Closure properties of Watson-Crick grammars

In this paper, we define Watson-Crick context-free grammars, as an extension of Watson-Crick regular grammars and Watson-Crick linear grammars with context-free grammar rules. We show the relation of Watson-Crick (regular and linear) grammars to the sticker systems, and study some of the important closure properties of the Watson-Crick grammars. We establish that the Watson-Crick regular grammars are closed under almost all of the main closure operations, while the differences between other Watson-Crick grammars with their corresponding Chomsky grammars depend on the computational power of the Watson-Crick grammars which still need to be studied

The computational power of Watson-Crick grammars: Revisited

A Watson-Crick finite automaton is one of DNA computational models using the Watson-Crick complementarity feature of deoxyribonucleic acid (DNA). We are interested in investigating a grammar counterpart of Watson-Crick automata. In this paper, we present results concerning the generative power of Watson-Crick (regular, linear, context-free) grammars. We show that the family of Watson-Crick context-free languages is included in the family of matrix languages

On the power of parallel communicating Watson–Crick automata systems

AbstractParallel communicating Watson–Crick automata systems were introduced in [E. Czeizler, E. Czeizler, Parallel communicating Watson–Crick automata systems, in: Z. Ésik, Z. Fülöp (Eds.), Proc. Automata and Formal Languages, Dobogókő, Hungary, 2005, pp. 83–96] as possible models of DNA computations. This combination of Watson–Crick automata and parallel communicating systems comes as a natural extension due to the new developments in DNA manipulation techniques. It is already known, see [D. Kuske, P. Weigel, The Role of the Complementarity Relation in Watson–Crick Automata and Sticker Systems, DLT 2004, Lecture Notes in Computer Science, Vol. 3340, Auckland, New Zealand, 2004, pp. 272–283], that for Watson–Crick finite automata, the complementarity relation plays no active role. However, this is not the case when considering parallel communicating Watson–Crick automata systems. In this paper we prove that non-injective complementarity relations increase the accepting power of these systems. We also prove that although Watson–Crick automata are equivalent to two-head finite automata, this equivalence is not preserved when comparing parallel communicating Watson–Crick automata systems and multi-head finite automata

Watson–Crick context-free grammars: Grammar simplifications and a parsing algorithm

A Watson–Crick (WK) context-free grammar, a context-free grammar with productions whose right-hand sides contain nonterminals and double-stranded terminal strings, generates complete double-stranded strings under Watson–Crick complementarity. In this paper, we investigate the simplification processes of Watson–Crick context-free grammars, which lead to defining Chomsky like normal form for Watson–Crick context-free grammars. The main result of the paper is a modified CYK (Cocke–Younger–Kasami) algorithm for Watson–Crick context-free grammars in WK-Chomsky normal form, allowing to parse double-stranded strings in O(n^6) time

Diseño e implementación de sistemas de anotación genómica basados en computación biomolecular y biocelular y técnicas de machine learning

[ES] El proyecto trata sobre el procesamiento de datos en formato FASTA y VCF y la transformación de estos datos al formato pvcf. Después estos datos serán usados para la generación de un modelo de lenguaje basado en los lenguajes k-explorables en sentido estricto. Esos modelos se utilizarán para la obtención de dos anotadores diferentes, uno basado en un autómata de Watson-Crick con una capa estocástica y otro en un autómata finito determinista con una capa estocástica. El análisis y la anotación de cadenas se realizará aplicando el algoritmo de Viterbi.[EN] The project will be based on data processing with FASTA and VCF format and the transformation of that data into a pvcf format. Then this data will be used for the generation of language model based on k-explorable languages in a strict sense. These models will be used for the obtention of two different annotators, one based on Watson-Crick automata with a stochastic layer and the other based on deterministic finite automata with a stochastic layer. The parsing and the annotation of strings will be done using the Viterbi algorithm.Granados Bañuls, A. (2021). Diseño e implementación de sistemas de anotación genómica basados en computación biomolecular y biocelular y técnicas de machine learning. Universitat Politècnica de València. http://hdl.handle.net/10251/171601TFG

On the Languages Accepted by Watson-Crick Finite Automata with Delays

[EN] In this work, we analyze the computational power of Watson-Crick finite automata (WKFA) if some restrictions over the transition function in the model are imposed. We consider that the restrictions imposed refer to the maximum length difference between the two input strands which is called the delay. We prove that the language class accepted by WKFA with such restrictions is a proper subclass of the languages accepted by arbitrary WKFA in general. In addition, we initiate the study of the language classes characterized by WKFAs with bounded delays. We prove some of the results by means of various relationships between WKFA and sticker systems.This work has been developed with the financial support of the European Union's Horizon 2020 research and innovation programme under grant agreement No. 952215 corresponding to the TAILOR project.Sempere Luna, JM. (2021). On the Languages Accepted by Watson-Crick Finite Automata with Delays. Mathematics. 9(8):1-12. https://doi.org/10.3390/math9080813S1129

Watson-crick petri net and place-labelled petri net controlled grammar using formal language theory

formal language theory is a branch of applied discrete mathematics and theoretical computer science. 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. a petri net is a model of information flow in systems that provides a useful mathematical formalism for modelling concurrent systems. in this thesis, the relation between watson-crick automata and petri nets is investigated to consider the massive parallelism in watson- crick automata. thus, a new concept called watson-crick petri net is introduced. besides that, the structural properties of watson-crick petri net are found, namely a single start place, a run place and the stop transition. also, the generative power of watson-crick petri net is determined. besides using watson-crick complementarity in petri nets, a context-free grammar is also considered in this research. a petri net controlled grammar is a type of a context-free grammar equipped with petri nets, where the successful derivation of the grammar can be simulated by the sequence of occurrences of the net. the production rules of a grammar, for all variants of petri net controlled grammars that have been introduced, are associated only with transitions of a petri net. therefore, a place-labelled petri net controlled grammar is introduced in this research. the place labelling enables the parallel application of production rules in petri net controlled grammars to be considered. the effects of labelling strategies and the set of final markings, along with lower and upper bounds are chosen in order to increase the generative power of place-labelled petri net controlled grammar. besides that, the structural properties and structural subclass of place-labelled petri net controlled grammar are also found in this thesis