Supervised variational relevance learning, an analytic geometric feature selection with applications to omic datasets

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

Determinação da estrutura de diferentes alcoóis terpênicos: um estudo teórico e experimental

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

Failure behavior modeling of slender reinforced concrete columns subjected to eccentric load

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Imagem de tensor de difusão na epilesia de lobo temporal mesial

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

Aprendizado de máquina baseado em tensores e suas aplicacções para floresta de caminhos ótimos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Theoretical and Experimental Studies in Nuclear Magnetic Resonance

Nuclear magnetic resonance (NMR) is a tool used to probe the physical and chemical environments of specific atoms in molecules. This research explored small molecule analogues to biological materials to determine NMR parameters using ab initio computations, comparing the results with solid-state NMR measurements. Models, such as dimethyl phosphate (DMP) for oligonucleotides or CuCl for the active site of the protein azurin, represented computationally unwieldy macromolecules. 31P chemical shielding tensors were calculated for DMP as a function of torsion angles, as well as for the phosphate salts, ammonium dihydrogen phosphate (ADHP), diammonium hydrogen phosphate, and magnesium dihydrogen phosphate. The computational DMP work indicated a problem with the current standard 31P reference of 85% H3PO4(aq.). Comparison of the calculations and experimental spectra for the phosphate salts indicated ADHP might be a preferable alternative as a solid state NMR reference for 31P. Experimental work included magic angle spinning experiments on powder samples using the UNL chemistry department’s Bruker Avance 600 MHz NMR to collect data to determine chemical shielding anisotropies. For the quadrupolar nuclei of copper and scandium, the electric field gradient was calculated in diatomic univalent metal halides, allowing determination of the minimal level of theory necessary to compute NMR parameters for these nuclei.

Magnetic fabrics and their relationship with the emplacement of the Piracaia pluton, SE Brazil

Magnetic fabric and rock-magnetism studies were performed on the four units of the 578 +/- 3-Ma-old Piracaia pluton (NW of Sao Paulo State, southern Brazil). This intrusion is roughly elliptical (similar to 32 km(2)), composed of (i) coarse-grained monzodiorite (MZD-c), (ii) fine-grained monzodiorite (MZD-f), which is predominant in the pluton, (iii) monzonite heterogeneous (MZN-het), and (iv) quartz syenite (Qz-Sy). Magnetic fabrics were determined by applying both anisotropy of low-field magnetic susceptibility (AMS) and anisotropy of anhysteretic remanent magnetization (AARM). The two fabrics are coaxial. The parallelism between AMS and AARM tensors excludes the presence of a single domain (SD) effect on the AMS fabric of the units. Several rock-magnetism experiments performed in one specimen from each sampled units show that for all of them, the magnetic susceptibility and magnetic fabrics are carried by magnetite grains, which was also observed in the thin sections. Foliations and lineations in the units were successfully determined by applying magnetic methods. Most of the magnetic foliations are steeply dipping or vertical in all units and are roughly parallel to the foliation measured in the field and in the country rocks. In contrast, the magnetic lineations present mostly low plunges for the whole pluton. However, for eight sites, they are steep up to vertical. Thin-section analyses show that rocks from the Piracaia pluton were affected by the regional strain during and after emplacement since magmatic foliation evolves to solid-state fabric in the north of the pluton, indicating that magnetic fabrics in this area of the pluton are related to this strain. Otherwise, the lack of solid-state deformation at outcrop scale and in thin sections precludes deformation in the SW of the pluton. This evidence allows us to interpret the observed magnetic fabrics as primary in origin (magmatic) acquired when the rocks were solidified as a result of magma flow, in which steeply plunging magnetic lineation suggests that a feeder zone could underlie this area.

