Showing papers by "Grzegorz Rozenberg published in 2006"

DNA Computing: New Computing Paradigms (Texts in Theoretical Computer Science. An EATCS Series)

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Spike trains in spiking neural p systems

Abstract: We continue here the study of the recently introduced spiking neural P systems, which mimic the way that neurons communicate with each other by means of short electrical impulses, identical in shape (voltage), but emitted at precise moments of time. The sequence of moments when a neuron emits a spike is called the spike train (of this neuron); by designating one neuron as the output neuron of a spiking neural P system II, one obtains a spike train of II. Given a specific way of assigning sets of numbers to spike trains of II, we obtain sets of numbers computed by II. In this way, spiking neural P systems become number computing devices. We consider a number of ways to assign (code) sets of numbers to (by) spike trains, and prove then computational completeness: the computed sets of numbers are exactly Turing computable sets. When the number of spikes present in the system is bounded, a characterization of semilinear sets of numbers is obtained. A number of research problems is also formulated.

Nanotechnology : science and computation

Abstract: Part 1 DNA Nanotechnology Algorithmic Self-assembly: Scaffolded DNA Origami: From Generalized Multi-crossovers to Polygonal Networks.- A Fresh Look at DNA Nanotechnology.- DNA Nanotechnology: An Evolving Field.- Self-healing Tile Sets.- Compact Error Resilient Computational DNA Tilings.- Forbidding-Enforcing Conditions in DNA Self-assembly of Graphs.- Part 2: Codes for DNA Nanotechnology: Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set.- Selection of Large Independent Sets of DNA Oligonucleotides.- Involution Solid Codes.- Part III: DNA Nanodevices: DNA-Based Motor Work at Bell Laboratories.- Nanoscale Molecular Transport by Synthetic DNA Machines.- Part IV: Electronics, Nanowires and DNA: A Supramolecular Approach to Metal Array Programming Using Artificial DNA.- Multicomponent Assemblies Including Long DNA and Nanoparrticles An Answer for the Integration Problem? Molecular Electronics From Physics to Computing.- Part V: Other Bio-molecules in Self-assembly: Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials.- Adding Functionality to DNA Arrays: The Developments of Semisynthetic DNA-Protein Conjugates.- Bacterial Surface Layer Proteins: A Simple but Versatile Biological Self-assembly System in Nature.- Part VI: Biomolecular Computational Models: Computing with Hairpins and Secondary Structures of DNA.- Bottom-up Approach to Complex Molecular Behaviors.- Aqueous Computing: Writing on Molecules Dissolved in Water.- Part VII: Computations Inspired by Cells: Turing Machines with Cells on the Tape.- Insights into a Biological Computer: Detangling Scrambled Genes of Ciliates.- Modeling Simple Operations for Gene Assembly.-

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 maxima] 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.

Process semantics for membrane systems

Abstract: A process model based on Petri nets is proposed to describe the structure of the behaviour of basic membrane systems. In [12], a systematic and structural link has been established between a basic class of membrane systems and Petri nets. To capture the compartmentisation of membrane systems, Place/Transition nets with explicit localities have been introduced. Each locality identifies a distinct set of transitions which may only be executed synchronously, i.e., in a locally maximal concurrent manner. Here, we develop the notion of a process for these nets. The resulting formalism should be of use in the investigation of the ways in which computations of membrane systems can evolve.

Membrane computing : 6th International Workshop, WMC 2005 : Vienna, Austria, July 18-21, 2005 : revised selected and invited papers

