Grzegorz Rozenberg

Event Structure Semantics for Dynamic Graph Grammars (2009)

Roberto Bruni, Hernán Melgratti, Ugo Montanari, Paolo Baldan, Hartmut Ehrig, Julia Padberg, ...

Abstract: Dynamic graph grammars (DGGs) are a reflexive extension of Graph Grammars that have been introduced to represent mobile reflexive systems and calculi at a convenient level of abstraction....

Uniformly scatered factors (2009)

Ilie, Lucian, Petre, Ion, Rozenberg, Grzegorz

http://www.tucs.fi/Publications/chapters/cIlPeRo99a.php

Circularity and other invariants of gene assembly in ciliates (2009)

Ehrenfeucht, Andrzej, Petre, Ion, Prescott, David M., Rozenberg, Grzegorz

Ciliates (an ancient group of single cell organisms) have two sorts of nuclei with different functionalities: the micronucleus and the macronucleus. After the cell mating the micronuclear genes are...

Characterizing the micronuclear gene patterns in ciliates (2009)

Ehrenfeucht, Andrzej, Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

The process of gene assembly in ciliates is one of the most complex examples of DNA processing known in any organism, and it is fascinating from the computational point of view - it is a prime...

Transitivity of Local Complementation and Switching on Graphs (2009)

Ehrenfeucht, Andrzej, Harju, Tero, Rozenberg, Grzegorz

The operations complementation C, local complementation lx and switching sx for the vertices x of a finite undirected graph are considered. The operation lx complements the subgraph induced by the...

Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs (2009)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

Gene assembly in ciliates is a life process fascinating from both the biological and the computational points of view. Several formal models of this process have been formulated and investigated,...

Computation in Living Cell: Gene Assembly in Ciliates (2009)

Ehrenfeucht, Andrzej, Harju, Tero, Petre, Ion, Prescot, David M., Rozenberg, Grzegorz

Natural Computing is concerned with computation that is taking place in Nature. The investigation of computations in living cells is one of the central and fastest growing areas of research in this...

Two Models for Gene Assembly in Ciliates (2009)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

Two models for gene assembly in ciliates have been proposed and investigated in the last few years. The DNA manipulations postulated in the two models are very different: one model is {\it...

Parallelism in Gene Assembly (2009)

Harju, Tero, Li, Chang, Petre, Ion, Rozenberg, Grzegorz

The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the...

Two Models for Gene Assembly (2009)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

Two models for gene assembly in ciliates have been proposed and investigated in the last few years. The DNA manipulations postulated in the two models are very different: one model is intramolecular...

Parallelism in Gene Assemby (2009)

Harju, Tero, Li, Chang, Petre, Ion, Rozenberg, Grzegorz

The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the...

Simple Operations for Gene Assembly (2009)

Harju, Tero, Petre, Ion, Rogojin, Vladimir, Rozenberg, Grzegorz

The intramolecular model for gene assembly in ciliates considers three operations, $\mld$, $\mhi$, and $\mdlad$ that can assemble any gene pattern through folding and recombination: the molecule is...

Modelling Simple Operations for Gene Assembly (2009)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

The intramolecular model (Ehrenfeucht et al, 2001) for gene assembly in ciliates considers three operations, $\mld$, $\mhi$, and $\mdlad$ that can assemble any micronuclear gene pattern through...

Computational processes in living cells: gene assembly in ciliates (2008)

Tero Harju, Grzegorz Rozenberg

Abstract. One of the most complex DNA processing in nature known to us is carried out by ciliates during the sexual reproduction when their micronuclear genome is transformed to the macronuclear...

Reversing graph transformations 2 (2008)

Paweł Sobociński, Paolo Baldan, Hartmut Ehrig, Julia Padberg, Grzegorz Rozenberg, Tiziana Margaria, ...

a general framework for backtracking in concurrent formalisms, thus allowing modelling of situations where deadlock can arise without the necessity of explicitly encoding the often involved...

Grammars Based on the Shu e Operation (2008)

Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa

Abstract: We consider generative mechanisms producing languages by starting from a nite set of words and shu ing the current words with words in given sets, depending on certain conditions. Namely,...

AND (2008)

Seymour Ginsburo, Grzegorz Rozenberg

Suppose given two of the following: a set L1 of start words, a set L ~ of target words, and a control set ~ of finite sequences of applications of a given finite set of homomorphisms (or finite...

IOS Press Interpreted Trajectories (2008)

Michael Domaratzki, Grzegorz Rozenberg, Kai Salomaa

Abstract. We introduce generalized trajectories where the individual symbols are interpreted as operations performed on the operand words. The various previously considered trajectory-based...