Stellar Models in General Relativity

Neutron stars are some of the most fascinating objects in Nature. Essentially all aspects of physics seems to be represented inside them. Their cores are likely to contain deconfined quarks, hyperons and other exotic phases of matter in which the strong interaction is the dominant force. The inner region of their solid crust is penetrated by superfluid neutrons and their magnetic fields may reach well over 1012 Gauss. Moreover, their extreme mean densities, well above the densities of nuclei, and their rapid rotation rates makes them truly relativistic both in the special as well as in the general sense. This thesis deals with a small subset of these phenomena. In particular the exciting possibility of trapping of gravita-tional waves is examined from a theoretical point of view. It is shown that the standard condition R < 3M is not essential to the trapping mechanism. This point is illustrated using the elegant tool provided by the optical geometry. It is also shown that a realistic equation of state proposed in the literature allows stable neutron star models with closed circular null orbits, something which is closely related to trapped gravitational waves. Furthermore, the general relativistic theory of elasticity is reviewed and applied to stellar models. Both static equilibrium as well as radially oscillating configurations with elasticsources are examined. Finally, Killing tensors are considered and their applicability to modeling of stars is discussed

Shallow and deep deformation in northern Apennines region using seismological data

For its particular position and the complex geological history, the Northern Apennines has been considered as a natural laboratory to apply several kinds of investigations. By the way, it is complicated to joint all the knowledge about the Northern Apennines in a unique picture that explains the structural and geological emplacement that produced it. The main goal of this thesis is to put together all information on the deformation - in the crust and at depth - of this region and to describe a geodynamical model that takes account of it. To do so, we have analyzed the pattern of deformation in the crust and in the mantle. In both cases the deformation has been studied using always information recovered from earthquakes, although using different techniques. In particular the shallower deformation has been studied using seismic moment tensors information. For our purpose we used the methods described in Arvidsson and Ekstrom (1998) that allowing the use in the inversion of surface waves [and not only of the body waves as the Centroid Moment Tensor (Dziewonski et al., 1981) one] allow to determine seismic source parameters for earthquakes with magnitude as small as 4.0. We applied this tool in the Northern Apennines and through this activity we have built up the Italian CMT dataset (Pondrelli et al., 2006) and the pattern of seismic deformation using the Kostrov (1974) method on a regular grid of 0.25 degree cells. We obtained a map of lateral variations of the pattern of seismic deformation on different layers of depth, taking into account the fact that shallow earthquakes (within 15 km of depth) in the region occur everywhere while most of events with a deeper hypocenter (15-40 km) occur only in the outer part of the belt, on the Adriatic side. For the analysis of the deep deformation, i.e. that occurred in the mantle, we used the anisotropy information characterizing the structure below the Northern Apennines. The anisotropy is an earth properties that in the crust is due to the presence of aligned fluid filled cracks or alternating isotropic layers with different elastic properties while in the mantle the most important cause of seismic anisotropy is the lattice preferred orientation (LPO) of the mantle minerals as the olivine. This last is a highly anisotropic mineral and tends to align its fast crystallographic axes (a-axis) parallel to the astenospheric flow as a response to finite strain induced by geodynamic processes. The seismic anisotropy pattern of a region is measured utilizing the shear wave splitting phenomenon (that is the seismological analogue to optical birefringence). Here, to do so, we apply on teleseismic earthquakes recorded on stations located in the study region, the Sileny and Plomerova (1996) approach. The results are analyzed on the basis of their lateral and vertical variations to better define the earth structure beneath Northern Apennines. We find different anisotropic domains, a Tuscany and an Adria one, with a pattern of seismic anisotropy which laterally varies in a similar way respect to the seismic deformation. Moreover, beneath the Adriatic region the distribution of the splitting parameters is so complex to request an appropriate analysis. Therefore we applied on our data the code of Menke and Levin (2003) which allows to look for different models of structures with multilayer anisotropy. We obtained that the structure beneath the Po Plain is probably even more complicated than expected. On the basis of the results obtained for this thesis, added with those from previous works, we suggest that slab roll-back, which created the Apennines and opened the Tyrrhenian Sea, evolved in the north boundary of Northern Apennines in a different way from its southern part. In particular, the trench retreat developed primarily south of our study region, with an eastward roll-back. In the northern portion of the orogen, after a first stage during which the retreat was perpendicular to the trench, it became oblique with respect to the structure.

Regularization strategies for discontinuity-preserving optical flow methods

[EN]The aim of this work is to study several strategies for the preservation of flow discontinuities in variational optical flow methods. We analyze the combination of robust functionals and diffusion tensors in the smoothness assumption. Our study includes the use of tensors based on decreasing functions, which has shown to provide good results. However, it presents several limitations and usually does not perform better than other basic approaches. It typically introduces instabilities in the computed motion fields in the form of independent \textit{blobs} of vectors with large magnitude...

