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Sharma, Shruti. "Unfolding and compaction in chaperonin-assisted protein folding followed by single molecule and ensemble FRET". Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-76225.
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Stenström, Harald. "Free ensemble improvisation /". Göteborg : Faculty of Fine, Applied and Performing Arts, Academy of Music and Drama, University of Gothenburg, 2009. http://hdl.handle.net/2077/20293.
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Stubblefield, Cedrick L. "Extracting value from ensembles for cloud-free forecasting". Monterey, California. Naval Postgraduate School, 2011. http://hdl.handle.net/10945/10796.
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The Air Force Weather Agency (AFWA) is currently producing cloud-free forecasts for several agencies, but operational forecasts do not incorporate forecast uncertainty. Uncertainty can be forecasted via an ensemble created with perturbed initial conditions. We combine AFWA's global cloud analysis and cloud advection model with the National Centers for Environmental Prediction's global weather ensemble to study the potential for ensemble cloud-free forecasting in support of space-based image collection. A year of ensemble forecasts forms the evaluation dataset. The operationally relevant cloud-free forecast threshold (cloud cover less than 30%) is evaluated over sets of 24-km grid boxes in three climatologically different regions. The analyses and forecasts favor cloud-cover values near 0% and 100% cloud cover, making skill metrics that assume normal statistics mostly inappropriate. Thus we focus on contingency table metrics at the 30% threshold and argue that the odds ratio is most appropriate. Because costs of satellite image collection are largely unknown or classified, and typical cost/loss models may not apply, we also invoke utility theory to quantify operator benefits obtainable from the ensemble. Ensemble skill is apparent, and utility for risk-averse users in persistently clear, cloudy, and variable regions/seasons yields up to a 20% increase in operational efficiency.
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Watson, Samuel Stewart 1986. "Conformal loop ensembles and the Gaussian free field". Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/97319.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 173-178).
The study of two-dimensional statistical physics models leads naturally to the analysis of various conformally invariant mathematical objects, such as the Gaussian free field, the Schramm-Loewner evolution, and the conformal loop ensemble. Just as Brownian motion is a scaling limit of discrete random walks, these objects serve as universal scaling limits of functions or paths associated with the underlying discrete models. We establish a new convergence result for percolation, a well-studied discrete model. We also study random sets of points surrounded by exceptional numbers of conformal loop ensemble loops and establish the existence of a random generalized function describing the nesting of the conformal loop ensemble. Using this framework, we study the relationship between Gaussian free field extrema and nesting extrema of the ensemble of Gaussian free field level loops. Finally, we describe a coupling between the set of all Gaussian free field level loops and a conformal loop ensemble growth process introduced by Werner and Wu. We prove that the dynamics are determined by the conformal loop ensemble in this coupling, and we use this result to construct a conformally invariant metric space.
by Samuel Stewart Watson.
Ph. D.
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Li, Rui. "OVERCOMING INITIAL HURDLES: STRATEGIES FOR DEVELOPING A UNIVERSITY FREE IMPROVISATION ENSEMBLE". UKnowledge, 2015. http://uknowledge.uky.edu/music_etds/52.
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New free improvisers may come across six major problems as they learn to improvise: imbalance between technique and music, incorrect perception of limitation, imbalance between rationality and emotion, lack of enthusiasm, inability to view criticism as a source of creativity, and misunderstanding of mistakes and risks. In this thesis, I propose a set of effective pedagogical tools as possible solutions for students and groups interested in exploring the beauty of free improvisation.
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Eriksson, Jesper. "My Improvisation Practice : the act of improvising in individual instrumental practice, collaboration projects and performance". Thesis, Kungl. Musikhögskolan, Institutionen för klassisk musik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kmh:diva-1654.
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In this study I research and reflect on the way I have been practicing with my saxophone, how I have been collaborating with others and how I’ve worked with performance during my two master years, with a focus on improvisation. The study is a presentation of my Professional Integration Project on NAIP-European Master of Music-program. I have had many different projects that will be presented. By playing, listening, and analyzing free improvisation I wanted to learn more about myself as a musician and about improvisation in general. I am also going to present individual exercises for improvisation I’ve been using, as well as exercises for group improvisation. I am going to present time-lines of events to see how one thing leads to another. I will present the product of a piece with improvised aspects, that led me and my collaborators to find our own ways of rehearsing. By summarizing the many aspects, I present my findings by describing what I want to learn, and how I want to learn it, and how I’ve been working with free improvisation groups and music collaboration, and what is important for me while performing improvisations. The findings of my studies suggest that I have developed my improvisational skills by playing free improvisation and doing exercises. My projects has also shown that you can combine written music with improvisational aspects in a classical setting by using different ways of rehearsing. Lastly, I found that it is important that, while improvising, musicians have a total mental presence to avoid energy loss in the music.Självständiga arbete, Master, 40 hp.
Program examenskonsert:
ImprovisationKvintett
Jesper Eriksson saxofon, Linnea Andreassen röst, Maiju Kopra röst, Viktor Rydén röst, Amanda Larsson röst.
Jesper ErikssonKvartett (2014), uruppförande
Alexander Rydberg violin, Jesper Eriksson saxofon, Emma Augustsson cello, Anton Svanberg tuba.
ImprovisationTrio
Jesper Eriksson saxofon, Jaan Krivel röst och klarinett, Kristoffer Linder slagverk
Extranummer: Friimprovisationsorkester
Jesper Eriksson saxofon, Alexander Rydberg violin, Emma Augustsson cello, Anton Svanberg tuba, Linnea Andreassen röst, Maiju Kopra röst, Viktor Rydén röst, Amanda Larsson röst, Jaan Krivel röst och klarinett, Kristoffer Linder slagverk, Bernhard Greter piano.
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Martínez, Monge Álvaro. "Free energy and information-content measurements in thermodynamic and molecular ensembles". Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667026.
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Single-molecule experiments have emerged as a powerful tool that allow researchers to investigate the physical behavior of individual molecules with unprecedented resolution. The feasibility exerting forces at the piconewton scale (10^-12 N) and measuring nanometric displacements in the sub-millisecond scale, offer a widespread range of exciting possibilities. The major part of this thesis is devoted to address fundamental topics of statistical physics using single-molecule experiments. In particular, in the first part of the thesis, we aimed to study one of the eldest questions in statistical mechanics: the issue of ensemble inequivalence. By performing single- molecule experiments on a well-known molecule (the CD4 DNA hairpin), we have been able of exploring two conjugate ensembles: the fixed-extension and the force-fixed ensemble. Both ensembles are conjugate with respect to energy since the product force times extension equals has energy dimensions. We carried out experiments in the fixed-force ensemble using both optical tweezers and magnetic tweezers, and in the fixed-extension using optical tweezers. We have found that these two conjugate ensembles are not equivalent at the level of thermodynamics nor in kinetics. Moreover, we showed that the often-neglected boundary terms in the definition of the thermodynamic work are essential to the validity of the fluctuation theorem. The second part of this thesis is also merely theoretical. Recent single-molecule assays confirmed the connection between information theory and statistical physics. Single- molecule experiments have turned out to be the perfect playground to explore the thermodynamic implications of having —or lacking— information. It is worthwhile to mention the experimental realization of the Szilard engine and the experimental verification of Landauer’s limit. With the current existing results, the information-to- energy connection is well established. We have been able to experimentally demonstrate, for the first time, the reversed implication. We have been able to quantify the information-content of neutral molecular ensembles by means of thermodynamic measurements. That is, we experimentally demonstrated the energy- to-information conversion. Our works are built on what we call ensemble force spectroscopy, a systematic procedure capable of obtaining a robust characterization of molecular ensembles in the best tradition of statistical physics, by measuring few tens of molecules. In the final part of the thesis we aimed to measure the specific binding energy of a metallic ion to the tertiary structure of a three-way RNA junction belonging
to the central domain of the 16S ribosomal RNA (rRNA). From the physics perspective, to the best of our knowledge, first time we have been able to discern the free energy contribution due to the specific binding of magnesium ions to an RNA substrate by means of single-molecule assays. On the other hand, such molecule is able to form, besides its native conformation, a force-induced misfolded state. Despite this fact was already pointed out in previous single-molecule studies, there was a lack of knowledge regarding the molecular kinetics and the folding pathway. Aiming to fill this gap, we performed a thorough study of the three-helix RNA junction using dynamic force spectroscopy. As a result, we have characterized the full folding pathway of the molecule, including both the native and the misfolded structure. Furthermore, we have experimentally confirmed the fact that the presence of magnesium promotes the stabilization of the native structure and we have measured this contribution. We have found that magnesium is able to rescue the native structure from the misfolded structure via electrostatic interactions due to magnesium binding. This fact is biologically relevant, since we have been able to characterize the conditions in which a misfolded molecule is able to recover its native conformation.En esta tesis hemos abordado cuestiones fundamentales de la física estadística. En particular, hemos estudiado el problema de la equivalencia entre colectivos estadísticos, la conversión de energía a información y el estudio de las energías específicas de unión de iones metálicos a sustratos de RNA. Esta tesis doctoral se ha llevado a cabo empleando dos de los instrumentos de molécula individual más conocidos, las pinzas ópticas y las pinzas magnéticas. Ambas son técnicas que permiten la aplicación controlada de fuerzas mecánicas a los extremos de una molécula individual. El poder aplicar fuerzas a sistemas moleculares permite llevar a cabo una profunda caracterización de las propiedades físicas de los llamados sistemas pequeños. Las dimensiones de estos sistemas abarcan desde unos pocos nanómetros —una millonésima parte del metro— hasta varios cientos de nanómetros. Además, los sistemas pequeños están lejos del llamado límite termodinámico y están dominados por las fluctuaciones térmicas del entorno. Por lo tanto, debido a estas peculiaridades, el estudio de sistemas pequeños mediante los instrumentos de molécula individual permite impulsar y extender los horizontes de la física de no equilibrio.
