Nurhidaya Mohamad Jan

A new variant of Petri net controlled grammars

A Petri net controlled grammar is a Petri net with respect to a context-free grammar where the successful derivations of the grammar can be simulated using the occurrence sequences of the net. In this paper, we introduce a new variant of Petri net controlled grammars, called a place-labeled Petri net controlled grammar, which is a context-free grammar equipped with a Petri net and a function which maps places of the net to productions of the grammar. The language consists of all terminal strings that can be obtained by parallelly applying multisets of the rules which are the images of the sets of the input places of transitions in a successful occurrence sequence of the Petri net. We study the effect of the different labeling strategies to the computational power and establish lower and upper bounds for the generative capacity of place-labeled Petri net controlled grammars.

Watson-Crick Petri net languages with finite sets of final markings

A Watson-Crick Petri net is a new formal model that enhances a Petri net with the Watson-Crick complementary feature adapted from DNA molecules. The transitions of a Watson-Crick Petri net are labeled with pairs of symbols, and a firing sequence of transitions of the Watson-Crick Petri net is considered as successful if and only if it produces complete double stranded sequences of symmetrically related symbols according to some mode of execution termination of the firing of transitions. As an execution termination mode, we can consider the set of all reachable markings and a finite set of final markings. In this research, we investigate the fundamental properties of Watson-Crick Petri net languages with finite sets of final markings.

Watson-Crick Petri net languages: the effect of labeling strategies

A Watson-Crick automaton is an automaton that works on tapes which are double stranded sequences of symbols related by Watson-Crick complementarity that are similar to the DNA molecules. However, this automaton cannot exploit the other fundamental features of DNA molecules such as the massive parallelism. Watson-Crick automata can be related to a model known as the Petri net. Petri net is a model based on the concepts of asynchronous and concurrent operation by the parts of a system and the realization by the parts can be represented by a graph or a net. From the relation between Watson-Crick automata and Petri net, a new model namely Watson-Crick Petri net has been developed. The language generated by Watson-Crick Petri net is a set of labeled sequences corresponding to the occurrence sequences of the model. In this research, some properties of languages generated by Watson-Crick Petri net are investigated.

Regular languages, regular grammars and automata in splicing systems

Splicing system is known as a mathematical model that initiates the connection between the study of DNA molecules and formal language theory. In splicing systems, languages called splicing languages refer to the set of double-stranded DNA molecules that may arise from an initial set of DNA molecules in the presence of restriction enzymes and ligase. In this paper, some splicing languages resulted from their respective splicing systems are shown. Since all splicing languages are regular, languages which result from the splicing systems can be further investigated using grammars and automata in the field of formal language theory. The splicing language can be written in the form of regular languages generated by grammar. Besides that, splicing systems can be accepted by automata. In this research, two restriction enzymes are used in splicing systems namely BfuCI and NcoI.