Grzegorz Rozenberg

Bio: Grzegorz Rozenberg is an academic researcher from Leiden University. The author has contributed to research in topics: Petri net & Formal language. The author has an hindex of 81, co-authored 679 publications receiving 31378 citations. Previous affiliations of Grzegorz Rozenberg include Åbo Akademi University & University of Warsaw.

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.

Beginnings of Molecular Computing

Abstract: “We can see only a short distance ahead, but we can see plenty there that needs to be done.” These words of Turing [213] can be taken as an underlying principle of any program for scientific development. Such an underlying principle is very characteristic for research programs in computer science. Advances in computer science are often shown by and remembered from some unexpected demonstration, rather than from a dramatic experiment as in physical sciences. As pointed out by Hartmanis [83], it is the role of such a demo to show the possibility or feasibility of doing what was previously thought to be impossible or not feasible. Often, the ideas and concepts brought about and tested in such demos determine or at least influence the research agenda in computer science. Adleman’s experiment [1] constituted such a demo. This book is about the short distance we can see ahead, and about the theoretical work already done concerning various aspects of molecular computing. The ultimate impact of DNA computing cannot yet be seen; this matter will be further discussed in Sect. 2.4.

DNA: Its Structure and Processing

Abstract: The term “genetic engineering” is a very broad generic term used to cover all kinds of manipulations of genetic material. For the purpose of this book this term describes the in vitro (hence outside living cell) manipulation of DNA and related molecules. These manipulations may be used to perform various kinds of computations.

Reduction graphs from overlap graphs for gene assembly in ciliates

Abstract: Ciliates are unicellular organisms having two types of functionally different nuclei: micronucleus and macronucleus. Gene assembly transforms a micronucleus into a macronucleus, thereby transforming each gene from its micronuclear form to its macronuclear form. Within a formal intramolecular model of gene assembly based on strings, the notion of reduction graph represents the macronuclear form of a gene, including byproducts, given only a description of the micronuclear form of that gene. For a more abstract model of gene assembly based on graphs, one cannot, in general, define the notion of reduction graphs. We show that if we restrict ourselves to the so-called realistic overlap graphs (which correspond to genes occurring in nature), then the notion of reduction graph can be defined in a manner equivalent to the string model. This allows one to carry over from the string model to the graph model several results that rely on the notion of reduction graph.

Petri nets: Properties, analysis and applications

Abstract: 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. >