Showing papers by "Grzegorz Rozenberg published in 2005"

Formal Methods in Software and Systems Modeling: Essays Dedicated to Hartmut Ehrig on the Occasion of His 60th Birthday (Lecture Notes in Computer Science)

Abstract: Graph Transformation.- On the Concurrent Semantics of Algebraic Graph Grammars.- From Graph Transformation to Software Engineering and Back.- Flexible Interconnection of Graph Transformation Modules.- Simulating Algebraic High-Level Nets by Parallel Attributed Graph Transformation.- Graph Processes with Fusions: Concurrency by Colimits, Again.- Graph Transformation with Variables.- Graph Transformation in Molecular Biology.- Changing Labels in the Double-Pushout Approach Can Be Treated Categorically.- Algebraic Specification and Logic.- Modules, Brains and Schemas.- From Conditional Specifications to Interaction Charts.- Algebraic Properties of Interfaces.- ? T -Integration of Logics.- Functorial Semantics of Rewrite Theories.- Expander2.- Relationships Between Equational and Inductive Data Types.- Cofree Coalgebras for Signature Morphisms.- Formal and Visual Modeling.- Nested Constraints and Application Conditions for High-Level Structures.- Synthesis Revisited: Generating Statechart Models from Scenario-Based Requirements.- Main Concepts of Networks of Transformation Units with Interlinking Semantics.- Embeddings and Contexts for Link Graphs.- Towards Architectural Connectors for UML.- Loose Semantics of Petri Nets.- A Formal Framework for the Development of Concurrent Object-Based Systems.- A Formal Description of the Basic Concepts of System Theory for Transportation.

Parallelism in gene assembly

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 the computational point of view, with ciliates even using the linked list data structure. Three molecular operations (Id, hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism of this process by investigating several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern, or how many steps are needed to assemble in parallel a micronuclear gene. We believe that the study of parallelism contributes to a better understanding of the nature of gene assembly, and in particular it provides a new insight in the complexity of this process.

Protein output for DNA computing

Abstract: In recent years, several strategies for DNA based molecular computing have been investigated. An important area of research is the detection and analysis of output molecules. We demonstrate how DNA computing can be extended with in vivo translation of the output. In the resulting proteins, the information per kilogram is about 15-fold higher than in the original DNA output. The proteins are therefore of correspondingly smaller mass, which facilitates their subsequent detection using highly sensitive mass spectrometry methods. We have tested this approach on an instance of the Minimal Dominating Set problem. The DNA used in the computation was constructed as an open reading frame in a plasmid, under the control of a strong inducible promoter. Sequential application of restriction endonucleases yielded a library of potential solutions to the problem instance. The mixture of plasmids was then used for expression of a protein representation. Using MALDI-TOF mass spectrometry, a protein corresponding to the correct solution could be detected. The results indicate the feasibility of the extension of DNA computing to include protein technology. Our strategy opens up new possibilities for both scaling of DNA computations and implementations that employ output of functional molecules or phenotypes.

Towards a petri net semantics for membrane systems

Abstract: We consider the modelling of the behaviour of membrane systems using Petri nets. First, a systematic, structural link is established between a basic class of membrane systems and Petri nets. To capture the compartmentisation of membrane systems, localities are proposed as an extension of Petri nets. This leads to a locally maximal concurrency semantics for Petri nets. We indicate how processes for these nets could be defined which should be of use in order to describe what is actually going on during a computation of a membrane system.

The breakpoint graph in ciliates

Abstract: The gene assembly process in ciliates (single-cell organisms) is interesting from both the biological and computational point of view. This paper studies the computational nature of the gene assembly process. Motivated by the breakpoint graph known from another branch of DNA transformation research, we introduce the reduction graph as a tool for the study of this process, and illustrate its usefulness by proving a number of properties of gene assembly.

Simple operations for gene assembly

Abstract: The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper some simpler variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.

Formal Methods in Software and Systems Modeling: essays dedicated to Hartmut Ehrig on the occasion of his 60th birthday

