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This dissertation presents and explores a technique to confine and manipulate single and multiple nano-objects in solution by exploiting the thermophoretic interactions with local temperature gradients. The method named thermophoretic trap uses an all-optically controlled heating via plasmonic absorption by a gold nano-structure designed for this purpose. The dissipation of absorbed laser light to thermal energy generates a localized temperature field. The spatial localization of the heat source thereby leads to strong temperature gradients that are used to drive a particle or molecule into a desired direction. The behavior of nano-objects confined by thermal inhomogeneities is explored experimentally as well as theoretically. The monograph treats three major experimental stages of development, which essentially differ in the way the heating laser beam is shaped and controlled. In a first generation, a static heating of an appropriate gold structure is used to induce a steady temperature profile that exhibits a local minimum in which particles can be confined. This simple realization illustrates the working principle best. In a second step, the static heating is replaced. A focused laser beam is used to heat a smaller spatial region. In order to confine a particle, the beam is steered in circles along a circular gold structure. The trapping dynamics are studied in detail and reveal similarities to the well-established Paul trap. The largest part of the thesis is dedicated to the third generation of the trap. While the hardware is identical to the second generation, using the real-time information on the position of the trapped object to heat only particular sites of the gold structure strongly increases the efficiency of the trap compared to the earlier versions. Beyond that, the optical feedback control allows for an active shaping of the effective virtual trapping potential by applying modified feedback rules, including e.g. a double-well or a box-like potential. This transforms the formerly pure trapping device to a versatile technique for micro and nano-fluidic manipulation. The physical and technical contributions to the limits of the method are explored. Finally, the feasibility of trapping single macro-molecules is demonstrated by the confinement of lambda-DNA for extended time periods over which the molecules center-of-mass motion as well as its conformational dynamics can be studied.

The tropical forests of Indochina harbor a suite of globally threatened tropical mammal species. These species are difficult to detect, and subsequently understudied. Noninvasive camera trapping was used to survey terrestrial mammals from a protected area in southeastern Lao PDR (Xe Sap National Protected Area). The presence-absence of four mammals (mainland serow Capricornis milneedwardsii, muntjac Muntiacus spp., macaque Macaca spp., and wild pig Sus scrofa) was modeled in an occupancy framework thereby accounting for detection probabilities. Our goals were to establish baseline occupancy data to assist with biological monitoring and to better understand the factors influencing the distribution of the target species. Naïve occupancy, or the proportion of sites at which the target species was detected, was 0.58 for muntjac, 0.55 for macaque, 0.38 for wild pig, and 0.30 for serow. True occupancy estimates (Ψ ± SE) from top-ranked models was 0.79 ± 0.21 for macaque, 0.74 ± 0.13 for muntjac, 0.51 ± 0.13 for wild pig, and 0.48 ± 0.18 for serow. The results underscore the importance of accounting for imperfect detection rates when studying rare or elusive species. I included two site covariates (forest type and distance to nearest village) in the occupancy models. Estimating occupancy as a function of site covariates improved model performance and provided insight into landscape-level factors that affect species occurrence. In the top-ranked models, serow occupancy was higher in hill evergreen forest (HEGF) than semi-evergreen forest (SEGF). Muntjac occupancy was higher in areas further from villages. Macaque occupancy was higher in areas closer to villages. Wild pig occupancy was higher in areas further from villages and in HEGF. I recommend using an occupancy framework to analyze occurrence data for difficult-to-study tropical mammal species. The results highlight the importance of Xe Sap NPA for large mammal conservation in the region. / text

Application of precision laser spectroscopy and optical clock technology to the ground and metastable, first excited state of the ²²⁹Th nucleus at < 10 eV has significant potential for use in optical frequency metrology and tests of variation of fundamental constants. This work is a report on the development of required technologies to realize such a nuclear optical clock with a single, trapped, laser cooled ²²⁹Th³⁺ ion. Creation, trapping, laser cooling, and precision spectroscopy are developed and refined first with the naturally occurring isotope, ²³²Th. These technologies are then extended to laser cooling and precision laser spectroscopy of the electronic structure of ²²⁹Th³⁺. An efficient optical excitation search protocol to directly observe this transition via the electron bridge is proposed. The extraordinarily small systematic clock shifts are estimated and the likely extraordinarily large sensitivity of the clock to variation of the fine structure constant is discussed.