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Westerlund, Annie M. "Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles". Licentiate thesis, KTH, Biofysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-234888.
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Ca2+ and calmodulin play important roles in many physiologically crucial pathways. The conformational landscape of calmodulin is intriguing. Conformational changes allow for binding target-proteins, while binding Ca2+ yields population shifts within the landscape. Thus, target-proteins become Ca2+-sensitive upon calmodulin binding. Calmodulin regulates more than 300 target-proteins, and mutations are linked to lethal disorders. The mechanisms underlying Ca2+ and target-protein binding are complex and pose interesting questions. Such questions are typically addressed with experiments which fail to provide simultaneous molecular and dynamics insights. In this thesis, questions on binding mechanisms are probed with molecular dynamics simulations together with tailored unsupervised learning and data analysis. In Paper 1, a free energy landscape estimator based on Gaussian mixture models with cross-validation was developed and used to evaluate the efficiency of regular molecular dynamics compared to temperature-enhanced molecular dynamics. This comparison revealed interesting properties of the free energy landscapes, highlighting different behaviors of the Ca2+-bound and unbound calmodulin conformational ensembles. In Paper 2, spectral clustering was used to shed light on Ca2+ and target protein binding. With these tools, it was possible to characterize differences in target-protein binding depending on Ca2+-state as well as N-terminal or C-terminal lobe binding. This work invites data-driven analysis into the field of biomolecule molecular dynamics, provides further insight into calmodulin’s Ca2+ and targetprotein binding, and serves as a stepping-stone towards a complete understanding of calmodulin’s Ca2+-dependent conformational ensembles.QC 20180912
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Nungesser, Ernesto [Verfasser]. "The future of some Bianchi A spacetimes with an ensemble of free falling particles / Ernesto Nungesser". Berlin : Freie Universität Berlin, 2012. http://d-nb.info/1027308546/34.
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Hartz, Barry C. "Cultivating Individual Musicianship and Ensemble Performance Through Notation-Free Learning in Three High School Band Programs". Case Western Reserve University School of Graduate Studies / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1435244359.
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Piedra, Olman E. "Creative Musical Improvisation in the Development and Formation of NEXUS Percussion Ensemble". Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1387545761.
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Lupu, Titus. "Ensembles poissoniens de boucles markoviennes". Thesis, Paris 11, 2015. http://www.theses.fr/2015PA112066/document.
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L'objet d'étude de cette thèse est une mesure infinie sur les boucles (lacets) naturellement associée à une large classe de processus de Markov et les processus ponctuels de Poisson d'intensité proportionnelle à cette mesure (paramètre d'intensité alpha>0). Ces processus ponctuels de Poisson portent le nom d'ensembles poissoniens de boucles markoviennes ou de soupes de boucles. La mesure sur les boucles est covariante par un certain nombre de transformations sur les processus de Markov, par exemple le changement de temps.Dans le cadre de soupe de boucles brownienne à l'intérieur d'un sous-domaine ouvert propre simplement connexe de C, il a été montré que les contours extérieurs des amas extérieurs de boucles sont, pour alpha<=1/2, des Conformal Loop Ensembles CLE(kappa), kappa dans (8/3,4]. D'autre part il a été montré pour une large classe de processus de Markov symétriques que lorsque alpha=1/2, le champ d'occupation d'une soupe de boucle (somme des temps passés par les boucles aux dessus des points) est le carré du champ libre gaussien. J'ai étudié d'abord les soupes de boucles associés aux processus de diffusion unidimensionnels, notamment leur champ d'occupation dont les zéros délimitent dans ce cas les amas de boucles. Puis j'ai étudié les soupes de boucles sur graphe discret ainsi que sur graphe métrique (arêtes remplacés par des fils continus). Sur graphe métrique on a d'une part une géométrie non triviale pour les boucles et d'autre part on a comme dans le cas unidimensionnel continu la propriété que les zéros du champ d'occupation délimitent les amas des boucles. En combinant les graphes métriques et l'isomorphisme avec le champ libre gaussien j'ai montré que alpha=1/2 est le paramètre d'intensité critique pour la percolation par soupe de boucles de marche aléatoire sur le demi plan discret Z*N (existence ou non d'un amas infini) et que pour alpha<=1/2 la limite d'échelle des contours extérieurs des amas extérieurs sur Z*N est un CLE(kappa) dans le demi-plan continuIn this thesis I study an infinite measure on loops naturally associated to a wide range of Markovian processes and the Poisson point processes of intensity proportional to this measure (intensity parameter alpha>0). This Poissson point processes are called Poisson ensembles of Markov loops or loop soups. The measure on loops is covariant with some transformation on Markovian processes, for instance the change of time. In the setting of Brownian loop soups inside a proper open simply connected domain of C it was shown that the outer boundaries of outermost clusters of loops are, for alpha1/2, Conformal Loop Ensembles CLE(kappa), kappa in (8/3,4]. Besides, it was shown for a wide range of symmetric Markovian processes that for alpha=1/2 the occupation field of a loop soup (the sum of times spent by loops over points) is the square of the Gaussian free field. First I studied the loop soups associated to one-dimensional diffusions, and particularly the occupation field and its zeroes that delimit in this case the clusters of loops. Then I studied the loop soups on discrete graphs and metric graphs (edges replaced by continuous lines). On a metric graph on one hand the loops have a non-trivial geometry and on the other hand one has the same property as in the setting of one-dimensional diffusions that the zeroes of the occupation field delimit the clusters of loops. By combing metric graphs and the isomorphism with the Gaussian free field I have shown that alpha=1/2 is the critical parameter for random walk loop soup percolation on the discrete half-plane Z*N (existence or not of an infinite cluster of loops) and that for alpha<= 1/2 the scaling limit of outer boundaries of outermost clusters on Z*N is a CLE(kappa) on the continuum half plane
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Brooks, Julian. "Being sound : FLOSS, flow and event in the composition and ensemble performance of free open computer music". Thesis, University of Huddersfield, 2016. http://eprints.hud.ac.uk/id/eprint/31370/.
