Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Computational Market Dynamics of Virtual Economies

The last two decades have provided a vast opportunity to live and explore the compulsive imaginary world or virtual world through massively multiplayer online role-playing games (MMORPGs). MMORPG gives a wide range of opportunities to its users to participate with multi-players on the same platform, to communicate and to do real time actions. There is a virtual economy in these games which is largely player-driven. In-game currency provides its users to build up their Avatars, to buy or sell the necessary goods to play, survive in the games and so on. As a part of virtual economies generated through EVE Online, this thesis mainly focuses on how the prices of the minerals in EVE Online behave by applying the Jabłonska- Capasso-Morale (JCM) mathematical simulation model. It is to verify up to what degree the model can reproduce the virtual economy behavior. The model is applied to buy and sell prices of two minerals namely, isogen and morphite. The simulation results demonstrate that JCM model ts reasonably well to the mineral prices, which lets us conclude that virtual economies behave similarly to the real ones.

From transcendental to practical intersubjectivity: a social psychological approach to Kant's musical aesthetics

It is well known that Kant’s aesthetics is framed intersubjectively because he upholds the claim of taste to universality. However, the transcendental foundation of this shared universality is a supersensible ground which is taken for granted but which cannot be brought directly into communicative experience. Kant’s reliance on the synthetic a priori structure of aesthetic judgment also removes it from the sphere of observable personal interaction. This argumentative strategy exposes it to skeptical challenge and generates inaccessible references to inner representations (be they intuitions, categories of the understanding or rational ideas). It is not sufficient, as Kant did, to propose a description of aesthetic experience that is subjectively plausible and thereby claim its intersubjective validity. It is indispensable to embody intersubjectivity in behavior and language. In practical intersubjectivity, aesthetic attitudes are dealt with in a concrete and accessible manner without relying on mentalistic assumptions as a foundation. Conceptual terms such as 'agreeable’, 'beauty’, 'sublime’, 'ugly’, 'universality’ acquire new meaning in a conversational context and aesthetic claims are tested in a dialogical game semantics model.

From absolutes to aesthetics : John Dewey and the art of experience /

In this thesis I sought to capture something of the integrity of John Dewey's larger vision. While recognizing this to be a difficult challenge, I needed to clear some of the debris of an overly narrow reading of Dewey's works by students of education. The tendency of reducing Dewey's larger philosophical vision down to neat theoretical snap shots in order to prop up their particular social scientific research, was in my estimation slowly damaging the larger integrity of Dewey's vast body of work. It was, in short, killing off the desire to read big works, because doing so was not necessary to satisfying the specialized interests of social scientific research. In this thesis then I made a plea for returning the Humanities to the center of higher education. It is there that students learn how to read and to think—skills required to take on someone of Dewey's stature. I set out in this thesis to do just that. I took Dewey's notion of experience as the main thread connecting all of his philosophy, and focused on two large areas of inquiry, science and its relation to philosophy, and aesthetic experience. By exploring in depth Dewey's understanding of human experience as it pertains to day-to-day living, my call was for a heightened mode of artful conduct within our living contexts. By calling on the necessity of appreciating the more qualitative dimensions of lived experience, I was hoping that students engaged in the Social Sciences might begin to bolster their research interests with more breadth and depth of reading and critical insight. I expressed this as being important to the survival and intelligent flourishing of democratic conduct.

Experimental and Computational Studies on Copper and Hydrobenzoin Derivatives in Catalytic Asymmetric Reactions

The use of theory to understand and facilitate catalytic enantioselective organic transformations involving copper and hydrobenzoin derivatives is reported. Section A details the use of theory to predict, facilitate, and understand a copper promoted amino oxygenation reaction reported by Chemler et al. Using Density Functional Theory (DFT), employing the hybrid B3LYP functional and a LanL2DZ/6-31G(d) basis set, the mechanistic details were studied on a N-tosyl-o-allylaniline and a [alpha]-methyl-[gamma]-alkenyl sulfonamide substrate. The results suggest the N-C bond formation proceeds via a cisaminocupration, and not through a radical-type mechanism. Additionally, the origin of diastereoselection observed with [alpha]-methyl-[gamma]-alkenyl sulfonamide arises from avoidance of unfavourable steric interactions between the methyl substituent and the N -protecting group. Section B details the computationally guided, experimental investigation of two hydrobenzoin derivatives as ligands/ catalysts, as well as the attempted synthesis of a third hydrobenzoin derivative. The bis-boronic acid derived from hydrobenzoin was successful as a Lewis acid catalyst in the Bignielli reaction and the Conia ene reaction, but provided only racemic products. The chiral diol derived from hydrobenzoin successfully increased the rate of the addition of diethyl zinc to benzaldehyde in the presence of titanium tetraisopropoxide, however poor enantioinduction was obseverved. Notably, the observed reactivity was successfully predicted by theoretical calculations.

