This thesis describes the design, construction and optimisation of two compact setups to produce ⁸⁷Rb Bose-Einstein condensates and dual ⁷Li-⁸⁷Rb Magneto- Optical Traps (MOTs). The motivation for compact systems is to have simplified systems to cool the atoms. The first experimental setup is based on a single pyrex glass cell without the need for atom chips. Fast evaporation will be achieved in a hybrid trap comprising of a magnetic quadrupole trap and an optical dipole trap created by a Nd:YVO4 laser and with future plans of using a Spatial Light Modulator (SLM). To enhance an efficient and rapid evaporation, we have investigated Light-Induced Atomic Desorption (LIAD) to modulate the Rb partial pressure during the cooling and trapping stage. With this technique, a ⁸⁷Rb MOT of 7 x 10⁷ atoms was loaded by shining violet light from a LED source into the glass cell, whose walls are coated with rubidium atoms. The atoms were then cooled by optical molasses and then loaded into a magnetic trap where lifetime measurements demonstrated that LIAD improves on magnetically-trapped atoms loaded from constant background pressure by a factor of six. This is quite encouraging and opens the possibility to do a rapid evaporation. In a second experiment, we have designed a compact system based on a stainless steel chamber to trap either ⁷Li or ⁶Li atoms in a MOT loaded from alkali-metal dispensers without the need of conventional oven-Zeeman slower. This setup can also load ⁸⁷Rb atoms, allowing future projects to simultaneously produce degenerate quantum gases of bosonic ⁸⁷Rb and fermionic ⁶Li atoms.

Selective gas-phase dissociation strategies have been developed for the characterization of cross-linked peptides and proteins in quadrupole ion trap mass spectrometers. An infrared chromogenic cross-linker (IRCX) containing a phosphotriester afforded rapid differentiation of cross-linked peptides from unmodified ones in proteolytic digests of cross-linked proteins by selective infrared multiphoton dissociation (IRMPD). Only the cross-linked peptides containing the chromogenic phosphate underwent IRMPD and unmodified peptides were not affected by IR irradiation. IRMPD of IRCX-cross-linked peptides yielded uncross-linked y-ion sequence tags of the constituent peptides due to secondary dissociation of all primary product ions which contained the chromophore, thus allowing successful de novo sequencing of the cross-linked peptides. Peptides cross-linked via a two-step conjugation strategy through the formation of a bis-arylhydrazone (BAH) bond were selectively dissociated by ultraviolet radiation at 355 nm. The BAH-cross-linked peptides could be distinguished from not only unmodified peptides but also dead-end modified peptides based on the selectivity of ultraviolet photodissociation. In a complementary approach, electron transfer dissociation of BAH-cross-linked peptides resulted in preferential cleavage of the hydrazone bond which produced two modified peptides. These modified peptides were subsequently interrogated by CID which allowed for the original site of cross-linking to be pinpointed. IRMPD was implemented in a dual pressure linear ion trap to demonstrate successful photodissociation of peptides having modest absorptivities. Peptides were observed to efficiently dissociation by IR irradiation exclusively in the low pressure cell whereas no dissociation was observed in the high pressure cell due to extensive collisional cooling. IRMPD provided greater sequence coverage of the peptides than CID and yielded product ion mass spectra which were predominantly composed of singly charged product ions which simplified spectral interpretation. IRMPD was further applied for the sequencing of small-interfering RNA. Complete sequence coverage was obtained and the results were compared to CID. / text

This thesis describes theoretical and experimental work whose main aim is the development of techniques for using trapped ⁴³Ca⁺ ions for quantum information processing. I present a rate equations model of ⁴³Ca⁺, and compare it with experimental data. The model is then used to investigate and optimise an electron-shelving readout method from a ground-level hyperfine qubit. The process is robust against common experimental imperfections. A shelving fidelity of up to 99.97% is theoretically possible, taking 100 μs. The laser pulse sequence can be greatly simplified for only a small reduction in the fidelity. The simplified method is tested experimentally with fidelities up to 99.8%. The shelving procedure could be applied to other commonly-used species of ion qubit. An entangling two-qubit quantum controlled-phase gate was attempted between a ⁴⁰Ca⁺ and a ⁴³Ca⁺ ion. The experiment did not succeed due to frequent decrystallisation of the ion pair, and strong motional decoherence. The source of the problems was never identified despite significant experimental effort, and the decision was made to suspend the experiments and continue them in an improved ion trap which is under construction. A sequence of pi-pulses, inspired by the Hahn spin-echo, was derived that is capable of greatly reducing dephasing of any qubit. If the qubit precession frequency varies with time as an nth-order polynomial, an (n+1) pulse sequence is theoretically capable of perfectly cancelling the resulting phase error. The sequence is used on a 43Ca+ magnetic-field-sensitive hyperfine qubit, with 20 pulses increasing the coherence time by a factor of 75 compared to an experiment without any spin-echo. In our ambient noise environment the well-known Carr-Purcell-Meiboom-Gill dynamic-decoupling method was found to be comparably effective.

