Grzegorz Rozenberg

Leiden University | LEI · Leiden Institute of Advanced Computer Science

Preface Gheorghe Păun, member of the Academy of Romania and member of Academia Europea, is one of the internationally most recognized Romanian computer scientists. His research has been influential in theoretical computer science, especially formal language theory and automata theory, in linguistics, and in natural computing. He single-handedly cre...

This book constitutes the refereed post-conference proceedings of the 20th International Conference on Membrane Computing, CMC 2020, held as a virtual event, in September 2020. The 10 full papers presented were selected from 31 submissions. The papers deal with all aspects on membrane computing and related areas.

Reaction systems is a formal model of computation which originated as a model of interactions between biochemical reactions in the living cell. These interactions are based on two mechanisms, facilitation and inhibition, and this is well reflected in the formulation of reaction systems. In this paper, we investigate the facilitation aspect of react...

Reaction systems originated as models of interactions between biochemical reactions in the living cell. Since then they were also successfully developed as models of interactive computation. Here, the interaction between a (reaction) system and its environment is modelled through context sequences provided by the environment – they influence the pr...

In this paper, we study the behavior (processes) of reaction systems where the context is not arbitrary, but it has its own structure. In particular, we consider a model where the context for a reaction system originates from a network of reaction systems. Such a network is formalized as a graph with reaction systems residing at its nodes, where ea...

In this paper, we introduce graph-based reaction systems as a generalization of set-based reaction systems, a novel and well-investigated model of interactive computation. Graph-based reaction systems allow us to introduce a new methodology for graph transformation, which is not based on the traditional “cut, add, and paste” approach, but rather on...

Reaction systems, motivated by the functioning of the living cell, became a novel model of interactive computation. In this paper, we pursue this line of research. More specifically, we present a systematic investigation of possible interactions of a reaction system with its environment (context). While in the original definition this interaction i...

This book offers an overview of the key ideas of Petri nets, how they were developed, and how they were applied in diverse applications. The chapters in the first part offer individual perspectives on the impact of Petri’s work. The second part of the book contains personal memories from researchers who collaborated with him closely, in particular...

This book constitutes revised selected papers from the 19th International Conference on Membrane Computing (CMC19), CMC 2018, which was held in Dresden, Germany, in September 2018. The 15 papers presented in this volume were carefully reviewed and selected from 20 submissions. The contributions aim to abstract computing ideas and models from the s...

Abstract. In this paper, we introduce graph-based reaction systems as a generalization of set-based reaction systems, a novel and well-investigated model of interactive computation. Graph-based reaction systems allow us to introduce a novel methodology for graph transformation, which is not based on the traditional "cut, add, and paste" approach, b...

Reaction systems were introduced as a formal model of interactions between biochemical reactions. These interactions, which are based on two mechanisms: facilitation and inhibition, determine the functioning of the living cell. Processes taking place in a reaction system are driven by the fixed set A of available reactions provided by . In this pap...

This book contains revised selected papers from the 17th International Conference on Membrane Computing, CMC 2017, held in Milan, Italy, in July 2016. The 19 full papers presented in this volume were carefully reviewed and selected from 28 submissions. They deal with membrane computing (P systems theory), an area of copmputer science aiming to abs...

In this paper we present a brief overview of a representative fragment of the theory of regions. Regions are a powerful tool for the synthesis of concurrent systems from a behavioural specification. To demonstrate the robustness of region based synthesis we survey some of the existing results for extensions of place/transition nets. We relate in pa...

Unpublished technical report part of which is published in a separate paper.

Abstract This paper defines a temporal logic for reaction systems (rsCTL). The logic is interpreted over the models for the context restricted reaction systems that generalize standard reaction systems by controlling context sequences. Moreover, a translation from the context restricted reaction systems into boolean functions is defined in order to...

Reaction systems are a formal framework for investigating dynamic bioprocesses which was inspired by the functioning of the living cell. Zoom structures formalize a static depository of knowledge of a discipline of knowledge/science and in particular they allow one to deal with the hierarchical nature of biology. Exploration systems combine reactio...

This book constitutes revised selected papers from the International Conference on Membrane Computing, CMC 2015, held in Valencia, Spain, in August 2015. The 22 full papers presented in this volume were carefully reviewed and selected from 34 submissions. The volume also contains 3 invited talks in full-paper length.

In this paper we extend the framework of reaction systems by introducing (extended) zoom structures which formalize a depository of knowledge of a discipline of science. The integrating structure of such a depository (which is a well-founded partial order) allows one to deal with the hierarchical nature of biology. This leads to the notion of an ex...