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This commentary describes my recent approach to writing compositions for the ensemble performance of computer music. Drawing on experimental music and improvisation, I contend that such music is best considered in terms of people’s situated and relational interplay. The compositional and performative question that permeates this thesis is ‘what can we do, in this time and space, with these tools available to us?’. As themes of equality and egalitarian access underpin this work throughout, I highlight my engagement with Free Libre Open Source Software (FLOSS) ideology and community, reflecting on how this achieves my aims. I describe my writing of text score compositions, making use of the term bounded improvisation, whose purposeful requirements for indeterminate realisation extends most current computer-based performance practice. Though no single strand of this research is perhaps unusual by itself, such an assemblage as that outlined above (incorporating composition, computer coding and ensemble performance practice) is, when allied to an understanding of electronic and computer music praxis, currently an underdeveloped approach. Such an approach I have thus chosen to term free open computer music. I incorporate two further pre-existing conceptual formulations to present a framework for constructing, reflecting on, and developing my work in this field. Firstly flow or 'immersed experience' is useful to explicate difficult to capture aspects of instrumental engagement and ensemble performance. Secondly, this portfolio of scores aims to produce well-constructed situations, facilitating spaces of flow which contain within their environments the opportunity for an event to take place. I present the outcomes of my practice as place-forming tactics that catalyse something to do, but not what to do, in performative spaces such as those described above. Such intentions define my aims for composition. These theoretical concerns, together with an allied consideration of the underpinning themes highlighted above, is a useful framework for refection and evaluation of this work.
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Salquebre, Quentin. "Développement d'un modèle de prédimensionnement d'un ensemble alternateur - machine Stirling à pistons libres". Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAT015/document.
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Le moteur Stirling a été développé il y’a 200 ans. Cependant son développement n’a jamais connu un grand essor. Le contexte énergétique actuel a relancé l’intérêt porté à ces machines. En effet la possibilité de le faire fonctionner à partir de n’importe quelle source de chaleur externe lui permet d’être associé à des sources d’énergie renouvelable comme l’énergie solaire. Au-delà des avantages écologiques, le développement par W. Beale à la fin des années 1960 d’un moteur Stirling à pistons libres (ou FPSE pour Free Piston Stirling Engine) a ajouté de nouveaux intérêts à un tel moteur. Cette nouvelle architecture permet au moteur de fonctionner sans système d’entrainement des pistons. Dans de telles machines, le mouvement des pistons n’est plus déterminé par la géométrie du système d’entrainement. Ces derniers sont mis en mouvement par les forces de pressions occurrents à l’intérieur du moteur. La dynamique des pistons et la thermodynamique du système sont alors couplées, rendant plus complexe la modélisation complète du système.Cette thèse présente une nouvelle technique de modélisation des machines Stirling à pistons libres, intitulée LHA5V pour Linear Harmonic Analysis 5 Volumes, permettant de coupler la thermodynamique du système et la réponse mécanique des pistons libres. Celle-ci repose alors sur la décomposition du moteur Stirling en cinq sous systèmes ouverts : deux espaces à volume variables, deux échangeurs de chaleur et le régénérateur. Nous supposons que les variables d’état varient périodiquement et le modèle détermine comment celles-ci varient en valeur moyenne, en amplitude et en phase afin de satisfaire les équations de conservation de la masse et de l’énergie. L’aspect innovant du modèle thermique repose sur la prise en compte implicite des pertes inhérentes au fonctionnement. Celles-ci ont en effet un impact direct sur le mouvement des pistons. Par ailleurs cette thèse présente également un modèle de génératrice électrique linéaire pouvant être couplé à la partie thermique. Le modèle électrique repose sur un calcul analytique de la force de poussée du stator sur la partie mobile. Le calcul des flux et du niveau d’induction dans le circuit magnétique est effectué à partir d’un réseau de perméances judicieusement paramétré.Que ce soit pour la modélisation thermique ou la modélisation électrique, chacun des modèles a été conçu pour avoir un temps de calcul faible, tout en restant le plus précis possible sur la prédiction des performances. Ceux-ci ont à chaque fois été confrontés à des données expérimentales, ou à d’autres techniques de modélisation plus fines de façon concluanteThough the Stirling engine was invented two centuries ago, it has never really grown to a fully marketable level. The current energy context has renewed the interest in this engine. Their ability to work with any external source of heat allow them to be associated with renewable energy such as solar energy. Beyond its ecological benefits, the invention of the free piston Stirling engine by W. Beale at the end of the 1960’s further increased the interest in Stirling engines. This novel structure allows the engine to operate without mechanical interface between pistons, which are driven entirely by the gas or other spring forces. In such engines, the pistons kinematics and the system thermodynamics are intimately coupled, thus increasing the complexity of the complete system computer modelling.This PhD presents an innovative technique to model a free piston Stirling engine that takes into account the coupling between the system thermodynamics and the mechanical response of the free pistons. This technique has been named LHA5V standing for Linear Harmonic Analysis 5 Volumes. It consists in splitting the engine in five open sub-systems: the compression and expansion spaces, the heater, the cooler and the regenerator. We hypothesize that the state variables are periodic, and the model then determines the variations of their mean, amplitude and phase values in order to satisfy the mass and energy conservation equations. This PhD also presents a model for a linear electric alternator, which can be coupled to the power piston. This electrical model is based on an analytical calculation of the thrust between the stator and the magnets. Magnetic flux and induction in the iron are determined by a carefully tuned reluctance network.Both thermal and electrical models have been designed to optimize both computing time and accuracy. The models generated have systematically been compared to experimental data or finite element analysis, with satisfactory results
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Cunha, João Victor de Souza. "Aplicação de Monte Carlo para a geração de ensembles e análise termodinâmica da interação biomolecular". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-25112016-143220/.
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As interações moleculares, em especial as de caráter não-covalente, são processos-chave em vários aspectos da biologia celular e molecular, desde a comunicação entre as células ou da velocidade e especificidade das reações enzimáticas. Portanto, há a necessidade de estudar e criar métodos preditivos para calcular a afinidade entre moléculas nos processos de interação, os quais encontram uma gama de aplicações, incluindo a descoberta de novos fármacos. No geral, entre esses valores de afinidade, o mais importante é a energia livre de ligação, que normalmente é determinada por modos computacionalmente rápidos, porém sem uma forte base teórica, ou por cálculos muito complexos, utilizando dinâmica molecular, onde mesmo com um grande poder de determinação da afinidade, é muito custoso computacionalmente. O objetivo deste trabalho é avaliar um modelo menos custoso computacionalmente e que promova um aprofundamento na avaliação de resultados obtidos a partir de simulações de docking molecular. Para esta finalidade, o método de Monte Carlo é empregado para a amostragem de orientações e conformações do ligante do sítio ativo macromolecular. A avaliação desta metodologia demonstrou que é possível calcular grandezas entrópicas e entálpicas e analisar a capacidade interativa entre complexos proteína-ligante de forma satisfatória para o complexo lisozima do bacteriófago T4.The molecular interactions, especially the ones with a non-covalent nature, are key processes in general aspects of cellular and molecular biology, including cellular communication and velocity and specificity of enzymatic reactions. So, there is a strong need for studies and development of methods for the calculation of the affinity on interaction processes, since these have a wide range of applications like rational drug design. The free energy of binding is the most important measure among the affinity measurements. It can be calculated by quick computational means, but lacking on strong theoretical basis or by complex calculations using molecular dynamics, where one can compute accurate results but at the price of an increased computer power. The aim of this project is to evaluate a computationally inexpensive model which can improve the results from molecular docking simulations. For this end, the Monte Carlo method is implemented to sample different ligand configurations inside the macromolecular binding site. The evaluation of this methodology showed that is possible to calculate entropy and enthalpy, along analyzing the interactive capacity between receptor-ligands complexes in a satisfactory way for the bacteriophage T4.
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Viveca, Lindahl. "Optimizing sampling of important events in complex biomolecular systems". Doctoral thesis, KTH, Fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-217837.