This thesis describes experimental demonstrations of high-fidelity readout of trapped ion quantum bits ("qubits") for quantum information processing. We present direct single-shot measurement of an "optical" qubit stored in a single calcium-40 ion by the process of resonance fluorescence with a fidelity of 99.991(1)% (surpassing the level necessary for fault-tolerant quantum computation). A time-resolved maximum likelihood method is used to discriminate efficiently between the two qubit states based on photon-counting information, even in the presence of qubit decay from one state to the other. It also screens out errors due to cosmic ray events in the detector, a phenomenon investigated in this work. An adaptive method allows the 99.99% level to be reached in 145us average detection time. The readout fidelity is asymmetric: 99.9998% is possible for the "bright" qubit state, while retaining 99.98% for the "dark" state. This asymmetry could be exploited in quantum error correction (by encoding the "no-error" syndrome of the ancilla qubits in the "bright" state), as could the likelihood values computed (which quantify confidence in the measurement outcome). We then extend the work to parallel readout of a four-ion string using a CCD camera and achieve the same 99.99% net fidelity, limited by qubit decay in the 400us exposure time. The behaviour of the camera is characterised by fitting experimental data with a model. The additional readout error due to cross-talk between ion images on the CCD is measured in an experiment designed to remove the effect of qubit decay; a spatial maximum likelihood technique is used to reduce this error to only 0.2(1)x10^{-4} per qubit, despite the presence of ~4% optical cross-talk between neighbouring qubits. Studies of the cross-talk indicate that the readout method would scale with negligible loss of fidelity to parallel readout of ~10,000 qubits with a readout time of ~3us per qubit. Monte-Carlo simulations of the readout process are presented for comparison with experimental data; these are also used to explore the parameter space associated with fluorescence detection and to optimise experimental and analysis parameters. Applications of the analysis methods to readout of other atomic and solid-state qubits are discussed.

