Showing papers by "Grzegorz Rozenberg published in 1998"

DNA Computing: New Computing Paradigms

Abstract: This is the first book on DNA computing, a molecular approach that may revolutionize computing-replacing silicon with carbon and microchips with DNA molecules. The book starts with an introduction to DNA computing, exploring the power of complementarity, the basics of biochemistry, and language and computation theory. It then brings the reader to the most advanced theories develop thus far in this emerging research area.

DNA computing, sticker systems, and universality ?

Abstract: 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]. Several types of sticker systems are shown to characterize (modulo a weak coding) the regular languages, hence the power of finite automata. One variant is proven to be equivalent to Turing machines. Another one is found to have a strictly intermediate power.

Introduction: DNA Computing in a Nutshell

Abstract: From silicon to carbon. From microchips to DNA molecules. This is the basic idea in DNA computing. Information-processing capabilities of organic molecules can be used in computers to replace digital switching primitives.

Lectures on Petri nets : advances in Petri nets

Abstract: Petri nets, process algebras and concurrent programming languages.- Petri nets and production systems.- Computer Supported Cooperative Work and Petri Nets.- Petri nets and digital hardware design.- An introduction to the practical use of coloured Petri Nets.- Protocol specification using P-graphs, a technique based on coloured Petri Nets.- Distributed algorithms for networks of agents.- Efficient performance analysis techniques for stochastic well-formed nets and stochastic process algebras.- Modelling and analysis of distributed software using GSPNs.

Bidirectional sticker systems.

Abstract: We introduce two-sided sticker systems, the two-sided variant of a computability model introduced as an abstraction of Adleman's style of DNA computing and of the matching of the so-called Watson-Crick complements. Several types of sticker systems are shown to have the same power as regular grammars, one variant is found to represent the linear languages, and another one is proved to be able to represent any recursively enumerable language. From this result we infer that any recursively enumerable language can be represented as the projection of the intersection of two minimal linear languages.

Complexity Issues in Switching of Graphs

Abstract: In the context of graph transformations we look at the operation of switching, which can be viewed as an elegant method for realizing global transformations of graphs through local transformations of the vertices. We compare the complexity of a number of problems on graphs with the complexity of these problems extended to the set of switches of a graph. Within this framework, we prove a modification of Yannakakis’ result and use it to show NP-completeness for the embedding problem. Finally we prove NP-completeness for the 3-colourability problem.

Lectures on Embedded Systems: European Educational Forum School on Embedded Systems, Veldhoven, The Netherlands, November 25-29, 1996

Abstract: Verification of clocked and hybrid systems.- Analyzing and synthesizing hybrid control systems.- Model checking timed automata.- On modeling real-time task systems.- A modular approach for programming embedded systems.- Proof-based system engineering and embedded systems.- A design notation and toolset for high-performance embedded systems development.- The maturity of object-oriented methodologies.- Object oriented development of embedded systems with the octopus method.- Engineering of real-time systems with an experiment in hybrid control.- Formal methods in the design of a storm surge barrier control system.- Statecharts in use: structured analysis and object-orientation.- Embedded systems in consumer products.- The long road from research to telecommunication applications.- Development of embedded software at ICT.

Double-Pullback Graph Transitions: A Rule-Based Framework with Incomplete Information

Abstract: Reactive systems perform their tasks through interaction with their users or with other systems (as parts of a bigger system) An essential requirement for modeling such systems is the ability to express this kind of interaction Classical rule-based approaches like Petri nets and graph transformation are not suited for this purpose because they assume to have complete control about the state and its transformation Therefore, in this paper we propose a general framework which extends a given rule-based approach by a loose semantics where the rules of the system (eg, graph productions or Petri net transitions) are considered as incomplete descriptions of the transformations to be performed: they still determine the changes to the matched substructure but for the remaining part (the context) unspecified changes are possible representing the application of (unknown) rules from the environment

Watson—Crick Automata

Abstract: In this chapter we investigate the automata counterpart of the sticker systems studied in the previous chapter. We consider a new type of automata, working on tapes which are double stranded sequences of symbols related by a complementarity relation, similar to a DNA molecule (such a data structure is called a Watson-Crick tape). The automata scan separately each of the two strands, in a correlated manner. They can also have a finite number of states controlling the moves and/or they can have an auxiliary memory which is also a Watson—Crick tape, used in a FIFO-like manner Combining such possibilities we obtain several types of automata. In most cases, these automata augmented with squeezing mechanisms, such as weak codings and deterministic sequential transducers, characterize the recursively enumerable languages.

