Showing papers by "Grzegorz Rozenberg published in 2002"

Computational Aspects of Gene (Un)Scrambling in Ciliates

Abstract: Ciliates, a very ancient group of organisms, have evolved extraordinary ways of organizing, manipulating, and replicating the DNA in their micronuclear genomes. The way that ciliates transform genes from their micronuclear (storage) form into their macronuclear (expression) form constitutes a very interesting case of “DNA computing in vivo”. In this paper we investigate in detail one aspect of this transformation, viz., gene (un)scrambling. In particular, we use the formal framework of pointer reduction systems to investigate the computational aspects of gene (un)scrambling.

Membrane systems with promoters/inhibitors

Abstract: The computational model of membrane computing (formalized through membrane systems, also called P systems) is based on the way that biological membranes define compartments, each having its set of molecules and (enzymes enhancing) reactions, with compartments communicating through the transport of molecules through membranes. In this paper we augment the basic model of membrane systems with promoters and inhibitors, which formalize the reaction enhancing and reaction prohibiting roles of various substances (molecules) present in cells. We formalize such membrane systems with promoters/inhibitors and investigate their basic properties. In particular we establish universality results, i.e., we provide characterizations of recursively enumerable sets (of vectors of natural numbers) using these systems. It turns out that systems with promoters/inhibitors achieve universal computations without using the standard “auxiliary” features of membrane systems, for instance, without using catalysts.

Computing by communication in networks of membranes

Abstract: In this paper we consider networks of membranes which compute by communication only, using symport/antiport rules. Such rules are used both for communication with the environment and for direct communication among membranes. It turns out that, rather surprisingly, networks with a small number of membranes are computationally universal. This is proved both for the case of three membranes where each membrane communicates with each other membrane, and for the case of four membranes consisting of two pairs such that only the membranes within each pair communicate directly. A single pair of communicating membranes can compute the Parikh images of matrix languages. Several open problems are also formulated.

String and graph reduction systems for gene assembly in ciliates

Abstract: Ciliates have developed a unique nuclear dualism, having two nuclei of different functionality: the germline micronucleus and the somatic macronucleus. The way that ciliates assemble the macronuclear genes after cell mating constitutes one of the most intricate DNA processings in living organisms. This processing is also very interesting from the computational point of view. In this paper, we investigate the operations of loop excision and hairpin excisionsreinsertion used in the assembly process. In particular, we consider three levels of formalization of this process, culminating in graph reduction systems.

Unifying Petri Nets: Advances in Petri Nets

Abstract: "What Is a Petri Net?" Informal Answers for the Informed Reader.- Application Oriented Approaches.- The ?Petri Net Baukasten?: An Overview.- Improving the Usability of Petri Nets with the ?Petri Net Baukasten?.- Implementation of Parameterized Net Classes with the Petri Net Kernel of the ?Petrinetz-Baukasten?.- Process Landscaping: Modelling Distributed Processes and Proving Properties of Distributed Process Models.- Unifying Frameworks.- Petri Nets over Partial Algebra.- Parameterized Net Classes: A Uniform Approach to Petri Net Classes.- Behavior and Realization Construction for Petri Nets Based on Free Monoid and Power Set Graphs.- Rewriting Logic as a Unifying Framework for Petri Nets.- Theoretical Approaches.- Generalized Automata and Their Net Representations.- On Concurrent Realization of Reactive Systems and Their Morphisms.- Transactions and Zero-Safe Nets.- Two Algebraic Process Semantics for Contextual Nets.- Continuous Petri Nets and Transition Systems.

Characterizing the Micronuclear Gene Patterns in Ciliates

Abstract: The process of gene assembly in ciliates is one of the most complex examples of DNA processing known in any organism, and it is fascinating from the computational point of view—it is a prime example of DNA computing in vivo. In this paper we continue to investigate the three molecular operations (ld, hi , and dlad ) that were postulated to carry out the gene assembly process in the intramolecular fashion. In particular, we focus on the understanding of the IES/ MDS patterns of micronuclear genes, which is one of the important goals of research on gene assembly in ciliates. We succeed in characterizing for each subset S of the three molecular operations those patterns that can be assembled using operations in S. These results enhance our understanding of the structure of micronuclear genes (and of the nature of molecular operations). They allow one to establish both similarity and complexity measures for micronuclear genes.

Membrane systems with coupled transport: universality and normal forms

Abstract: This paper continues research on membrane systems which function by communication only, meaning that there are no evolving rules for molecules. The whole computation process relies on passage of molecules through membranes - this provides communication between regions of the membrane system. Next to transport of single molecules through membranes (uniport) we also study a coupled transport of molecules, with two molecules passing either in the same direction (symport) or in opposite directions (antiport). We study the computational power of such membrane systems and prove that using only symport one gets Turing universality. Moreover, we prove that five membranes suffice to get Turing universality, and the number of membranes can be decreased to three if forbidding context conditions for transport are used.

Evolutionary Computation as a Paradigm for DNA-Based Computing

Abstract: Evolutionary Computation focuses on probabilistic search and optimization methods gleaned from the model of organic evolution. Genetic algorithms, evolution strategies, and evolutionary programming are three independently developed representatives of this class of algorithms, with genetic programming and classifier systems as additional paradigms in the field.