Towards reverse engineering of Photosystem II: Synergistic Computational and Experimental Approaches

ABSTRACT Photosystem II (PSII) of oxygenic photosynthesis has the unique ability to photochemically oxidize water, extracting electrons from water to result in the evolution of oxygen gas while depositing these electrons to the rest of the photosynthetic machinery which in turn reduces CO2 to carbohydrate molecules acting as fuel for the cell. Unfortunately, native PSII is unstable and not suitable to be used in industrial applications. Consequently, there is a need to reverse-engineer the water oxidation photochemical reactions of PSII using solution-stable proteins. But what does it take to reverse-engineer PSII’s reactions? PSII has the pigment with the highest oxidation potential in nature known as P680. The high oxidation of P680 is in fact the driving force for water oxidation. P680 is made up of a chlorophyll a dimer embedded inside the relatively hydrophobic transmembrane environment of PSII. In this thesis, the electrostatic factors contributing to the high oxidation potential of P680 are described. PSII oxidizes water in a specialized metal cluster known as the Oxygen Evolving Complex (OEC). The pathways that water can take to enter the relatively hydrophobic region of PSII are described as well. A previous attempt to reverse engineer PSII’s reactions using the protein scaffold of E. coli’s Bacterioferritin (BFR) existed. The oxidation potential of the pigment used for the BFR ‘reaction centre’ was measured and the protein effects calculated in a similar fashion to how P680 potentials were calculated in PSII. The BFR-RC’s pigment oxidation potential was found to be 0.57 V, too low to oxidize water or tyrosine like PSII. We suggest that the observed tyrosine oxidation in BRF-RC could be driven by the ZnCe6 di-cation. In order to increase the efficiency of iii tyrosine oxidation, and ultimately oxidize water, the first potential of ZnCe6 would have to attain a value in excess of 0.8 V. The results were used to develop a second generation of BFR-RC using a high oxidation pigment. The hypervalent phosphorous porphyrin forms a radical pair that can be observed using Transient Electron Paramagnetic Resonance (TR-EPR). Finally, the results from this thesis are discussed in light of the development of solar fuel producing systems.

Modeling Metal Protein Complexes from Experimental Extended X-ray Absorption Fine Structure using Computational Intelligence

Experimental Extended X-ray Absorption Fine Structure (EXAFS) spectra carry information about the chemical structure of metal protein complexes. However, pre- dicting the structure of such complexes from EXAFS spectra is not a simple task. Currently methods such as Monte Carlo optimization or simulated annealing are used in structure refinement of EXAFS. These methods have proven somewhat successful in structure refinement but have not been successful in finding the global minima. Multiple population based algorithms, including a genetic algorithm, a restarting ge- netic algorithm, differential evolution, and particle swarm optimization, are studied for their effectiveness in structure refinement of EXAFS. The oxygen-evolving com- plex in S1 is used as a benchmark for comparing the algorithms. These algorithms were successful in finding new atomic structures that produced improved calculated EXAFS spectra over atomic structures previously found.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

Computational prediction of neural progenitor cell fates

Understanding how stem and progenitor cells choose between alternative cell fates is a major challenge in developmental biology. Efforts to tackle this problem have been hampered by the scarcity of markers that can be used to predict cell division outcomes. Here we present a computational method, based on algorithmic information theory, to analyze dynamic features of living cells over time. Using this method, we asked whether rat retinal progenitor cells (RPCs) display characteristic phenotypes before undergoing mitosis that could foretell their fate. We predicted whether RPCs will undergo a self-renewing or terminal division with 99% accuracy, or whether they will produce two photoreceptors or another combination of offspring with 87% accuracy. Our implementation can segment, track and generate predictions for 40 cells simultaneously on a standard computer at 5 min per frame. This method could be used to isolate cell populations with specific developmental potential, enabling previously impossible investigations.

