Processing of Synthetic Aperture Radar Images by a Multiscale Boundary Contour System and Feature Contour System

An improved Boundary Contour System (BCS) and Feature Contour System (FCS) neural network model of preattentive vision is applied to large images containing range data gathered by a synthetic aperture radar (SAR) sensor. The goal of processing is to make structures such as motor vehicles, roads, or buildings more salient and more interpretable to human observers than they are in the original imagery. Early processing by shunting center-surround networks compresses signal dynamic range and performs local contrast enhancement. Subsequent processing by filters sensitive to oriented contrast, including short-range competition and long-range cooperation, segments the image into regions. The segmentation is performed by three "copies" of the BCS and FCS, of small, medium, and large scales, wherein the "short-range" and "long-range" interactions within each scale occur over smaller or larger distances, corresponding to the size of the early filters of each scale. A diffusive filling-in operation within the segmented regions at each scale produces coherent surface representations. The combination of BCS and FCS helps to locate and enhance structure over regions of many pixels, without the resulting blur characteristic of approaches based on low spatial frequency filtering alone.

A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.

Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. An element located within a DNase I-hypersensitive site (DHS) 10 kb into the first intron was previously shown to augment CFTR promoter activity in a tissue-specific manner. Here, we reveal the mechanism by which this element influences CFTR transcription. We employed a high-resolution method of mapping DHS using tiled microarrays to accurately locate the intron 1 DHS. Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. Moreover, using chromosome conformation capture (3C) analysis, we show that this element interacts with the CFTR promoter in CFTR-expressing cells. These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression.

Caractérisation structurale et thermodynamique de la reconnaissance du substrat par le ribozyme VS de Neurospora

Les interactions ARN/ARN de type kissing-loop sont des éléments de structure tertiaire qui jouent souvent des rôles clés chez les ARN, tant au niveau fonctionnel que structural. En effet, ce type d’interaction est crucial pour plusieurs processus dépendant des ARN, notamment pour l’initiation de la traduction, la reconnaissance des ARN antisens et la dimérisation de génome rétroviral. Les interactions kissing-loop sont également importantes pour le repliement des ARN, puisqu’elles permettent d’établir des contacts à longue distance entre différents ARN ou encore entre les domaines éloignés d’un même ARN. Ce type d’interaction stabilise aussi les structures complexes des ARN fonctionnels tels que les ARNt, les riborégulateurs et les ribozymes. Comme d’autres ARN fonctionnels, le ribozyme VS de Neurospora contient une interaction kissing-loop importante. Celle-ci est impliquée dans la reconnaissance du substrat et se forme entre la tige-boucle I (stem-loop I, SLI) du substrat et la tige-boucle V (stem-loop V, SLV) du domaine catalytique. Des études biochimiques ont démontré que l’interaction kissing-loop I/V, dépendante du magnésium, implique trois paires de bases Watson-Crick (W-C). De plus, cette interaction est associée à un réarrangement de la structure du substrat, le faisant passer d’une conformation inactive dite unshifted à une conformation active dite shifted. Les travaux présentés dans cette thèse consistent en une caractérisation structurale et thermodynamique de l’interaction kissing-loop I/V du ribozyme VS, laquelle est formée de fragments d’ARN représentant les tige-boucles I et V dérivées du ribozyme VS (SLI et SLV). Cette caractérisation a été réalisée principalement par spectroscopie de résonance magnétique nucléaire (RMN) et par titrage calorimétrique isotherme (isothermal titration calorimetry, ITC) en utilisant différents complexes SLI/SLV dans lesquels l’ARN SLV est commun à tous les complexes, alors que différentes variations de l’ARN SLI ont été utilisées, soit en conformation shiftable ou preshifted. Les données d’ITC ont permis de démontrer qu’en présence d’une concentration saturante de magnésium, l’affinité d’un substrat SLI preshifted pour SLV est extrêmement élevée, rendant cette interaction plus stable que ce qui est prédit pour un duplexe d’ARN équivalent. De plus, l’étude effectuée par ITC montre que des ARN SLI preshifted présentent une meilleure affinité pour SLV que des ARN SLI shiftable, ce qui a permis de calculer le coût énergétique associé au réarrangement de structure du substrat. En plus de confirmer la formation des trois paires de bases W-C prédites à la jonction I/V, les études de RMN ont permis d’obtenir une preuve structurale directe du réarrangement structural des substrats SLI shiftable en présence de magnésium et de l’ARN SLV. La structure RMN d’un complexe SLI/SLV de grande affinité démontre que les boucles terminales de SLI et SLV forment chacune un motif U-turn, ce qui facilite l’appariement W-C intermoléculaire. Plusieurs autres interactions ont été définies à l’interface I/V, notamment des triplets de bases, ainsi que des empilements de bases. Ces interactions contribuent d’ailleurs à la création d’une structure présentant un empilement continu, c’est-à-dire qui se propage du centre de l’interaction jusqu’aux bouts des tiges de SLI et SLV. Ces études de RMN permettent donc de mieux comprendre la stabilité exceptionnelle de l’interaction kissing-loop I/V au niveau structural et mènent à l’élaboration d’un modèle cinétique de l’activation du substrat par le ribozyme VS. En considérant l’ensemble des données d’ITC et de RMN, l’étonnante stabilité de l’interaction I/V s’explique probablement par une combinaison de facteurs, dont les motifs U-turn, la présence d’un nucléotide exclu de la boucle de SLV (U700), la liaison de cations magnésium et l’empilement de bases continu à la jonction I/V.