This paper discusses research frontiers of membrane computing by presenting current open problems and research topics, together with the relevant background and motivation.

Natural Computing (cf., e.g., [12,13]) is concerned with human-designed computing inspired by nature as well as with computation taking place in nature, i.e., it investigates models, computational techniques, and computational technologies inspired by nature as well as it investigates, in terms of information processing, phenomena/processes taking...

Ciliates are a very diverse and ancient group of unicellular eukaryotic organisms. A feature that is essentially unique to ciliates is the nuclear dualism, meaning that they have two functionally different types of nuclei, the macronucleus and the micronucleus. During sexual reproduction a micronucleus is transformed into a macronucleus – this proc...

Boolean nets are a family of Petri net models with very simple markings which are sets of places. We investigate several classes of boolean nets distinguished by different kinds of individual connections between places and transitions, as well as different ways in which these connections are combined in order to specify the effect of executing step...

This paper continues an investigation into bridging two research areas concerned with natural computing: membrane computing and reaction systems. More specifically, the paper considers a transfer of two assumptions/axioms of reaction systems, non-permanency and the threshold assumption, into the framework of membrane computing. It is proved that: 1...

Carl Adam Petri was a visionary who founded an extraordinarily fruitful domain of study in the field of distributed discrete event systems. He was the first computer scientist to identify concurrency as a fundamental aspect of computing. He did so in his seminal PhD thesis from 1962 where in fact he outlined a whole new foundations for computer sci...

This chapter is dedicated to the memory of Professor Zdzisław Pawlak, founder of the Polish school of Artificial Intelligence and one of the pioneers in Computer Engineering and Computer Science with worldwide influence. To capture the spirit of Professor Pawlak’s creative genius, this chapter contains testimonies of many collaborators, colleagues...

Reaction systems are a formal model for processes inspired by the functioning of the living cell. The underlying idea of this model is that the functioning of the living cell is determined by the interactions of biochemical reactions, and these interactions are based on the mechanisms of facilitation and inhibition. In this chapter, we first review...

In this paper we present in a tutorial fashion the framework of reaction systems – a formal approach to investigating processes instigated by the living cell. The main idea behind this approach is that this functioning is determined by interactions between biochemical reactions, and these interactions are based on two mechanisms, facilitation and i...

Automated synthesis from behavioural specifications is an attractive and powerful way of constructing concurrent systems. Here we focus on the problem of synthesising a membrane system from a behavioural specification given in the form of a transition system which specifies the desired state space of the system to be constructed. We demonstrate how...

Reaction systems are an abstract model of biochemical reactions in the living cell within a framework of finite (though often large) discrete dynamical systems. In this setting, this paper provides an analytical and experimental study of stability. The notion of stability is defined in terms of the way in which small perturbations to the initial st...

Natural Computing is concerned with both human-designed computing inspired by nature and computing taking place in nature. The former research strand investigates computational techniques, models of computation and computational devices inspired by nature. The latter research strand investigates, in terms of information processing, processes taking...

Reaction systems formally model the functioning of the living cell. By representing sets of reactions by trees, we obtain a useful tool to investigate the state spaces of reaction systems. In particular, we give an upper bound on the fraction of inactive states within a subspace of the state space. This subspace represents partial knowledge of the...

Natural Computing is the field of research that investigates both human-designed computing inspired by nature and computing taking place in nature, i.e., it investigates models and computational techniques inspired by nature and also it investigates phenomena taking place in nature in terms of information processing.Examples of the first strand of...

Most computational problems for matrix semigroups and groups are inherently difficult to solve and even undecidable starting from dimension three. The questions about the decidability and complexity of problems for two-dimensional matrix semigroups remain ...

Reaction systems are a formal model for processes inspired by the functioning of the living cell. These processes are determined by the iteration of the state transition functions of reaction systems, also called rs functions. In this paper we provide mathematical characterisations of rs functions implemented/defined by "minimal reaction systems",...

Reaction systems are a model for the investigation of processes carried out by biochemical reactions in living cells. A reaction system consists of a set of reactions which transform a current system’s state (a set of entities) into the successor state. In this paper we investigate which entities are actually relevant from the point of view of gene...

This book constitutes the proceedings of the 6th International Conference on Graph Transformations, ICGT 2012, held in Bremen, Germany, in September 2012. The 30 papers and 3 invited papers presented were carefully reviewed and selected from numerous submissions. The papers are organized in topical sections on behavioural analysis, high-level graph...

