Field imperfection induced axial secular frequency shifts in nonlinear ion traps

This article develops a simple analytical expression that relates ion axial secular frequency to field aberration in ion trap mass spectrometers. Hexapole and octopole aberrations have been considered in the present computations. The equation of motion of the ions in a pseudopotential well with these superpositions has the form of a Duffing-like equation and a perturbation method has been used to obtain the expression for ion secular frequency as a function of field imperfections. The expression indicates that the frequency shift is sensitive to the sign of the octopole superposition and insensitive to the sign of the hexapole superposition. Further, for weak multipole superposition of the same magnitude, octopole superposition causes a larger frequency shift in comparison to hexapole superposition.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

The effect of environmental coupling on tunneling of quasiparticles in Josephson junctions

We study quasiparticle tunneling in Josephson tunnel junctions embedded in an electromagnetic environment. We identify tunneling processes that transfer electrical charge and couple to the environment in a way similar to that of normal electrons, and processes that mix electrons and holes and are thus creating charge superpositions. The latter are sensitive to the phase difference between the superconductors and are thus limited by phase diffusion even at zero temperature. We show that the environmental coupling is suppressed in many environments, thus leading to lower quasiparticle decay rates and better superconductor qubit coherence than previously expected. Our approach is nonperturbative in the environmental coupling strength.

Resonant and Secular Orbital Interations

In stable solar systems, planets remain in nearly elliptical orbits around their stars. Over longer timescales, however, their orbital shapes and sizes change due to mutual gravitational perturbations. Orbits of satellites around a planet vary for the same reason. Because of their interactions, the orbits of planets and satellites today are different from what they were earlier. In order to determine their original orbits, which are critical constraints on formation theories, it is crucial to understand how orbits evolve over the age of the Solar System. Depending on their timescale, we classify orbital interactions as either short-term (orbital resonances) or long-term (secular evolution). My work involves examples of both interaction types. Resonant history of the small Neptunian satellites In satellite systems, tidal migration brings satellite orbits in and out of resonances. During a resonance passage, satellite orbits change dramatically in a very short period of time. We investigate the resonant history of the six small Neptunian moons. In this unique system, the exotic orbit of the large captured Triton (with a circular, retrograde, and highly tilted orbit) influences the resonances among the small satellites very strongly. We derive an analytical framework which can be applied to Neptune's satellites and to similar systems. Our numerical simulations explain the current orbital tilts of the small satellites as well as constrain key physical parameters of both Neptune and its moons. Secular orbital interactions during eccentricity damping Long-term periodic changes of orbital shape and orientation occur when two or more planets orbit the same star. The variations of orbital elements are superpositions of the same number of fundamental modes as the number of planets in the system. We investigate how this effect interacts with other perturbations imposed by external disturbances, such as the tides and relativistic effects. Through analytical studies of a system consisting of two planets, we find that an external perturbation exerted on one planet affects the other indirectly. We formulate a general theory for how both orbits evolve in response to an arbitrary externally-imposed slow change in eccentricity.

Quantitative analysis of proton imaging measurements of laser-induced plasmas

A method for obtaining quantitative information about electric field and charge distributions from proton imaging measurements of laser-induced plasmas is presented. A parameterised charge distribution is used as target plasma. The deflection of a proton beam by the electric field of such a plasma is simulated numerically as well as the resulting proton density, which will be obtained on a screen behind the plasma according to the proton imaging technique. The parameters of the specific charge distributions are delivered by a combination of linear regression and nonlinear fitting of the calculated proton density distribution to the measured optical density of a radiochromic film screen changed by proton exposure. It is shown that superpositions of spherical Gaussian charge distributions as target plasma are sufficient to simulate various structures in proton imaging measurements, which makes this method very flexible.

Electron recombination, photoionization, and scattering via many-electron compound resonances

Highly excited eigenstates of atoms and ions with open f shell are chaotic superpositions of thousands, or even millions, of Hartree-Fock determinant states. The interaction between dielectronic and multielectronic configurations leads to the broadening of dielectronic recombination resonances and relative enhancement of photon emission due to opening of thousands of radiative decay channels. The radiative yield is close to 100% for electron energy <1 eV and rapidly decreases for higher energies due to opening of many autoionization channels. The same mechanism predicts suppression of photoionization and relative enhancement of the Raman scattering. Results of our calculations of the recombination rate are in agreement with the experimental data for W20+ and Au25+.