Nanoaperture optical tweezers are emerging as useful tools for the detection and identification of biological molecules and their interactions at the single molecule level. Nanoaperture optical tweezers provide a low-cost, scalable, straight-forward, high-speed platform for single molecule studies without the need to use tethers or labeling. This thesis gives a general description of conventional optical tweezers and how they are limited in terms of their capability to trapping biological molecules. It also looks at nanoaperture-based optical tweezers which have been suggested to overcome the limitations of conventional optical tweezers. The thesis then focuses on the double nanohole optical tweezer as a tool for trapping biological molecules and studying their behaviour and interactions with other molecules. The double nanohole aperture trap integrated with microfluidic channels has been used to detect single protein binding. In that experiment a double-syringe pump was used to deliver biotin-coated polystyrene particles to the double nanohole trapping site. Once stable trapping of biotin-coated polystyrene particle was achieved, the double-syringe pump was used to flow in streptavidin solution to the trapping site and binding was detected by measuring the transmission through the double nanohole aperture. In addition, the double nanohole optical tweezer has been used to observe the real-time dynamic variations in protein-small molecule interaction (PSMI) with the primary focus on the effect of single and multiple binding events on the dynamics of the protein in the trap. Time traces of the bare form of the streptavidin showed slower timescale dynamics as compared to the biotinylated forms of the protein. Furthermore, the double nanohole aperture tweezer has been used to study the real-time binding kinetics of PSMIs and to determine their disassociation constants. The interaction of blood protein human serum albumin (HSA) with tolbutamide and phenytoin was considered in that study. The dissociation constants of the interaction of HSA with tolbutamide and phenytoin obtained using our technique were in good agreement with the values reported in the literature. These results would open up new windows for studying real-time binding kinetics of protein-small molecule interactions in a label-free, free-solution environment, which will be of interest to future studies including drug discovery. / Graduate

Calcium (Ca2+)/calmodulin-dependent kinase 2 (CaMK-II) is one member of a family of Ca2+/calmodulin-dependent protein kinases that responds to intracellular Ca2+ signals (Hudmon, A. and H. Schulman (2002)). CaMK-II is a multifunctional regulator of transcription, cell cycle progression, cell motility and neuronal development. (Wang, C., et al. (2008), Easley, C. A. IV, et al. (2008), Osterhoff, M., et al. (2003), Faison, M. O., et al. (2002)). Recently, CaMK-II has been shown to be important in the early development of vertebrates. In developing zebrafish, disruption of CaMK-II expression has been shown to induce phenotypes similar to those documented in several human diseases. The identification of the tissue-specific binding partners and substrates of CaMK-II which are responsible for specific developmental fates remains a key step in understanding this important protein kinase family. In this thesis research, specific “substrate-trapping” mutants of CaMK-II were designed, introduced into a variety of rodent and human cell lines in culture and used in conjunction with tandem mass spectrometry to identify binding partners, such as β-actin, tropomodulin-3 and Fli-I as well as novel, putative substrates, such as the tumor suppressor protein 53 (p53). This approach was subsequently applied to zebrafish embryos where an overlapping subset of CaMK-II binding proteins to those found in mammalian cell culture were identified. This project represents one of the first studies to identify binding proteins in zebrafish embryos using epitope tagging and mass spectrometry. This research has also established a technical framework for the use of mass spectrometry to characterize the developmental proteome of whole zebrafish embryos or specific zebrafish tissues at any developmental time point.