Depinning transition of dislocation assemblies: Pileups and low-angle grain boundaries

We investigate the depinning transition occurring in dislocation assemblies. In particular, we consider the cases of regularly spaced pileups and low-angle grain boundaries interacting with a disordered stress landscape provided by solute atoms, or by other immobile dislocations present in nonactive slip systems. Using linear elasticity, we compute the stress originated by small deformations of these assemblies and the corresponding energy cost in two and three dimensions. Contrary to the case of isolated dislocation lines, which are usually approximated as elastic strings with an effective line tension, the deformations of a dislocation assembly cannot be described by local elastic interactions with a constant tension or stiffness. A nonlocal elastic kernel results as a consequence of long-range interactions between dislocations. In light of this result, we revise statistical depinning theories of dislocation assemblies and compare the theoretical results with numerical simulations and experimental data.

Conservative force fields in non-Gaussian statistics

In this Letter, we determine the kappa-distribution function for a gas in the presence of an external field of force described by a potential U(r). In the case of a dilute gas, we show that the kappa-power law distribution including the potential energy factor term can rigorously be deduced in the framework of kinetic theory with basis on the Vlasov equation. Such a result is significant as a preliminary to the discussion on the role of long range interactions in the Kaniadakis thermostatistics and the underlying kinetic theory. (C) 2008 Elsevier B.V. All rights reserved.

Estudo de sistemas complexos com interações de longo alcance : percolação, redes e tráfego

In this thesis we investigate physical problems which present a high degree of complexity using tools and models of Statistical Mechanics. We give a special attention to systems with long-range interactions, such as one-dimensional long-range bondpercolation, complex networks without metric and vehicular traffic. The flux in linear chain (percolation) with bond between first neighbor only happens if pc = 1, but when we consider long-range interactions , the situation is completely different, i.e., the transitions between the percolating phase and non-percolating phase happens for pc < 1. This kind of transition happens even when the system is diluted ( dilution of sites ). Some of these effects are investigated in this work, for example, the extensivity of the system, the relation between critical properties and the dilution, etc. In particular we show that the dilution does not change the universality of the system. In another work, we analyze the implications of using a power law quality distribution for vertices in the growth dynamics of a network studied by Bianconi and Barabási. It incorporates in the preferential attachment the different ability (fitness) of the nodes to compete for links. Finally, we study the vehicular traffic on road networks when it is submitted to an increasing flux of cars. In this way, we develop two models which enable the analysis of the total flux on each road as well as the flux leaving the system and the behavior of the total number of congested roads

Size limiting in Tsallis statistics

Power law scaling is observed in many physical, biological and socio-economical complex systems and is now considered an important property of these systems. In general, power law exists in the central part of the distribution. It has deviations from power law for very small and very large variable sizes. Tsallis, through non-extensive thermodynamics, explained power law distribution in many cases including deviation from the power law. In case of very large steps, the used the heuristic crossover approach. In the present we present an alternative model in which we consider that the entropy factor 9 decreases with variable size due to the softening of long range interactions or memory. We apply this model for distribution of citation index of scientists and examination scores and are able to explain the distribution for entire variable range. In the present model, we can have very sharp cut-off without interfering with power law in its central part as observed in many cases. (C) 2008 Elsevier B.V. All rights reserved.