Paleoclimatic archives, such as lake sediments, extend our understanding of terrestrial and aquatic ecosystem dynamics in relation to climate variability beyond the period covered by instrumental data. In this context, annually laminated (i.e. varved) lake sediments are particularly valuable, as they offer high temporal resolution and undisturbed sediment. However, in order to extract reliable climate information from lake sediments, a careful calibration with the processes controlling the sediment formation is essential. This thesis combines limnological and paleolimnological data from a varved, boreal lake in northern Sweden (Nylandssjön, Nordingrå) collected over different time scales. The main aim of the thesis is to gain a more refined insight into which processes are reflected in the sedimentary diatom assemblage. More specifically, sequential sediment trap records were coupled with physical, chemical and biological lake monitoring and environmental data for comparison and validation with the varved sediment record. The main result of the thesis is that timing, succession and inter-annual variability of key limnological and environmental processes (e.g. ice-cover duration, lake over-turn or catchment run-off) are of major importance for the sedimentary diatom assemblage formation. Continuous monitoring of physico-chemical parameters over three consecutive years identified varying winter air temperature as a major factor influencing in-lake processes and hence the diatom record. Timing of lake over-turn and catchment run-off seemed to be the driver for monospecific diatom blooms, which are reflected in the annual sediment signal. The integrated annual diatom signal in the sediment was dominated by spring or autumn blooms, resulting either from a Cyclotella glomerata dominated spring bloom after relatively warm winter conditions, or a Asterionella formosa dominated autumn bloom after relatively cold winter conditions. The analysis of the diatom stratigraphy in the varved sediment over several decades corroborated the importance of climatic variables (late winter air temperature and NAO), even though the variables with the most predictive power for variance in the diatom data were associated with sediment composition (C, N and sedimentation rate) and pollution (Pb and Cu). Overall, the analysis of the drivers of inter-annual and decadal diatom assemblage fluctuations emphasizes the importance of winter air temperature, indicating that weather extremes may be disproportionately represented in annual sediment records in contrast to nutrient concentrations or sedimentation rate.

Using a cryogenic linear 22-pole rf ion trap, rate coefficients for H/D exchange reactions of OH− with D2 (1) and OD− with H2 (2) have been measured at temperatures between 11 K and 300 K with normal hydrogen. Below 60 K, we obtained k1 = 5.5 × 10−10 cm3 s−1 for the exoergic reaction (1). Upon increasing the temperature above 60 K, the data decrease with a power law, k1(T) [similar] T−2.7, reaching ≈1 × 10−10 cm3 s−1 at 200 K. This observation is tentatively explained with a decrease of the lifetime of the intermediate complex as well as with the assumption that scrambling of the three hydrogen atoms is restricted by the topology of the potential energy surface. The rate coefficient for the endoergic reaction (2) increases with temperature from 12 K up to 300 K, following the Arrhenius equation, k2 = 7.5 × 10−11 exp(−92 K/T) cm3 s−1 over two orders of magnitude. The fitted activation energy, EA-Exp = 7.9 meV, is in perfect accordance with the endothermicity of 24.0 meV, if one accounts for the thermal population of the rotational states of both reactants. The low mean activation energy in comparison with the enthalpy change in the reaction is mainly due to the rotational energy of 14.7 meV contributed by ortho-H2 (J = 1). Nonetheless, one should not ignore the reactivity of pure para-H2 because, according to our model, it already reaches 43% of that of ortho-H2 at 100 K. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Pollinating insects are important for many plants and for the human population. To be able to monitor pollinators and assess improvements made for them, it is important to get information about pollinator population changes. Therefore, it is essential that the methods used to collect data are accurate (i.e. that they represent the pollinator fauna). One commonly used method is pan-traps, but this method is suggested to be affected by the abundance of surrounding flowers. The results in the present study showed that catches in pan-traps can be affected by flower cover and the colour of the flowers, depending on which colours are preferred by the insects. The effects differed when looking at a larger scale (2-6 ha) and a smaller scale (25 m2) around the pan-traps. When comparing cover of flowers with catches in pan-traps in the small scale there were some results that showed linear positive correlations (expected), but also, negative linear and quadratic correlations. In contrast, in the large scale there were no significant positive linear correlations. When comparing catches in hand-net and pan-traps, only in one out of six taxonomical groups there were a correlation. The results in this study show that catches in pan-traps can be misleading if catches are done to survey pollinator population fauna and the cover of flowers is not considered.