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Proteins and DNA are large, complex molecules that carry out biological functions essential to all life. Their successful operation relies on adopting specific structures, stabilized by intra-molecular interactions between atoms. The spatial and temporal resolution required to study the mechanics of these molecules in full detail can only be obtained using computer simulations of molecular models. In a molecular dynamics simulation, a trajectory of the system is generated, which allows mapping out the states and dynamics of the molecule. However, the time and length scales characteristic of biological events are many orders of magnitude larger than the resolution needed to accurately describe the microscopic processes of the atoms. To overcome this problem, sampling methods have been developed that enhance the occurrence of rare but important events, which improves the statistics of simulation data. This thesis summarizes my work on developing the AWH method, an algorithm that adaptively optimizes sampling toward a target function and simultaneously finds and assigns probabilities to states of the simulated system. I have adapted AWH for use in molecular dynamics simulations. In doing so, I investigated the convergence of the method as a function of its input parameters and improved the robustness of the method. I have also worked on a generally applicable approach for calculating the target function in an automatic and non-arbitrary way. Traditionally, the target is set in an ad hoc way, while now sampling can be improved by 50% or more without extra effort. I have also used AWH to improve sampling in two biologically relevant applications. In one paper, we study the opening of a DNA base pair, which due to the stability of the DNA double helix only very rarely occurs spontaneously. We show that the probability of opening depends on both nearest-neighbor and longer-range sequence effect and furthermore structurally characterize the open states. In the second application the permeability and ammonia selectivity of the membrane protein aquaporin is investigated and we show that these functions are sensitive to specific mutations.QC 20171117
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Nicolas, Adrien. "Optical quantum memories with cold atomic ensembles : a free space implementation for multimode storage, or a nanofiber-based one for high collection efficiency". Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066494/document.
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Nous étudions expérimentalement deux mémoires quantiques pour la lumière utilisant la transparence électromagnétiquement induite (EIT) dans des nuages froids de césium.Nous expliquons la pertinence des mémoires quantiques pour le développement de réseaux quantiques à longue distance, et décrivons la théorie de l’EIT en soulignant les paramètres essentiels pour l’implémentation de mémoires quantiques.Notre premier cas d’étude est un piège magnéto-optique en espace libre. Notre principal résultat est la démonstration du caractère multimode de ce système pour le stockage quantique de la lumière. Pour cela, nous utilisons des faisceaux de Laguerre-Gauss (LG), porteurs de moment angulaire orbital (OAM). Dans une première étape, nous avons montré que l’état de moment orbital d’impulsions lumineuses en régime de photons uniques est préservé lors du stockage dans la mémoire. Ensuite, nous avons implémenté un bit quantique comme une superposition de modes LG ayant des hélicités opposées. Nous avons développé un système original pour mesurer ces bits quantiques qui nous a permis de caractériser l’action de la mémoire. Nous avons ainsi pu montrer que le stockage quantique de ces bits quantiques.Le second système, également un nuage d’atomes froids, a la particularité que les atomes sont piégés optiquement autour d’un nano-guide d’onde. Ce design innovant permet une plus grande interaction entre lumière et matière, et facilite l’interfaçage des photons dans et hors de la mémoire. Nous décrivons la construction de ce dispositif et les premiers pas vers son utilisation en tant que mémoire quantiqueWe present an experimental study of two optical quantum memory systems based on electromagnetically induced transparency (EIT) in cold cesium atoms.We explain the relevance of quantum memories for the development of large-scale quantum networks, we give a comprehensive theory of the EIT phenomenon and underline the role of relevant parameters regarding the implementation of quantum memories.The first system under study is prepared in a free-space magneto-optical trap. The main result of this thesis is the demonstration of the spatial multimode capability of this system at the quantum level. For this, we used Laguerre-Gaussian (LG) light beams, i.e. beams possessing a non-zero value of orbital angular momentum (OAM). In a first step, we showed that the orbital angular momentum of stored light pulses is preserved by the memory, deep in the single photon regime. In a second step, we encoded information in the orbital angular momentum state of a weak light pulse and defined a qubit using two LG beams of opposite helicities. We developed an original setup for the measurement of this OAM qubit and used it to characterize the action of the memory during the storage of such a light pulse. Our results show that the memory performs the quantum storage of such a qubit.The second system under study, also a cloud of cold atoms, has the specificity that the atoms are trapped optically in the vicinity of a nano-waveguide. This innovative design ensures a higher light-matter interaction and facilitates the interfacing of photons into and out of the memory. We describe the building of this setup and the first steps towards quantum memory implementations
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Wu, Hao. "Autour les relations entre SLE, CLE, champ libre Gaussien, et les conséquences". Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00856599.
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Cette thèse porte sur les relations entre les processus SLE, les ensembles CLE et le champ libre Gaussien. Dans le chapitre 2, nous donnons une construction des processus SLE(k,r) à partir des boucles des CLE(k) et d'échantillons de restriction chordale. Sheffield et Werner ont prouvé que les CLE(k) peuvent être construits à partir des processus d'exploration symétriques des SLE(k,r).Nous montrons dans le chapitre 3 que la configuration des boucles construites à partir du processus d'exploration asymétrique des SLE(k,k-6) donne la même loi CLE(k). Le processus SLE(4) peut être considéré comme les lignes de niveau du champ libre Gaussien et l'ensemble CLE(4) correspond à la collection des lignes de niveau de ce champ libre Gaussien. Dans la deuxième partie du chapitre 3, nous définissons un paramètre de temps invariant conforme pour chaque boucle appartenant à CLE(4) et nous donnons ensuite dans le chapitre 4 un couplage entre le champ libre Gaussien et l'ensemble CLE(4) à l'aide du paramètre de temps. Les processus SLE(k) peuvent être considérés comme les lignes de flot du champ libre Gaussien. Nous explicitons la dimension de Hausdorff de l'intersection de deux lignes de flot du champ libre Gaussien. Cela nous permet d'obtenir la dimension de l'ensemble des points de coupure et des points doubles de la courbe SLE, voir le chapitre 5. Dans le chapitre 6, nous définissons la mesure de restriction radiale, prouvons la caractérisation de ces mesures, et montrons la condition nécessaire et suffisante de l'existence des mesures de restriction radiale.
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Åberg, K. Magnus. "Variance Reduction in Analytical Chemistry : New Numerical Methods in Chemometrics and Molecular Simulation". Doctoral thesis, Stockholm University, Department of Analytical Chemistry, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-283.
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This thesis is based on five papers addressing variance reduction in different ways. The papers have in common that they all present new numerical methods.
Paper I investigates quantitative structure-retention relationships from an image processing perspective, using an artificial neural network to preprocess three-dimensional structural descriptions of the studied steroid molecules.
Paper II presents a new method for computing free energies. Free energy is the quantity that determines chemical equilibria and partition coefficients. The proposed method may be used for estimating, e.g., chromatographic retention without performing experiments.
Two papers (III and IV) deal with correcting deviations from bilinearity by so-called peak alignment. Bilinearity is a theoretical assumption about the distribution of instrumental data that is often violated by measured data. Deviations from bilinearity lead to increased variance, both in the data and in inferences from the data, unless invariance to the deviations is built into the model, e.g., by the use of the method proposed in paper III and extended in paper IV.
Paper V addresses a generic problem in classification; namely, how to measure the goodness of different data representations, so that the best classifier may be constructed.
Variance reduction is one of the pillars on which analytical chemistry rests. This thesis considers two aspects on variance reduction: before and after experiments are performed. Before experimenting, theoretical predictions of experimental outcomes may be used to direct which experiments to perform, and how to perform them (papers I and II). After experiments are performed, the variance of inferences from the measured data are affected by the method of data analysis (papers III-V).
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Reynolds, Ryan Michael. "Moving targets: Political theatre in a post-political age". Thesis, University of Canterbury. Theatre and Film Studies, 2006. http://hdl.handle.net/10092/898.
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This thesis gauges the contemporary landscape of political theatre at a time in which everything, and consequently nothing, is political. That is, almost all theatres today proclaim a politics, and yet there is widespread resignation regarding the inevitability of capitalism. This thesis proposes a theory of political action via the theatre: radical theatre today must employ a strategy of "moving targets". Theatrical actions must be adaptable and mobile to seek out the moving targets of capital and track down target audiences as they move through public space. In addition, political theatre must become a moving target to avoid amalgamation into the capitalist system of exchange. I approached this topic through four case studies. Two of the case studies, Reverend Billy's Church of Stop Shopping and the Critical Art Ensemble, are based in the United States. I studied their work via materials - books, essays, videos, websites, interviews, and more - but not in person. The other two case studies are lifted from my own experience with the Christchurch Free Theatre: an original production of Christmas Shopping and a devised production of Karl Kraus' play The Last Days of Mankind. These latter two case studies served as laboratory experiments through which I was able to test ideas and problematics of political theatre that arose through my research. These case studies led to the determination that creating aesthetic experiences and actions - as opposed to having explicitly political content - can be a strategy or foundation for a radical political theatre that resists, undermines, and at times transcends the seeming inevitability of consumer capitalism. In an age in which any political intervention is seen as senseless disruption, a form of pointless violence, this theatre has adopted the strategies of terrorist actions to have a disruptive effect without positing a specific alternative social structure.
