DNA Computing: Modelling in Formal Languages and Combinatorics on Words, and Complexity Estimation

DNA computing, an essential area of unconventional computing research, encodes problems using DNA molecules and solves them using biological processes. This thesis contributes to the theoretical research in DNA computing by modelling biological processes as computations and by studying formal language and combinatorics on words concepts motivated by DNA processes. It also contributes to the experimental research in DNA computing by a scaling comparison between DNA computing and other models of computation. First, for theoretical DNA computing research, we propose a new word operation inspired by a DNA wet lab protocol called cross-pairing polymerase chain reaction (XPCR). We define and study a word operation called word blending that models and generalizes an unexpected outcome of XPCR. The input words are uwx and ywv that share a non-empty overlap w, and the output is the word uwv. Closure properties of the Chomsky families of languages under this operation and its iterated version, the existence of a solution to equations involving this operation, and its state complexity are studied. To follow the XPCR experimental requirement closely, a new word operation called conjugate word blending is defined, where the subwords x and y are required to be identical. Closure properties of the Chomsky families of languages under this operation and the XPCR experiments that motivate and implement it are presented. Second, we generalize the sequence of Fibonacci words inspired by biological concepts on DNA. The sequence of Fibonacci words is an infinite sequence of words obtained from two initial letters f(1) = a and f(2)= b, by the recursive definition f(n+2) = f(n+1)*f(n), for all positive integers n, where * denotes word concatenation. After we propose a unified terminology for different types of Fibonacci words and corresponding results in the extensive literature on the topic, we define and explore involutive Fibonacci words motivated by ideas stemming from theoretical studies of DNA computing. The relationship between different involutive Fibonacci words and their borderedness and primitivity are studied. Third, we analyze the practicability of DNA computing experiments since DNA computing and other unconventional computing methods that solve computationally challenging problems often have the limitation that the space of potential solutions grows exponentially with their sizes. For such problems, DNA computing algorithms may achieve a linear time complexity with an exponential space complexity as a trade-off. Using the subset sum problem as the benchmark problem, we present a scaling comparison of the DNA computing (DNA-C) approach with the network biocomputing (NB-C) and the electronic computing (E-C) approaches, where the volume, computing time, and energy required, relative to the input size, are compared. Our analysis shows that E-C uses a tiny volume compared to that required by DNA-C and NB-C, at the cost of the E-C computing time being outperformed first by DNA-C and then by NB-C. In addition, NB-C appears to be more energy efficient than DNA-C for some input sets, and E-C is always an order of magnitude less energy efficient than DNA-C

Promised streaming algorithms and finding pseudo-repetitions

As the size of data available for processing increases, new models of computation are needed. This motivates the study of data streams, which are sequences of information for which each element can be read only after the previous one. In this work we study two particular types of streaming variants: promised graph streaming algorithms and combinatorial queries on large words. We give an &omega(n) lower bound for working memory, where n is the number of vertices of the graph, for a variety of problems for which the graphs are promised to be forests. The crux of the proofs is based on reductions from the field of communication complexity. Finally, we give an upper bound for two problems related to finding pseudo-repetitions on words via anti-/morphisms, for which we also propose streaming versions

Antropofagia and Constructive Universalism: A Diptych

This study proposes a rethinking of the word-image relation through an examination of Joaquin Torres-García’s Constructive Universalism (ca.1934-1949) and the Brazilian Modernist movement of Antropofagia (1928-ca.1934). By placing both in the close relation of a ‘diptych,’ I argue for a new reading of Torres-García’s visual work as well as a different understanding of Antropofagia. In the first part of this work, I argue, through a close reading and viewing of Torres-García’s work, that the constitutive instability between word/image has been overlooked in favour of, on the one hand, an appropriation in terms of a ‘deviation’ from the canon of Geometric Abstraction and on the other hand as a paradigm of Pre-Columbian, Inca abstraction. Both discursive gestures repress the matter of visual aesthesis. Against this strategy of legibility, I propose a counter-reading through the concepts of ‘graphism’ (Leroi-Gourhan), ‘manuscription’ (Sarabia), the ‘sensory field’ (Lyotard) and the hypericon. These concepts allow contingency to find its way back into Torres-García’s oeuvre in opposition to neo-Classicist misappropriations. Throughout my argument, it will become evident that Torres-García’s paintings bespeak an irrepressible mestizaje, an intertwining of the figural with the abstract. It is this tension animating Torres-García’s work that has been neglected by the disciplining of discourse’s ‘logic of illustration.’ In the second part of the study, I take Antropofagia not so much as a historically determinate period in the narrative of Brazilian Modernism, but as a heuristic for the thinking through of the ‘inconstancy’ of the relation between word and image in its New World Baroque vertigo. This vertigo is politically charged, and amounts to a ‘counter-Conquest’ (Lezama Lima) of the clear and distinct distribution of legibility and visibility inherited through coloniality. The metaphoric economy of cannibalism in Oswald de Andrade’s “Manifesto Antropófago” (1928) in conjunction with the visual work of Tarsila do Amaral and the ‘re-discovery’ of Barroco Mineiro by the Brazilian avant-garde deconstructs the narrative of rupture so as to engage in a complex ‘route to roots’ highlighting the artifice of origin. This same artifice marks Torres-García’s oeuvre, and by ‘closing’ the diptych, I show how abstraction folds back into a Baroque superimposition

