These ...

Parameterized matching between two strings occurs when it is possible to reduce the first one to the second by a renaming of the alphabet symbols. We present an algorithm for searching for parameterized occurrences of a patten in a textstring when both ...

The simple intramolecular model for gene assembly in ciliates consists of three molecular operations, simple ld, simple hi and simple dlad. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the ...

We investigate shuffle-decomposability into two words. We give an algorithm which takes as input a DFA M (under certain conditions) and determines the unique candidate decomposition into words u and v such that L(M)=uv if M is shuffle decomposable, in ...

The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper, we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem of ...

We consider sequences of local and edge complementations on graphs with loops (we allow local complementation only on looped vertices). We recall that these operations together form the matrix operation of principal pivot transform (or pivot) restricted ...

Euler's integer partition theorem, which states that the number of partitions of an integer into odd integers is equal to the number of partitions into distinct integers, ranks 16 in Wells' list of the most beautiful theorems (Wells, 1990) [15]. In this ...

We investigate the power of (1-reversal) counter machines (finite automata with multiple counters, where each counter can ''reverse'' only once, i.e., once a counter decrements, it can no longer increment) and one-way multihead finite automata (finite ...

We consider the family of rational relations on words, i.e., relations recognized by multitape automata, which have rational trace on any finite intersection of rational relations. We prove that this family consists of finite unions of relations which ...

Reaction systems are a formal model based on the regulation mechanisms of facilitation and inhibition between biochemical reactions, which underlie the functioning of living cells. The aim of this paper is to explore the expressive power of reaction ...

The palindromization map @j in a free monoid A^* was introduced in 1997 by the first author in the case of a binary alphabet A, and later extended by other authors to arbitrary alphabets. Acting on infinite words, @j generates the class of standard ...

The class of Church-Rosser congruential languages has been introduced by McNaughton, Narendran, and Otto in 1988. A language L is Church-Rosser congruential (belongs to CRCL), if there is a finite, confluent, and length-reducing semi-Thue system S such ...

The linear program dual variables for weighted matching and its generalization to f-factors are shown to be the weights of certain subgraphs: y duals are the weights of certain maximum matchings or f-factors; z duals are the weights of certain 2-factors ...

In this paper, we continue our study on the state complexity of combined operations on regular languages. We study the state complexities of @?"i"="1^kL"i^2, @?"i"="1^kL"i^2, @?"i"="1^kL"i^R, and @?"i"="1^kL"i^R, for regular languages L"i, 1@?i@?k, k>=...

We consider a recently defined notion of k-abelian equivalence of words in connection with avoidability problems. This equivalence relation, for a fixed natural number k, takes into account the numbers of occurrences of the different factors of length k ...

Multidimensional combinatorial substitutions are rules that replace symbols by finite patterns of symbols in Z^d. We focus on the case where the patterns are not necessarily rectangular, which requires a specific description of the way they are glued ...

Automated synthesis from behavioural specifications, such as transition systems, is an attractive way of constructing correct concurrent systems. In this paper, we investigate the synthesis of Petri nets which use special connections between transitions ...

We prove that characteristic Sturmian words are extremal for the Critical Factorization Theorem (CFT) in the following sense. If p"x(n) denotes the local period of an infinite word x at point n, we prove that x is a characteristic Sturmian word if and ...

Reaction automata are a formal model that has been introduced to investigate the computing powers of interactive behaviors of biochemical reactions (Okubo et al. (2012) [19]). Reaction automata are language acceptors with multiset rewriting mechanism ...

We continue here the investigation of P automata, in their non-extended case, a class of devices which characterize non-universal family of languages. First, a recent conjecture is confirmed: any recursively enumerable language is obtained from a ...

Tree automata operating on unranked trees use regular languages, called horizontal languages, to define the transitions of the vertical states that define the bottom-up computation of the automaton. It is well known that the deterministic tree automaton ...

We discuss the role of interactions in the modeling of perception processes. Interactive information systems, introduced in this paper, play the important role in this modeling. Moreover, the proposed approach opens a new research direction in rough set ...