Creep and damage models for the service behaviour of structural members

Deformability is often a crucial to the conception of many civil-engineering structural elements. Also, design is all the more burdensome if both long- and short-term deformability has to be considered. In this thesis, long- and short-term deformability has been studied from the material and the structural modelling point of view. Moreover, two materials have been handled: pultruded composites and concrete. A new finite element model for thin-walled beams has been introduced. As a main assumption, cross-sections rigid are considered rigid in their plane; this hypothesis replaces that of the classical beam theory of plane cross-sections in the deformed state. That also allows reducing the total number of degrees of freedom, and therefore making analysis faster compared with twodimensional finite elements. Longitudinal direction warping is left free, allowing describing phenomena such as the shear lag. The new finite-element model has been first applied to concrete thin-walled beams (such as roof high span girders or bridge girders) subject to instantaneous service loadings. Concrete in his cracked state has been considered through a smeared crack model for beams under bending. At a second stage, the FE-model has been extended to the viscoelastic field and applied to pultruded composite beams under sustained loadings. The generalized Maxwell model has been adopted. As far as materials are concerned, long-term creep tests have been carried out on pultruded specimens. Both tension and shear tests have been executed. Some specimen has been strengthened with carbon fibre plies to reduce short- and long- term deformability. Tests have been done in a climate room and specimens kept 2 years under constant load in time. As for concrete, a model for tertiary creep has been proposed. The basic idea is to couple the UMLV linear creep model with a damage model in order to describe nonlinearity. An effective strain tensor, weighting the total and the elasto-damaged strain tensors, controls damage evolution through the damage loading function. Creep strains are related to the effective stresses (defined by damage models) and so associated to the intact material.

Strahlungskorrekturen zu Polarisationsobservablen schwerer Quarks

Das Thema der Dissertation ist die analytische Berechnung von QCD-Strahlungskorrekturen erster Ordnung zurPolarisation schwerer und leichter Quarks in der $e^+ e^-$-Vernichtung,und der Polarisation von Gluonen, die bei der Produktion von leichten oderschweren Quarkpaaren in der $e^+ e^-$-Vernichtung abgestrahlt werden. Der erste Teil der Arbeit (Kapitel 1 und 2) befaßt sich mitder vollständigen Analyse der Gluonpolarisation für den Prozeß $e^+ e^- to q bar q G$ und $ Q bar Q G$. Es werdenBerechnungen derQCD-Bremsstrahlungskorrekturen zur ersten Ordnung in$alpha_s$ zur Gluonpolarisation im Prozeß $e^+ e^- to q bar q G$ und$ Q bar Q G$ durchgeführt. Ferner werden die lineare und die zirkulareGluonpolarisation in der Hadronebene und Leptonebene untersucht. Anschließend werden die Polarwinkelabhängigkeit und dieStrahlpolarisationsabhängigkeit der Gluonpolarisation analysiert. Im zweiten Teil der Arbeit (Kapitel 3 und 4) finden sich die Berechnungen der QCD-Strahlungskorrekturen erster Ordnungfür massive Quarkszur Longitudinal-Longitudinal Spin-Korrelation für dieProzeße $e^+ e^- to q bar q$ und $Q bar Q$. In Kapitel 3 wirdeine Mittelung überdie Polarwinkel durchgeführt, während in Kapitel 4 die Polarwinkel-Abhängigkeit explizit untersucht wird. ImKapitel 3 und 4 wird der Effekt der $O(alpha_s)$-Korrektur zur spin-flip-Konfiguration der verschiedenen Komponenten derHadrontensoren diskutiert. Der vorgelegten Arbeit kommt im Rahmen der für die Zukunftgeplanten Hochpräzisionsexperimente eine besondere Bedeutung zu, dasie Vorhersagen für Spinobservablen liefert, die in Experimentenan den geplanten $e^+ e^-$-Linearbeschleunigern gemessen werden können.