Application of the Google matrix methods for characterization of directed networks

La théorie des réseaux complexes est un domaine récent et important de la recherche qui consiste étudier divers systèmes naturels ou artificiels d'un point de vue des graphes en considérant une collection d'objets interdépendants. Parmi les différents aspects de la théorie des réseaux complexes, cette thèse se concentre sur l'analyse des propriétés structurelles des réseaux dirigés. L'outil principal utilisé dans ce travail est la méthode de la matrice Google qui est une méthode dérivée de la théorie des chaînes de Markov. La construction de cette matrice et son lien avec les chaînes de Markov sont expliqués dans le second chapitre et les propriétés spectrales des valeurs propres y sont également discutées. L'accent est mis sur le vecteur propre principal dela matrice (le PageRank). La base du système de ranking donné par le Page Rank y est expliquée en détail et illustrée à travers plusieurs exemples dans les chapitres suivants. Les systèmes considérés ici sont: les séquences d'ADN de quelques espèces animales,le système nerveux du vers C.elegans ainsi que l'antique jeu de stratégie sur plateau, le jeu de go. Dans le premier cas nous analysons les propriétés statistiques des chaînes symboliques sous le point de vue des réseaux dirigés et nous proposons une mesure simple de similarité entre les espèces basée sur le PageRank. Dans le second cas nous introduisons le concept du ranking complémentaire (le CheiRank) permettant de caractériser en deux dimensions les réseaux dirigés. Dans le troisième cas nous utilisons les vecteurs propres principaux pour mettre en évidence les coups importants joués lors d'une partie de Go et nous montrons que les vecteurs propres suivants peuvent contenir des informations de communautés de coups. Ces diverses applications montrent que l'information apportée par le PageRank peut s'avérer utile dans de nombreuses situations différentes affin d'obtenir un aperçu du problème sous un angle différent, qui est l'approche des réseaux dirigés, enrichissant ainsi notre compréhension des systèmes étudiés.The complex network theory is a recent field of great importance to study various systems under a graph perspective by considering a collection of interdependent objects. Among the different aspects of the complex networks, this thesis is focused on the analysis of structural properties of directed networks. The primary tool used in this work is the Google matrix method which is derived from the Markov chain theory. The construction of this matrix and its link with Markov chains are explored and the spectral properties of the eigenvalues are discussed with an emphasis on the dominant eigenvalue with its associated eigenvector(PageRank vector). The ranking system given by the PageRank is explained in detail and illustrated through several examples. The systems considered here are the DNA sequences of some animal species, the neural system of the C.elegans worm and the ancient strategy board game : the game of Go. In the first case, the statistical properties of symbolic chains are analyzed through a directed network viewpoint and a similarity measure of species based on PageRank is proposed. In the second case, the complementary ranking system (CheiRank vector) is introduced to provide a two dimensional characterization of the directed networks. In the third case, the dominant eigenvectors are used to highlight the most important moves during a game of Go and it is shown that those eigenvectors contain more information than mere frequency counts of the moves. It is also discussed that eigenvectors other than the dominant ones might contain information about some community structures of moves. These applications show how the information brought by the PageRank can be useful in various situations to gain some interesting or original insight about the studied system and how it is helping to understand the organization of the underlying directed network

Storytelling revivalism in England and Wales : history, performance and interpretation.

This study discusses the storytelling movement in England and Wales as an example of the traditional arts "revival." "Revivals" are qualitatively different from mature traditions, but this distinction eludes theorisation. This creates shortcomings in the literature, which are identified and discussed. It is concluded that mature traditions and "revivals" are both subcategories of traditional milieu. The "revival" is distinguished, firstly, by its attenuated diachronic chains of transmission and synchronic bonds of social cohesion, resulting in a loss of deep aesthetic consensus in the participant group; and, secondly, by its self-traditionalisation: its selfconscious self-presentation as a traditional form socioculturally opposed to a traditionless mainstream modernity. The "revival" is therefore often understood as a nostalgic and symbolic re-enactment of desired sociocultural conditions. The study is an inductive, transparent consideration of storytelling revivalism in England and Wales in the light of this preliminary conclusion, considering three issues: the history of the movement; the whole-group performance of storytelling events; and emic interpretations and understandings of involvement, elicited in interview. The evidence is that storytelling revivalism is part of a long-lived appropriative process transcending sociocultural distinctions; that its performative idioms do not express but mediate - eventually, undermine - its iconoclastic separateness from modernity, integrating the formally "revived" form into the informal mainstream; and that interviews demonstrated nostalgic sociocultural beliefs to be contingent and of secondary importance to aesthetic experience. In conclusion, revivalistic communities indulge selfconscious self-traditionalisation sparingly and reluctantly. Emically, it is an uninteresting implication or a necessary cognitive and behavioural stopgap facilitating a deeper experiential familiarity with the form itself "Revival," although occupying an intellectually enfranchised milieu, is properly a nascent non-intellectual, aesthetic and social form. This conclusion overturns the preliminary conclusion, and suggests the general fallaciousness of assuming that cultural forms are primarily coded representations of sociocultural conditions