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Li, Qiang. "Direct and Large-Eddy Simulations of Turbulent Boundary Layers with Heat Transfer". Doctoral thesis, KTH, Mekanik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-41156.
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Aru, Juhan. "Géométrie du champ libre Gaussien en relation avec les processus SLE et la formule KPZ". Thesis, Lyon, École normale supérieure, 2015. http://www.theses.fr/2015ENSL1007/document.
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Cette thèse porte sur la géométrie du champ libre Gaussien. Le champ libre Gaussien est un objet central en théorie quantique des champs et représente entre autre les fluctuations naturelles d'un potentiel électrique ou d’un modèle de dimères. La thèse commence dans le discret avec la démonstration d'un principe de Donsker en dimension plus grande que 1. Ce résultat est établi grâce à une nouvelle façon de représenter le champ libre en exprimant son gradient comme la partie gradient d'un champ de bruits blancs. Ensuite, les processus d'exploration du champ libre - ou ensembles locaux - introduits par Schramm-Sheffield sont étudiés en détail. Ces ensembles locaux généralisent de façon naturelle le concept de temps d'arrêt. On formalise cette théorie d'une nouvelle manière en procédant par analogie au cas 1D. Pour mieux comprendre le comportement du champs libre près des points d'intersection des ensembles locaux, un étude fine des oscillations du champ libre 2D près du bord s'avère utile. Enfin, la partie principale de cette thèse étudie des processus d'explorations particuliers – les processus SLE qui sont couplés naturellement avec le champ libre. On peut donner par exemple un sens aux lignes de niveau en utilisant le processus SLE_4 (Schramm-Sheffield). Nous avons utilisé ce couplage pour mieux comprendre la relation dite de KPZ qui intervient dans la théorie de la gravité quantique de Liouville. A l ‘aide de résultats fins sur l’enroulement des SLEs, nous avons montré comment adapter la relation de KPZ à la famille ci-dessus de processus d’explorations du champ libre. On peut interpréter ces résultats aussi comme une description de la géométrie du champ libre près des ces lignes d’explorationIn this thesis we study the geometry of the Gaussian free field (GFF). After a gentle general introduction, we describe what we call the Hodge decomposition of the white noise – a way to represent the white noise vector field as a sum of a gradient and a rotation of independent GFFs. This decomposition gives rise to the Donsker invariance principle for the GFF.Next, we revisit from a slightly different angle the theory of so-called local sets of the GFF, introduced by Schramm and Sheffield. These random sets allow one to study the geometry of the GFF in a Markovian way. We also go a step further in describing the behaviour of the field near the boundary of possibly several local sets. The first chapter ends with a study of boundary oscillations of the GFF.The GFF is only a generalized function, yet it comes out that one can still make sense of it as a „random landscape“. In particular, Schramm and Sheffield gave meaning to the level lines of the GFF in terms of a coupling with SLE_4 process. In chapter 2 we study this coupling and describe the existent proofs and a non-proof of measurability of the SLE_4 process in this coupling. The rest of this chapter contains one of the most technical parts of the thesis – we obtain fine estimates on the winding of the SLE curves, conditioned to pass closely by a fixed point.This technical work is put in use in chapter 3, where we study the so called KPZ relation. In this context, the KPZ formula relates fractal dimensions of sets under the Euclidean geometry and under the „quantum geometry“ given by the exponential of the GFF. So far the KPZ formula was derived for planar sets independent of the quantum geometry. Here, we determine the KPZ formulas for sets that are naturally coupled with the quantum geometry – for the flow and level lines of the GFF. The family of KPZ formulas obtained resemble but still differ from the KPZ formula for independent sets
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Hamy, Anne-Sophie. "Identification of Factors Predicting Sensitivity or Resistance to Neoadjuvant Chemotherapy in Breast Cancer Neoadjuvant treatment : the future of patients with breast cancer Neoadjuvant treatment for intermediate/high-risk HER2-positive and triple-negative breast cancers: no longer an “option” but an ethical obligation Long-term outcome of the REMAGUS 02 trial, a multicenter randomised phase II trial in locally advanced breast cancer patients treated with neoadjuvant chemotherapy with or without celecoxib or trastuzumab according to HER2 status BIRC5 (survivin) : a pejorative prognostic marker in stage II/III breast cancer with no response to neoadjuvant chemotherapy Beyond Axillary Lymph Node Metastasis, BMI and Menopausal Status Are Prognostic Determinants for Triple-Negative Breast Cancer Treated by Neoadjuvant Chemotherapy Pathological complete response and prognosis after neoadjuvant chemotherapy for HER2-positive breast cancers before and after trastuzumab era: results from a real-life cohort The presence of an in situ component on pre-treatment biopsy is not associated with response to neoadjuvant chemotherapy for breast cancer Chemosensitivity, tumor infiltrating lymphocytes (TILs), and survival of postpartum PABC patients treated by neoadjuvant chemotherapy Lymphovascular invasion after neoadjuvant chemotherapy is strongly associated with poor prognosis in breast carcinoma New insight for pharmacogenomics studies from the transcriptional analysis of two large-scale cancer cell line panels Biological network-driven gene selection identifies a stromal immune module as a key determinant of triple-negative breast carcinoma prognosis A Stromal Immune Module Correlated with the Response to Neoadjuvant Chemotherapy, Prognosis and Lymphocyte Infiltration in HER2-Positive Breast Carcinoma Is Inversely Correlated with Hormonal Pathways Stromal lymphocyte infiltration after neoadjuvant chemotherapy is associated with aggressive residual disease and lower disease-free survival in HER2-positive breast cancer Interaction between molecular subtypes, stromal immune infiltration before and after treatment in breast cancer patients treated with neoadjuvant chemotherapy COX2/PTGS2 Expression Is Predictive of Response to Neoadjuvant Celecoxib in HER2-negative Breast Cancer Patients Celecoxib With Neoadjuvant Chemotherapy for Breast Cancer Might Worsen Outcomes Differentially by COX-2 Expression and ER Status: Exploratory Analysis of the REMAGUS02 Trial Comedications influence immune infiltration and pathological response to neoadjuvant chemotherapy in breast cancer". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS129.
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La chimiothérapie néoadjuvante (CNA) est utilisée dans les cancers du sein agressifs ou localement avancés (CS). Au delà des bénéfices cliniques, elle représente une opportunité pour monitorer in vivo la sensibilité d’une tumeur à un traitement.A partir de l’analyse de sets de données de patients traités par CNA, nous souhaitons identifier des mécanismes associes à la résistance ou sensibilité au traitement. Dans la première partie, nous avons évalué des paramètres, cliniques, anatomopathologiques et transcriptomiques. Nous avons démontré que des éléments non explorés comme la présence d’embols après CNA revêtaient une information pronostique importante. Dans une 2ème partie, nous avons analysé l’impact de l’infiltrat immunitaire dans le cancer du sein, et avons décrit les changements observés entre des échantillons avant et après CNA. Nous avons montré que l’impact pronostique des TILs était différent avant et après CNA, et était opposé dans les CS triple négatif ou HER2-positif. Finalement, nous avons analysé l’impact des comédications pendant la CNA. Nous avons trouvé des effets positifs – via l’augmentation de l’infiltrat immunitaire et la réponse au traitement – et des effets négatifs avec des effets délétères dans certains sous groupes de patients. En conclusion, la situation néoadjuvante représente une plateforme pour générer et potentiellement valider des hypothèses de recherche. La mise à disposition de jeux de données de patients traités par chimiothérapie néoadjuvante constituerait une ressource majeure pour accélérer la recherche contre le cancer du seinNeoadjuvant chemotherapy (NAC i.e. chemotherapy before surgery) is increasingly being used for aggressive or locally advanced breast cancer (BCs). Beyond clinical benefits, it represents an opportunity to monitor in vivo sensitivity to treatment. Based on the analysis of datasets of BCs patients treated with NAC, we aimed at identifying mechanisms associated with resistance or sensitivity to treatment.In the first part, we evaluated biological, clinical, pathological and transcriptomic patterns. We demonstrated that unexplored pathological features such as post-NAC lymphovascular invasion may carried an important prognostic information.In a second part, we analyzed impact of imune infiltration in BC and we described extensively the changes of tumor infiltrating lymphocytes (TILs) between pre and post-NAC samples. We showed that the prognostic impact of TILs was different before and after NAC, and was opposite in TNBC and HER2-positive BCs. Finally, we investigated the impact of comedications use during NAC. We found both positive effects - while enhancing immune infiltration and response to treatment - and negative effects with deleterisous oncologic outcomes in specific patients subgroups. In conclusion, the neoadjuvant setting represents a platform to both generate and potentially validate research hypotheses aiming at increasing the efficacy of treatment. The public release of real-life datasets of BC patients treated with NAC would represent a major resource to accelerate BC research
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Mohammadridha, Taghreed. "Automatic Glycemia Regulation of Type I Diabetes". Thesis, Ecole centrale de Nantes, 2017. http://www.theses.fr/2017ECDN0008.