Mounting evidence suggests that large carnivores regulate the abundance and diversity of species at multiple trophic levels through cascading top-down effects. The fear large carnivores inspire in their prey may be a critical component of these top-down effects, buffering lower trophic levels from overconsumption by suppressing large herbivore and mesopredator foraging. However, the evidence that the fear of large carnivores cascades through food webs has been repeatedly challenged because it remains experimentally untested. My collaborators and I exploited a natural experiment – the presence or absence of mesopredator raccoons (Procyon lotor) on islands in the Gulf Islands of British Columbia, Canada – to examine the breadth of mesopredator impacts in a system from which all native large carnivores have been extirpated. By comparing prey abundance on islands with and without raccoons, we found significant negative effects of raccoon presence on terrestrial (songbirds and corvids), intertidal (crabs and fish) and shallow subtidal (red rock crabs Cancer productus) prey, demonstrating that, in the absence of native large carnivores, mesopredator impacts on islands can extend across ecosystem boundaries to affect both terrestrial and marine communities. To test whether fear of large carnivores can mitigate these community-level impacts of mesopredators, we experimentally manipulated fear in free-living raccoon populations using month-long playbacks of large carnivore vocalizations and monitored the effects on raccoon behaviour and the intertidal community. Fear of large carnivores reduced raccoon foraging to the benefit of the raccoon’s prey, which in turn affected a competitor and prey of the raccoon’s prey. By experimentally restoring the fear of large carnivores in our study system, we succeeded in reversing the impacts of raccoons, reinforcing the need to protect large carnivores given the conservation benefits the fear of them provides. Our experimental work demonstrated that fine-scale behavioural changes in prey in response to predation risk can have community-level effects relevant to biodiversity conservation. However, experimentally testing animal responses to predators and other sources of risk in free-living wildlife presents considerable logistical challenges. To address these challenges, my collaborators and I developed an Automated Behavioural Response system, which integrates playback experiments into camera trap studies, allowing researchers to collect experimental data from wildlife populations without requiring the presence of an observer. Here I describe tests of this system in Uganda, Canada and the USA, and discuss novel research opportunities in ecology and conservation biology made available by this new technology. / Graduate

Le comportement des thons tropicaux autour des objets flottants : De l'étude des comportements individuels et collectifs à l'étude du piège écologiqueLes recherches en halieutique ont pour objectif d'améliorer les connaissances sur le fonctionnement des populations de poissons afin de transférer celle-ci vers des outils de gestion. Ce travail de thèse repose sur un ensemble d'expériences et de modélisations destinées à approfondir notre compréhension générale du comportement associatif de poissons grands pélagiques avec des objets flottantes à la surface de l'océan. Notre objectif est de tester si les milliers d'objets flottants artificiels déployés par les pêcheurs (DCP - Dispositifs de Concentration de Poissons) constituent des pièges écologiques pour les thons tropicaux. Pour mener à bien ce travail, nous avons dans le premier chapitre caractérisé le comportement individuel de thons dans un réseau de DCP ancrés. L'analyse de données de marquage acoustique de 96 thons albacores (Thunnus albacares) (30-96 cm) à Hawaii montre que les thons présentent une plasticité comportementale forte face aux DCP qu'ils rencontrent mais également que le temps de résidence sous les DCP diminue avec la taille des individus. Afin de quantifier l'impact de l'augmentation de la densité de DCP il est essentiel de comprendre les mécanismes et les facteurs qui influencent les temps de résidences sous les DCP. Dans le second chapitre, des expériences de choix binaires suggèrent un rôle de la biomasse agrégée dans la formation, la maintenance et la dispersion des agrégations que forment les thons sous les objets flottants. La quantification de la dynamique des arrivées et des départs des poissons aux DCP permettra de valider les hypothèses que nous proposons concernant les mécanismes sociaux sous-jacents d'une part et d'autre part de tester l'influence de la qualité de l'environnement et de la densité de DCP sur les temps de résidences individuels et la distribution spatiale des populations. Dans le troisième chapitre, la comparaison de facteurs de condition de listaos (Katsuwonus pelamis) matures capturés en bancs libres et sous objets flottants dans une zone naturellement riche en objets flottants, et