Stavros Konstantinidis

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The input data for DNA computing must be encoded into the form of single or double DNA strands. As complementary parts of single strands can bind together forming a double-stranded DNA sequence, one has to impose restrictions on these sets of DNA words (languages) to prevent them from interacting in undesirable ways. We recall a list of known properties of(More)
The computation language of a DNA-based system consists of all the words (DNA strands) that can appear in any computation step of the system. In this work we define properties of languages which ensure that the words of such languages will not form undesirable bonds when used in DNA computations. We give several characterizations of the desired properties(More)
This paper explores different means of representation for algebraic transductions, i.e., word relations realized by pushdown transducers. The relevance of this work lies more in its point of view rather than any particular result. We are aiming at giving specific techniques for obtaining, or perhaps explaining, decompositions of algebraic (and incidentally,(More)
When the words of a language are communicated via a noisy channel, the language property of error-detection ensures that no word of the language can be transformed to another word of the language. On the other hand, the property of error-correction ensures that the channel cannot transform two different words of the language to the same word. In this work(More)
We formalize the notion of a DNA hairpin secondary structure, examining its mathematical properties. Two related secondary structures are also investigated, taking into the account imperfect bonds (bulges, mismatches) and multiple hairpins. We characterize maximal sets of hairpin-forming DNA sequences, as well as hairpin-free ones. We study their algebraic(More)
The problem of negative design of DNA languages is addressed, that is, properties and construction methods of large sets of words that prevent undesired bonds when used in DNA computations. We recall a few existing formalizations of the problem and then define the property of sim-bond-freedom, where sim is a similarity relation between words. We show that(More)
The paper examines the concept of hairpin-free words motivated from the biocomputing and bioinformatics fields. Hairpin (-free) DNA structures have numerous applications to DNA computing and molecular genetics in general. A word is called hairpin-free if it cannot be written in the form xvyθ(v)z, with certain additional conditions, for an involution θ (a(More)
We use some ‘natural’ language operations, such as shuffle (scattered insertion) and scattered deletion to model 9 noisy channels, that is, nondeterministic processes transforming words to words. In this spirit, we also introduce the operation of scattered substitution and derive the closure properties of the language families in the Chomsky 11 hierarchy(More)
Motivated by the general need to identify and classify species based on molecular evidence, genome comparisons have been proposed that are based on measuring mostly Euclidean distances between Chaos Game Representation (CGR) patterns of genomic DNA sequences. We provide, on an extensive dataset and using several different distances, confirmation of the(More)