Showing papers by "Grzegorz Rozenberg published in 2007"
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TL;DR: The paper provides the basic definitions, illustrates them by biology and computer science oriented examples, relates reaction systems to some traditional models of computation, and proves some basic properties of reaction systems.
Abstract: Interactions between biochemical reactions lie at the heart of functioning of a living cell. In order to formalize these interactions we introduce reaction systems. We motivate them by explicitely stating a number of assumptions/axioms that (we believe) hold for a great number of biochemical reactions - we point out that these assumptions are very different from the ones underlying traditional models of computation. The paper provides the basic definitions, illustrates them by biology and computer science oriented examples, relates reaction systems to some traditional models of computation, and proves some basic properties of reaction systems.
201 citations
TL;DR: In this article, the authors introduce the notion of a module and investigate the formation and evolution of modules in a self-organizing reaction system, where the organizing goal is to ensure a specific property of the set of all modules (of a state of a process).
66 citations
Proceedings Article•
01 Jan 2007
TL;DR: It is proved that reaction systems can be viewed as self-organizing systems, where the organizing goal is to ensure a specific property of the set of all modules (of a state of a process).
Abstract: Reaction systems are a formal model of interactions between biochemical reactions. They are based on the observation that two basic mechanisms behind the functioning of biochemical reactions are facilitation and inhibition. In this paper we continue the investigation of reaction systems, and in particular we introduce the notion of a module, and then we investigate the formation and evolution of modules. Among others we prove that reaction systems can be viewed as self-organizing systems, where the organizing goal is to ensure a specific property of the set of all modules (of a state of a process).
59 citations
TL;DR: It is demonstrated how the computations can be extended by in vivo translation of the DNA library into protein, which allows for multi-criterion optimization of knapsack computations, one of the most complex computations performed by natural systems.
Abstract: One line of DNA computing research focuses on parallel search algorithms, which can be used to solve many optimization problems. DNA in solution can provide an enormous molecular library, which can be searched by molecular biological techniques. We have implemented such a parallel search for solutions to knapsack problems, which ask for the best way to pack a knapsack of limited volume. Several instances of knapsack problems were solved using DNA. We demonstrate how the computations can be extended by in vivo translation of the DNA library into protein. This combination of DNA and protein allows for multi-criterion optimization. The knapsack computations performed can then be seen as protein optimizations, one of the most complex computations performed by natural systems.
32 citations
TL;DR: It is shown that membrane systems which differ from conventional membrane systems by the following features are computationally universal and that if only the second feature is used then one can generate at least the family of Parikh images of the languages generated by programmed grammars without appearance checking.
22 citations
Book•
01 Jan 2007
TL;DR: The Handbook of Theoretical Computer Science as discussed by the authors provides professionals and students with a comprehensive overview of the main results and developments in this rapidly evolving field, including models of computation, complexity theory, data structures, and efficient computation in many recognized subdisciplines of theoretical computer science.
Abstract: "Of all the books I have covered in the Forum to date, this set is the most unique and possibly the most useful to the SIGACT community, in support both of teaching and research.... The books can be used by anyone wanting simply to gain an understanding of one of these areas, or by someone desiring to be in research in a topic, or by instructors wishing to find timely information on a subject they are teaching outside their major areas of expertise." -- Rocky Ross, "SIGACT News" "This is a reference which has a place in every computer science library." -- Raymond Lauzzana, "Languages of Design" The Handbook of Theoretical Computer Science provides professionals and students with a comprehensive overview of the main results and developments in this rapidly evolving field. Volume A covers models of computation, complexity theory, data structures, and efficient computation in many recognized subdisciplines of theoretical computer science. Volume B takes up the theory of automata and rewriting systems, the foundations of modern programming languages, and logics for program specification and verification, and presents several studies on the theoretic modeling of advanced information processing. The two volumes contain thirty-seven chapters, with extensive chapter references and individual tables of contents for each chapter. There are 5,387 entry subject indexes that include notational symbols, and a list of contributors and affiliations in each volume.
14 citations
TL;DR: The study of the spiking neural P systems considered as transducers of binary strings or binary infinite sequences is continued, and their ability to compute morphisms is investigated.
Abstract: We continue the study of the spiking neural P systems considered as transducers of binary strings or binary infinite sequences, and we investigate their ability to compute morphisms. The class of computed morphisms is rather restricted: length preserving or erasing, and the so-called 2-block morphisms can be computed; however, non-erasing non-length-preserving morphisms cannot be computed.
11 citations
Journal Article•
TL;DR: The model deals with aggregates of cells which are defined as undirected graphs where a multiset over a fixed alphabet is assigned to each vertex, and properties of the sets of graphs generated by these systems are characterised.
Abstract: We present a model for self-assembly of graphs based on multisets and the formalism of membrane systems The model deals with aggregates of cells which are defined as undirected graphs where a multiset over a fixed alphabet is assigned to each vertex The evolution of these aggregates is determined by an application of multiset-based aggregation rules to enlarge the current structure as well as an application of membrane-systems-based communication rules to enable cells to exchange objects alongside the edges of the graph We compare the generative power of selfassembly membrane systems with and without communication rules, and we characterise properties of the sets of graphs generated by these systems We also introduce two notions of stability for self-assembly processes that capture the idea of having produced a stable structure Finally, we investigate self-assembly membrane systems where the alphabet is a singleton
9 citations
TL;DR: Two efficient algorithms for evaluating precycles and defects are given: one is an algorithm due to Contejean and Devie, the other is a novel branch-and-bound tree search procedure.