Abstract: Invited Lectures.- Computational Power of Symport/Antiport: History, Advances, and Open Problems.- Structural Operational Semantics of P Systems.- Some Recent Results Concerning Deterministic P Systems.- Membrane Algorithms.- On Evolutionary Lineages of Membrane Systems.- Regular Presentations.- Number of Protons/Bi-stable Catalysts and Membranes in P Systems. Time-Freeness.- Symbol/Membrane Complexity of P Systems with Symport/Antiport Rules.- On P Systems as a Modelling Tool for Biological Systems.- Encoding-Decoding Transitional Systems for Classes of P Systems.- On the Computational Power of the Mate/Bud/Drip Brane Calculus: Interleaving vs. Maximal Parallelism.- A Membrane Computing System Mapped on an Asynchronous, Distributed Computational Environment.- P Systems with Memory.- Algebraic and Coalgebraic Aspects of Membrane Computing.- P Systems and the Modeling of Biochemical Oscillations.- P Systems, Petri Nets, and Program Machines.- On the Power of Dissolution in P Systems with Active Membranes.- A Linear Solution for QSAT with Membrane Creation.- On Symport/Antiport P Systems and Semilinear Sets.- Boolean Circuits and a DNA Algorithm in Membrane Computing.- Towards a Petri Net Semantics for Membrane Systems.- Quantum Sequential P Systems with Unit Rules and Energy Assigned to Membranes.- Editing Distances Between Membrane Structures.- Relational Membrane Systems.- On the Rule Complexity of Universal Tissue P Systems.- Non-cooperative P Systems with Priorities Characterize PsET0L.

Modelling Simple Operations for Gene Assembly

Abstract: The intramolecular model (Ehrenfeucht et al, 2001) for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any micronuclear 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 may consist of many coding and non-coding blocks. We consider in this paper some restricted variants of the three operations, where only one coding block is rearranged at a time. We present in this paper the molecular model of these simple operations. We also introduce a mathematical model for the simple operations, on three levels of abstractions: MDS descriptors, signed permutations, and signed double occurrence strings. 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 strategy. TUCS Laboratory Computational Biomodelling Discrete Mathematics for Information Technology

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 lists data structure. Three molecular operations (ld, hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising 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. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.

Complexity measures for gene assembly

Abstract: The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and separated by non-coding sequences to form micronuclear genes. Assembling the coding blocks from micronuclear genes to form functional macronuclear genes is facilitated by an impressive in-vivo implementation of the linked list data structure of computer science. Complexity measures for genes may be defined in many ways, including the number of MDSs, the number of loci, etc. We take a different approach in this paper and propose four complexity measures for genes in ciliates, based on the 'effort' required to assemble the gene. We consider: (a) the types of operations used in the assembly, (b) the number of operations used in the assembly, (c) the length of the molecular folds involved, and (d) the length of the shortest possible parallel assembly for that gene. "One of the oldest forms of life on Earth has been revealed as a natural born computer programmer."

Processes of Petri Nets with Localities

Abstract: We consider a class of Petri nets suitable for the modelling and behavioural analysis of globally asynchronous locally synchronous (GALS) systems. The proposed model of PTL-nets is basically that of Place/Transition-nets (PT-nets) equipped with an explicit notion of locality. Each locality identifies a distinct set of transitions which may only be executed synchronously, i.e. in a maximally concurrent manner. We investigate how to capture the non-sequential semantics of PTL-nets using techniques similar to those used in the standard treatment of PT-nets. As a result, we postulate that processes based on occurrence nets augmented with additional information about localities and enabledness of non-fired transitions can provide a satisfactory basis for a causality semantics of PTL-nets. Abstract We consider a class of Petri nets suitable for the modelling and behavioural analysis of globally asynchronous locally synchronous (GALS) systems. The proposed model of PTL-nets is basically that of Place/Transition-nets (PT-nets) equipped with an explicit notion of locality. Each locality identifies a distinct set of transitions which may only be executed synchronously, i.e. in a maximally concurrent manner. We investigate how to capture the non-sequential semantics of PTL-nets using techniques similar to those used in the standard treatment of PT-nets. As a result, we postulate that processes based on occurrence nets augmented with additional information about localities and enabledness of non-fired transitions can provide a satisfactory basis for a causality semantics of PTL-nets. Abstract. We consider a class of Petri nets suitable for the modelling and behavioural analysis of globally asynchronous locally synchronous (GALS) systems. The proposed model of PTL-nets is basically that of Place/Transition-nets (PT-nets) equipped with an explicit notion of locality. Each locality identifies a distinct set of transitions which may only be executed synchronously, i.e., in a maximally concurrent manner. We investigate how to capture the non-sequential semantics of PTL-nets using techniques similar to those used in the standard treatment of PT-nets. As a result, we postulate that processes based on occurrence nets augmented with additional information about localities and enabledness of non-fired transitions can provide a satisfactory basis for a causality semantics of PTL-nets.

