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Showing papers by "Grzegorz Rozenberg published in 2000"


Journal ArticleDOI
TL;DR: A new method of computing using DNA plasmids is introduced, applicable to a wide variety of algorithmic problems, and the potential advantages are listed.
Abstract: A new method of computing using DNA plasmids is introduced and the potential advantages are listed. The new method is illustrated by reporting a laboratory computation of an instance of the NP-complete algorithmic problem of computing the cardinal number of a maximal independent subset of the vertex set of a graph. A circular DNA plasmid, specifically designed for this method of molecular computing, was constructed. This computational plasmid contains a specially inserted series of DNA sequence segments, each of which is bordered by a characteristic pair of restriction enzyme sites. For the computation reported here, the DNA sequence segments of this series were used to represent the vertices of the graph being investigated. By applying a scheme of enzymatic treatments to the computational plasmids, modified plasmids were generated from which the solution of the computational problem was selected. This new method of computing is applicable to a wide variety of algorithmic problems. Further computations in this style are in progress.

148 citations



Journal ArticleDOI
TL;DR: The fundamental properties of computations in such P systems with external output are investigated, including the computing power, normal forms, and basic decision problems.
Abstract: A membrane computing system (also called P 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 membrane Each cell is an independent computing agent with its own computing program, which produces objects The interaction between cells consists of the exchange of objects through membranes The output of a computation is a partially ordered set of objects which leave the system through its external membrane The fundamental properties of computations in such P systems with external output are investigated These include the computing power, normal forms, and basic decision problems

67 citations


Book ChapterDOI
13 Jun 2000
TL;DR: By keeping track of the strands as they weave back and forth through the assembly, it is shown that surprisingly sophisticated calculations can be performed using linear self-assembly.
Abstract: This paper investigates computation by linear assemblies of complex DNA tiles, which we call string tiles. By keeping track of the strands as they weave back and forth through the assembly, we show that surprisingly sophisticated calculations can be performed using linear self-assembly. Examples range from generating an addition table to providing O(1) solutions to CNF-SAT and DHPP. We classify the families of languages that can be generated by various types of DNA molecules, and establish a correspondence to the existing classes ET0Lml and ET0Lfin. Thus, linear self-assembly of string tiles can generate the output languages of finite-visit Turing Machines.

48 citations


Journal ArticleDOI
TL;DR: It is given that a language L is k -poly-slender if the number of words of length n in L is of order ${\cal O}.
Abstract: 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 ${\cal O}(n^k)$ . We give a precise characterization of the k -poly-slender context-free languages. The well-known characterization of the k -poly-slender regular languages is an immediate consequence of ours.

24 citations


Journal ArticleDOI
TL;DR: It is shown that every switching class, except the class of all complete bipartite graphs, contains a pancyclic graph, which implies that deciding whether a switching class contains a hamiltonian graph can be done in polynomial time although this problem is NP-complete for graphs.

10 citations


Book
01 Jan 2000
TL;DR: This paper discussesGraph-Based Models for Managing Development Processes, Resources, and Products, and Software Engineering, and Graph Transformation Techniques for Integrating Information from the WWW.
Abstract: Graph Languages.- Some Remarks on the Generative Power of Collage Grammars and Chain-Code Grammars.- Tree Languages Generated by Context-Free Graph Grammars.- Neighborhood Expansion Grammars.- Neighborhood-Preserving Node Replacements.- Graph Theory.- Complexity Issues in Switching of Graphs.- The Power of Local Computations in Graphs with Initial Knowledge.- Categorical Approaches.- Double-Pullback Graph Transitions: A Rule-Based Framework with Incomplete Information.- Double-Pushout Approach with Injective Matching.- Node Replacement in Hypergraphs: Translating NCE Rewriting into the Pullback Approacht.- Pushout Complements for Arbitrary Partial Algebras.- Concurrency and Distribution.- Unfolding of Double-Pushout Graph Grammars is a Coreflection.- Local Views on Distributed Systems and Their Communication.- Dynamic Change Management by Distributed Graph Transformation: Towards Configurable Distributed Systems.- A Framework for NLC and ESM: Local Action Systems.- Artificial Intelligence.- Redundancy and Subsumption in High-Level Replacement Systems.- Knowledge Representation and Graph Transformation.- Utilizing Constraint Satisfaction Techniques for Efficient Graph Pattern Matching.- Visual Languages.- Conceptual Model of the Graphical Editor GenGEd for the Visual Definition of Visual Languages.- From Formulae to Rewriting Systems.- Hypergraphs as a Uniform Diagram Representation Model.- Specification Concepts.- Story Diagrams: A New Graph Rewrite Language Based on the Unified Modeling Language and Java.- A Fully Abstract Model for Graph-Interpreted Temporal Logic.- More About Control Conditions for Transformation Units.- Integrity Constraints in the Multi-Paradigm Language PROGRES.- Modularity and Refinement.- A Framework for Adding Packages to Graph Transformation Approaches.- Refinements of Graph Transformation Systems via Rule Expressions.- Simple Modules for Grace.- UML Packages for PROgrammed Graph REwriting Systems.- Incremental Development of Safety Properties in Petri Net Transformations.- Software Engineering.- Using Graph Transformation Techniques for Integrating Information from the WWW.- A Model Making Automation Process (MMAP) Using a Graph Grammar Formalism.- Graph-Based Models for Managing Development Processes, Resources, and Products.- Deriving Software Performance Models from Architectural Patterns by Graph Transformations.

6 citations


Book ChapterDOI
13 Dec 2000
TL;DR: Natural Computing is computing inspired by (or gleaned from) nature, while DNA Computing is much bolder: it is using novel paradigms from molecular biology, but it also aims at the implementation of algorithms based on these paradigm in biological hardware (bioware).
Abstract: Natural Computing is computing inspired by (or gleaned from) nature. During the last decade the area of Natural Computing became one of the most active areas of computer science, and without doubt it will become central for computing in the coming years. Characteristic for Natural Computing is the metaphorical use of concepts, principles and mechanisms underlying natural systems. Thus, e.g., evolutionary algorithms use the concepts of mutation, recombination, and natural selection from biology, while neural networks are inspired by the highly interconnected neural structures in the brain and nervous system. In both areas, the algorithms are implemented on traditional silicon-based computers. On the other hand, DNA Computing (or more generally, Molecular Computing) is much bolder: it is using novel paradigms (coming from molecular biology), but it also aims at the implementation of algorithms based on these paradigms in biological hardware (bioware).

2 citations



Book ChapterDOI
01 Jan 2000
TL;DR: Investigating the borderline between their finite and infinite antichains is able to fully characterize the property of being well partial order, and the result generalizes Higman’s theorem.
Abstract: 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 case in between and put some restrictions on the number of factors as to which u is allowed to be scattered. A large class of partial orders which are generalizations of factors and subwords is obtained. Investigating the borderline between their finite and infinite antichains, we are able to fully characterize the property of being well partial order. The result generalizes Higman’s theorem.