Proposal for a Noninterferometric Test of Collapse Models in Optomechanical Systems

The test of modifications to quantum mechanics aimed at identifying the fundamental reasons behind the unobservability of quantum mechanical superpositions at the macroscale is a crucial goal of modern quantum mechanics. Within the context of collapse models, current proposals based on interferometric techniques for their falsification are far from the experimental state of the art. Here we discuss an alternative approach to the testing of quantum collapse models that, by bypassing the need for the preparation of quantum superposition states might help us addressing nonlinear stochastic mechanisms such as the one at the basis of the continuous spontaneous localization model. 

Macroscopicity in an optomechanical matter-wave interferometer

We analyse a proposal that we have recently put forward for an interface between matter-wave and optomechanical technologies from the perspective of macroscopic quantumness. In particular, by making use of a measure of macroscopicity in quantum superpositions that is particularly well suited for continuous variables systems, we demonstrate the existence of working points for our interface at which a quantum mechanical superposition of genuinely mesoscopic states is achieved. Our proposal thus holds the potential to affirm itself as a viable atom-to-mechanics transducer of quantum coherences.

Limitations of a measurement-assisted optomechanical route to quantum macroscopicity of superposition states

Optomechanics is currently believed to provide a promising route towards the achievement of genuine quantum effects at the large, massive-system scale. By using a recently proposed figure of merit that is well suited to address continuous-variable systems, in this paper we analyze the requirements needed for the state of a mechanical mode (embodied by an end-cavity cantilever or a membrane placed within an optical cavity) to be qualified as macroscopic. We show that, according to the phase space-based criterion that we have chosen for our quantitative analysis, the state achieved through strong single-photon radiation-pressure coupling to a quantized field of light and conditioned by measurements operated on the latter might be interpreted as macroscopically quantum. In general, though, genuine macroscopic quantum superpositions appear to be possible only under quite demanding experimental conditions

Solutions de rang k et invariants de Riemann pour les systèmes de type hydrodynamique multidimensionnels

Dans ce travail, nous adaptons la méthode des symétries conditionnelles afin de construire des solutions exprimées en termes des invariants de Riemann. Dans ce contexte, nous considérons des systèmes non elliptiques quasilinéaires homogènes (de type hydrodynamique) du premier ordre d'équations aux dérivées partielles multidimensionnelles. Nous décrivons en détail les conditions nécessaires et suffisantes pour garantir l'existence locale de ce type de solution. Nous étudions les relations entre la structure des éléments intégraux et la possibilité de construire certaines classes de solutions de rang k. Ces classes de solutions incluent les superpositions non linéaires d'ondes de Riemann ainsi que les solutions multisolitoniques. Nous généralisons cette méthode aux systèmes non homogènes quasilinéaires et non elliptiques du premier ordre. Ces méthodes sont appliquées aux équations de la dynamique des fluides en (3+1) dimensions modélisant le flot d'un fluide isentropique. De nouvelles classes de solutions de rang 2 et 3 sont construites et elles incluent des solutions double- et triple-solitoniques. De nouveaux phénomènes non linéaires et linéaires sont établis pour la superposition des ondes de Riemann. Finalement, nous discutons de certains aspects concernant la construction de solutions de rang 2 pour l'équation de Kadomtsev-Petviashvili sans dispersion.

L’univers dans un point noir : esthétique et matérialité dans l’oeuvre de Jack Kirby

Notre recherche étudie les particularités esthétiques et matérialistes de l’oeuvre du bédéiste américain Jack Kirby (1917-1994) et la manière dont elles répondent d’agencements qui visent à déconstruire et reconstruire les formes sur la page. Contemporain de Will Eisner, Kirby est largement considéré comme l'auteur et dessinateur le plus influent de son époque, co-signant les premières aventures de certains des super-héros qui perdurent et qui sont aujourd’hui la manne de l’industrie hollywoodienne (Captain America, les Fantastic Four, Hulk, etc.). Son oeuvre protéiforme est composée de superpositions de textures, d’objets récupérés, de figures déviées et trouve dans son rapport à la matière les principaux axiomes qui la définissent. Cherchant dans son travail à cerner les fonctions des nombreux amoncellements de points noirs (baptisés kirby dots par la critique et l’industrie), nous nous écartons des modèles d’analyse sémiologiques pour constituer une approche écosophique de la bande dessinée. Dans cette dernière, nous avons recours à la schizo-analyse théorisée par Gilles Deleuze et Félix Guattari dans leur ouvrage L’Anti-OEdipe (1972) afin de cerner les conditions de la production de sens et de non-sens du point kirbyen. Pour ce faire, nous proposons de reconsidérer la BD comme une écologie séquentialisée, composée de cases sans icônes, c’est-à-dire d’un espace pris au plus près de la planche, pour soi et en soi, sans rapport de causalité fixe ou de structure prédéterminée. Nous envisageons ensuite les territorialités archaïques de la bande dessinée pour mieux définir son ontogénie, puis pour étudier les rapports machiniques et schizos qu’entretiennent entre eux les différents espaces (que nous distinguons en espaces striés et en espaces lisses) ainsi que les différents traits de la planche. Finalement, nous expliquerons en quoi le point kirbyen apparaît comme une machine abstraite, c’est-à-dire une instance capable d’auto-générer, d’auto-poïétiser, son propre mystère représentationnel.

