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. >

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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

Reaction systems are a formal model for processes inspired by the functioning of the living cell. These processes are determined by the iteration of the state transition functions of reaction systems, also called rs functions. In this paper we provide mathematical characterisations of rs functions implemented/defined by "minimal reaction systems", i.e., reaction systems with reactions using the minimal number of reactants, or the minimal number of inhibitors, or the minimal number of resources (i.e., reactants and inhibitors together).

Minimal reaction systems

This second volume of the Handbook of Formal Languages contains the most fundamental applications of language theory. Various aspects of linguistics and parsing, both natural and programming languages, symbolic manipulation, and pattern matching are discussed. A special feature is the recently very active field of DNA computing.

Handbook of formal languages, vol. 2: linear modeling: background and application

Ciliates (an ancient group of single cell organisms) have two sorts of nuclei with different functionalities: the micronucleus and the macronucleus. After the cell mating the micronuclear genes are converted into the macronuclear genes in the process called gene assembly. This is one of the most complex examples of DNA processing known in any organisms, and it is fascinating from the computational point of view. This paper continues the investigation of gene assembly in the framework of three molecular operations: ld-excision, hi-excision/reinsertion, and dlad-excision/reinsertion. In general, for a given micronuclear gene there exists many strategies for using these three operations to accomplish gene assembly. Since it is not known yet which strategies are actually used by ciliates, it is important to study the invariants of gene assembly, i.e., those properties of gene assembly that are common to all these strategies. A macronuclear gene (before its excision and capping with telomeres) can be assembled either in a linear or in a circular molecule. We prove in this paper that the circularity property (whether or not a given gene will be assembled in a circular molecule) is an invariant. We give a simple decision algorithm for the circularity property, and discuss a number of other related invariants.

Circularity and Other Invariants of Gene Assembly in Ciliates.

DNA computing aims at using nucleic acids for computing. Since micromolar DNA solutions can act as billions of parallel nanoprocessors, DNA computers can in theory solve optimization problems that require vast search spaces. However, the actual parallelism currently being achieved is at least a hundred million-fold lower than the number of DNA molecules used. This is due to the quantity of DNA molecules of one species that is required to produce a detectable output to the computations. In order to miniaturize the computation and considerably reduce the amount of DNA needed, we have combined DNA computing with single-molecule detection. Reliable hybridization detection was achieved at the level of single DNA molecules with fluorescence cross-correlation spectroscopy. To illustrate the use of this approach, we implemented a DNA-based computation and solved a 4-variable 4-clause instance of the computationally hard Satisfiability (SAT) problem.

/pdf/dna-computing-using-single-molecule-hybridization-detection-38vmotp0x7.pdf

Grzegorz Rozenberg

Papers

Minimal reaction systems

Handbook of formal languages, vol. 2: linear modeling: background and application

Circularity and Other Invariants of Gene Assembly in Ciliates.

DNA computing using single-molecule hybridization detection

A relationship between ET0L and EDT0L languages