Taylor's power law for ecological communities: an explanation on nonextensive/nonlinear statistical grounds

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Simulação de Monte Carlo: de modelos de spin à teoria de campos na rede

Pós-graduação em Física - IFT

Percolation transition in quantum Ising and rotor models with sub-Ohmic dissipation

We investigate the influence of sub-Ohmic dissipation on randomly diluted quantum Ising and rotor models. The dissipation causes the quantum dynamics of sufficiently large percolation clusters to freeze completely. As a result, the zero-temperature quantum phase transition across the lattice percolation threshold separates an unusual super-paramagnetic cluster phase from an inhomogeneous ferromagnetic phase. We determine the low-temperature thermodynamic behavior in both phases, which is dominated by large frozen and slowly fluctuating percolation clusters. We relate our results to the smeared transition scenario for disordered quantum phase transitions, and we compare the cases of sub-Ohmic, Ohmic, and super-Ohmic dissipation.

Supersymmetric extension of the quantum spherical model

In this work, we present a supersymmetric extension of the quantum spherical model, both in components and also in the superspace formalisms. We find the solution for short- and long-range interactions through the imaginary time formalism path integral approach. The existence of critical points (classical and quantum) is analyzed and the corresponding critical dimensions are determined.

Quantum Correlations in Field Theory and Integrable Systems

In this thesis we will investigate some properties of one-dimensional quantum systems. From a theoretical point of view quantum models in one dimension are particularly interesting because they are strongly interacting, since particles cannot avoid each other in their motion, and you we can never ignore collisions. Yet, integrable models often generate new and non-trivial solutions, which could not be found perturbatively. In this dissertation we shall focus on two important aspects of integrable one- dimensional models: Their entanglement properties at equilibrium and their dynamical correlators after a quantum quench. The first part of the thesis will be therefore devoted to the study of the entanglement entropy in one- dimensional integrable systems, with a special focus on the XYZ spin-1/2 chain, which, in addition to being integrable, is also an interacting model. We will derive its Renyi entropies in the thermodynamic limit and its behaviour in different phases and for different values of the mass-gap will be analysed. In the second part of the thesis we will instead study the dynamics of correlators after a quantum quench , which represent a powerful tool to measure how perturbations and signals propagate through a quantum chain. The emphasis will be on the Transverse Field Ising Chain and the O(3) non-linear sigma model, which will be both studied by means of a semi-classical approach. Moreover in the last chapter we will demonstrate a general result about the dynamics of correlation functions of local observables after a quantum quench in integrable systems. In particular we will show that if there are not long-range interactions in the final Hamiltonian, then the dynamics of the model (non equal- time correlations) is described by the same statistical ensemble that describes its statical properties (equal-time correlations).