8 citations
TL;DR: A specific repair scheme is proposed, and it is proposed that this repair scheme applied to a coiled structure of a DNA molecule that has undergone multiple breaks can produce IES insertions and/or scrambled/inverted MIC gene patterns.
13 Aug 2007
27 Aug 2007
TL;DR: It is shown that the reduction graph can be defined within the GPRS if one restricts ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature), which allows one to carry over from the SPRS to the G PRS several results that rely on the reductiongraph.
Abstract: The string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS) are important formal models of gene assembly in ciliates. The reduction graph is a useful tool for the analysis of the SPRS, providing valuable information about the way that gene assembly is performed for a given gene. The GPRS is more abstract than the SPRS - not all information present in the SPRS is retained in the GPRS. As a consequence the reduction graph cannot be defined for the GPRS in general, but we show that it can be defined if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature). Defining the reduction graph within the GPRS allows one to carry over from the SPRS to the GPRS several results that rely on the reduction graph.
Posted Content•
TL;DR: It is shown that the reduction graph can be defined (in an equivalent manner as defined for the SPRS) if the authors restrict ourselves to so-called realistic overlap graphs, which correspond to genes occurring in nature.
Abstract: 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 valuable tool within the SPRS, revealing much information about how gene assembly is performed for a given gene. The GPRS is more abstract than the SPRS and not all information present in the SPRS is retained in the GPRS. As a consequence the reduction graph cannot be defined for the GPRS in general, but we show that it can be defined (in an equivalent manner as defined for the SPRS) if we restrict ourselves to so-called realistic overlap graphs. Fortunately, only these graphs correspond to genes occurring in nature. Defining the reduction graph within the GPRS allows one to carry over several results within the SPRS that rely on the reduction graph.
01 Jan 2007
18 Jun 2007
TL;DR: Natural computing refers to computation taking place in nature and to humandesigned computation inspired by nature, and human-designed computing inspired byNature has had already a big impact on the development of computer science.
Abstract: Natural computing refers to computation taking place in nature and to humandesigned computation inspired by nature. When complex phenomena going on in nature are viewed as computational processes, our understanding of these phenomena and of the essence of computation is enhanced. On the other hand human-designed computing inspired by nature has had already a big impact on the development of computer science (think, e.g., about neural computing, evolutionary computing, molecular computing and quantum computing).
18 Jun 2007
TL;DR: Two main mechanisms behind the functioning of biochemical reactions are facilitation and inhibition; these mechanisms are also central for the interaction between biochemical reactions.
Abstract: Two main mechanisms behind the functioning of biochemical reactions are facilitation and inhibition; these mechanisms are also central for the interaction between biochemical reactions. This observation underlies the theory of reaction systems which is a formal framework for the investigation of biochemical reactions, and especially interactions between them.
Journal Article•
TL;DR: A correspondence framework between three-valued logics and similarity-based approximate reasoning and a possibility-theoretic view of formal concept analysis for disagreement and exhaustiveness are presented.
Abstract: Arrow logic with arbitrary intersections : applications to Pawlak's information systems p. 1 Rough set approach to behavioral pattern identification p. 27 Multiset-based self-assembly of graphs p. 49 Entropies and co-entropies of coverings with application to incomplete information systems p. 77 Rough sets and learning by unification p. 107 Rough dialogue and implication lattices p. 123 On string languages generated by spiking neural P systems p. 141 Relative nondeterministic information logic is EXPTIME-complete p. 163 A correspondence framework between three-valued logics and similarity-based approximate reasoning p. 179 A possibility-theoretic view of formal concept analysis p. 195 A multi-modal logic for disagreement and exhaustiveness p. 215 Complexity issues in multiagent logics p. 239 Reaction systems p. 263 Cooperative world modeling in dynamic multi-robot environments p. 281 Towards a pragmatic mereology p. 295 Pawlak's information systems in terms of Galois connections and functional dependencies p. 315 Z. Pawlak, a precursor of DNA computing and of picture grammars p. 331 Locally derivable graphs p. 335 On construction of partial reducts and irreducible partial decision rules p. 357 Retracts of algebras p. 375 Bridging the gap between non-symbolic and symbolic processing-how could human being acquire language? p. 385 Near sets : special theory about nearness of objects p. 407 Concept approximation in mathematics and computer science. An essay in homage to Zdzislaw Pawlak p. 435 Approaches to conflict dynamics based on rough sets p. 453 Subword balance in binary words, languages and sequences p. 469 Histogram thresholding using beam theory and ambiguity measures p. 483 On generating all binary trees p. 505
TL;DR: It is shown that every symmetric function g has a unique minimal semimetric switch, and, moreover, there is a switch of g that is isometric to a finite Manhattan metric.