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Cette thèse étudie le contrôle en boucle fermée pour la régulation de la glycémie du diabète de type 1 (DT1). Deux catégories principales de commande sont conçues: l'une est basée sur un modèle et l'autre non. Pour tester leur efficacité, les deux types sont testés in silico sur deux simulateurs de DT1. Le premier est un modèle à long terme qui est dérivé des données cliniques des sujets de DT1 et le second est le simulateur Uva/Padova. Tout d'abord, la commande sans modèle (CSM) est conçue. Après avoir montré qu'un régulateur proportionnel intelligent (iP) à référence constante peut être mis en défaut sur un simple second ordre, nous avons conçu un régulateur iP à référence variable. Une solution alternative est un régulateur proportionnel-intégral-dérivé intelligent (iPID) à référence constante. Une meilleure performance globale est obtenue avec iPID par rapport à iP et par rapport à un PID classique. Deuxièmement, une commande par modes glissants (CMG) garantie positive est conçue pour la première fois pour la régulation de la glycémie. La conception de cette commande est basée sur un modèle. La commande CMG est choisie pour la régulation de la glycémie en raison de ses propriétés de robustesse bien connues. Cependant, notre contribution majeure est l'assurance d'une commande rigoureusement positive. La commande CMG est conçue pour être positive partout dans un ensemble invariant du sous-système d'insulinémie du plasma. Enfin, un régulateur positif par retour d'état est calculé pour la première fois pour la régulation de la glycémie. Le plus grand ensemble positif invariant (EPI) est trouvé. Non seulement la positivité de la commande est révisée, mais plutôt un contrôle glycémique serré est atteint. Lorsque l'état initial du système appartient à l’EPI, l'hypoglycémie est évitée. Dans le cas contraire, l'hypoglycémie future est prédite pour tout état initial en dehors de l'EPIThis thesis investigates closed-loop control for glycemia regulation of Type1 Diabetes Mellitus (T1DM). Two main controller categories are designed: non-model-based and model-based. To test their efficiency, both types are tested in silico on two T1DM simulators. The first is a long-term model that is derived from clinical data of T1DM subjects and the second is the Uva/Padova simulator. Firstly, Model-free Control (MFC) is designed: a variable reference intelligent Proportional (iP) control and a constant reference intelligent Proportional-Integral-Derivative (iPID). Better overall performance is yielded with iPID over iP and over a classic PID. Secondly, a positive Sliding Mode Control SMC is designed for the first time for glycemia regulation. The model-based controller is chosen for glycemia regulation due to its well-known robustness properties. More importantly, our main contribution is that SMC is designed to be positive everywhere in the positively invariant set for the plasma insulin subsystem. Finally, a positive state feedback controller is designed for the first time to regulate glycemia. The largest Positively Invariant Set (PIS) is found. Not only control positivity is respected but rather a tight glycemic control is achieved. When the system initial condition belongs to the PIS, hypoglycemia is prevented, otherwise future hypoglycemia is predicted for any initial condition outside the PIS
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Pouilly-Cathelain, Maxime. "Synthèse de correcteurs s’adaptant à des critères multiples de haut niveau par la commande prédictive et les réseaux de neurones". Electronic Thesis or Diss., université Paris-Saclay, 2020. http://www.theses.fr/2020UPASG019.
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Cette thèse porte sur la commande des systèmes non linéaires soumis à des contraintes non différentiables ou non convexes. L'objectif est de pouvoir réaliser une commande permettant de considérer tout type de contraintes évaluables en temps réel.Pour répondre à cet objectif, la commande prédictive a été utilisée en ajoutant des fonctions barrières à la fonction de coût. Un algorithme d'optimisation sans gradient a permis de résoudre ce problème d'optimisation. De plus, une formulation permettant de garantir la stabilité et la robustesse vis-à-vis de perturbations a été proposée dans le cadre des systèmes linéaires. La démonstration de la stabilité repose sur les ensembles invariants et la théorie de Lyapunov.Dans le cas des systèmes non linéaires, les réseaux de neurones dynamiques ont été utilisés comme modèle de prédiction pour la commande prédictive. L'apprentissage de ces réseaux ainsi que les observateurs non linéaires nécessaires à leur utilisation ont été étudiés. Enfin, notre étude s'est portée sur l'amélioration de la prédiction par réseaux de neurones en présence de perturbations.La méthode de synthèse de correcteurs présentée dans ces travaux a été appliquée à l’évitement d’obstacles par un véhicule autonomeThis PhD thesis deals with the control of nonlinear systems subject to nondifferentiable or nonconvex constraints. The objective is to design a control law considering any type of constraints that can be online evaluated.To achieve this goal, model predictive control has been used in addition to barrier functions included in the cost function. A gradient-free optimization algorithm has been used to solve this optimization problem. Besides, a cost function formulation has been proposed to ensure stability and robustness against disturbances for linear systems. The proof of stability is based on invariant sets and the Lyapunov theory.In the case of nonlinear systems, dynamic neural networks have been used as a predictor for model predictive control. Machine learning algorithms and the nonlinear observers required for the use of neural networks have been studied. Finally, our study has focused on improving neural network prediction in the presence of disturbances.The synthesis method presented in this work has been applied to obstacle avoidance by an autonomous vehicle
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Amrane, Amazigh. "Posets série-parallèles transfinis : automates, logiques et théories équationnelles". Thesis, Normandie, 2020. http://www.theses.fr/2020NORMR102.
