Search results for "Computation theory"
showing 10 items of 336 documents
A detailed experimental study of a DNA computer with two endonucleases
2017
Abstract Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro’s group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity – increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effe…
Biomolecular computers with multiple restriction enzymes
2017
Abstract The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton t…
Bacteria classification using minimal absent words
2017
Bacteria classification has been deeply investigated with different tools for many purposes, such as early diagnosis, metagenomics, phylogenetics. Classification methods based on ribosomal DNA sequences are considered a reference in this area. We present a new classificatier for bacteria species based on a dissimilarity measure of purely combinatorial nature. This measure is based on the notion of Minimal Absent Words, a combinatorial definition that recently found applications in bioinformatics. We can therefore incorporate this measure into a probabilistic neural network in order to classify bacteria species. Our approach is motivated by the fact that there is a vast literature on the com…
Discovering unbounded unions of regular pattern languages from positive examples
1996
The problem of learning unions of certain pattern languages from positive examples is considered. We restrict to the regular patterns, i.e., patterns where each variable symbol can appear only once, and to the substring patterns, which is a subclass of regular patterns of the type xαy, where x and y are variables and α is a string of constant symbols. We present an algorithm that, given a set of strings, finds a good collection of patterns covering this set. The notion of a ‘good covering’ is defined as the most probable collection of patterns likely to be present in the examples, assuming a simple probabilistic model, or equivalently using the Minimum Description Length (MDL) principle. Ou…
DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
2019
Abstract Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gai…
Propositions pour une littérature d’investigation
2017
Le temps semble a l’alliance de la litterature et des sciences sociales. Mais les modalites en sont encore incertaines. Au lieu de considerer l’anthropologie comme une forme de litterature, on peut envisager la litterature comme une enquete. Cette « litterature d’investigation » se donne notamment pour objectif de documenter des formes de vie et de monter des dispositifs rendant compte d’aspects inapercus de phenomenes sociaux. Elle occupe ainsi une position intermediaire : elle se menage a la fois une liberte et une creativite relatives vis-a-vis des protocoles d’enquete propres aux sciences sociales et une certaine mefiance pour un respect trop reverencieux envers la litterature.
Additivity of affine designs
2020
We show that any affine block design $$\mathcal{D}=(\mathcal{P},\mathcal{B})$$ is a subset of a suitable commutative group $${\mathfrak {G}}_\mathcal{D},$$ with the property that a k-subset of $$\mathcal{P}$$ is a block of $$\mathcal{D}$$ if and only if its k elements sum up to zero. As a consequence, the group of automorphisms of any affine design $$\mathcal{D}$$ is the group of automorphisms of $${\mathfrak {G}}_\mathcal{D}$$ that leave $$\mathcal P$$ invariant. Whenever k is a prime p, $${\mathfrak {G}}_\mathcal{D}$$ is an elementary abelian p-group.
Symmetric and asymmetric cryptographic key exchange protocols in the octonion algebra
2019
AbstractWe propose three cryptographic key exchange protocols in the octonion algebra. Using the totient function, defined for integral octonions, we generalize the RSA public-key cryptosystem to the octonion arithmetics. The two proposed symmetric cryptographic key exchange protocols are based on the automorphism and the derivation of the octonion algebra.
Finitary shadows of compact subgroups of $$S(\omega )$$
2020
AbstractLet LF be the lattice of all subgroups of the group $$SF(\omega )$$SF(ω) of all finitary permutations of the set of natural numbers. We consider subgroups of $$SF(\omega )$$SF(ω) of the form $$C\cap SF(\omega )$$C∩SF(ω), where C is a compact subgroup of the group of all permutations. In particular, we study their distribution among elements of LF. We measure this using natural relations of orthogonality and almost containedness. We also study complexity of the corresponding families of compact subgroups of $$S(\omega )$$S(ω).