The Aesthetics of Madame de Staël and Mary Shelley

L’esthétique de Madame de Staël and Mary Shelley discute l’art de l’improvisation et le concept de l’enthousiasme dans les écrits de ces deux auteurs. Dans ce projet, j’explore l’esthétique d’improvisation et d’enthousiasme de Madame de Staël dans Corinne, en me référant à son autre roman Delphine, à sa pièce de théâtre Sapho, et à ses nouvelles ainsi qu’à ses textes philosophiques comme De l’Allemagne, De l’influence des passions, et De la littérature. J’argumente que Madame de Staël représente à travers le caractère de Corinne une esthétique anti-utilitaire. J’explique qu’elle évoque des valeurs cosmopolites qui valorisent une culture indigène qui est en opposition avec l’impérialisme de Napoléon. De plus, j’examine comment les improvisations de Corinne dérivent d’un enthousiasme qui est associé à la définition que Platon offre du terme. Ceci est évident par la signification que Madame de Staël présente du terme dans De L’Allemagne. J’interprète la maladie de Corinne comme étant d’origine psychosomatique qui est manifesté par la perte de son génie et par un suicide lent qui est une expression de colère contre la patriarchie. Le caractère de Corinne permet à Madame de Staël d’explorer le conflit que les femmes artistes éprouvaient entre ayant une carrière artistique et adhérant à l’idéologie domestique. Chapitre deux se concentre sur l’intérêt que Shelley démontre sur l’art de l’improvisation comme elle l’exprime dans ses lettres à propos de l’improvisateur Tommaso Sgricci. Malgré sa fascination avec la poésie extemporanée, Shelley regrette que cette forme d’art soit évanescente. Aussi, j’examine son enthousiasme pour un autre artiste, Nicolò Paganini. Son enchantement avec se violoniste virtuose est lié à des discours concernant le talent surnaturel des improvisateurs. J’argumente qu’il y a un continuum d’improvisation entre les balades orales du peuple et les improvisations de culture sophistiqué des improvisateurs de haute société. J’estime que les Shelleys collaboraient à définir une théorie d’inspiration à travers leurs intérêts pour l’art de l’improvisation. Chapitre trois considère le lien entre cosmologie et esthétique d’inspiration à travers la fonction de la musique, spécialement La Création de Joseph Haydn, dans The Last Man de Shelley. J’examine la représentation du sublime des Alpes dans le roman à travers de discours qui associent les Alpes avec les forces primordiales de la création. Les rôles de la Nécessité, Prophétie, et du Temps peuvent être compris en considérant la musique des sphères. Chapitre quatre explore les différentes définitions de terme enthousiasme dans les écrits de Shelley, particulièrement Valperga et The Last Man. Je discute l’opinion de Shelley sur Madame de Staël comme suggéré dans Lives. J’analyse les caractères qui ressemblent à Corinne dans les écrits de Shelley. De plus, je considère les sens multiples du mot enthousiasme en relation avec la Guerre civil d’Angleterre et la Révolution française. Je présente comment le terme enthousiasme était lié au cours du dix-septième siècle avec des discours médicales concernant la mélancolie et comment ceci est reflété dans les caractères de Shelley.

A computational fluid dynamic study on the filtering mechanics in suspension feeding marine invertebrates

Les suspensivores ont la tâche importante de séparer les particules de l'eau. Bien qu'une grande gamme de morphologies existe pour les structures d'alimentation, elles sont pratiquement toutes constituées de rangées de cylindres qui interagissent avec leur environnement fluide. Le mécanisme de capture des particules utilisé dépend des contraintes morphologiques, des besoins énergétiques et des conditions d'écoulement. Comme nos objectifs étaient de comprendre ces relations, nous avons eu recours à des études de comparaison pour interpréter les tendances en nature et pour comprendre les conditions qui provoquent de nouveaux fonctionnements. Nous avons utilisé la dynamique des fluides numérique (computational fluid dynamics, CFD) pour créer des expériences contrôlées et pour simplifier les analyses. Notre première étude démontre que les coûts énergétiques associés au pompage dans les espaces petits sont élevés. De plus, le CFD suggère que les fentes branchiales des ptérobranches sont des structures rudimentaires, d'un ancêtre plus grande. Ce dernier point confirme l'hypothèse qu'un ver se nourrit par filtration tel que l'ancêtre des deuterostomes. Notre deuxième étude détermine la gamme du nombre de Reynolds number critique où la performance d'un filtre de balane change. Quand le Re est très bas, les différences morphologiques n'ont pas un grand effet sur le fonctionnement. Cependant, une pagaie devient une passoire lorsque le Re se trouve entre 1 et 3,5. Le CFD s’est dévoilé être un outil très utile qui a permis d’obtenir des détails sur les microfluides. Ces études montrent comment la morphologie et les dynamiques des fluides interagissent avec la mécanisme de capture ou de structures utilisées, ainsi que comment des petits changements de taille, de forme, ou de vitesse d'écoulement peuvent conduire à un nouveau fonctionnement.