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Nous étudions dans cette thèse des structures généralisant la notion classique de mot. Elles sont construites à partir d’un ensemble partiellement ordonné (partially ordered set ou poset) vérifiant les propriétés suivantes : — elles ne contiennent pas 4 éléments distincts x, y, z, t dont l’ordre relatif est exactement x < y, z < y, z < t (posets dits sans N) ; — les chaînes sont des ordres linéaires dénombrables et dispersés ; — les antichaînes sont finies ; et chaque élément est étiqueté par une lettre d’un alphabet fini. De manière équivalente, la classe des posets que nous considérons est la plus petite construite à partir du poset vide et du singleton, fermée par les produits séquentiel et parallèle finis, et le produit ω et son renversé −ω (posets série-parallèles). Elle est une généralisation à la fois des posets série-parallèles finis étiquetés, en y ajoutant l’infinitude, et des mots transfinis, en affaiblissant l’ordre total des éléments en ordre partiel. En informatique, les posets série-parallèles finis trouvent leur intérêt dans la modélisation des processus concurrents basés sur les primitives fork/join, et les mots transfinis dans l’étude de la récursivité. Les langages rationnels de ces posets étiquetés sont définis à partir d’expressions et d’automates équivalents introduits par Bedon et Rispal, qui généralisent le cas des mots transfinis (Bruyère et Carton) et celui des posets finis (Lodaya et Weil). Dans cette thèse nous les étudions du point de vue de la logique. Nous généralisons en particulier le théorème de Büchi, Elgot et Trakhtenbrot, établissant pour le cas des langages de mots finis l’égalité entre la classe des langages rationnels et celle des langages définissables en logique monadique du second ordre (MSO). La logique mise en oeuvre est une extension de MSO par de l’arithmétique de Presburger. Nous nous intéressons également à certaines variétés d’algèbres de posets. Nous montrons que l’algèbre dont l’univers est la classe des posets série-parallèles transfinis et dont les opérations sont les produits séquentiel et parallèle finis et les produits (resp. puissances) ω et − ω est libre dans la variété correspondante V (resp. V 0). Nous en déduisons la liberté de la même algèbre sans le produit parallèle ou le produit − ω. Enfin, nous montrons que la théorie équationnelle de V 0 est décidable. Ce sont notamment des généralisations de résultats similaires de Bloom et Choffrut pour la variété d’algèbres de mots de longueur inférieure à ω!, de Choffrut et Ésik pour la variété d’algèbres de posets sans N dont les antichaînes sont finies et les chaînes sont de longueur inférieure à ω! et ceux de Bloom et Ésik pour la variété d’algèbres de mots sur les ordres linéaires dénombrables et dispersésWe study in this thesis structures extending the classical notion of word. They are built from a partially ordered set (poset) verifying the following properties : — they do not contain 4 distinct elements x, y, z, t whose relative order is exactly x < y, z < y, z < t (posets called N-free) ; — their chains are countable and scattered linear orderings ; — their antichains are finite ; and each element is labeled by a letter of a finite alphabet. Equivalently, the class of posets which we consider is the smallest one built from the empty poset and the singleton, and being closed under sequential and parallel products, and ω product and its backward ordering −ω (series-parallel posets). It is a generalization of both of finite series-parallel labeled posets, by adding infinity, and transfinite words, by weakening the total ordering of the elements to a partial ordering. In computer science, series-parallel posets find their interest in modeling concurrent processes based on fork/join primitives, and transfinite words in the study of recursion. The rational languages of these labeled posets are defined from expressions and equivalent automata introduced by Bedon and Rispal, which generalize thecase of transfinite words (Bruyère and Carton) and the one of finite posets (Lodaya and Weil). In this thesis we study such structures from the logic point of view. In particular, we generalize the Büchi-Elgot-Trakhtenbrot theorem, establishing in the case of finite words the correspondence between the class of rational languages and the one of languages definable in monadic second order logic (MSO). The implemented logic is an extension of MSO by Presburger arithmetic. We focus on some varieties of posets algebras too. We show that the algebra whose universe is the class of transfinite series-parallel posets and whose operations are the sequential and parallel products and the ω and −ω products (resp. powers) is free in the corresponding variety V (resp. V 0). We deduce the freeness of the same algebra without parallel or −ω product. Finally, we showthat the equational theory of V 0 is decidable. These results are, in particular, generalizations of similar results of Bloom and Choffrut on the variety of algebras of words whose length are less than ω!, of Choffrut and Ésik on the variety of algebras of N-free posets whose antichains are finite and whose chains are less than ω! and those of Bloom and Ésik on the variety of algebras of words indexed by countable and scattered linear orderings
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MEDEIROS, Rex Antonio da Costa. "Zero-Error capacity of quantum channels". Universidade Federal de Campina Grande, 2008. http://dspace.sti.ufcg.edu.br:8080/jspui/handle/riufcg/1320.
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REX ANTONIO DA COSTA MEDEIROS - TESE PPGEE 2008..pdf: 1089371 bytes, checksum: ea0c95501b938e0d466779a06faaa4f6 (MD5)Made available in DSpace on 2018-08-01T21:11:37Z (GMT). No. of bitstreams: 1 REX ANTONIO DA COSTA MEDEIROS - TESE PPGEE 2008..pdf: 1089371 bytes, checksum: ea0c95501b938e0d466779a06faaa4f6 (MD5) Previous issue date: 2008-05-09
Nesta tese, a capacidade erro-zero de canais discretos sem memória é generalizada para canais quânticos. Uma nova capacidade para a transmissão de informação clássica através de canais quânticos é proposta. A capacidade erro-zero de canais quânticos (CEZQ) é definida como sendo a máxima quantidade de informação por uso do canal que pode ser enviada através de um canal quântico ruidoso, considerando uma probabilidade de erro igual a zero. O protocolo de comunicação restringe palavras-código a produtos tensoriais de estados quânticos de entrada, enquanto que medições coletivas entre várias saídas do canal são permitidas. Portanto, o protocolo empregado é similar ao protocolo de Holevo-Schumacher-Westmoreland. O problema de encontrar a CEZQ é reformulado usando elementos da teoria de grafos. Esta definição equivalente é usada para demonstrar propriedades de famílias de estados quânticos e medições que atingem a CEZQ. É mostrado que a capacidade de um canal quântico num espaço de Hilbert de dimensão d pode sempre ser alcançada usando famílias compostas de, no máximo,d estados puros. Com relação às medições, demonstra-se que medições coletivas de von Neumann são necessárias e suficientes para alcançar a capacidade. É discutido se a CEZQ é uma generalização não trivial da capacidade erro-zero clássica. O termo não trivial refere-se a existência de canais quânticos para os quais a CEZQ só pode ser alcançada através de famílias de estados quânticos não-ortogonais e usando códigos de comprimento maior ou igual a dois. É investigada a CEZQ de alguns canais quânticos. É mostrado que o problema de calcular a CEZQ de canais clássicos-quânticos é puramente clássico. Em particular, é exibido um canal quântico para o qual conjectura-se que a CEZQ só pode ser alcançada usando uma família de estados quânticos não-ortogonais. Se a conjectura é verdadeira, é possível calcular o valor exato da capacidade e construir um código de bloco quântico que alcança a capacidade. Finalmente, é demonstrado que a CEZQ é limitada superiormente pela capacidade de Holevo-Schumacher-Westmoreland.
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Sharma, Shruti [Verfasser]. "Unfolding and compaction in chaperonin-assisted protein folding followed by single molecule and ensemble FRET / Shruti Sharma". 2007. http://d-nb.info/987979825/34.
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Srinivasa, Ramya. "Flavivirus RNA replication: Probe development, structural dynamics, and role of zinc ions". Thesis, 2023. https://etd.iisc.ac.in/handle/2005/6085.
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Flaviviruses share a typical genome architecture where the highly conserved UTRs flank a central coding region. They also share a common genome replication strategy called genome cyclization where the UTRs interact to form a long-range, dynamic, 3D RNA interactome. Recent studies focused on the involvement of the capsid coding region in modulating these UTR interactions. Along similar lines, we have investigated the effect of CCR on the UTRs interactions in Dengue using ensemble FRET with cyanine dye-labeled Dengue UTRs. As a part of this study, we have developed a novel, generic chemoenzymatic, bead-based method for base-specific modification of RNA called “T7 RNA polymerase extension-based RNA modification (TERM)”. Here, we describe TERM development, demonstrate the synthesis of single, site-specific cyanine dye-labeled Dengue UTRs and discuss the UTR interaction studies performed using the TERM-synthesized cyanine dye-labeled UTRs. Our results bridge the knowledge gap in understanding the role of the capsid coding region in Flavivirus UTRs.
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Menezes, José. "Creative Process in Free Improvisation". Master's thesis, 2010. http://hdl.handle.net/10174/6051.
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This research investigates the creative and communicational processes used by improvisers in free improvised performance and the ideologies behind those processes. Two studies were conducted: In Study 1 quantitative data was extracted from a recorded performance with Music Information Retrieval (M.I.R) software with special focus on moments consensually considered by the musicians as “best”. Study 2 analysed qualitative data extracted from interviews with improvisers and retrospective verbal protocol regarding the whole performance with special focus on “best moments”. The results of Study 1 reveal the use of alterations of musical features such as energy, note density and spectral changes in order to create points of qualitative change in improvised music. Creative strategies revealed by Study 2 include reiteration, the use of error as a motor for generation of music materials, real-time use of processes of musical composition and automatic playing.
Improved conditions of separation of recorded instruments are advised in future research on this subject.
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Giovannelli, Edoardo. "Sampling methods and free energy estimators for computer simulations: development and applications". Doctoral thesis, 2018. http://hdl.handle.net/2158/1124398.
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Benedix, Alexander [Verfasser]. "Free energy prediction of biomolecular systems using ensembles of structures / von Alexander Benedix". 2009. http://d-nb.info/997942266/34.
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Swann, Ellen Therese. "Development and application of statistical and quantum mechanical methods for modelling molecular ensembles". Phd thesis, 2018. http://hdl.handle.net/1885/142784.