A Bakhtinian reading of fantasy chronotopes in modern children’s fantasy literature

Drawing on Bakhtin’s theory of the literary artistic chronotope and the interdisciplinary spatiotemporal theories of geocriticism, this study identifies three particular modes of the fantasy spatiotemporality presented in modern children’s fantasy works. They are the epic chronotope, the “fantastic” time-travel chronotope and the heterotopian chronotope. Each fantasy chronotope is examined in the specific but interrelated textual contexts of selected children’s fantasy works in relation to the three main research questions: (i) How is the fantasy chronotope embodied and strategically deployed in the focused children’s fantasy works? (ii) What ideas and values are conveyed by its syntagmatic interplay with other chronotopes that characterise the textual quotidian world? (iii) How do characters, through their spatiotemporal practices, negotiate with the divergent chronotopic values that converge and wrestle in the textual universes? This study builds on existing works in relation to chronotopic considerations and develops the understanding of the fantasy chronotope in these particular ways: a) It moves the study of the fantasy chronotope from generalities to specific instances, so that the inner diversity of the fantasy spatiotemporal arrangements can be perceived and explored. b) It examines the syntagmatic spatiotemporal relations constructed between the fantasy and the “real” in individual children’s fantasy works and their connotations. In so doing, it reveals how each of the identified fantasy chronotopes can be strategically deployed in fantasy cartographies to convey meanings and values. c) This study also delves into the spatiotemporal embedding of human actions that is distinctively shown in fantasy chronotopes. This is done by reading characters’ spatiotemporal practices in and their negotiations with the projected fantasy worlds. d) Taking Bakhtin’s literary artistic chronotope as the link, my reading of the fantasy chronotopes also demonstrates an interpenetrative and reciprocal relation between fantasy spatiotemporal imaginations and the theoretical interpretations of space and time in geocriticism

Wonder and Scepticism in the Long Twelfth Century

This thesis considers the interaction between wonder and scepticism in long twelfth-century Europe. Wonder is presented as necessitating a cognitive reaction that involves a process of evidence and fact-checking, which leads to a subjective assessment of a phenomenon’s truth or falsehood, or its probability or improbability. Brewer explores a variety of wonder stories from the Middle Ages to chart this reaction. Such stories include green children, monsters, wild men, miraculous healings, and marvelous tales of the exotic East. Brewer proposes that medieval people reacted to novel and unexplained phenomena using a transhistorical epistemological process, but that there were nevertheless significant synchronic differences in terms of what phenomena were accounted bizarre, what the normative reactions to various phenomena were considered to be, and the overall availability of sense-derived knowledge. In particular, the burgeoning empiricism of the long twelfth century created tension with the pervasive idea of faith as a necessity to understanding God’s creation. Brewer therefore proposes that, in some ways, evolutionary mechanisms such as the emotion of wonder were at odds with medieval cultural pretensions

Koncepce prostoru viktoriánských románů

The dissertation focuses on two general categories of defining space: on space expression according to the expressive approach to aesthetics and, secondly, on space representation based on the mimetic aesthetics. The exploration of the surface structure of space employs the philosophical categories of smooth and striated space, formulated by Deleuze and Guattari in their Treatise on Nomadology, while the depths of the inner spaces, including the spaces of the human mind, are treated within the framework of Gaston Bachelard's phenomenology, stressing the importance of the symbolic meanings hidden in the unconscious. The primary texts in which the concept of space is explored range from the Brontë sisters' novels (Wuthering Heights, Jane Eyre) to Thomas Hardy's Wessex novels, and further on to the last novel of George Eliot, Daniel Deronda. Attention is given to the role of natural elements constituting space, with emphasis on the element of water.Práce se zabývá koncepcí prostoru vybraných viktoriánských románů nejprve v jeho povrchové struktuře a posléze zkoumá hloubkové vztahy těchto struktur k archetypálním a symbolickým složkám prostoru v literatuře. Ke zkoumání "povrchu" byla využita filosofie pojetí prostoru Deleuze a Guattariho rozlišující prostor hladký (nomádský) a zvrstvený (civilizačními zásahy). Další část práce využívá filosofickou perspektivu vnímání prostoru Gastona Bachelarda, jehož Poetika prostoru zachycuje fenomenologii básnického obrazu s důrazem na archetypální pojetí hloubky prostoru a jeho funkci v lidském podvědomí. Práce se zaměřuje na vybrané romány viktoriánské doby, které nesou jisté společné znaky (centralizace prostoru, otevřenost krajiny, vztah k místu nebo určitému regionu), a v tomto směru podrobuje analýze romány sester Brontëových (Na Větrné hůrce, Jana Eyrová), Thomase Hardyho a George Eliot (Mlýn na řece Floss, Daniel Deronda).Ústav anglistiky a amerikanistikyFilozofická fakultaFaculty of Art