The mid-infrared (MIR) system presented in the thesis is based on a sub-100-fs erbium-doped fiber laser operating at 1.55 µm. The output of the laser is split in two, each arm seeding an erbium-doped fiber amplifier. The output of the first amplifier is sent to a grating-based stretcher to be stretched to 50 ps before seeding the optical parametric chirped-pulse amplifier (OPCPA). The output of the second amplifier is coupled to a highly nonlinear fiber to generate the 1 µm needed to seed the a neodymium-doped yttrium lithium fluoride (Nd:YLF) system. This work represents the first time this synchronization scheme is used, and the timing jitter between the two arms at the OPCPA is reduced to 333 fs. The pump laser for the OPCPA is a regenerative amplifier producing 1.6 W followed by a double-pass amplifier, for a final output power of 2.5 W at 1 kHz. Etalons were inserted into the cavity of the regenerative amplifier to stretch the pulses to 50 ps The OPCPA consists of two potassium titanyl arsenate crystals in a noncollinear configuration. With three passes, the gain is 3.8 · 10 6 . Using a grating compressor, the pulse duration is reduced to 140 fs, with a power of 300 mW. Because of the reduction of the timing jitter, the amplitude stability is 1 %, which is a great improvement compare to existing systems. To generate ultrafast light in the MIR, an optical parametric amplifier is used, pumped ii by the output of the OPCPA and seeded with its 3-µm idler. Two crystals were tested, both in a single-pass configuration. For the first crystal, a 4-mm thick silver thiogallate, an efficiency of 7.4 % was reached, with 8.76 mW in the signal and 7.2 mW in the idler. For the second crystal, a 2-mm thick lithium gallium selenide, the efficiency was higher, reaching 10.8 %. The power for the signal was 11.5 mW, and for the idler, 11.11 mW. Using this new scheme, energies on par with current systems are achieved with much higher efficiencies.

Introduction: Currently, there are no objective techniques to assess burn depth. An early assessment of burn depth would enable accurate management decisions, which would improve patient outcomes. Near infrared (NIR) technology has shown promise as a non-invasive monitor of oxygenation and perfusion, and its potential to assess the depth of burn injuries has been investigated clinically over the past five years. The purpose of the thesis was to determine the capacity of NIR technology to differentiate acute thermal injuries. Methods: Burn sites (n=5) and control sites (n=5) were created on the dorsum of sixteen animals with brass rods held at constant pressure and heated to 100°C and 37.5°C respectively. NIR data was collected from the burns and control sites pre-burn, immediately post-burn, and 1, 12, 24, 36, 48 and 96 hours after the burn injury. Biopsies of the burn and control sites were acquired at each time point and used to confirm the depth of injury. NIR data was processed for the content of water, oxy-, deoxy- and methemoglobin. Results: Oxyhemoglobin and total hemoglobin decreased as burn depth increased. The proportion of oxy- and deoxyhemoglobin to total hemoglobin showed that the ratio of oxy- to deoxyhemoglobin decreased as burn injury increased. Methemoglobin levels as a ratio of total hemoglobin also showed that as the severity of injury increased the proportion of methemoglobin also increased. Finally, superficial partial thickness injuries (3 s and 12 s) showed early peak levels of water, which rapidly declined towards baseline. The deep partial thickness injuries (20 s and 30 s) do not experience peak levels and retain water over the course of the experiment. The full thickness injuries water levels remain close or below baseline levels throughout the experiment. Conclusion: NIR spectroscopy could distinguish burn depth using water, oxy-, met- and total hemoglobin as separate entities. The presence of methemoglobin in the burn wounds is a novel finding that has not been described previously in burn literature.