Simple operations for gene assembly

Abstract: The intramolecular model for gene assembly in ciliates considers three operations, Id, hi, and diad 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.

Interpreted Trajectories

Abstract: We introduce generalized trajectories where the individual symbols are interpreted as operations performed on the operand words. The various previously considered trajectory-based operations can all be expressed in this formalism. It is shown that the generalized operations can simulate Turing machine computations. We consider the equivalence problem and a notion of unambiguity that is sufficient to make equivalence decidable for regular sets of trajectories under nonincreasing interpretations.

Graph transformations : Third International Conference, ICGT 2006, Natal, Rio Grande do Norte, Brazil, September 17-23, 2006 : proceedings

Abstract: Invited Papers.- Nested Quantification in Graph Transformation Rules.- Idioms of Logical Modelling.- New Algorithms and Applications of Cyclic Reference Counting.- New Graph Transformation Models.- Sesqui-Pushout Rewriting.- Automata on Directed Graphs: Edge Versus Vertex Marking.- Conflict Detection for Graph Transformation with Negative Application Conditions.- Adaptive Star Grammars.- Structure Manipulation.- Narrowing Data-Structures with Pointers.- Molecular Analysis of Metabolic Pathway with Graph Transformation.- Matrix Approach to Graph Transformation: Matching and Sequences.- String Generating Hypergraph Grammars with Word Order Restrictions.- Borrowed Contexts and Adhesive Categories.- Composition and Decomposition of DPO Transformations with Borrowed Context.- Process Bisimulation Via a Graphical Encoding.- Toposes Are Adhesive.- Extensions for Distributed and Global Computing.- Graph Transactions as Processes.- Categorical Foundations of Distributed Graph Transformation.- Dynamic Graph Transformation Systems.- Autonomous Units and Their Semantics - The Sequential Case.- Software Engineering Methods and Tools.- Termination Analysis of Model Transformations by Petri Nets.- Non-functional Analysis of Distributed Systems in Unreliable Environments Using Stochastic Object Based Graph Grammars.- Temporal Graph Queries to Support Software Evolution.- On the Use of Alloy to Analyze Graph Transformation Systems.- Model-Driven Development.- Non-materialized Model View Specification with Triple Graph Grammars.- Model-Driven Monitoring: An Application of Graph Transformation for Design by Contract.- Model View Management with Triple Graph Transformation Systems.- Efficient Implementation.- Graph Transformation in Constant Time.- GrGen: A Fast SPO-Based Graph Rewriting Tool.- Realizing Graph Transformations by Pre- and Postconditions and Command Sequences.- Heuristic Search for the Analysis of Graph Transition Systems.- Logics.- Satisfiability of High-Level Conditions.- Weakest Preconditions for High-Level Programs.- Tutorial and Workshops.- Introductory Tutorial on Foundations and Applications of Graph Transformation.- Workshop on Graph Computation Models.- Workshop on Graph-Based Tools.- Workshop on Petri Nets and Graph Transformations.- 3rd International Workshop on Software Evolution Through Transformations: Embracing Change.

Formalizing spherical membrane structures and membrane proteins populations

Abstract: We present a formalization of membrane structure by using a parametric 2-dimensional spherical surface, where membrane proteins reside and can move, according to prescribed operations. A more detailed formalization of membrane proteins acting as transporters is also given, thus possibly allowing a global scale analysis of ion flows across a membrane. Several other applications, both biology and computation oriented, are proposed.

Covers from templates

Abstract: 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 which is a molecular operation that provides a solution for a molecular implementation of gene assembly in ciliates.

The Construction 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. We determine lower bounds on their lengths and explain how we construct these minimal DNA expressions.

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.

Communication membrane systems with active symports

Abstract: We consider membrane systems where the generation/transformation of objects can take place only if it is linked to communication rules. More specifically, all the rules move objects through membranes and, moreover, the membranes can modify the objects as they pass through. The intuitive interpretation of such rules is that a multiset of objects can move from a region to an adjacent one, and moreover objects can engage into (biochemical) reactions while passing through (are in "contact" with) a membrane. Therefore such "twofold" rules are called symport-rewriting (in short, sr) rules, where symport refers to a coordinated passage of a "team" of molecules through a membrane. In this paper we investigate the influence of the form of sr rules on the power of membrane systems that employ them (sometime in combination with simple antiport rules which allow a synchronized exchange, through a membrane, of two molecules residing in two adjacent regions). A typical restriction on the form of an sr rule requires that the passage described by the rule is such that the sort of exiting molecules is a subset of the sort of entering molecules (however the multiplicities of sorts do not have to be related). We also compare the sequential passage mode with the maximally parallel passage mode.