The monstrous archive. Aesthetics of decay and horror in found footage films

Ce texte a été présenté à la table ronde « Contested Footage: Snuff, Disease, the Avant-Garde, and the Archive » lors du congrès annuel de la PCA/ACA (Popular Culture Association/American Culture Association) qui se tenait à la Nouvelle-Orléans, du 1er au 4 avril 2015. La participation à ce congrès s’inscrivait dans le cadre du projet de recherche « Archives et création : nouvelles perspectives sur l’archivistique » sous la direction d’Yvon Lemay. Ce projet est financée par le Conseil de recherches en sciences humaines du Canada (CRSH) dans le cadre du programme Savoir (2013-2016).

Computational models for the prediction of severe thunderstorms over east indian region

Thunderstorm is one of the most spectacular weather phenomena in the atmosphere. Many parts over the Indian region experience thunderstorms at higher frequency during pre-monsoon months (March- May), when the atmosphere is highly unstable because of high temperatures prevailing at lower levels. Most dominant feature of the weather during the pre-monsoon season over the eastern Indo-Gangetic plain and northeast India is the outburst of severe local convective storms, commonly known as ‘Nor’wester’ or ‘Kalbaishakhi’. The severe thunderstorms associated with thunder, squall line, lightning and hail cause extensive losses in agriculture, damage to structure and also loss of life. The casualty due to lightning associated with thunderstorms in this region is the highest in the world. The highest numbers of aviation hazards are reported during occurrence of these thunderstorms. In India, 72% of tornadoes are associated with this thunderstorm.

The Aesthetics Of Paul Verlaine And Changampuzha Krishnapillai - A Comparative Perspective

The present study is entitled The Aesthetics of Paul Verlaine and Changampuzha Krishnapillai - a comparative perspective. The purpose of the study is to compare the poetic genius of the French poet Paul Verlaine (1844-1896) and that of the Malayalam poet Changampuzha Krishnapillai (1911-1948), within a descriptive framework. The investigation will hopefully answer the questions- Has Changampuzha been indeed influenced by Verlaine, if so, to what extent? Can the aesthetic appreciation be justified in both poets as illustrated in their works? The comparative methodology of juxtaposing the selected oeuvres of the poets is largely adopted in the study. Since the span of analysis is across national and linguistic borders, the distinguishing as well as exclusive traits of the individual poets will be of much importance in formulating the comparative assumption in this work. The vastly differing geographical, linguistic and cultural milieus of these two poets,-one a national French poet and the other, a regional Indian poet writing in Malayalam prima facie,endow the theme of the dissertation with an innate hue of diversity. Such an ambitious task would naturally entail a renewed research into the dedication of the poets to their muses and their ultimate contributions to poetics. The analysis, while attempting to illuminate from a fresh angle, the amply researched oeuvre of Verlaine and the lesser studied one of Changampuzha, cannot but be aware of the limitations of the task at hand. The present study is the first of its kind on the specific theme of analysis, and is hoped that it would be of relevance since no work has so far been known to have been undertaken on the topic. At a time when the birth centenary celebrations of Changampuzha have just concluded, this study is hoped to assume significance as it would help in isolating the originality of the poet's works, extricating the garb of the French influence. Ultimately, this study aims at creating a wider appreciation of the impact that the French writers have had on Malayalam writers, thus shedding new light on the benign foreign influences that served to enhance the beauty of our cultural heritage

Vibrational spectroscopic studies and computational study of quinoline-2-carbaldehyde benzoyl hydrazone

FT-IR spectrum of quinoline-2-carbaldehyde benzoyl hydrazone (HQb H2O) was recorded and analyzed. The synthesis and crystal structure data are also described. The vibrational wavenumbers were examined theoretically using the Gaussian03 package of programs using HF/6-31G(d) and B3LYP/6-31G(d) levels of theory. The data obtained from vibrational wavenumber calculations are used to assign vibrational bands obtained in infrared spectroscopy of the studied molecule. The first hyperpolarizability, infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated values. The changes in the CAN bond lengths suggest an extended p-electron delocalization over quinoline and hydrazone moieties which is responsible for the non-linearity of the molecule