relativement peu impactée par le déploiement de DCP (Le Canal du Mozambique), nous a permis d'établir un point de référence essentiel pour estimer les effets des perturbations actuelles. Plus généralement, les résultats obtenus dans les différents chapitres tendent à conforter l'hypothèse d'un rôle social et non trophique des objets flottants dans l'écologie de thonidés. Les résultats obtenus durant cette thèse amènent à poser un regard nouveau sur l'hypothèse du piège écologique. Notre travail s'est principalement intéressé à un modèle biologique de choix, les thons tropicaux. Cependant le cadre théorique des questions abordées, les outils d'observations et les méthodes d'analyses développées sont assez génériques pour être appliqués aux autres espèces rencontrées sous les objets flottants. Cette recherche s'intègre plus généralement dans les problématiques visant à mieux comprendre les stratégies comportementales et la distribution des populations dans des environnements multi-sites. / Research in fisheries science aims at investigating the functioning of fish population with the objective of using this knowledge to propose sustainable management measures. This PhD thesis relies on a collection of experiments and modelling designed to further our knowledge on the aggregative behaviour of large pelagic fish with floating structures at the surface of the ocean. The overall objective is to test whether the thousands of man-made floating structures deployed by fishermen (also referred as Fish Aggregating Device –FAD) act as ecological traps for tropical tunas. To archive this main objective, it was first necessary to characterize the individual behaviour of tuna in a network of FAD. In the first chapter, the analysis of 96 acoustically tagged yellowfin tuna (Thunnus albacares) between 30-96 cm FL in the array of anchored FADs around Oahu (Hawaii, US) shows that individuals tuna exhibited behavioural plasticity while in the array and that behaviour around FAD is size dependent. In order to assess the impact of the increasing density of FAD, the major habitat modification, it is essential to understand the factors that influence the residence time at FADs. In the second chapter, binary choice experiments suggest that the aggregated biomass under the FAD play a role in the aggregative process. Nonetheless, quantification of arrival and departure dynamics of fish to FAD are required to validate the assumptions we proposed on the underlying social mechanism. Such model would, then, allow testing the effect of FAD density and environmental conditions on individual residence time and spatial distribution of population. In the third chapter, the comparison of skipjack tuna (Katsuwonus pelamis) condition between individual associated with logs and in free swimming schools in the Mozambique Channel, an area known to be naturally enriched with logs with few FADs, highlights the need for estimating reference points prior to assessing the impacts of anthropogenic modifications to habitats on animals.Combining the different chapters, our results tend to favour a social rather than a trophic role of floating objects in the ecology of tunas. More generally, we discuss what novel insight our results bring up on the ecological trap hypothesis. Tropical tunas represent an interesting model species on which we focused. However, the theoretical framework of the questions we addressed, the observation and analytical tools we developed are generic enough to be applied to the others species that are encountered around floating structures. In a broader extent, this work meets the general topic of studying behavioural strategies and distribution of population in multi-patch environment.

The central bank is not able to further ease monetary conditions once it ex- hausts the space for managing short-term policy rate. Then it has to turn its attention to unconventional measures. The thesis provides a discussion about the suitability of different unconventional policy tools in the Czech situation while the foreign exchange (FX) interventions have proven to be the most appropriate choice. A New Keynesian small open economy DSGE model estimated for the Czech Republic is enhanced to model the FX interventions and to compare dif- ferent monetary policy rules at the zero lower bound (ZLB). The thesis provides three main findings. First, the volatility of the real and nominal macroeconomic variables is magnified in the response to the domestic demand shock, the for- eign financial shock and the foreign inflation shock. Second, the volatility of prices decreases significantly if the central bank adopts price-level or exchange rate targeting rule. Third, intervening to fix the nominal exchange rate on some particular target or to correct a misalignment of the real exchange rate from its fundamentals serves as a good stabilizer of prices while intervening to smooth the nominal exchange rate movements increases the overall macroeconomic volatility at the ZLB. 1