In this paper we introduce a variation of Watson-Crick automata in which both heads read the doubled DNA strand form 5' to 3'. The sensing version of these automata recognize exactly the linear context-free languages. The deterministic version is not so powerful, but all fixed-rated linear (for instance even-linear) languages can be accepted by them. Relation to other variations of Watson-Crick automata and pushdown automata are presented. The full-reading version of sensing 5′ → 3′ automata recognizes non context-free languages as well.

background

Watson-Crick finite automata.

On 5' → 3' sensing Watson-Crick finite automata

This paper surveys some known results in Watson-Crick automata theory. In particular, we concentrate on the computational power, complexity measures, decidability problems, and systems of Watson-Crick automata working together on the same input. This selection of topics is not exhaustive, reflecting the research interests of the authors. A series of open problems and questions is also included.

A Short Survey on Watson-Crick Automata.

Molecular computing is a new paradigm to perform calculations using nanotechnology. This paper presents the overall research direction from which molecular inference and expert systems are emerging. It introduces the subject matter and a general description of the problems involved. This includes selected methods of knowledge representation by DNA oligonucleotides, strategies of the inference mechanism, concept of the inference engine based on circular DNA molecules, particularly derived from plasmids, practical experience in DNA inference engine implementation, and discussion of the experimental results. The approach allows evaluating logical statements and drawing inferences for generating other statements via DNA computing. A series of experiments have been conducted to confirm practical utility of this approach. In these experiments, parameters of biochemical reactions were varied to determine truth/false recognition accuracy. In addition, we discuss the fundamental issues of inference engine and try ...

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The inference based on molecular computing

In [4, page166], it is asked what influence the complementarity relation plays as far as the expressiveness of sticker systems and Watson-Crick automata are concerned. Here, we give the answer: (almost) none! More precisely, we show that every language L of a sticker system or a Watson-Crick automaton is the language of such a system with a one-to-one complementarity relation. Our second group of results shows that L is the inverse block coding of a language from the same family over any nontrivial fixed complementarity relation. Finally, we prove that any Watson-Crick automaton can be transformed into an equivalent simple and all-final one. This implies the collapse of parts of the hierarchy introduced in [4].

Watson-Crick finite automata.

Citations

On 5' → 3' sensing Watson-Crick finite automata

A Short Survey on Watson-Crick Automata.

The inference based on molecular computing

The role of the complementarity relation in Watson-Crick automata and sticker systems

On a hierarchy of 5′ → 3′ sensing Watson–Crick finite automata languages

Related Papers (5)

DNA Computing: New Computing Paradigms

A Short Survey on Watson-Crick Automata.

5′ → 3′ Watson-Crick Automata With Several Runs

Introduction to Automata Theory, Languages, and Computation

Molecular computation of solutions to combinatorial problems