The study and applications of surface plasmon polaritons (SP) – also known as plasmonics – has attracted the interest of a wide range of researchers in various fields such as biology, physics, and engineering. Unfortunately, the large propagation losses of the SP severely limit the usefulness of plasmonics for many practical applications. In this dissertation a new wave guiding mechanism is proposed in order to address the large propagation losses of the plasmonic guides. Possible applications of this guiding scheme are also investigated. The proposed hybrid plasmonic waveguide (HPWG) consists of a metal layer separated from a high index slab by a low index spacer. A detailed analysis is carried out to clarify the wave guiding mechanism and it is established that the mode guided by the HPWG results from the coupling of a SP mode and a dielectric waveguide mode. A two dimensional HPWG is proposed and the effects of various parameters on the HPWG performance are analyzed in detail. This structure offers the possibility of integrating plasmonic devices on a silicon platform. The proposed waveguide supports two different modes: a hybrid TM mode and a conventional TE mode. The hybrid TM mode is concentrated in the low index layer, whereas the conventional TE mode is concentrated in the high index region. This polarization diversity is used to design a TM- and a TE-pass polarizer and a polarization independent coupler on a silicon-on-insulator (SOI) platform. Moreover, the performance of a HPWG bend is investigated and is compared with plasmonic waveguide bends. The proposed devices are very compact and outperform previously reported designs. The application of HPWG for biosensing is also explored. By utilizing the polarization diversity, the HPWG biosensor can overcome some of the limitations of plasmonic sensors. For example, unlike plasmonic sensors, the HPWG biosensor can remove the interfering bulk and surface effects.

Doctor of Philosophy / Department of Physics / Itzhak Ben-Itzhak / Lasers are being used widely for the study and manipulation of the dynamics of atomic and molecular targets, and advances in laser technology makes it possible to explore new areas of research — for example attosecond physics. In order to probe the fragmentation dynamics of molecular ions, we have developed a coincidence three-dimensional momentum imaging method that allows the kinematically complete study of all fragments except electrons. Recent upgrades to this method allow the measurement of slow dissociation fragments, down to nearly zero velocity, in intense ultrafast laser fields. Evidences for the low energy breakup are presented using the benchmark molecules diatomic H[subscript]2[superscript]+ and polyatomic H[subscript]3[superscript]+ . The low energy fragments in H[subscript]2[superscript]+ dissociation are due to the intriguing zero-photon dissociation phenomenon. This first experimental evidence for the zero-photon dissociation is further supported by sophisticated theoretical treatment. We have explored the laser pulse length, intensity, wavelength, and chirp dependence of zero-photon dissociation of H[subscript]2[superscript]+, and the results are well described by a two-photon process based on stimulated Raman scattering. Similar studies of the slow dissociation of H[subscript]3[superscript]+ reveal that two-body dissociation is dominant over three-body dissociation. The most likely pathways leading to low-energy breakup into H[superscript]++H[subscript]2, in contradiction to the assessments of the channels in at least one previous study, are explored by varying the laser pulse duration and the wavelength. In addition, we have investigated the dissociation and single ionization of N[subscript]2[superscript]+ , and an interesting high energy feature in addition to the low energy has been observed at higher intensities. Such high energy results from the breakup of molecules in excited states are accessible at higher intensities where their potential energy is changing rapidly with the internuclear distance. We have extended the intense field ionization studies to other molecular ions N[subscript]2[superscript]+ , CO[superscript]+, NO[superscript]+, and O[subscript]2[superscript]+ . The dissociative ionization of these molecules follow a general mechanism, a stairstep ionization mechanism. Utilizing the capability of the upgraded experimental method we have measured the non-dissociative and dissociative ionization of CO[superscript]+ using different pulse lengths. The results suggest that dissociative ionization can be manipulated by suppressing some ionization paths.

Doctor of Philosophy / Department of Physics / Kristan L. Corwin / Optical frequency references have been widely used in applications such as navigation, remote sensing, and telecommunication industry. For stable frequency references in the near-infrared (NIR), lasers can be locked to narrow absorption features in gases such as acetylene. Currently, most Near NIR references are realized in free space setups. In this thesis, a low-loss hollow-core optical fiber with a diameter of sub millimeters is integrated into the reference setup to provide long interaction lengths between the filling gas and the laser field, also facilitate the optical interaction with low power levels. To make portable NIR reference, gas can be sealed inside the hollow-core fiber, by creating a photonic microcell. This work has demonstrated all-fiber optical frequency references in the Near IR by fabricating and integrating gas sealed photonic microcells in the reference setup. Also, a thoughtful study regarding the lineshape of the fiber-based reference has been accomplished. According the proper modeling of a shift due to lineshape, a correction was applied to our previous absolute frequency measurement of an NIR optical frequency reference. Furthermore, effects of the hollow-core fibers, including mode-dependence frequency shift related to surface modes are explored. In addition, angle splicing techniques, which will improve the performance of the fiber-based frequency reference have been created. Low transmission and return loss angle splices of photonic bandgap fiber, single mode PCF, and large core kagome to SMF-28 are developed and those fibers are demonstrated to be promising for photonic microcell based optical frequency references. Finally, a potentially portable optical metrology system is demonstrated by stabilizing a fiber-laser based frequency comb to an acetylene-filled optical fiber frequency reference. Further work is necessary to fabricate an all-fiber portable optical metrology system with high optical transmission and low molecular contamination.