Quantum effects and dynamics in hydrogen-bonded systems: a first-principles approach to spectroscopic experiments

Computer simulations have become an important tool in physics. Especially systems in the solid state have been investigated extensively with the help of modern computational methods. This thesis focuses on the simulation of hydrogen-bonded systems, using quantum chemical methods combined with molecular dynamics (MD) simulations. MD simulations are carried out for investigating the energetics and structure of a system under conditions that include physical parameters such as temperature and pressure. Ab initio quantum chemical methods have proven to be capable of predicting spectroscopic quantities. The combination of these two features still represents a methodological challenge. Furthermore, conventional MD simulations consider the nuclei as classical particles. Not only motional effects, but also the quantum nature of the nuclei are expected to influence the properties of a molecular system. This work aims at a more realistic description of properties that are accessible via NMR experiments. With the help of the path integral formalism the quantum nature of the nuclei has been incorporated and its influence on the NMR parameters explored. The effect on both the NMR chemical shift and the Nuclear Quadrupole Coupling Constants (NQCC) is presented for intra- and intermolecular hydrogen bonds. The second part of this thesis presents the computation of electric field gradients within the Gaussian and Augmented Plane Waves (GAPW) framework, that allows for all-electron calculations in periodic systems. This recent development improves the accuracy of many calculations compared to the pseudopotential approximation, which treats the core electrons as part of an effective potential. In combination with MD simulations of water, the NMR longitudinal relaxation times for 17O and 2H have been obtained. The results show a considerable agreement with the experiment. Finally, an implementation of the calculation of the stress tensor into the quantum chemical program suite CP2K is presented. This enables MD simulations under constant pressure conditions, which is demonstrated with a series of liquid water simulations, that sheds light on the influence of the exchange-correlation functional used on the density of the simulated liquid.

Theoretical studies of fluid membrane mechanics

Biologische Membranen sind Fettmolekül-Doppelschichten, die sich wie zweidimensionale Flüssigkeiten verhalten. Die Energie einer solchen fluiden Oberfläche kann häufig mit Hilfe eines Hamiltonians beschrieben werden, der invariant unter Reparametrisierungen der Oberfläche ist und nur von ihrer Geometrie abhängt. Beiträge innerer Freiheitsgrade und der Umgebung können in den Formalismus mit einbezogen werden. Dieser Ansatz wird in der vorliegenden Arbeit dazu verwendet, die Mechanik fluider Membranen und ähnlicher Oberflächen zu untersuchen. Spannungen und Drehmomente in der Oberfläche lassen sich durch kovariante Tensoren ausdrücken. Diese können dann z. B. dazu verwendet werden, die Gleichgewichtsposition der Kontaktlinie zu bestimmen, an der sich zwei aneinander haftende Oberflächen voneinander trennen. Mit Ausnahme von Kapillarphänomenen ist die Oberflächenenergie nicht nur abhängig von Translationen der Kontaktlinie, sondern auch von Änderungen in der Steigung oder sogar Krümmung. Die sich ergebenden Randbedingungen entsprechen den Gleichgewichtsbedingungen an Kräfte und Drehmomente, falls sich die Kontaktlinie frei bewegen kann. Wenn eine der Oberflächen starr ist, muss die Variation lokal dieser Fläche folgen. Spannungen und Drehmomente tragen dann zu einer einzigen Gleichgewichtsbedingung bei; ihre Beiträge können nicht mehr einzeln identifiziert werden. Um quantitative Aussagen über das Verhalten einer fluiden Oberfläche zu machen, müssen ihre elastischen Eigenschaften bekannt sein. Der "Nanotrommel"-Versuchsaufbau ermöglicht es, Membraneigenschaften lokal zu untersuchen: Er besteht aus einer porenüberspannenden Membran, die während des Experiments durch die Spitze eines Rasterkraftmikroskops in die Pore gedrückt wird. Der lineare Verlauf der resultierenden Kraft-Abstands-Kurven kann mit Hilfe der in dieser Arbeit entwickelten Theorie reproduziert werden, wenn der Einfluss von Adhäsion zwischen Spitze und Membran vernachlässigt wird. Bezieht man diesen Effekt in die Rechnungen mit ein, ändert sich das Resultat erheblich: Kraft-Abstands-Kurven sind nicht länger linear, Hysterese und nichtverschwindende Trennkräfte treten auf. Die Voraussagen der Rechnungen könnten in zukünftigen Experimenten dazu verwendet werden, Parameter wie die Biegesteifigkeit der Membran mit einer Auflösung im Nanometerbereich zu bestimmen. Wenn die Materialeigenschaften bekannt sind, können Probleme der Membranmechanik genauer betrachtet werden. Oberflächenvermittelte Wechselwirkungen sind in diesem Zusammenhang ein interessantes Beispiel. Mit Hilfe des oben erwähnten Spannungstensors können analytische Ausdrücke für die krümmungsvermittelte Kraft zwischen zwei Teilchen, die z. B. Proteine repräsentieren, hergeleitet werden. Zusätzlich wird das Gleichgewicht der Kräfte und Drehmomente genutzt, um mehrere Bedingungen an die Geometrie der Membran abzuleiten. Für den Fall zweier unendlich langer Zylinder auf der Membran werden diese Bedingungen zusammen mit Profilberechnungen kombiniert, um quantitative Aussagen über die Wechselwirkung zu treffen. Theorie und Experiment stoßen an ihre Grenzen, wenn es darum geht, die Relevanz von krümmungsvermittelten Wechselwirkungen in der biologischen Zelle korrekt zu beurteilen. In einem solchen Fall bieten Computersimulationen einen alternativen Ansatz: Die hier präsentierten Simulationen sagen voraus, dass Proteine zusammenfinden und Membranbläschen (Vesikel) bilden können, sobald jedes der Proteine eine Mindestkrümmung in der Membran induziert. Der Radius der Vesikel hängt dabei stark von der lokal aufgeprägten Krümmung ab. Das Resultat der Simulationen wird in dieser Arbeit durch ein approximatives theoretisches Modell qualitativ bestätigt.