La sensibilité à l’hydrogène d’un acier de type S690QL a été étudiée par une approche locale de la rupture. Des essais de fatigue ont été réalisés à l’air et en milieu salin sous protection cathodique sur des éprouvettes micro-entaillées. La fissure a été contrôlée en cours d’essai par une méthode de suivi électrique. La réponse mécanique du matériau en avant de l’entaille a été simulée par calculs par éléments finis.Les mécanismes de fatigue ont été étudiés par une méthode permettant d’isoler une contrainte interne et deux composantes de la contrainte effective, activée et non-activée thermiquement. L’effet de l’hydrogène sur ces contraintes a également été étudié.Pour comprendre le phénomène de piégeage de l’hydrogène dans la microstructure de cet acier, des tests de perméation électrochimique et de désorption thermique ont été réalisés. Les paramètres expérimentaux ainsi déterminés sont utilisés dans un modèle phénoménologique de la diffusion. Il a été développé pour simuler la répartition locale de l’hydrogène sur des géométries complexes.Les résultats montrent une forte dépendance de l’amorçage de la fissure avec l’accumulation de déformation plastique. Pour les essais de fatigue réalisés sur les éprouvettes entaillées, il ressort que le piégeage dans le champ élastique des dislocations est le phénomène prépondérant dans le mécanisme de fragilisation. Dans le cas d’éprouvettes lisses sollicitées en fatigue oligocyclique, le piégeage dans les murs de cellules de dislocations est majoritaire et l’amorçage de la fissure est certainement localisé sur ces défauts. L’hydrogène affecte également les deux composantes, thermique et athermique, de la contrainte effective. / The sensitivity to hydrogen embrittlement of S690QL steels is studied by local approach to fracture. Fatigue tests in air and in saline solution under cathodic protection are performed on micro-notched specimens. Crack is monitored by direct current potential drop method. The mechanical response of the material at the notch-tip is simulated by finite elements calculations.Fatigue mechanisms are investigated by a decomposition method of the flow stress to extract internal stress and the thermal and athermal components of the effective stress. Hydrogen effects on these stresses are also studied.Hydrogen trapping in the microstructure is investigated using electrochemical permeation tests and thermal desorption spectrometry. A phenomenological model is developed thanks to experimental results. This model is able to simulate the local hydrogen concentration in samples with complex geometry.Our results show that crack initiation is highly dependent on the plastic strain accumulation. For fatigue tests on micro-notched specimens, hydrogen trapping in dislocations elastic field is the predominant phenomena in the embrittlement mechanism. For smooth specimens under low cycle fatigue testing, hydrogen trapping in dislocations cells walls is significant and crack initiation is probably localized in this microstructural defect. Both components of the effective stress are also influenced by hydrogen.

Arthur Ashkin's Nobel Prize-winning single-beam gradient force optical tweezers have revolutionized research in many fields of science. The invention has enabled various atomic and single molecular studies, proving to be an essential tool for observing and understanding nature at the nanoscale. This thesis showcases the uniqueness of single-beam gradient force traps and the advances necessary to overcome the limitations inherent in conventional techniques of optical trapping. With decreasing particle sizes, the power required for a stable trap increases and could potentially damage a particle. This is a significant limitation for studying biomolecules using conventional optical traps. Plasmonic nanoaperture optical trapping using double-nanohole apertures is introduced as a solution to overcoming these limitations. Achievements in double-nanohole optical trapping made possible by the pioneering work of Gordon et. al are highlighted as well. This thesis focuses on the advances in nanoaperture fabrication methods and improvements to experimental techniques adopted in single molecular optical trapping studies. The technique of colloidal lithography is discussed as a cost-effective high-throughput alternative method for nanofabrication. The limitation in using this technique for producing double-nanohole apertures with feature sizes essential for optical trapping is analyzed. Improvements to enable tuning of aperture diameter and cusp separation is one of the main achievements of the work detailed in this thesis. Furthermore, the thesis explains the modified fabrication process tailor-made for designing double-nanohole apertures optimized for optical trapping. Transmission characterization of various apertures fabricated using colloidal lithography is carried out experimentally and estimated by computational electrodynamics simulations using the finite-difference time-domain (FDTD) method. Optical trapping with double-nanohole apertures fabricated using colloidal lithography is demonstrated with distinct results revealing trapping of a single polystyrene molecule, a rubisco enzyme and a bovine serum albumin (BSA) protein. / Graduate