Master of Science / Physics / Vinod Kumarappan / This report includes the experimental details and results of two experiments. The first experiment addresses carrier envelope phase (CEP) effects in higher order harmonic generation (HHG), and the second experiment is a pump-probe experiment on CO₂ molecules using ultrashort laser pulses. Ultrashort laser pulses that are only a few optical cycles long are of interest for studying different atomic and molecular processes. The CEP of such a pulse is an important parameter that can affect the experimental results. Because the laser pulses we used in the HHG experiment have random CEP, we tagged a given harmonic spectrum with the CEP of the fundamental laser pulse that generated it by measuring both shot-by-shot. The first chapter of this report is about the experimental details and the results we got from our CEP-tagged HHG experiment that enabled us to observe the interference of different quantum pathways. In the second experiment, discussed in the second chapter of this report, we tried to study the structure of the CO₂⁺ ion created by strong field ionization in a pump-probe experiment. For this experiment, we used an ultrashort laser pulse to ionize CO₂ molecules, and after various time delays we probed the ionic wave packet by ionizing CO₂⁺ with another ultrashort laser pulse. By performing Fourier analysis on the delay-dependent CO₂⁺⁺ yield, we were able to identify the populated states of CO₂⁺.

Doctor of Philosophy / Department of Physics / Zenghu Chang / The observation and control of dynamics in atomic and molecular targets requires the use of laser pulses with duration less than the characteristic timescale of the process which is to be manipulated. For electron dynamics, this time scale is on the order of attoseconds where 1 attosecond = 10[superscript]-18 seconds. In order to generate pulses on this time scale, different gating methods have been proposed. The idea is to extract or “gate” a single pulse from an attosecond pulse train and switch off all the other pulses. While previous methods have had some success, they are very difficult to implement and so far very few labs have access to these unique light sources. The purpose of this work is to introduce a new method, called double optical gating (DOG), and to demonstrate its effectiveness at generating high contrast single isolated attosecond pulses from multi-cycle lasers. First, the method is described in detail and is investigated in the spectral domain. The resulting attosecond pulses produced are then temporally characterized through attosecond streaking. A second method of gating, called generalized double optical gating (GDOG), is also introduced. This method allows attosecond pulse generation directly from a carrier-envelope phase un-stabilized laser system for the first time. Next the methods of DOG and GDOG are implemented in attosecond applications like high flux pulses and extreme broadband spectrum generation. Finally, the attosecond pulses themselves are used in experiments. First, an attosecond/femtosecond cross correlation is used for characterization of spatial and temporal properties of femtosecond pulses. Then, an attosecond pump, femtosecond probe experiment is conducted to observe and control electron dynamics in helium for the first time.

Ultrafast electron diffraction is a novel pump-probe technique which aims to determine transient structures during photoinduced chemical reactions and other structural transitions. This technique provides structural information at the atomic level of inspection by using an electron pulse as a diffractive probe. The atomic motions of interest happen on the 100 fs = 10^(−13) s time scale. To observe these atomic motions, a probe which matches this time scale is required. In this thesis, I describe the development of an electron diffractometer which is capable of 200 fs temporal resolution while maintaining high signal level per electron pulse. This was made possible by the construction of an ultra-compact photoactivated 60 keV femtosecond electron gun. Traditional electron pulse characterization methods are unsuitable for high number density femtosecond electron pulses such as the pulses produced by this electron gun. I developed two techniques based on the laser ponderomotive force to reliably determine the duration of femtosecond electron pulses into the sub-100 fs range. These techniques produce a direct cross-correlation trace between the electron pulse and a laser pulse. The results of these measurements confirmed the temporal resolution of the newly developed femtosecond electron diffractometer. This cross-correlation technique was also used to calibrate a method for the determination of the temporal overlap of electron and laser pulses. These techniques provide the pulse diagnostics necessary to utilize the temporal resolution provided by femtosecond electron pulses. Owing to their high charge-to-mass ratio, electrons are a sensitive probe for electric fields. I used femtosecond electron pulses in an electron deflectometry experiment to directly observe the transient charge distributions produced during femtosecond laser ablation of a silicon (100) surface. We found an electric field strength of 3.5 × 10^6 V/m produced by the emission of 5.3 × 10^11 electrons/cm^2 just 3 ps after an excitation pulse of 5.6 J/cm^2 . This observation allowed us to rule out Coulomb explosion as the mechanism for ablation under the conditions present in this experiment.