How ciliates manipulate their own DNA – A splendid example of natural computing

Abstract: DNA computing is a novel and vivid research area which is genuinely interdisciplinary – computer scientists and molecular scientists collaborate to investigate the use of DNA molecules for the purpose of computing. DNA computing in vivo is the investigation of computations taking place naturally in a living cell, with the goal of understanding computational properties of DNA molecules in their native environment. Gene assembly in ciliates (single cell organisms) is perhaps the most involved process of DNA manipulation yet known in living organisms. The computational nature of this process has attracted much attention in recent years. The results obtained so far demonstrate that this process of gene assembly is a splendid example of computing taking place in nature, i.e., Natural Computing. Indeed, DNA computing in vivo may be far more widespread in nature than we currently recognize. This paper is a tutorial on (computational nature of the) gene assembly in ciliates, which is intended for a broad audience of researchers interested in Natural Computing. In particular, no knowledge of molecular biology is assumed on the part of the motivated reader.

Concurrency and Hardware Design

Abstract: We introduce a simple formal framework for specifying and implementing concurrent systems. The framework enables the specification of safety and progress properties and is based on Enhanced Characteristic Functions. The use of Enhanced Characteristic Functions leads to simple definitions of operations such as hiding and various process compositions. We discuss two compositions: the network composition for building networks of processes and the specification composition for building specifications of processes. A central notion in our framework is the notion of a snippet. A snippet represents a part behavior of a process satisfying one specific constraint. A specification of a concurrent process satisfying all constraints is expressed by means of a specification composition of snippets. We present various properties of the specification and network compositions that can be helpful in the specification and implementation of concurrent systems. We illustrate our design approach with the design of some asynchronous circuits.

Concurrency and Hardware Design, Advances in Petri Nets

Abstract: Formal Models- Composing Snippets- A Programming Approach to the Design of Asynchronous Logic Blocks- Asynchronous Circuits- GALA (Globally Asynchronous - Locally Arbitrary) Design- Synthesis of Reactive Systems: Application to Asynchronous Circuit Design- Decomposition in Asynchronous Circuit Design- Embedded System Design- Functional and Performance Modeling of Concurrency in VCC- Modeling and Designing Heterogeneous Systems- Timed Verification and Performance Analysis- Timed Verification of Asynchronous Circuits- Performance Analysis of Asynchronous Circuits Using Markov Chains

Computational processes in living cells: gene assembly in ciliates

Abstract: One of the most complex DNA processing in nature known to us is carried out by ciliates during the sexual reproduction when their micronuclear genome is transformed to the macronuclear genome. This process of gene assembly is intriguing and captivating also from the computational point of view.We investigate here three intramolecular molecular operations (ld, hi, and dlad) postulated to accomplish gene assembly. The formal models for these operations are formulated on three different abstraction levels: MDS descriptors, legals strings and overlap graphs. In general both legal strings and overlap graphs contain strings and graphs that do not model any micronuclear gene. After a short survey of gene assembly we study the problem of recognizing whether a general legal string or a general overlap graph is a formalization of a micronuclear gene.

Models of molecular computing based on molecular reactions

Abstract: We discuss two models of molecular computing. The first one is based on an abstract formulation of two sorts of molecular reactions: enforcing and forbidden. The enforcing reactions are reactions that may happen, and are allowed to happen, in a given molecular system, while the forbidden reactions are detrimental for the system (e.g., leading to "incorrect" computations) and thus must be avoided. Hence computations in such a forbidding-enforcing system are driven by enforcing conditions (describing the enforcing reactions), but they are restrained by forbidding conditions (describing the forbidden reactions). The second model, called molecular landscapes, is geared towards the display of solutions. It consists of organisms (computing agents) functioning in a common environment which plays the role of a common communication medium for the organisms. When a molecular landscapes system works on a specific computational problem, each organism is working on this problem. But as soon as an organism M will get its solution to the problem, it modifies the environment, which from this moment on supports only the organisms that get the same solution as M. This is done through a selection mechanism that relies on selective competition which "kills" the losers. Since this selection mechanism interacts with the solution mechanism from the moment that computations are initiated, it can drastically increase the density of good solutions (molecules). In this way the molecular landscapes system achieves the goal of displaying solutions.

Formal and Natural Computing: Essays Dedicated to Grzegorz Rozenberg

Abstract: Words, Languages, Automata.- Balanced Grammars and Their Languages.- Safety and Liveness Properties for Real Traces and a Direct Translation from LTL to Monoids.- The Delta Operation: From Strings to Trees to Strings.- Infinite Solutions of Marked Post Correspondence Problem.- The Branching Point Approach to Conway's Problem.- A Survey of Some Quantitative Approaches to the Notion of Information.- Nondeterministic Trajectories.- Binary Patterns in Infinite Binary Words.- Graph Transformations.- A Sight-seeing Tour of the Computational Landscape of Graph Transformation.- Local Action Systems and DPO Graph Transformation.- Bisimulation Equivalences for Graph Grammars.- Petri Nets.- High-Level Net Processes.- Petri Net Control for Grammar Systems.- Regular Event Structures and Finite Petri Nets: A Conjecture.- Concurrent Computing.- Towards Team-Automata-Driven Object-Oriented Collaborative Work.- Grammars as Processes.- Temporal Concurrent Constraint Programming: Applications and Behavior.- Molecular Computing.- Rewriting P Systems with Conditional Communication.- An Aqueous Algorithm for Finding the Bijections Contained in a Binary Relation.- Upper Bounds for Restricted Splicing.- Codes, Involutions, and DNA Encodings.- DNA Manipulations in Ciliates.- A Magic Pot : Self-assembly Computation Revisited.

Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates

Abstract: DNA computing, or more generally molecular computing, is a novel exciting area of research at the intersection of mathematics, computer science and molecular biology. The area of DNA computing studies the use of biomolecules for the purpose of computing (in vitro or in vivo). Molecular biologists assists here computer scientists in their attempt to replace or to complement the silicon-based computers by DNA-based computers. The hardware for such computations consists of biomolecules ( bioware).