Diminuer l'épaisseur de la couche d'absorbeur est une solution attractive pour produire des cellules photovoltaïques à coût réduit. Cela permet également de réduire la quantité de matériau actif utilisé ainsi que d'améliorer la collection du courant dans la cellule. Cette thèse s'est focalisée sur la conception de nanostructures pour exalter l'absorption de la lumière dans des couches de semiconducteur d'épaisseur réduite et ainsi proposer des cellules ultraminces efficaces.Dans un premier temps, nous avons proposé une approche originale pour piéger la lumière dans une cellule ultra-fine (≤ 100 nm) en silicium amorphe. Un réseau métallique est placé en face avant de la cellule déposée sur un miroir métallique afin d'obtenir une absorption multi-résonante large bande pour les deux polarisations de la lumière. Nous proposons aussi d'utiliser le réseau métallique comme une électrode transparente alternative afin de réduire les pertes optiques dans le contact avant de la cellule. Une analyse numérique approfondie des mécanismes résonants en jeu a été menée ainsi que la fabrication et la caractérisation optique de démonstrateurs.Dans un deuxième temps, nous avons appliqué ce concept de contact avant multi-résonant à des couches ultra-fines en arsenure de gallium (GaAs). Nous avons montré numériquement et expérimentalement le potentiel d'une nanogrille métallique bi-dimensionnelle pour le confinement efficace de la lumière dans 25 nm de GaAs.Enfin, nous avons étudié la possibilité de réduire l'épaisseur de cellules en silicium cristallin d'un facteur 10 à 100 par rapport à l'état de l'art. Nous avons développé un procédé pour transférer des couches de silicium cristallin de quelques microns d'épaisseur épitaxiées par PECVD sur un substrat hôte bas coût. Nous avons également travaillé à la structuration contrôlée de nanopyramides en vue d'un piégeage optique efficace dans ces couches minces. / Reducing the absorber thickness is an attractive solution to decrease the production cost of solar cells. Furthermore, it allows to reduce the amount of material needed and improve the current collection in the cell. This thesis has been focused on the design of nanostructures to enhance light absorption in very small semiconductor volumes in order to achieve efficient ultra-thin solar cells. First, we have proposed an original light-trapping concept for ultra-thin amorphous silicon (a-Si:H) solar cells. A one-dimensional metallic grating is patterned on the front surface of the cell deposited on a metallic mirror. Broadband multi-resonant absorption has been demonstrated for both light polarizations. The metallic grating is also used as an alternative transparent electrode in order to reduce optical losses in the front contact. A detailed analysis of the multi-resonant absorption mechanism has been carried out through numerical calculations. The fabrication and optical characterization of ultra-thin a-Si:H solar cells with metallic gratings have validated the multi-resonant approach.Second, we have proposed a design with a two-dimensional metallic grid as a resonant front contact for very thin (25 nm) gallium arsenide (GaAs) layers. We have shown through the design and fabrication of a proof-of-concept structure the potential of metallic nanogrids to confine efficiently light absorption with an ultra-thin GaAs layer.Finally, advanced light-trapping structures could also allow a thickness reduction of crystalline silicon wafers of a factor 20 to 100 with respect to state-of-the-art cells. We have developed a process to transfer micron-thick epitaxial crystalline silicon (c-Si) layers onto a low-cost host substrate. Inverted nanopyramids have also been fabricated in crystalline silicon in order to achieve a broadband anti-reflection effect. It opens promising perspectives towards the realization of double-sided nanopatterned ultra-thin c-Si cells.