Les cellules sont capables de détecter les distributions spatiales de protéines et ainsi de migrer ou s’étendre dans la direction appropriée. Une compréhension de la réponse cellulaire aux modifications de ces distributions spatiales de protéines est essentielle pour l’avancement des connaissances dans plusieurs domaines de recherches tels que le développement, l’immunologie ou l’oncologie. Un exemple particulièrement complexe est le guidage d’axones se déroulant pendant le développement du système nerveux. Ce dernier nécessite la présence de plusieurs distributions de molécules de guidages étant attractives ou répulsives pour connecter correctement ce réseau complexe qu’est le système nerveux. Puisque plusieurs indices de guidage collaborent, il est particulièrement difficile d’identifier la contribution individuelle ou la voie de signalisation qui est déclenchée in vivo, il est donc nécessaire d’utiliser des méthodes pour reproduire ces distributions de protéines in vitro. Plusieurs méthodes existent pour produire des gradients de protéines solubles ou liées aux substrats. Quelques méthodes pour produire des gradients solubles sont déjà couramment utilisées dans plusieurs laboratoires, mais elles limitent l’étude aux distributions de protéines qui sont normalement sécrétées in vivo. Les méthodes permettant de produire des distributions liées au substrat sont particulièrement complexes, ce qui restreint leur utilisation à quelques laboratoires. Premièrement, nous présentons une méthode simple qui exploite le photoblanchiment de molécules fluorescentes pour créer des motifs de protéines liées au substrat : Laser-assisted protein adsorption by photobleaching (LAPAP). Cette méthode permet de produire des motifs de protéines complexes d’une résolution micrométrique et d’une grande portée dynamique. Une caractérisation de la technique a été faite et en tant que preuve de fonctionnalité, des axones de neurones du ganglion spinal ont été guidés sur des gradients d’un peptide provenant de la laminine. Deuxièmement, LAPAP a été amélioré de manière à pouvoir fabriquer des motifs avec plusieurs composantes grâce à l’utilisation de lasers à différentes longueurs d’onde et d’anticorps conjugués à des fluorophores correspondants à ces longueurs d’onde. De plus, pour accélérer et simplifier le processus de fabrication, nous avons développé LAPAP à illumination à champ large qui utilise un modulateur spatial de lumière, une diode électroluminescente et un microscope standard pour imprimer directement un motif de protéines. Cette méthode est particulièrement simple comparativement à la version originale de LAPAP puisqu’elle n’implique pas le contrôle de la puissance laser et de platines motorisées, mais seulement d’envoyer l’image du motif désiré au modulateur spatial. Finalement, nous avons utilisé LAPAP pour démontrer que notre technique peut être utilisée dans des analyses de haut contenu pour quantifier les changements morphologiques résultant de la croissance neuronale sur des gradients de protéines de guidage. Nous avons produit des milliers de gradients de laminin-1 ayant différentes pentes et analysé les variations au niveau du guidage de neurites provenant d’une lignée cellulaire neuronale (RGC-5). Un algorithme pour analyser les images des cellules sur les gradients a été développé pour détecter chaque cellule et quantifier la position du centroïde du soma ainsi que les angles d’initiation, final et de braquage de chaque neurite. Ces données ont démontré que les gradients de laminine influencent l’angle d’initiation des neurites des RGC-5, mais n’influencent pas leur braquage. Nous croyons que les résultats présentés dans cette thèse faciliteront l’utilisation de motifs de protéines liées au substrat dans les laboratoires des sciences de la vie, puisque LAPAP peut être effectué à l’aide d’un microscope confocal ou d’un microscope standard légèrement modifié. Cela pourrait contribuer à l’augmentation du nombre de laboratoires travaillant sur le guidage avec des gradients liés au substrat afin d’atteindre la masse critique nécessaire à des percées majeures en neuroscience. / Cells are able to sense spatial distribution of proteins and accordingly migrate or extend in the appropriate direction. Understanding cellular responses to modifications in molecular spatial distributions is essential for advances in several fields such as development, immunology and oncology. A particularly complex example is axonal guidance that occurs during the development of the nervous system, which relies on distributions of attractive and repulsive guidance molecules to correctly wire this intricate network. Since several guidance cues collaborate to development of the nervous system, it is particularly difficult to assess the individual contribution of each cue and the signaling cascade each trigger in vivo; therefore methods to reproduce those distributions individually in vitro are necessary to study in detail the effect of each guidance cue. Several methods exist to produce graded distributions of protein that are either soluble or substrate-bound. A few methods making solution gradients are already widely used in several laboratories to perform experiments with the guidance cues that are normally diffusing in vivo. However, current methods allowing the fabrication of substrate-bound gradients are quite complex, which restrict their use to a few laboratories. First, we present a straightforward method exploiting photobleaching of a fluorescently tagged molecule using a visible laser to generating substrate-bound protein patterns: Laser-assisted protein adsorption by photobleaching (LAPAP). This method allows producing complex patterns of protein with micron spatial resolution and high dynamic range. An extensive characterization of the technique was performed and as proof of functionality, axons from dorsal root ganglions cells were guided on laminin peptide gradients. Secondly, LAPAP was improved in order to produce multicomponent patterns by using lasers at different wavelengths and antibodies conjugated to fluorophores corresponding to these wavelengths. Moreover, to speed-up the fabrication process and simplify the device, we developed widefield illumination LAPAP which uses a spatial light modulator, a light emitting diode and a standard microscope to directly print patterns. This patterning method is relatively simple compared to the original LAPAP setup, since it does not involve controlling the laser power or a motorized stage, but only sends an image of the desired pattern to a spatial light modulator. Finally, we used LAPAP to show how it could be used in automated high-content screening assays to quantify the morphological changes resulting from axon growth on gradients of guidance proteins. We produced thousands of laminin-1 gradients of different slopes and analyzed the variations in neurite guidance of neuron-like cells (RGC-5). An image analysis algorithm was developed to process bright field microscopy images, detecting each cell and quantifying the soma centroid and the initiation, terminal and turning angles of the maximal neurite. This data showed that laminin gradients influence the initiation angle of neurite extension of RGC-5, but does not contribute to its turning. We believe that the results presented in this thesis will facilitate the use of substrate- bound protein patterning in typical life science laboratories, since a confocal microscope or a slightly modified standard microscope is the only specialized equipment needed to fabricate patterns by LAPAP. This could increase the number of laboratories working with substrate-bound protein patterns in order to reach the critical mass necessary for major advances in neuroscience.