Feasibility studies of the pp pi 0 e + e - electromagnetic channel at PANDA

Among all possible realizations of quark and antiquark assembly, the nucleon (the proton and the neutron) is the most stable of all hadrons and consequently has been the subject of intensive studies. Mass, shape, radius and more complex representations of its internal structure are measured since several decades using different probes. The proton (spin 1/2) is described by the electric GE and magnetic GM form factors which characterise its internal structure. The simplest way to measure the proton form factors consists in measuring the angular distribution of the electron-proton elastic scattering accessing the so-called Space-Like region where q2 < 0. Using the crossed channel antiproton proton <--> e+e-, one accesses another kinematical region, the so-called Time-Like region where q2 > 0. However, due to the antiproton proton <--> e+e- threshold q2th, only the kinematical domain q2 > q2th > 0 is available. To access the unphysical region, one may use the antiproton proton --> pi0 e+ e- reaction where the pi0 takes away a part of the system energy allowing q2 to be varied between q2th and almost 0. This thesis aims to show the feasibility of such measurements with the PANDA detector which will be installed on the new high intensity antiproton ring at the FAIR facility at Darmstadt. To describe the antiproton proton --> pi0 e+ e- reaction, a Lagrangian based approach is developed. The 5-fold differential cross section is determined and related to linear combinations of hadronic tensors. Under the assumption of one nucleon exchange, the hadronic tensors are expressed in terms of the 2 complex proton electromagnetic form factors. An extraction method which provides an access to the proton electromagnetic form factor ratio R = |GE|/|GM| and for the first time in an unpolarized experiment to the cosine of the phase difference is developed. Such measurements have never been performed in the unphysical region up to now. Extended simulations were performed to show how the ratio R and the cosine can be extracted from the positron angular distribution. Furthermore, a model is developed for the antiproton proton --> pi0 pi+ pi- background reaction considered as the most dangerous one. The background to signal cross section ratio was estimated under different cut combinations of the particle identification information from the different detectors and of the kinematic fits. The background contribution can be reduced to the percent level or even less. The corresponding signal efficiency ranges from a few % to 30%. The precision on the determination of the ratio R and of the cosine is determined using the expected counting rates via Monte Carlo method. A part of this thesis is also dedicated to more technical work with the study of the prototype of the electromagnetic calorimeter and the determination of its resolution.