Molecular dynamics simulations of sheared brush-like systems

Mit Hilfe von Molekulardynamik-Simulationen untersuchen wir bürstenartige Systeme unter guten Lösungsmittelbedingungen. Diese Systeme sind, dank ihren vielfältigen Beschaffenheiten, die von Molekularparametern und äußeren Bedingungen abhängig sind, wichtig für viele industrielle Anwendungen. Man vermutet, dass die Polymerbürsten eine entscheidende Rolle in der Natur wegen ihrer einzigartigen Gleiteigenschaften spielen. Ein vergröbertes Modell wird verwendet, um die strukturellen und dynamischen Eigenschaften zweier hochkomprimierter Polymerbürsten, die eine niedrige Reibung aufweisen, zu untersuchen. Allerdings sind die Lubrikationseigenschaften dieser Systeme, die in vielen biologischen Systemen vorhanden sind, beeinflußt. Wir untersuchen so-genannte "weiche Kolloide", die zwischen den beiden Polymerbürsten eingebettet sind, und wie diese Makroobjekte auf die Polymerbürsten wirken.rnrnNicht-Gleichgewichts-Molekulardynamik-Simulationen werden durchgeführt, in denen die hydrodynamischen Wechselwirkungen durch die Anwendung des DPD-Thermostaten mit expliziten Lösungsmittelmolekülen berücksichtigt werden. Wir zeigen, dass die Kenntnis der Gleichgewichtseigenschaften des Systems erlaubt, dynamische Nichtgleichgewichtsigenschaften der Doppelschicht vorherzusagen.rnrnWir untersuchen, wie die effektive Wechselwirkung zwischen kolloidalen Einschlüßen durch die Anwesenheit der Bürsten (in Abhängigkeit der Weichheit der Kolloide und der Pfropfdichte der Bürsten) beeinflußt wird. Als nächsten Schritt untersuchen wir die rheologische Antwort von solchen komplexen Doppelschichten auf Scherung. Wir entwickeln eine Skalen-Theorie, die die Abhängigkeit der makroskopischen Transporteigenschaften und der lateralen Ausdehnung der verankerten Ketten von der Weissenberg Zahl oberhalb des Bereichs, in dem die lineare Antwort-Theorie gilt, voraussagt. Die Vorhersagen der Theorie stimmen gut mit unseren und früheren numerischen Ergebnissen und neuen Experimenten überein. Unsere Theorie bietet die Möglichkeit, die Relaxationszeit der Doppelschicht zu berechnen. Wenn diese Zeit mit einer charakteristischen Längenskala kombiniert wird, kann auch das ''transiente'' (nicht-stationäre) Verhalten beschrieben werden.rnrnrnWir untersuchen die Antwort des Drucktensors und die Deformation der Bürsten während der Scherinvertierung für grosse Weissenberg Zahlen. Wir entwickeln eine Vorhersage für die charakteristische Zeit, nach der das System wieder den stationären Zustand erreicht.rnrnrnElektrostatik spielt eine bedeutende Rolle in vielen biologischen Prozessen. Die Lubrikationseigenschaften der Polymerbürsten werden durch die Anwesenheit langreichweitiger Wechselwirkungen stark beeinflusst. Für unterschiedliche Stärken der elektrostatischen Wechselwirkungen untersuchen wir rheologische Eigenschaften der Doppelschicht und vergleichen mit neutralen Systemen. Wir studieren den kontinuierlichen Übergang der Systemeigenschaften von neutralen zu stark geladenen Bürsten durch Variation der Bjerrumlänge und der Ladungsdichte.

Excitatory–inhibitory network in the visual cortex: Psychophysical evidence

At early stages in visual processing cells respond to local stimuli with specific features such as orientation and spatial frequency. Although the receptive fields of these cells have been thought to be local and independent, recent physiological and psychophysical evidence has accumulated, indicating that the cells participate in a rich network of local connections. Thus, these local processing units can integrate information over much larger parts of the visual field; the pattern of their response to a stimulus apparently depends on the context presented. To explore the pattern of lateral interactions in human visual cortex under different context conditions we used a novel chain lateral masking detection paradigm, in which human observers performed a detection task in the presence of different length chains of high-contrast-flanked Gabor signals. The results indicated a nonmonotonic relation of the detection threshold with the number of flankers. Remote flankers had a stronger effect on target detection when the space between them was filled with other flankers, indicating that the detection threshold is caused by dynamics of large neuronal populations in the neocortex, with a major interplay between excitation and inhibition. We considered a model of the primary visual cortex as a network consisting of excitatory and inhibitory cell populations, with both short- and long-range interactions. The model exhibited a behavior similar to the experimental results throughout a range of parameters. Experimental and modeling results indicated that long-range connections play an important role in visual perception, possibly mediating the effects of context.

Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism

I attempt to reconcile apparently conflicting factors and mechanisms that have been proposed to determine the rate constant for two-state folding of small proteins, on the basis of general features of the structures of transition states. Φ-Value analysis implies a transition state for folding that resembles an expanded and distorted native structure, which is built around an extended nucleus. The nucleus is composed predominantly of elements of partly or well-formed native secondary structure that are stabilized by local and long-range tertiary interactions. These long-range interactions give rise to connecting loops, frequently containing the native loops that are poorly structured. I derive an equation that relates differences in the contact order of a protein to changes in the length of linking loops, which, in turn, is directly related to the unfavorable free energy of the loops in the transition state. Kinetic data on loop extension mutants of CI2 and α-spectrin SH3 domain fit the equation qualitatively. The rate of folding depends primarily on the interactions that directly stabilize the nucleus, especially those in native-like secondary structure and those resulting from the entropy loss from the connecting loops, which vary with contact order. This partitioning of energy accounts for the success of some algorithms that predict folding rates, because they use these principles either explicitly or implicitly. The extended nucleus model thus unifies the observations of rate depending on both stability and topology.