LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

Communicating Distributed H Systems with
Alternating Filters
Sergey Verlan
Laboratoire d’Informatique Théorique et Appliquée
Université de Metz, France
verlan@sciences.univ-metz.fr
Abstract. We present a variant of communicating distributed H systems
where each filter is substituted by a tuple of filters. Such systems
behave like original ones with the difference that at each moment we use
one element of the tuple for the filtering process and this element is replaced
after each use, periodically. We show that it suffices to use tuples
of two filters in order to generate any recursively enumerable language,
with two tubes only. We also show that it is possible to obtain the same
result having no rules in the second tube which acts as a garbage collector.
Moreover, the two filters in a tuple differ only in one letter. We also
present different improvements and open questions.
1 Introduction
Splicing systems (H systems) were the first theoretical model of biomolecular
computing and they were introduced by T. Head. [5,6]. The molecules from
biology are replaced by words over a finite alphabet and the chemical reactions
are replaced by a splicing operation. An H system specifies a set of rules used to
perform a splicing and a set of initial words or axioms. The computation is done
by applying iteratively the rules to the set of words until no more new words
can be generated. This corresponds to a bio-chemical experiment where we have
enzymes (splicing rules) and initial molecules (axioms) which are put together
in a tube and we wait until the reaction stops.
Unfortunately, H systems are not very powerful and a lot of other models
introducing additional control elements were proposed (see [14] for an overview).
One of these well-known models are communicating distributed H systems (CDH
systems) or test tube systems (TT systems) introduced in [1]. This model introduces
tubes (or components). Each tube contains a set of strings and a set of
splicing rules and evolves as an H system. The result of its work can be redistributed
to other tubes according to a certain filter associated with each tube.
Each filter is an alphabet and a string will enter a tube only if it is composed
only by symbols present in the filter associated with the tube. After that these
strings form the new starting molecules for the corresponding tube.
In the same paper it was shown that the model can generate any recursively
enumerable language using a finite set of strings and a finite set of splicing rules.
N. Jonoska et al. (Eds.): Molecular Computing (Head Festschrift), LNCS 2950, pp. 367–384, 2004.
c○ Springer-Verlag Berlin Heidelberg 2004