A series of rapid, high sensitivity capillary electrophoresis (CE) separation systems have been developed for the analysis of biological analytes and systems. A majority of the work has focused on development of novel instrumentation, in which new injection and detection strategies were investigated to improve the sensitivity of fast CE. A novel optical injection interface for capillary zone electrophoresis based upon the photophysical activation of caged dye attached to the target analyte was developed. The primary advantage of this approach is the lower background and background-associated noise resulting from reduced caged-fluorescein emission in conjunction with the high quantum yield of the resulting fluorescein. Improved detection limits were obtained compared to those observed in photobleaching-based optical gating. A primary drawback of photolytic optical gating CE is the lack of available caged-dye analogs with sufficiently fast reaction kinetics for online derivatization. To overcome this limitation, we have developed a chemical derivatization scheme for primary amines that couples the fast kinetic properties of o-phthaldialdehyde (OPA) with the photophysical properties of visible, high quantum yield, fluorescent dyes. The feasibility of this approach was evaluated by using an OPA/fluorescent thiol reaction, which was used to monitor neurotransmitter mixtures and proteins. The utilization of a high power ultraviolet light emitting diode for fluorescence detection in CE separations has been introduced to analyze a range of environmentally and biologically important compounds, including polyaromatic hydrocarbons and biogenic amines, such as neurotransmitters, amino acids and proteins, that have been derivatized with UV-excited fluorogenic labels. To understand cellular chemistry, it is imperative that single cells should be studied. This work was focused on developing CE based method to characterize the cellular uptake of TAT-EGFP. We demonstrated TAT mediated delivery of EGFP protein into HeLa cells and TAT-EGFP loaded single cell was analyzed by CE-LIF to determine the intracellular EGFP content. An application of CE-LIF for the determination of biogenic amine levels in the antennal lobes of the Manduca sexta is also explored and methods were developed to analyze a single antennal lobe dissected from moths. The lobe was digested and contents were labeled with the fluorogenic dye prior to CZE analysis.

This thesis contains two components of research: studies of supercontinuum pulses generated in the novel microstructure fiber, and research on spatio-temporal coupling in ultrafast laser beams. One of the most exciting developments in optics in recent years has been the invention of the microstructure optical fiber. By controlling the structural parameters of these novel fibers in design and manufacturing, their dispersion profile can be freely tailored, opening up a huge application base. One particularly interesting effect in the microstructure fiber is the generation of ultrabroadband supercontinuum with only nJ-level Ti:sapphire oscillator pulse pump. This supercontinuum is arguably the most complicated ultrafast pulse ever generated, with its huge time-bandwidth product (> 1000 from a 16-cm-long fiber). Although many applications have been demonstrated or envisioned with this continuum, its generation is a very complicated process that is poorly understood, and the characteristics of the continuum pulses are not clearly known. In this work, we make a full-intensity-and-phase measurement of the continuum pulses using cross-correlation frequency-resolved optical gating (XFROG). The results reveal surprising unstable fine spectral structure in the continuum pulses, which is confirmed by single-shot measurements. Our study on the coherence of the continuum, on the other hand, shows that the spectral phase of the supercontinuum is fairly stable. Numerical simulations are carried out whose results are in good agreement with experiments. The second component of this thesis is the study of spatio-temporal coupling in ultrafast beams. We propose two definitions of spatial chirp, point out their respective physical meanings, and derive their relationship. On the common perception of the equivalence between pulse-front tilt and angular dispersion, we show that the equivalence only holds for plane waves. We establish a generalized theory of ultrafast laser beams with first-order spatio-temporal couplings, and discover a new pulse-front tilt effect associated with the combination of spatial chirp and temporal chirp. For the measurement of spatio-temporal distortions, the effects of such distortions in the input beam to a GRENOUILLE trace are carefully studied. An algorithm is proposed and tested to retrieve information about the distortions from the GRENOUILLE trace.

Neurological and neuroendocrine disorders result from signaling dysregulation at the molecular, cellular, and multi-cellular levels. This dissertation presents the development of separation methods, using capillary zone electrophoresis (CZE) and capillary liquid chromatography (CLC), for detecting and quantifying small molecules, peptides, and proteins involved in cellular signaling. CZE is a rapid separation technique, making it ideal for monitoring cellular dynamics with high temporal resolution. An ultraviolet - light emitting diode was used for photolytic optical gating of caged fluorophore-labeled biogenic amines, common functional groups in neurotransmitters. Additionally, a novel caged fluorophore with faster reaction kinetics than commercially available dyes was used to label reduced thiols and primary amines in the presence of o-phthalaldehyde. Together this light source and novel caged dye illustrate the utility of these methods for monitoring chemical dynamics during continuous sampling. Many cellular second messengers, including inositol phosphates, are known to exist within the cell, but their dynamics and intermolecular interactions are poorly understood since they lack chromophores or electroactive functional groups making direct detection difficult. Utilizing CZE with capacitive coupled contactless conductivity detection (C4D), biological phosphates were separated and detected based on their high anionic charge, suggesting the utility of C4D in label-free detection of biological molecules. The techniques described above require higher sensitivity to monitor physiologically relevant analyte concentrations; therefore, Hadamard transform capillary electrophoresis (HTCE) was used as a multiplexing method in which multiple separations were performed simultaneously. HTCE resulted in increased sensitivity by decreasing the random background noise. Peptides and proteins propagate signals within or between cells; yet, they are difficult to separate and detect by CZE since their highly charged surfaces result in non-specific adsorption to the capillary wall. To minimize these interactions, stable hybrid phospholipid bilayers were prepared as capillary coatings for CZE separations of cationic proteins. Additionally, stabilized phospholipid bilayer coatings were formed on silica particles through redox polymerization of synthetic, polymerizable lipids. These bilayers were stable after exposure to surfactant, organic solvents, and after storage for one month, suggesting their value as lipid chromatography stationary phases for future incorporation of transmembrane proteins to analyze binding interactions with small molecules.