Membrane systems with external control

Abstract: We consider the idea of controlling the evolution of a membrane system. In particular, we investigate a model of membrane systems using promoted rules, where a string of promoters (called the control string) “travels” through the regions, activating the rules of the system. This control string is present in the skin region at the beginning of the computation – one can interpret that it has been inserted in the system before starting the computation – and it is “consumed”, symbol by symbol, while traveling through the system. In this way, the inserted string drives the computation of the membrane system by controlling the activation of evolution rules. When the control string is entirely consumed and no rule can be applied anymore, then the system halts – this corresponds to a successful computation. The number of objects present in the output region is the result of such a computation. In this way, using a set of control strings (a control program), one generates a set of numbers. We also consider a more restrictive definition of a successful computation, and then study the corresponding model. In this paper we investigate the influence of the structure of control programs on the generative power. We demonstrate that different structures yield generative powers ranging from finite to recursively enumerable number sets. In determining the way that the control string moves through the regions, we consider two possible “strategies of traveling”, and prove that they are similar as far as the generative power is concerned.

Workshop on Petri Nets and Graph Transformations

Abstract: The Workshop on Petri Nets and Graph Transformations, which is currently at its second edition, is focussed on the mutual relationship between two prominent specification formalisms for concurrency and distribution, namely Petri nets and graph transformation systems It belongs to the folklore that Petri nets can be seen as rewriting systems over (multi)sets, the rewriting rules being the transitions, and, as such, they can be seen as special graph transformation systems, acting over labelled discrete graphs The basic notions of Petri nets like marking, enabling, firing, steps and step sequences can be naturally “translated” to corresponding notions of graph transformation systems Due to this close correspondence there has been a mutual influence between the two fields, which has lead to a fruitful cross-fertilisation

Embedding linear orders in grids

Abstract: A grid (or a mesh) is a two-dimensional permutation: an m× n-grid of size mn is an m× n-matrix where the entries run through the elements {1,2, …, mn}. We prove that if δ1 and δ2 are any two linear orders on {1,2, …, N}, then they can be simultaneously embedded (in a well defined sense) into a unique grid having the smallest size.

The Embedding Problem for Switching Classes of Graphs

Abstract: In the context of graph transformation we look at the operation of switching, which can be viewed as a 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 subgraph. However, when considering graphs up to isomorphism, we immediately run into the graph isomorphism problem for which no efficient solution is known. Surprisingly enough however, in some cases the decision process can be simplified by transforming the query graph into a "smaller" graph without changing the answer. The main lesson learned is that the size of the query graph is not the dominating factor, but its cycle rank. Although a number of our results hold specifically for undirected, unlabelled graphs, we propose a more general framework and give many positive and negative results for more general cases, where the graphs are labelled with elements of a (finitely generated abelian) group.

Reaction Cycles in Membrane Systems and Molecular Dynamics

Abstract: 1 Leiden University, Mathematical Institute Niels Bohrweg 1, 2333 CA Leiden, The Netherlands muskulus@math.leidenuniv.nl 2 Vrije Universiteit Amsterdam, Faculteit der Bewegingswetenschappen Van der Boechorststraat 9, 1081 BT Amsterdam, The Netherlands s.houweling@fbw.vu.nl 3 Leiden University, Leiden Institute of Advanced Computer Science Niels Bohrweg 1, 2333 CA Leiden, The Netherlands {rbrijder,rozenber}@liacs.nl 4 Universita degli Studi di Milano Dipartimento di Informatica e Comunicazione Via Comelico 39, 20135 Milano, Italy besozzi@dico.unimi.it 5 Universita degli Studi di Milano Dipartimento di Informatica, Sistemistica e Comunicazione Via Bicocca degli Arcimboldi 8, 20126 Milano, Italy {pescini,cazzaniga}@disco.unimib.it