Formal Properties of Gene Assembly: Equivalence problem for overlap graphs (2008)

Tero Harju, Ion Petre, Grzegorz Rozenberg

Summary. Gene assembly in ciliates is a life process fascinating from both the biological and the computational points of view. Several formal models of this process have been formulated and...

Membrane Systems with External Control (2008)

Robert Brijder, Matteo Cavaliere, Agustín Riscos-núñez, Grzegorz Rozenberg

Abstract. We consider the idea of controlling the evolution of a membrane system. In particular, we investigate a model of membrane systems using promoted rules, where a string of promoters (called...

Tutorial on DNA Computing and Graph Transformation (2008)

Tero Harju, Ion Petre, Grzegorz Rozenberg

DNA computing, or more generally Molecular computing is an exciting research area at the intersection of mathematics, computer science and molecular biology. Research in DNA computing can be roughly...

Under consideration for publication in Math. Struct. in Comp. Science String and graph reduction systems for gene assembly in ciliates (2008)

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg

Ciliates have developed a unique nuclear dualism- two nuclei of di erent functionality: the germline micronucleus and the somatic macronucleus. The way that ciliates assemble the macronuclear genes...

Bidirectional sticker systems (2008)

Rudolf Freund, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa

We introduce two-sided sticker systems, the two-sided variant of a computability model introduced 5 as an abstraction of Adleman's style of DNA computing 1 and of the matching of the so-called...

Event Structure Semantics for Dynamic Graph Grammars (2008)

Roberto Bruni, Hernán Melgratti, Ugo Montanari, Paolo Baldan, Hartmut Ehrig, Julia Padberg, ...

Abstract: Dynamic graph grammars (DGGs) are a reflexive extension of Graph Grammars that have been introduced to represent mobile reflexive systems and calculi at a convenient level of abstraction....

Evolutionary Computation as a Paradigm for DNA-Based Computing (2007)

Thomas Bäck, Joost N. Kok, Grzegorz Rozenberg

. Evolutionary Computation focuses on probabilistic search and optimization methods gleaned from the model of organic evolution. Genetic algorithms, evolution strategies and evolutionary programming...

2 (2007)

Clarence A. Ellis, Jetty Kleijn, Grzegorz Rozenberg

Abstract. Team automata have been proposed in [Ell97] as a formal framework for modeling both the conceptual and the architectural level of groupware systems. Here we dene team automata in a...

2 (2007)

Clarence A. Ellis, Jetty Kleijn, Grzegorz Rozenberg

Team automata are a mathematical modeling tool for capturing notions of coordination, collaboration, and cooperation. They are based upon the concept of "shared actions". In this...

On strongly context-free languages 1 (2007)

Lucian Ilie, Grzegorz Rozenberg, Arto Salomaa

We investigate the context-free languages whose complements are also context-free. We call them strongly context-free languages. The family of strongly linear languages is similarly defined. After...

Membrane Computing with External Output (2007)

Gheorghe P, Grzegorz Rozenberg, Arto Salomaa

A super-cell system consists of computing cells which are organized hierarchically by the inclusion relation: cells may include cells, which again may include cells, etc. Each cell is enclosed by its...

On Strongly Context-Free Languages (2007)

Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa

Starting from the question (inspired by the so-called computing by carving, from the DNA-based computing area) "which is easier to generate, a language or its complement?", we...

Theory Group: Mathematical Structures in Computer Science (2007)

Lucian Ilie, Grzegorz Rozenberg, Arto Salomaa, Turku Centre, Computer Science

Solving an open problem of [3], we prove that any slender context-free language L is strongly linear, i.e., both L and its complement are linear languages.

On the Crossover Distance (2007)

Victor Mitrana, Grzegorz Rozenberg, Arto Salomaa, Turku Centre, Computer Science

A basic problem in the area of combinatorial algorithms for genome evolution is to determine the minimum number of large scale evolutionary events (genome rearrangements) that transform a genome into...

Generating Strings by Replication: A Simple Case (2007)

Valeria Mihalache, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa

We consider the following new way of generating a language: start with a string w and a given set of insertion contexts (u; v); if uv appears as a substring of w, then we can insert in between u and...

Complexity Measures for Gene Assembly (2007)

Harju, Tero, Li, Chang, Petre, Ion, Rozenberg, Grzegorz

The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and...

How Overlap Determines the Macronuclear Genes in Ciliates (2007)

Brijder, Robert, Hoogeboom, Hendrik Jan, Rozenberg, Grzegorz

Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a...

Complexity Measures for Gene Assembly (2007)

Harju, Tero, Li, Chang, Petre, Ion, Rozenberg, Grzegorz

The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and...

Simple Operations for Gene Assembly (2006)

Harju, Tero, Petre, Ion, Rogojin, Vladimir, Rozenberg, Grzegorz

The intramolecular model for gene assembly in ciliates considers three operations, $mld$, $mhi$, and $mdlad$ that can assemble any gene pattern through folding and recombination: the molecule is...

Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph (2006)

Brijder, Robert, Hoogeboom, Hendrik Jan, Rozenberg, Grzegorz

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the...

Parallelism in gene assembly (2006)

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg

Abstract. The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from...

Spike trains in spiking neural P systems (2006)

Gheorghe Păun, Grzegorz Rozenberg

Abstract. We continue here the study of the recently introduced spiking neural P systems, which mimic the way that neurons communicate with each other by means of short electrical impulses, identical...

Modelling Simple Operations for Gene Assembly (2005)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

The intramolecular model (Ehrenfeucht et al, 2001) for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any micronuclear gene pattern through folding and...

THE EMBEDDING PROBLEM FOR SWITCHING CLASSES (2005)

Andrzej Ehrenfeucht, Jurriaan Hage, Tero Harju, Grzegorz Rozenberg

1 In the context of graph transformation we look at the operation of switching, which can be viewed as an elegant method for realizing global transformations of (group-labelled) graphs through local...

Formal Specification and Rule-Based Refinement of Software Components (2005)

Kumulierte Habilitation, Fakultät Iv, Elektrotechnik Und Informatik, Theoretische Informatik, Habiltationscolloquium Februar, ...

Software components are a useful and widely accepted abstraction mechanism during the entire software life cycle from analysis to maintenance. They need to be backed by thorough formal concepts and...

Finite Metrics in Switching Classes (2004)

Ehrenfeucht, Andrzej, Harju, Tero, Rozenberg, Grzegorz

Let D be a finite set together with a real valued function g with g(x,x)=0 and g(x,y) = g(y,x). A switch of g is obtained by transforming g using a local valuation s: gs (x,y) = s(x) + g(x,y) + s(y)...

Embedding Linear Orders in Grids (2004)

Ehrenfeucht, Andrzej, Harju, Tero, Rozenberg, Grzegorz

A grid is a two-dimensional permutation: an m×n-grid of size mn is an m×n-matrix where the entries run through the elements {1,2, ... , mn}. We prove that if d1 and d2 are any two linear...

Zebra Factorizations in Free Semigroups (2004)

Ehrenfeucht, Andrzej, Harju, Tero, Rozenberg, Grzegorz

Let S be a semigroup of words over an alphabet A. Let W(S) consist of those elements w of S for which every prefix and suffix of w belongs to S. We show that W(S) is a free semigroup. Moreover, S is...

DNA computing using single-molecule hybridization detection (2004)

Schmidt, Kristiane A., Henkel, Christiaan V., Rozenberg, Grzegorz, Spaink, Herman P.

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that...

Gene Assembly in Ciliates: Molecular Operations (2003)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

"If you look inside the cell you find a bunch of amazing little tools. The cell is a treasure chest." (Leonard Adleman in CNN Science and Space, August 17, 2003). Natural Computing is concerned...

Gene Assembly in Ciliates: Formal Frameworks (2003)

Harju, Tero, Petre, Ion, Rozenberg, Grzegorz

This is the second part of a review of the research on formal modelling of gene assembly in ciliates. In the first part, we provided the basic biological background and introduced molecular...

Synchronizations in team automata for groupware systems (2003)

Clarence A. Ellis, Jetty Kleijn, Grzegorz Rozenberg

Abstract. Team automata have been proposed in (Ellis, 1997) as a formal framework for modeling both the conceptual and the architectural level of groupware systems. Here we dene team automata in a...

Team Automata for CSCW (2001)

Clarence A. Ellis, Jetty Kleijn, Grzegorz Rozenberg

Team automata have been proposed as a formal framework for modelling both the conceptual and the architectural level of groupware systems. They are dened in terms of component automata together with...

Behavior and Realization Construction for Petri Nets Based on Free Monoid and Power Set Graphs (2001)

Julia Padberg, Hartmut Ehrig, Grzegorz Rozenberg

Starting from the algebraic view of Petri nets as monoids (as advocated by Meseguer and Montanari in [MM90]) we present the marking graphs of place transition nets as free monoid graphs and the...

Nonconventional computing paradigms in a new millennium: a roundtable,” Computing (2001)

C Omputing, Y. Zomaya, James A. Anderson, David B. Fogel, Gerard J. Milburn, Grzegorz Rozenberg

For the past 50 years, we have based most (if not all) of the world’s computers on the von Neumann model, which Alan Turing’s theoretical model in turn inspired in the first half of the 20th...

Team Automata for Spatial Access Control Maurice H. ter Beek (2001)

Clarence A. Ellis, Jetty Kleijn, Grzegorz Rozenberg

Team automata provide a framework for capturing notions like coordination, collaboration, and cooperation in distributed systems. They consist of an abstract specification of components of a system...

