Starts with a brief review of the history and the application areas considered in the literature. The author then proceeds with introductory modeling examples, behavioral and structural properties, three methods of analysis, subclasses of Petri nets and their analysis. In particular, one section is devoted to marked graphs, the concurrent system model most amenable to analysis. Introductory discussions on stochastic nets with their application to performance modeling, and on high-level nets with their application to logic programming, are provided. Also included are recent results on reachability criteria. Suggestions are provided for further reading on many subject areas of Petri nets. >

/pdf/petri-nets-properties-analysis-and-applications-43jwyjdxr0.pdf

Petri nets: Properties, analysis and applications

Data Mining Practical Machine Learning Tools and Techniques

https://cmi.ac.in/~madhavan/courses/verification-2011/alur-dill-tcs-94.pdf

A theory of timed automata

物件導向軟體之架構(Object-Oriented Software Construction)探討

The Temporal Logic of Reactive and Concurrent Systems: Specification

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

/pdf/modelling-simple-operations-for-gene-assembly-4x882j6wdp.pdf

Modelling Simple Operations for Gene Assembly

Reaction systems, motivated by the functioning of the living cell, became a novel model of interactive computation. In this paper, we pursue this line of research. More specifically, we present a systematic investigation of possible interactions of a reaction system with its environment (context). While in the original definition this interaction is one-way, i.e., the behavior of a reaction system is influenced by its environment, we investigate now also the influence of the system on its environment, where a possible time delay of this influence is also considered. To understand the behavior of reaction systems when such a two-way interaction takes place, we establish its relationship to their context-independent behavior (i.e., the behavior which is not influenced by the environment).

Reaction systems with influence on environment

On representing recursively enumerable languages by internal contextual languages

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.

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

Abstract The degree of a graph H is the maximum among the degrees of its nodes. A set of graphs L is of bounded degree if there exists a positive integer n such that the degree of each graph in L does not exceed n . We demonstrate that it is decidable whether or not the (graph) language of an arbitrary node label controlled (NLC) grammar is of bounded degree. Moreover, it is shown that, given an arbitrary NLC grammar G generating the language L(G) of bounded degree, one can effectively compute the maximum integer which appears as the degree of a graph in L(G) .

Grzegorz Rozenberg

Papers

Modelling Simple Operations for Gene Assembly

Reaction systems with influence on environment

On representing recursively enumerable languages by internal contextual languages

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

The Bounded Degree Problem for NLC Grammars Is Decidable ; CU-CS-267-84