Reaction systems are a formal model of interactions between biochemical reactions. They consist of sets of reactions, where each reaction is classified by its set of reactants (needed for the reaction to take place), its set of inhibitors (each of which prevents the reaction from taking place), and its set of products (produced when the reaction ta...

We study the problem of covering a word f by a set F of available segments. In particular we demonstrate that each F induces a unique structure (scaffold) on f which determines how all "succint" coverings of f (by elements of F) are positioned on f. Our motivation for this study comes from the formalization of the template–guided recombination whic...

Reaction systems are a formal framework for investigating processes carried out by biochemical reactions. This paper is an introduction to reaction systems. It provides basic notions together with the underlying intuition and motivation as well as two examples (a binary counter and transition systems) of "programming" with reaction systems. It also...

In this talk we are concerned with the intrinsic similarities and differences between Petri nets on the one hand, and membrane systems and reaction systems on the other hand.

We continue the formal study of multiset-based self-assembly. The process of self-assembly of graphs, where iteratively new nodes are attached to a given graph, is guided by rules operating on nodes labelled by multisets. In this way, the multisets and rules model connection points (such as “sticky ends”) and complementarity/affinity between connec...

Natural Computing is an interdisciplinary field of research that investigates human-designed computing inspired by nature as well as computation taking place in nature. In other words, Natural Computing investigates models, computational techniques, and computational technologies inspired by nature as well as it investigates, in terms of informatio...

A reaction system is essentially a finite set of reactions, where each reaction consists of a finite set of reactants (needed for the reaction to take place), a finite set of inhibitors (each of which inhibits the reaction from taking place), and a finite set of products produced when the reaction takes place. A crucial feature of a reaction system...

geometrical computation involves drawing colored line segments (traces of signals) according to rules: signals with similar color are parallel and when they intersect, they are replaced according to their colors. Time and space are continuous and accumulations can be devised to unlimitedly accelerate a computation and provide, in a finite duration,...

A Petri net model is referred to as Boolean if the only pos-sible markings are sets, i.e., places are marked or not without further quantification; moreover, also the enabling conditions and firing rule are based on this principle of set-based token arithmetic. Elementary Net systems are an example of a class of Boolean nets, and so are the re-cent...

We investigate how Petri nets could he used to provide a faithful semantics of reaction systems, a formal framework for the investigation of processes carried by biochemical reactions. We propose and discuss possible approaches to this problem using some existing Petri net classes and concurrency concepts, such as maximal parallelism. After that we...

Petri nets are a general and well-established model of concurrent and distributed computation and behaviour, including that taking place in biological systems. In this survey paper, we are concerned with intrinsic relationships between Petri nets and two formal models inspired by aspects of the functioning of the living cell: membrane systems and r...

This book constitutes the thoroughly refereed post-conference proceedings of the 11th International Conference on Membrane Computing, CMC11, held in Jena, Germany, in August 2010 - continuing the fruitful tradition of 10 previous editions of the International Workshop on Membrane Computing (WMC). The 23 revised full papers presented together with 4...

Natural Computing (see, e.g., [5] or [6]) is concerned with human-designed computing inspired by nature as well as with computation taking place in nature. In other words, natural computing investigates models and computational techniques inspired by nature as well as it investigates, in terms of information processing, processes taking place in na...

Reaction systems are a functional model of interactions between biochemical reactions. They define functions on finite sets (over a common finite domain). In this paper, we investigate combinatorial properties of functions defined by reaction systems. In particular, we provide analytical approximations of combinatorial properties of random reaction...

Reaction systems are a formal model of interactions between biochemical reactions. In this note we initiate an investigation of causalities in reaction systems which reflect the way that elements (entities) of a reaction system influence each other.

This paper presents a formal framework for investigating processes driven by interactions between biochemical reactions in living cells. These interactions are based on the mechanisms of facilitation and inhibition, which underlie the definition of reaction systems – the central construct of our framework. We discuss in this paper the basic setup f...

ene Assembly in Ciliates refers to the process of transforming the micronuclear genome into the macronuclear genome during the sexual activity of conjugation in ciliates (single-celled eukaryotes). The special structure of the micronuclear genes closely resembles the linked list data structure from computer science, and the DNA rearrangements perfo...

The 9th International Conference on Unconventional Computation, UC 2010, was organized under the auspices of EATCS and Academia Europaea, by the University of Tokyo (Tokyo, Japan), and the Center for Discrete Mathematics and Theoretical Computer Science (Auckland, New Zealand). It was held in Tokyoduring June 21–25,2010(seehttp://arn.local.frs.rike...