Les peignes de longueurs d'onde, produisant des dizaines de porteuses optiques régulièrement espacées à partir d'une seule source laser, présentent un grand intérêt pour les systèmes de communication à haut débit. Ce travail de thèse porte sur les peignes générés par les diodes laser à blocage de modes basées sur des nanostructures semi-conductrices à basse dimensionnalité. Dans cette étude, les performances en verrouillage de modes de lasers Fabry-Pérot mono-section basés sur différents systèmes de matériaux sont comparées sur la base de la largeur du spectre optique d'émission et de la capacité à produire des impulsions courtes à faible gigue temporelle. En remarquant que les lasers à base de bâtonnets quantiques InAs sur InP présentent de meilleures caractéristiques par rapport aux autres matériaux examinés, leurs propriétés spécifiques en termes de stabilité des peignes de fréquences optiques et de chirp des impulsions sont étudiées plus en détail. Le chirp est d'abord étudié par la technique FROG (frequency-resolved optical gating). Ensuite, la dispersion chromatique du matériau laser est évaluée afin de vérifier si elle peut expliquer les grandes valeurs de chirp mesurées par FROG. Pour cela la technique de réflectométrie optique dans le domaine fréquentiel est utilisée et ses capacités uniques de mesure ont été étudiées et validées. Enfin, ces lasers sont employés avec succès pour les transmissions haut débit à l'aide de la technique de modulation optique OFDM (orthogonal frequency-division multiplexing) en détection directe. Débits de l'ordre du térabit par seconde, ainsi que le faible coût de l’architecture du système, sont très prometteurs pour les data centers / Optical frequency combs, generating tens of equally spaced optical carriers from a single laser source, are very attractive for next-generation wavelength division multiplexing (WDM) communication systems. This PhD thesis presents a study on the optical frequency combs generated by mode-locked laser diodes based on low-dimensional semiconductor nanostructures. In this work, the mode-locking performances of single-section Fabry-Pérot lasers based on different material systems are compared on the basis of the optical spectrum width, the timing jitter and pulse generation capabilities. Then, noticing that InAs quantum dashes grown on InP exhibit on average better characteristics than other examined materials, their unique properties in terms of comb stability and pulse chirp are studied in more detail. Laser chirp, in particular, is first investigated by frequency resolved optical gating (FROG) characterizations. Then, chromatic dispersion of the laser material is assessed in order to verify whether it can account for the large chirp values measured by FROG. For that, a high sensitivity optical frequency-domain reflectometry setup is used and its measurement capabilities are extensively studied and validated. Finally, the combs generated by quantum dash mode-locked lasers are successfully employed for high data rate transmissions using direct-detection optical orthogonal frequency division multiplexing. Terabit per second capacities, as well as the low cost of this system architecture, appear to be particularly promising for future datacom applications

We demonstrate four experimentally simple methods for measuring very complex ultrashort light pulses. Although each method is comprised of only a few optical elements, they permit the measurement of extremely complex pulses with time-bandwidth products greater than 65,000. First, we demonstrate an extremely simple frequency-resolved-optical gating (GRENOUILLE) device for measuring the intensity and phase of pulses up to ~20ps in length. In order to achieve the required high spectral resolution and large temporal range, it uses a few-cm-thick second harmonic-generation crystal in the shape of a pentagon. This has the additional advantage of reducing the device's total number of components to three. Secondly, we introduce a variation of spectral interferometry (SI) using a virtually imaged phased array and grating spectrometer for measuring long complex ultrashort pulses up to 80 ps in length. Next, we introduce a SI technique for measuring the complete intensity and phase of relatively long and very complex ultrashort pulses. It involves making multiple measurements using SI (in its SEA TADPOLE variation) at numerous delays, measuring many temporal pulselets within the pulse, and concatenating the resulting pulselets. Its spectral resolution is the inverse delay range--many times higher than that of the spectrometer used. The waveforms were measured with ~ fs temporal resolution over a temporal range of ~ns and had time-bandwidth products exceeding 65,000, which to our knowledge is the largest time-bandwidth product ever measured with ~fs temporal resolution. Finally, we demonstrate a single-shot measurement technique that temporally interleaves hundreds of measurements with ~fs temporal resolution. It is another variation of SI for measuring the complete intensity and phase of relatively long and complex ultrashort pulses in a single shot. It uses a grating to introduce a transverse time delay into a reference pulse which gates the unknown pulse by interfering it at the image plane of an imaging spectrometer. It provided ~125 fs temporal resolution and a temporal range of 70 ps using a low-resolution spectrometer.