Contexts on Trajectories

Abstract: 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 obtain also a very general class of contextual grammars such that most of the fundamental classes of contextual grammars, for instance, internal contextual grammars, external contextual grammars, n-contextual grammars, are particular cases of contextual grammars with contexts shuffled on trajectories. The approach is very flexible, able to model various aspects from linguistics.

Insertion-Deletion Systems

Abstract: In this chapter we consider computing models based on two operations which were already considered in formal language theory, mainly with motivation from linguistics. These operations — insertion and deletion, with context dependence — can also be encountered in the genetic area and they can be performed, at least theoretically, in the following ways.

Introduction to Formal Language Theory

Abstract: The mathematical theory of DNA computing presented in Part II of this book is developed in the framework of formal language theory. As we have seen in Chap. 1, DNA molecules have a natural representation through “double” strings satisfying certain assumptions (Watson-Crick complementarity and opposite directionality). Also, various enzymatic operations on DNA molecules can be naturally represented as operations on (double) strings. Consequently, using DNA molecules and their manipulation for the purpose of DNA computing can be conveniently and naturally expressed in the framework of (double) strings and operations on them. This leads to formal language theory as a natural framework for formalizing and investigating DNA computing.

Beginnings of Molecular Computing

Abstract: “We can see only a short distance ahead, but we can see plenty there that needs to be done.” These words of Turing [213] can be taken as an underlying principle of any program for scientific development. Such an underlying principle is very characteristic for research programs in computer science. Advances in computer science are often shown by and remembered from some unexpected demonstration, rather than from a dramatic experiment as in physical sciences. As pointed out by Hartmanis [83], it is the role of such a demo to show the possibility or feasibility of doing what was previously thought to be impossible or not feasible. Often, the ideas and concepts brought about and tested in such demos determine or at least influence the research agenda in computer science. Adleman’s experiment [1] constituted such a demo. This book is about the short distance we can see ahead, and about the theoretical work already done concerning various aspects of molecular computing. The ultimate impact of DNA computing cannot yet be seen; this matter will be further discussed in Sect. 2.4.

DNA: Its Structure and Processing

Abstract: The term “genetic engineering” is a very broad generic term used to cover all kinds of manipulations of genetic material. For the purpose of this book this term describes the in vitro (hence outside living cell) manipulation of DNA and related molecules. These manipulations may be used to perform various kinds of computations.

On the Crossover Distance

Abstract: 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 another. The present paper is a contribution to the algorithmic study of genom evolution by crossovers (translocations). Crossover is the biological process of exchanging material of the end of two (homologous) chromosomes \cite{hfs}. In this paper we consider chromosomes as being linear strings that exchange each other prefixes in the crossover process. Two types of crossover distance between two sets of strings (genomes) are introduced; we examine the complexity of computing these distances in the case of uniform crossover, that is at each step the strings exchange prefixes of the same length. We present exact polynomial algorithms based on the "greedy" strategy when the target set is a singleton. When considering arbitrary target sets an 2-approximation algorithm is provided for computing the sequential crossover distance. Some open problems are also formulated.

Characterizations of re languages starting from internal contextual languages

Abstract: We investigate the problem of expressing an arbitrary recursively enumerable language L 0in terms of an internal contextual language. It has been shown previously that L 0is a gsm image of a language generated by an internal contextual grammar with finite selectors. We first prove several variants of this characterization of recursively enumerable languages. We then establish two entirely new characterizations in terms of internal contextual grammars with finite selectors, applying either (1) leftmost (or prefix) derivations, or (2) erased contexts. The characterization obtained in (2) is particularly simple because one-sided grammars are sufficient in this case.