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Self-assembly is the process in which simple objects autonomously aggregate into large structures and it has become one of the major tools for nano-scale engineering. We propose in this paper a string-based framework inspired by the principle of selfassembly: two strings with a common overlap, say uv and vw, yield a string uvw; we say that string uvw has(More)
The heat shock response is a primordial defense mechanism against cell stress and protein misfolding. It proceeds with the minimum number of mechanisms that any regulatory network must include, a stress-induced activation and a feedback regulation, and can thus be regarded as the archetype for a cellular regulatory process. We propose here a simple(More)
Using the fact that the Parikh matrix mapping is not an injective mapping, the paper investigates some properties of the set of words with the same Parikh matrix; these words are called “amiable”. The presented results extend the results obtained in [1] for the binary case. In particular it is shown that all the words having the same Parikh matrix can be(More)
We prove two results on commutation of languages. First, we show that the maximal language commuting with a three-element language, i.e. its centralizer, is rational, thus giving an a5rmative answer to a special case of a problem proposed by Conway in 1971. Second, we characterize all languages commuting with a three-element code. The characterization is(More)
The process of gene assembly in ciliates is one of the most complex examples of DNA processing known in any organism, and it is fascinating from the computational point of view—it is a prime example of DNA computing in vivo. In this paper we continue to investigate the three molecular operations (ld, hi , and dlad ) that were postulated to carry out the(More)
Ciliates have developed a unique nuclear dualism two nuclei of di erent functionality the germline micronucleus and the somatic macronucleus The way that ciliates assemble the macronuclear genes after cell mating constitutes one of the most intricate DNA processings in living organisms This processing is also very interesting from the computational point of(More)
The way that ciliates transform genes from their micronuclear to the macronuclear form is very interesting (and unique), also from a computational point of view. In this paper, we describe the model of gene assembly in ciliates presented in [2], [3], and [4]. Moreover, we prove that the set of three operations underlying this model is universal, in the(More)
Ciliates (an ancient group of single cell organisms) have two sorts of nuclei with different functionalities: the micronucleus and the macronucleus. After the cell mating the micronuclear genes are converted into the macronuclear genes in the process called gene assembly. This is one of the most complex examples of DNA processing known in any organisms, and(More)
The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked lists data structure. Three molecular operations (ld, hi, and dlad) have been postulated for the gene(More)