An apparatus that combines single molecule fluorescence, optical trapping and bright-field microscopy is presented. Given the spread over orders of magnitude of the light intensities for the different techniques, special considerations in choosing the spectral regions for each were taken. Moreover, imaging single molecules in a background of intense light from the infra red laser used for the optical trap has been shown to result in enhanced photo-bleaching due to two-photon processes. A scheme for fast time-sharing was implemented in which the fluorescence excitation light and the trap light alternate in fast succession. This eliminates two-photon effects and enables stable manipulation using the optical trap. The simultaneous use of the bright-field imaging in differential interference contrast arrangement enables observation of refractile objects in the sample over large distances. The apparatus was designed for future use in studies of molecular motor regulation. However, to demonstrate the functionality of the system, the rotational diffusion of a micro-sphere fluorescently labelled at one spot was measured. / text

This thesis describes the advances made towards a dual-species magneto-optical trap (MOT) of Li and Rb for use in photoassociation spectroscopy, Feshbach resonance studies, and, as long-term aspirations, the formation of ultracold heteronuclear polar molecules. The initial discussion will focus on a brief theoretical overview of laser cooling and trapping and the production of ultracold molecules from a cold atom source. Subsequently, details of the experimental system, including those pertaining to the required laser light, the vacuum chamber, and the computer control system will be presented. Finally, preliminary optimization and characterization measurements showing the performance of a single species Li MOT are introduced. These measurements demonstrated the loading of over 8 x 107 Li atoms directly into a MOT without the need for a Zeeman slower.

This thesis describes the advances made towards a dual-species magneto-optical trap (MOT) of Li and Rb for use in photoassociation spectroscopy, Feshbach resonance studies, and, as long-term aspirations, the formation of ultracold heteronuclear polar molecules. The initial discussion will focus on a brief theoretical overview of laser cooling and trapping and the production of ultracold molecules from a cold atom source. Subsequently, details of the experimental system, including those pertaining to the required laser light, the vacuum chamber, and the computer control system will be presented. Finally, preliminary optimization and characterization measurements showing the performance of a single species Li MOT are introduced. These measurements demonstrated the loading of over 8 x 107 Li atoms directly into a MOT without the need for a Zeeman slower.

Casimir and Casimir-Polder effects are forces between electrically neutral bodies and particles in vacuum, arising entirely from quantum fluctuations. The modification to the vacuum electromagnetic-field modes imposed by the presence of any particle or surface can result in these mechanical forces, which are often the dominant interaction at small separations. These effects play an increasingly critical role in the operation of micro- and nano-mechanical systems as well as miniaturized atomic traps for precision sensors and quantum-information devices. Despite their fundamental importance, calculations present theoretical and numeric challenges, and precise atom-surface potential measurements are lacking in many geometric and distance regimes. The spectroscopic measurement of Casimir-Polder-induced energy level shifts in optical-lattice trapped atoms offers a new experimental method to probe atom-surface interactions. Strontium, the current front-runner among optical frequency metrology systems, has demonstrated characteristics ideal for such precision measurements. An alkaline earth atom possessing ultra-narrow intercombination transitions, strontium can be loaded into an optical lattice at the “magic” wavelength where the probe transition is unperturbed by the trap light. Translation of the lattice will permit controlled transport of tightly-confined atomic samples to well-calibrated atom- surface separations, while optical transition shifts serve as a direct probe of the Casimir-Polder potential. We have constructed a strontium magneto-optical trap (MOT) for future Casimir-Polder experiments. This thesis will describe the strontium apparatus, initial trap performance, and some details of the proposed measurement procedure.

This thesis describes the advances made towards a dual-species magneto-optical trap (MOT) of Li and Rb for use in photoassociation spectroscopy, Feshbach resonance studies, and, as long-term aspirations, the formation of ultracold heteronuclear polar molecules. The initial discussion will focus on a brief theoretical overview of laser cooling and trapping and the production of ultracold molecules from a cold atom source. Subsequently, details of the experimental system, including those pertaining to the required laser light, the vacuum chamber, and the computer control system will be presented. Finally, preliminary optimization and characterization measurements showing the performance of a single species Li MOT are introduced. These measurements demonstrated the loading of over 8 x 107 Li atoms directly into a MOT without the need for a Zeeman slower. / Science, Faculty of / Physics and Astronomy, Department of / Graduate