Les pintures rupestres prehistòriques del Zemmur (Sahara Occidental)

El treball de tesi ha tingut per objectiu estudiar les pintures rupestres del Zemmur, al Sahara Occidental. El Zemmur és una regió muntanyosa molt rica en abrics, que s'obren a les cingleres dels seus turons de gres baixos, aplanats i allargassats. Aquestes pintures foren descobertes al 1995, quan el personal del ministeri de Cultura de la República Àrab Sahrauí i Democràtica les va mostrar a un equip d'arqueòlegs i antropòlegs de la Universitat de Girona. Les campanyes d'estudi continuades que s'han realitzat en aquests jaciments de pintura rupestre prehistòrica des d'aleshores han proporcionat les dades per aquesta investigació. En total es tracta d'un conjunt de 2734 figures repartides en 130 abrics de 5 jaciments diferents: Uad Ymal, Uadi Kenta, Rekeiz Ajahfun, Rekeiz Lemgasem i Asako. Les hipòtesis a contrastar eren dues. La primera que al Zemmur hi havia diversos estils de pintura rupestre. La segona que la majoria d'aquests estils dataven de la prehistòria. Ambdues han pogut ser verificades i s'han aportat arguments que demostren que eren certes. El treball de tesi ha consistit en fotografiar les pintures, digitalitzar-les, reproduir-les i estudiar-les. Concretament l'estudi ha consistit en descriure-les, classificar-les estilísticament i datar-les. La classificació s'ha realitzat a partir d'una sèrie de criteris morfològics i tècnics. Posteriorment les imatges han estat atribuïdes a diversos estils, que també havien estat definits amb criteris morfotècnics a partir de l'observació de les imatges. La seva existència, i per tant la verificació de la primera hipòtesi, es dedueix de la presència de recurrències morfotècniques en les representacions. Més tard aquests estils han estat ordenats de manera relativa tot estudiant les seves superposicions. La seqüència dels cinc estils identificats, de més antic a més recent és: Balladors, Modelats, Tracejats, Figures Fosques i Linial. Posteriorment s'ha intentat datar cadascun dels estils a partir de les representacions ja que les anàlisis efectuades indicaren que no era possible datar les imatges per tècniques radiomètriques a causa de la manca de matèria orgànica en les pintures. En qualsevol cas, gràcies a les representacions d'armes, d'animals i els textos escrits hem pogut verificar que la majoria d'elles són prehistòriques, tal com apuntàvem en la nostra segona hipòtesi. Finalment s'ha arribat a la conclusió que l'estil dels Balladors data, de manera molt aproximada, d'ara fa entre 3800 i 3200 anys tal com indiquen les representacions d'alabardes. L'estil Linial, el més recent, data d'entre ara fa 2400 i 2000 anys perquè és acompanyat de textos líbico-berbers però no de representacions de camells. Els estils Modelat, Tracejat i Figures Fosques es daten entremig. A part de les conclusions obtingudes, un dels resultats més importants d'aquest treball ha estat la realització del corpus de pintura prehistòrica del Zemmur que consta, com ja hem dit, de milers d'imatges. Per tant aquesta recerca, a més de tractar sobre un material inèdit i d'un gran interès històric, hauria d'ésser útil per a la gestió de tot aquest patrimoni.

Flavor mixing in a Lee-type model

An exactly solvable quantum field theory (QFT) model of Lee type is constructed to study how neutrino flavor eigenstates are created through interactions and how the localization properties of neutrinos follows from the parent particle that decays. The two-particle states formed by the neutrino and the accompanying charged lepton can be calculated exactly as well as their creation probabilities. We can show that the coherent creation of neutrino flavor eigenstates follows from the common negligible contribution of neutrino masses to their creation probabilities. on the other hand, it is shown that it is not possible to associate a well-defined flavor to coherent superpositions of charged leptons.

