Search results for " COMPUTATION"
showing 10 items of 1478 documents
FLYCOP: metabolic modeling-based analysis and engineering microbial communities
2018
10 p.-5 fig.-2 tab.
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…
A computational approach for the assessment of executive functions in patients with obsessive-compulsive disorder
2019
Previous studies on obsessive–compulsive disorder (OCD) showed impairments in executive domains, particularly in cognitive inhibition. In this perspective, the use of virtual reality showed huge potential in the assessment of executive functions; however, unfortunately, to date, no study on the assessment of these patients took advantage of the use of virtual environments. One of the main problems faced within assessment protocols is the use of a limited number of variables and tools when tailoring a personalized program. The main aim of this study was to provide a heuristic decision tree for the future development of tailored assessment protocols. To this purpose, we conducted a study that…
GIS Infomobility for Travellers
2016
Geographical Information Systems (GIS) are essential systems to support decisions on territorial and environmental aspects. But they not always have been properly used for this purpose. Only in recent years GIS have been getting better used for the planning, management and control of the territory. The application of GIS to the transport sector has become relevant both for management and decision-making in support of Public Administration (PA) and citizens. GIS are particularly useful for roads and routing graphs management capabilities as well as for searching the most suitable path. The results achieved in this research activity aimed to evaluate different road graphs, proprietary and fre…
Packing colorings of subcubic outerplanar graphs
2018
Given a graph $G$ and a nondecreasing sequence $S=(s_1,\ldots,s_k)$ of positive integers, the mapping $c:V(G)\longrightarrow \{1,\ldots,k\}$ is called an $S$-packing coloring of $G$ if for any two distinct vertices $x$ and $y$ in $c^{-1}(i)$, the distance between $x$ and $y$ is greater than $s_i$. The smallest integer $k$ such that there exists a $(1,2,\ldots,k)$-packing coloring of a graph $G$ is called the packing chromatic number of $G$, denoted $\chi_{\rho}(G)$. The question of boundedness of the packing chromatic number in the class of subcubic (planar) graphs was investigated in several earlier papers; recently it was established that the invariant is unbounded in the class of all sub…
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.