Abstract: Graph Transformation.- On the Concurrent Semantics of Algebraic Graph Grammars.- From Graph Transformation to Software Engineering and Back.- Flexible Interconnection of Graph Transformation Modules.- Simulating Algebraic High-Level Nets by Parallel Attributed Graph Transformation.- Graph Processes with Fusions: Concurrency by Colimits, Again.- Graph Transformation with Variables.- Graph Transformation in Molecular Biology.- Changing Labels in the Double-Pushout Approach Can Be Treated Categorically.- Algebraic Specification and Logic.- Modules, Brains and Schemas.- From Conditional Specifications to Interaction Charts.- Algebraic Properties of Interfaces.- ? T -Integration of Logics.- Functorial Semantics of Rewrite Theories.- Expander2.- Relationships Between Equational and Inductive Data Types.- Cofree Coalgebras for Signature Morphisms.- Formal and Visual Modeling.- Nested Constraints and Application Conditions for High-Level Structures.- Synthesis Revisited: Generating Statechart Models from Scenario-Based Requirements.- Main Concepts of Networks of Transformation Units with Interlinking Semantics.- Embeddings and Contexts for Link Graphs.- Towards Architectural Connectors for UML.- Loose Semantics of Petri Nets.- A Formal Framework for the Development of Concurrent Object-Based Systems.- A Formal Description of the Basic Concepts of System Theory for Transportation.

Combinatorial aspects of minimal DNA expressions

Abstract: We describe a formal language/notation for DNA molecules that may contain nicks and gaps. The elements of the language, DNA expressions, denote formal DNA molecules. Different DNA expressions may denote the same formal DNA molecule. We analyse the shortest DNA expressions denoting a given formal DNA molecule: what is their length, how are they constructed, how many of them are there, and how can they be characterized.

Main concepts of networks of transformation units with interlinking semantics

Abstract: The aim of this paper is to introduce a modelling concept and structuring principle for rule-based systems the semantics of which is not restricted to a sequential behavior, but can be applied to various types of parallelism and concurrency. The central syntactic notion is that of a transformation unit that encapsulates a set of rules, imports other transformation units, and regulates the use and interaction of both by means of a control condition. The semantics is given by interlinking the applications of rules with the semantics of the imported units using a given collection of semantic operations. As the main result, the interlinking semantics turns out to be the least fixed point of the interlinking operator. The interlinking semantics generalizes the earlier introduced interleaving semantics of rule-based transformation units, which is obtained by the sequential composition of binary relations as only semantic operation.

Membrane Computing: 5th International Workshop, WMC 2004, Milan, Italy, June 14-16, 2004, Revised Selected and Invited Papers

Abstract: Invited Lectures.- ?P Systems and Typed ?-Calculus.- P Automata.- Asynchronous P Systems and P Systems Working in the Sequential Mode.- Evolution and Oscillation in P Systems: Applications to Biological Phenomena.- An Approach to Computational Complexity in Membrane Computing.- LMNtal: A Language Model with Links and Membranes.- Regular Presentations.- Executable Specifications of P Systems.- On the Efficiency of P Systems with Active Membranes and Two Polarizations.- Communicative P Systems with Minimal Cooperation.- Ultimately Confluent Rewriting Systems. Parallel Multiset-Rewriting with Permitting or Forbidding Contexts.- Unstable P Systems: Applications to Linguistics.- A P System Description of the Sodium-Potassium Pump.- Inhibiting/De-inhibiting Rules in P Systems.- Time-Independent P Systems.- On Two-Dimensional Mesh Networks and Their Simulation with P Systems.- Exploring Computation Trees Associated with P Systems.- Approximating Non-discrete P Systems.- Reducing the Size of Extended Gemmating P Systems.- P Systems Generating Trees.- On Descriptive Complexity of P Systems.- P Systems with Symport/Antiport: The Traces of RBCs.- Conservative Computations in Energy-Based P Systems.- General Multi-fuzzy Sets and Fuzzy Membrane Systems.- Trading Polarization for Bi-stable Catalysts in P Systems with Active Membranes.- Modelling Dynamic Organization of Biology-Inspired Multi-agent Systems with Communicating X-Machines and Population P Systems.- On the Size of P Systems with Minimal Symport/Antiport.

Application of mismatch detection methods in DNA computing

Abstract: In many implementations of DNA computing, reliable detection of hybridization is of prime importance. We have applied several well-established DNA mutation scanning methods to this problem. Since they have been developed for speed and accuracy, these technologies are very promising for DNA computing. We have benchmarked a heteroduplex migration assay and enzymatic detection of mismatches on a 4 variable instance of 3SAT, using a previously described blocking algorithm. The first method is promising, but yielded ambiguous results. On the other hand, we were able to distinguish all perfect from imperfect duplexes by means of a CEL I mismatch endonuclease assay.

The Embedding Problem For Switching Classes

Abstract: 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 transformations of the vertices. In case vertices are given an identity, various relatively efficient algorithms exist for deciding whether a graph can be switched so that it contains some other graph, the query graph, as an induced sub- graph. However, when considering graphs up to isomorphism, we immediately run into the graph