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The development of new quantum chemical methods requires
extensive benchmarking to establish the accuracy and limitations
of a method. Current benchmarking practices in computational
chemistry use test sets that are subject to human biases and as
such can be fundamentally flawed. This work presents a thorough
benchmark of diffusion Monte Carlo
(DMC) for a range of systems and properties as well as a novel
method for developing new, unbiased test sets using multivariate
statistical techniques. Firstly, the hydrogen abstraction of
methanol is used as a test system to develop a more efficient
protocol that minimises the computational cost of DMC without
compromising accuracy. This protocol is then applied to three
test sets of reaction energies, including 43 radical
stabilisation energies, 14 Diels-Alder reactions and 76 barrier
heights of hydrogen and non-hydrogen transfer reactions. The
average mean absolute error for all three databases is just 0.9
kcal/mol.
The accuracy of the explicitly correlated trial wavefunction used
in DMC is demonstrated using the ionisation potentials and
electron affinities of first- and second-row atoms. A
multi-determinant trial wavefunction reduces the errors for
systems with strong multi-configuration character, as well as
for predominantly single-reference systems. It is shown that the
use of pseudopotentials in place of all-electron basis sets
slightly increases the error for these systems. DMC is then
tested with a set of eighteen challenging reactions.
Incorporating more determinants in the trial wavefunction reduced
the errors for most systems but results are highly dependent on
the active space used in the CISD wavefunction. The accuracy of
multi-determinant DMC for strongly multi-reference systems is
tested for the isomerisation of diazene. In this case no method
was capable of reducing the error of the strongly-correlated
rotational transition state.
Finally, an improved method for selecting test sets is presented
using multivariate statistical techniques. Bias-free test sets
are constructed by selecting archetypes and prototypes based on
numerical representations of molecules. Descriptors based on the
one-, two- and three-dimensional structures of a molecule are
tested. These new test sets are
then used to benchmark a number of methods.
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Martins, João Ricardo Gonçalves. "Study of the Förster resonance energy transfer in ensembles of colloidal PbS quantum dots, emitting in the near-infrared spectral range". Master's thesis, 2020. http://hdl.handle.net/1822/73680.
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Dissertação de mestrado em PhysicsFörster resonance energy transfer (FRET) is a non-radiative energy transfer mechanism between two light-emitting systems, such as two quantum dots (QDots) or molecules. This mechanism involves an excited donor fluorophore (e.g., a QDot or a dye molecule) which transfers its energy of excitation to an acceptor (another QDot or molecule which is in resonance with the donor), via dipole-dipole coupling. FRET is the dominant type of energy transfer between emitters at a nanometre proximity. Other factors that influence the efficiency of this energy transfer mechanism include the spectral overlap of the donor emission spectrum and the acceptor absorption spectrum and the relative orientation of the dipole moment of both particles. In nature, for instance, FRET plays a dominant role in the energy transfer in photosynthetic apparatus of plants and bacteria. Some interesting applications of FRET can be found in photovoltaics, probing of molecular distances and molecular interactions, and storage and transfer of quantum information. The main goal of this master thesis lies in detecting the presence of the FRET mechanism when two different colloidal QDot samples of PbS (short for Lead Sulfide), with different QDot size, are linked together via surface chemistry. This chemical procedure activates carboxyl or phosphate groups, which promote the binding of primary amines of organic glutathione QDot shell molecules. In other words, it promotes a cross-linkage between the organic shells of two, or more, quantum dots at a distance at which FRET is present. Using PbS quantum dots, which emit in the near-infrared (NIR) region of the light spectrum, these experiments can be reported as one of the first attempts to find The FRET mechanism in a near-infrared system of QDots. Most previous reports of FRET mechanisms were concerned with QDots which emit in the visible range, such as CdTe and CdSe QDots. The NIR spectral range, for instance, promotes interesting applications in photonic crystals, where FRET can be enhanced by spontaneous emission inhibition, in photovoltaics, in order to greatly absorb infrared light, and in the production of near-infrared QDot lasers. In order to find evidences of the presence of the FRET mechanism, emission spectra and time-resolved measurements, using the time correlated single photon counting technique (TCSPC), of cross-linked colloidal PbS QDot solutions have been performed and will be shown in this master thesis. Along with the experimental results, a study of statistical moments of the PbS quantum dot photoluminescence kinetics will be presented in this thesis, which experimental kinetics were acquired with TCSPC. With this statistical analysis, it is possible to evaluate and compare various decay properties, such as the average decay time, the mean-squared value of the decay and the measure of asymmetry of the time-resolved distribution. In order to understand the obtained results, some donor decay models were developed and studied, alongside with other decay functions found in the literature. A theoretical description of the FRET mechanism will be presented in order to understand the proposed decay models.
A transferência ressonante de energia de Förster (em inglês, Förster resonance energy transfer, ou, simplesmente, FRET) é um mecanismo de transferência de energia não radiativo presente entre duas unidades fluorescentes, como dois pontos quânticos ou duas moléculas. Neste mecanismo, um dador excitado (por exemplo, um ponto quântico ou uma molécula) transfere a sua energia de excitação para um aceitador (outro ponto quântico ou molécula) com o qual se encontre em ressonância, por acoplamento dipolo-dipolo. O FRET é um mecanismo dominante entre emissores distanciados entre si a uma ordem dos nanómetros. Outros fatores dominantes que influenciam a eficiência deste mecanismo de transferência são a sobreposição do espetro de emissão do dador com o espetro de absorção do aceitador e a orientação relativa do momento dipolar de ambas as partículas. Este mecanismo tem também um papel fundamental em processos biológicos como a fotossíntese em plantas e bactérias. Algumas aplicações de FRET podem ser encontradas em sistemas fotovoltaicos, na análise de distâncias e interações moleculares, e no armazenamento de informação quântica. O objetivo principal desta tese de mestrado é a deteção do mecanismo de FRET numa mistura coloidal de duas amostras pontos quânticos de PbS (símbolo químico para Galena, ou sulfeto de chumbo) com diferentes tamanhos, que são unidas por processos de química de superfícies. Estes processos químicos promovem, neste caso específico, ligações cruzadas físicas entre dois, ou mais, pontos quânticos, a uma distância da ordem dos nanómetros, que promove a presença de FRET. A deteção de FRET em sistemas de pontos quânticos que emitem no espetro infravermelho próximo (isto é, com comprimentos de onda entre 0.7 1.4mm), como os pontos quânticos de PbS, não é amplamente encontrada na literatura, a qual foca na deteção de mecanismos de FRET em pontos quânticos que emitem no espetro visível, como pontos quânticos de CdTe ou CdSe. O espetro infravermelho próximo permite, como exemplo, aplicações em cristais fotónicos, aonde o mecanismo de FRET é predominante pela inibição da emissão radiativa espontânea, assim como a aplicação em lasers que emitem no infravermelho e absorção de luz no infravermelho em sistemas fotovoltaicos. De forma a detetar a presença de FRET nas amostras de pontos quânticos, foram medidos espetros de emissão e cinéticas fotoluminescentes, estas obtidas por técnicas de resolução temporal de fotoluminescência como TCSPC (em inglês, Time Correlated Single Photon Counting). Em conjunto com os resultados experimentais obtidos, é apresentado nesta tese o estudo estatístico das cinéticas fotoluminescentes das amostras de pontos quânticos PbS, cujas cinéticas foram obtidas pela técnica de TCSPC. A partir desta análise estatística, é possível de avaliar e comparar várias propriedades das cinéticas, tais como o tempo médio de decaimento, o erro quadrático médio e a medida da assimetria da cinética obtida. De forma a compreender os resultados obtidos, alguns modelos de decaimentos do dador foram desenvolvidos e estudados, em conjunto com outras funções de decaimento que são encontradas na literatura. De forma a sustentar os modelos teóricos de decaimento, é também apresentado um tratamento teórico do mecanismo de FRET.
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Brown, Mark R. "An analysis of freedom in Jean-Paul Sartre's Critique of dialectical reason, Volume 1: theory of practical ensembles /". 1997.
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Reynolds, R. M. "Moving targets : political theatre in a post-political age : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in the University of Canterbury /". 2006. http://library.canterbury.ac.nz/etd/adt-NZCU20060926.133947.
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