Estudo cefalométrico com implantes metálicos das alterações esqueléticas, a longo prazo, após o uso do bionator de Balters

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Near-field mediated enhancement effects on plasmonic nanostructures

In dieser Arbeit wird eine detaillierte Untersuchung und Charakterisierung der Zwei-Photonen-induzierten Fluoreszenzverstärkung von organischen Farbstoffen auf plasmonischen Nanostrukturen vorgestellt. Diese Fluoreszenzverstärkung ist insbesondere für hochaufgelöste Fluoreszenzmikroskopie und Einzelmolekülspektroskopie von großer Bedeutung. Durch die Zwei-Photonen-Anregung resultiert eine Begrenzung des Absorptionsprozesses auf das fokale Volumen. In Kombination mit dem elektrischen Nahfeld der Nanostrukturen als Anregungsquelle entsteht eine noch stärkere Verringerung des Anregungsvolumens auf eine Größe unterhalb der Beugungsgrenze. Dies erlaubt die selektive Messung ausgewählter Farbstoffe. Durch die Herstellung der Nanopartikel mittels Kolloidlithografie wird eine definierte, reproduzierbare Geometrie erhalten. Polymermultischichten dienen als Abstandshalter, um die Farbstoffe an einer exakten Distanz zum Metall zu positionieren. Durch die kovalente Anbindung des Farbstoffs an die oberste Schicht wird eine gleichmäßige Verteilung des Farbstoffs in geringer Konzentration erhalten. rnEs wird eine Verstärkung der Fluoreszenz um den Faktor 30 für Farbstoffe auf Goldellipsen detektiert, verglichen mit Farbstoffen außerhalb des Nahfelds. Sichelförmige Nanostrukturen erzeugen eine Verstärkung von 120. Dies belegt, dass das Ausmaß der Fluoreszenzverstärkung entscheidend von der Stärke des elektrischen Nahfelds der Nanostruktur abhängt. Auch das Material der Nanostruktur ist hierbei von Bedeutung. So erzeugen Silberellipsen eine 1,5-fach höhere Fluoreszenzverstärkung als identische Goldellipsen. Distanzabhängige Fluoreszenzmessungen zeigen, dass die Zwei-Photonen-angeregte Fluoreszenzverstärkung an strukturspezifischen Abständen zum Metall maximiert wird. Elliptische Strukturen zeigen ein Maximum bei einem Abstand von 8 nm zum Metall, wohingegen bei sichelförmigen Nanostrukturen die höchste Fluoreszenzintensität bei 12 nm gemessen wird. Bei kleineren Abständen unterliegt der Farbstoff einem starken Löschprozess, sogenanntes Quenching. Dieses konkurriert mit dem Verstärkungsprozess, wodurch es zu einer geringen Nettoverstärkung kommt. Hat die untersuchte Struktur Dimensionen größer als das Auflösungsvermögen des Mikroskops, ist eine direkte Visualisierung des elektrischen Nahfelds der Nanostruktur möglich. rnrnEin weiterer Fokus dieser Arbeit lag auf der Herstellung neuartiger Nanostrukturen durch kolloidlithografische Methoden. Gestapelte Dimere sichelförmiger Nanostrukturen mit exakter vertikaler Ausrichtung und einem Separationsabstand von etwa 10 nm wurden hergestellt. Die räumliche Nähe der beiden Strukturen führt zu einem Kopplungsprozess, der neue optische Resonanzen hervorruft. Diese können als Superpositionen der Plasmonenmoden der einzelnen Sicheln beschrieben werden. Ein Hybridisierungsmodell wird angewandt, um die spektralen Unterschiede zu erklären. Computersimulationen belegen die zugrunde liegende Theorie und erweitern das Modell um experimentell nicht aufgelöste Resonanzen. rnWeiterhin wird ein neuer Herstellungsprozess für sichelförmige Nanostrukturen vorgestellt, der eine präzise Formanpassung ermöglicht. Hierdurch kann die Lage der Plasmonenresonanz exakt justiert werden. Korrelationen der geometrischen Daten mit den Resonanzwellenlängen tragen zum grundlegenden Verständnis der Plasmonenresonanzen bei. Die vorgestellten Resultate wurden mittels Computersimulationen verifiziert. Der Fabrikationsprozess erlaubt die Herstellung von Dimeren sichelförmiger Nanostrukturen in einer Ebene. Durch die räumliche Nähe überlappen die elektrischen Nahfelder, wodurch es zu kopplungs-induzierten Shifts der Plasmonenresonanzen kommt. Der Unterschied zu theoretisch berechneten ungekoppelten Nanosicheln kann auch bei den gegenüberliegenden sichelförmigen Nanostrukturen mit Hilfe des Plasmonenhybridisierungsmodells erklärt werden.