L’ADN et l’ARN double brin (ADNdb, ARNdb) subissent des transitions de surétirement avec des forces d’environ 60 pN. Nous effectuons des mesures de force à l'aide d'un piège optique à double faisceau contenant deux billes reliées par une seule molécule. Un brin du duplex est attaché aux deux extrémités aux deux billes, tandis que l’autre brin n’est attaché qu’à une seule extrémité. Quatre cas différents sont comparés: ADNdb, ARNdb, hybride ARN- ADN avec ADN sous tension et hybride ADN- ARN avec ARN sous tension.Un surétirement se produit pour les quatre duplex. La différence la plus remarquable est que les ARNdb présentent un plateau lisse, alors que les autres duplex présentent des motifs en dents de scie. Nous constatons que les ARNdb s'étirent par un mécanisme différent et expliquons pourquoi cette propriété pourrait aider les structures d'ARN à s'assembler et à jouer leurs rôles biologiques.Un surétirement de l'hybride ARN-ADN libère progressivement un brin d'ARN. Les structures formées au sein de cet ARN naissant sont visibles dans le signal de force lors du re- recuit. Pour la première fois à notre connaissance, nous imitons donc et étudions le repliement de l'ARN co-transcriptionnel dans un test in vitro. En se concentrant sur le stade précoce de l’assemblage des grandes sous- unités ribosomales de E. coli (domaines I-II de l’ARNr 23S et des protéines r L4, L13, L20, L22, L24), on observe plus souvent un recuit partiel avec les protéines r. Nos résultats indiquent que les cinq protéines r de liaison précoce agissent comme des auxiliaires de repliement bien avant que l’ARN 23S complet ne soit transcrit. / Double-stranded DNA and RNA (dsDNA, dsRNA) undergo overstretching transitions at forces around 60 pN. We perform force measurements using a dual-beam optical trap that holds two beads linked by a single molecule. One strand of the duplex is attached at both extremities to the beads, while the other strand is attached only at one extremity. Four different cases are compared: dsDNA, dsRNA, RNA-DNA hybrid with DNA under tension, and DNA-RNA hybrid with RNA under tension. Overstretching occurs for all four duplexes. The most remarkable difference is that dsRNA exhibits a smooth plateau, while the other duplexes show saw-tooth patterns. We find that dsRNA overstretches by a different mechanism and explain why this property could help RNA structures to assemble and play their biological roles.Overstretching the RNA-DNA hybrid progressively liberates an RNA strand. Structures formed within this nascent RNA are seen in the force signal upon re-annealing. For the first time to our knowledge, we thus mimic and study co-transcriptional RNA folding in an in-vitro assay. Focusing on the early stage of E.coli large ribosomal subunit assembly (domains I-II of 23S rRNA and r-proteins L4, L13, L20, L22, L24), partial re-annealing is observed more frequently with r-proteins than without. Our results indicate that the five early- binding r-proteins act as folding helpers well before the entire 23S RNA is transcribed.

This thesis provides a summary of the laser system constructed in the Quantum Degenerate Gases Laboratory for laser cooling and trapping of 85/87Rband 6Li as well as of experiments that have been pursued in our lab to date. The first chapter provides an overview of the experimental focus of the QDG lab. The second and third chapters provide the fundamental theory behind laser cooling and trapping. The fourth chapter provides details of the laser system. The fifth chapter describes an experiment performed on the subject of dual-injection, performed in collaboration with Dr. James Booth of the British Columbia Institute of Technology (BCIT) involving the dual-injection of a single slave amplifier. The last chapter describes the progress made on the experimental setup needed for the study of Feshbach resonances between 85/87Rb and 6Li and the photoassociative formation of molecules.

This research presents the development of an advanced, state-of-the-art optical trap for use in biological materials and nanosystems investigation. An optical trap is an instrument capable of manipulating microscopic particles using the inherent momentum of light. First introduced by Askin et al., the single beam gradient optical trap is capable of generating small forces (~1-100 pN) in a noninvasive manner. As a result, the optical trap is often used to manipulate biological specimen. This research presents the process for the construction of a custom optical trap, the methods to build a controllable optical trap through a traditional fixed gain controller as well as an adaptive controller, and also enables the application of torque to trapped particles. A method of using adaptive techniques for system identification and calibration is also presented. This research has the potential to use forces and torques to affect our understanding of the mechanics of single molecules and motor proteins. This instrument provides a more precise means of manipulating biological specimen as well as a tool for nanofabrication and has the potential to expand the knowledge base of DNA, chromosomes, biomotors, motor proteins, reversible polymers, and can be used to control chemical reactions. The research presented here documents the creation of an optical trap that is sensitive for applications requiring precise displacements and forces, adaptable to a variety of current and future research applications, and useable by anyone interested in researching micro- and nanosytems. / Dissertation

Laser beams with precisely controlled intensity profiles are essential for many areas. We developed a beam shaping system based on the digital micromirror device (DMD) for ultra-cold atom experiments and other potential applications. The binary DMD pattern was first designed by the error diffusion algorithm based on an accurate measurement of the quasi-Gaussian incident beam from a real-world laser. The DMD pattern was projected to the image plane by a bandwidth-limited 4f telescope that converted this pattern to the grayscale image. The system bandwidth determined the theoretical limit of image precision by the digitization error. In addition, it controlled the spatial shape of the point spread function (PSF) that reflected the tradeoff between image precision and spatial resolution. PSF was used as a non-orthogonal basis set for iterative pattern refinement to seek the best possible system performance. This feedback process, along with stable performance of DMD, the blue-noise spectrum of the error diffusion algorithm, and low-pass filtering, guaranteed high-precision beam shaping performance. This system was used to produce various beam profiles for different spatial frequency spectra. First, we demonstrated high-precision slowly-varying intensity beam profiles with an unprecedented high intensity accuracy. For flattop and linearly-tilted flattop beams, we achieved 0.20-0.34% root-mean-square (RMS) error over the entire measurement region. Second, two-dimensional sinusoidal-flattop beams were used to evaluate image precision versus system bandwidth. System evaluation confirmed that this system was capable of producing any spatial pattern with <3% RMS error for the most system bandwidth. This experiment extended the beam shaping to any system bandwidth and provided a reference to estimate the output image quality based on its spatial spectrum. Later experiment using a Lena-flattop beam profile demonstrated the arbitrary beam profile generation. We implemented this system for applications on the homogenous optical lattice and dynamic optical trap generation. The DMD pattern was optimized by the iterative refinement process at the image feedback arm, and projected through a two-stage imaging system to form the desired beam profile at the working plane. Experiments demonstrated a high-precision beam shaping as well as a fast and dynamic control of the generated beam profile. / text

No description available.