Doctor of Philosophy / Department of Physics / Brian R. Washburn / Optical frequency combs produced by mode-locked fiber lasers are useful tools for high precision frequency metrology and molecular spectroscopy in a robust and portable format. We have specifically investigated erbium doped fiber mode-locked lasers that use single-walled carbon nanotubes as a saturable absorber. We have, for the first time, developed and phase- stabilized a carbon nanotube fiber laser (CNFL) frequency comb. The carbon nanotube saturable absorber, which was fabricated using an optically driven deposition method, permits a high repetition frequency (>150 MHz) since an optical nonlinearity of fibers is not used for mode-locking. The CNFL comb combined with a parabolic pulse erbium doped fiber amplifier (EDFA) has shown a compact, robust, and cost-effective supercontinuum source. The amplified pulse from the parabolic pulse EDFA was compressed with a hollow-core photonic bandgap fiber, which produced a wave-breaking-free pulse with an all-fiber set-up. The stabilized comb has demonstrated a fractional instability of 1.2 ×10[superscript]-11 at 1 sec averaging time, the reference-limited instability. We have performed optical frequency metrology with the CNFL comb and have measured an optical frequency, P(13) which is a molecular overtone transition of C2H2. The measured frequency has shown a good agreement with the known value within an uncertainty of 10 kHz. In order to extend the application of the CNFL comb such as multi-heterodyne dual comb spectroscopy, we have investigated the noise of the CNFL comb and particularly, the broad carrier envelope offset frequency (f[subscript]0) linewidth of the CNFL comb. The primary noise source is shown to be white amplitude noise on the oscillator pump laser combined with the sensitivity of the mode-locked laser to pump power fluctuations. The control bandwidth of f[subscipt]0 was limited by the response dynamics of the CNFL comb. The significant reduction of comb noise has been observed by implementing a phase-lead compensation to extend control bandwidth of the comb and by reducing the pump relative intensity noise simultaneously. Therefore the f[subscipt]0 linewidth has been narrower from 850 kHz to 220 kHz. The integrated phase noise for the f[subscipt]0 lock is 1.6 radians from 100 Hz to 102 kHz.