A characterization of poly-slender context-free languages, Theor (2000)

Lucian Ilie, Grzegorz Rozenberg, Arto Salomaa

For a non-negative integer k, we say that a language L is k-poly-slender if the number of words of length n in L is of order O(n k). We give a precise characterization of the k-poly-slender...

Uniformly scattered factors (2000)

Lucian Ilie, Ion Petre, Grzegorz Rozenberg, Turku Centre, Computer Science

A word u appears as a factor of another word v as it is; in one piece. When u is a subword of v, u may be scattered as several factors. We consider the in-between case and put some restrictions on...

Uniformly scattered factors (1999)

Ilie, Lucian, Petre, Ion, Rozenberg, Grzegorz

http://www.tucs.fi/Publications/techreports/TR243.php

DNA computing: new ideas and paradigms (1999)

Rozenberg, Grzegorz, Salomaa, Arto

http://www.tucs.fi/Publications/proceedings/pRoSa99a.php

On the Crossover Distance (1998)

Mitrana, Victor, Rozenberg, Grzegorz, Salomaa, Arto

http://www.tucs.fi/Publications/techreports/TR223.php

Contexts on Trajectories (1998)

Carlos Martin-vide, Alexandru Mateescu, Grzegorz Rozenberg, Arto Salomaa, Turku Centre, Computer Science

We introduce and investigate a new way of generating mildly context-sensitive languages. The main idea is that the contexts are adjoined by shuffling them on certain trajectories. In this way we...

Shuffle on trajectories: Syntactic constraints (1998)

Alexandru Mateescu, Grzegorz Rozenberg, Arto Salomaa

We introduce and investigate new methods to define parallel composition of words and languages. The operation of parallel composition leads to new shuffle-like operations defined by syntactic...

X-Families: An Approach to the Study of Families of Syntactically Similar Languages (1998)

Carlos Martin-Vide, Gheorghe Paun, Grzegorz Rozenberg, Grzegorz Rozenberg, Arto Salomaa, Arto Salomaa

. All classes of grammars investigated in formal language theory generate a language by starting from #nite sets of axioms and iteratively applying certain production rules which transform...

Petri Nets and Business Process Management (1998)

Jörg Desel, Andreas Oberweis, Wolfgang Reisig, Grzegorz Rozenberg

ion morphisms: Lakos 1997) We stress that we aim at less but powerful principles, that we set out to trace their consequences as far as possible and that we want to formalize them by mathematical...

DNA Computing, Sticker Systems, and Universality (1998)

Lila Kari, Gheorghe Paun, Gheorghe P, Grzegorz Rozenberg, Arto Salomaa, Sheng Yu

. We introduce the sticker systems, a computability model, which is an abstraction of the computations using the Watson-Crick complementarity as in Adleman's DNA computing experiment, [1]....

Formal Language Theory, special issue (1997)

Rozenberg, Grzegorz, Salomaa, Arto

http://www.tucs.fi/Publications/journals/jRoSA97.php

Shuffle-Like Operations on Omega-Words (1997)

Alexandru Mateescu, George Daniel Mateescu, Grzegorz Rozenberg, Arto Salomaa

We introduce and investigate some shuffle-like operations on !-words and !-languages. The approach is applicable to concurrency, providing a method to define the parallel composition of processes. It...

DNA computing, matching systems, and universality (1996)

Lila Kari, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa, Sheng Yu

We introduce the matching systems, a computability model which is an abstraction of the way of using the Watson-Crick complementarity when computing with DNA in the Adleman style, [1]. Several types...

Reductions for primitive 2-structures (1994)

Harju, Tero, Rozenberg, Grzegorz

http://www.tucs.fi/Publications/journals/HaRo94b.php

Genetic L-System Programming (1994)

Christian Jacob, Aristid Lindenmayer, Grzegorz Rozenberg

. We present the Genetic L-System Programming (GLP) paradigm for evolutionary creation and development of parallel rewrite systems (Lsystems, Lindenmayer-systems) which provide a commonly used...

Equality languages and fixed point languages (1979)

Engelfriet, Joost, Rozenberg, Grzegorz

This paper considers equality languages and fixed-point languages of homomorphisms and deterministic gsm mappings. It provides some basic properties of these classes of languages. We introduce a new...

DNA computing using single-molecule hybridization detection

Schmidt, Kristiane A., Henkel, Christiaan V., Rozenberg, Grzegorz, Spaink, Herman P.

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that...

DNA computing using single-molecule hybridization detection

Schmidt, Kristiane A., Henkel, Christiaan V., Rozenberg, Grzegorz, Spaink, Herman P.

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that...