I present a series of experimental and theoretical advances in the field of quantum state estimation. Techniques for measuring the quantum state of light that were originally developed for distinguishable photons fail when the particles are indistinguishable. I develop new methods for handling indistinguishability in quantum state estimation. The technique I present provides the first complete description of states of experimentally indistinguishable photons. It allows me to derive the number of parameters needed to describe an arbitrary state and to quantify distinguishability. I demonstrate its use by applying it to the measurement of the quantum polarization state of two and three-photon systems. State characterization is optimal when no redundant information is collected about the state of the system. I present the results of the first optimal characterization of the polarization state of a two-photon system. I show an improved estimation power over the previous state of the art. I also show how the optimal measurements lead to a new description of the quantum state in terms of a discrete Wigner function. It is often desirable to describe the quantum state of a system in terms of properties that are not themselves quantum-mechanical observables. This usually requires a full characterization of the state followed by a calculation of the properties from the parameters characterizing the state. I apply a technique that allows such properties to be determined directly, without a full characterization of the state. This allows one such property, the purity, to be determined in a single measurement, regardless of the size of the system, while the conventional method of determining purity requires a number of measurements that scales exponentially with the system size.

I present in this thesis the design, implementation and measurement results of a narrowband quantum light source based on cavity-enhanced Parametric Down-Conversion (PDC). Spontaneous Parametric Down-Conversion (SPDC) is the workhorse in the field of optical quantum information and quantum computation, yet it is not suitable for applications where deterministic nonlinearities are required due to its low spectral brightness. By placing the nonlinear crystal inside a cavity, the spectrum of down-conversion is actively modified, such that all the non-resonant modes of down-conversion experience destructive interference, while the resonant mode sees constructive interference, resulting in great enhancement in spectral brightness. I design and construct such a cavity-enhanced down-conversion source with record high spectral brightness, making it possible to use cold atoms as the interaction medium to achieve large nonlinearity between photons. The frequency of the photons is tunable and their coherence time is measured to be on the order of 10 nanoseconds, matching the lifetime of the excited state of typical alkali atoms. I characterize extensively the output of the source by measuring the second-order correlation function, quantifying two-photon indistinguishability, performing quantum state tomography of entangled states, and showing different statistics of the source. The unprecedented long coherence time of the photon pairs has also made possible the encoding of quantum information in the time domain of the photons. I present a theoretical proposal of multi-dimensional quantum information with such long-coherence-time photons and analyze its performance with realistic parameter settings. I implement this proposal with the quantum light source I have built, and show for the first time that a qutrit can be encoded in the time domain of the single photons. I demonstrate the coherence is preserved for the qutrit state, thus ruling out any classical probabilistic explanation of the experimental data. Such an encoding scheme provides an easy access to multi-dimensional systems and can be used as a versatile platform for many quantum information and quantum computation tasks.

I present a series of experimental and theoretical advances in the field of quantum state estimation. Techniques for measuring the quantum state of light that were originally developed for distinguishable photons fail when the particles are indistinguishable. I develop new methods for handling indistinguishability in quantum state estimation. The technique I present provides the first complete description of states of experimentally indistinguishable photons. It allows me to derive the number of parameters needed to describe an arbitrary state and to quantify distinguishability. I demonstrate its use by applying it to the measurement of the quantum polarization state of two and three-photon systems. State characterization is optimal when no redundant information is collected about the state of the system. I present the results of the first optimal characterization of the polarization state of a two-photon system. I show an improved estimation power over the previous state of the art. I also show how the optimal measurements lead to a new description of the quantum state in terms of a discrete Wigner function. It is often desirable to describe the quantum state of a system in terms of properties that are not themselves quantum-mechanical observables. This usually requires a full characterization of the state followed by a calculation of the properties from the parameters characterizing the state. I apply a technique that allows such properties to be determined directly, without a full characterization of the state. This allows one such property, the purity, to be determined in a single measurement, regardless of the size of the system, while the conventional method of determining purity requires a number of measurements that scales exponentially with the system size.

I present in this thesis the design, implementation and measurement results of a narrowband quantum light source based on cavity-enhanced Parametric Down-Conversion (PDC). Spontaneous Parametric Down-Conversion (SPDC) is the workhorse in the field of optical quantum information and quantum computation, yet it is not suitable for applications where deterministic nonlinearities are required due to its low spectral brightness. By placing the nonlinear crystal inside a cavity, the spectrum of down-conversion is actively modified, such that all the non-resonant modes of down-conversion experience destructive interference, while the resonant mode sees constructive interference, resulting in great enhancement in spectral brightness. I design and construct such a cavity-enhanced down-conversion source with record high spectral brightness, making it possible to use cold atoms as the interaction medium to achieve large nonlinearity between photons. The frequency of the photons is tunable and their coherence time is measured to be on the order of 10 nanoseconds, matching the lifetime of the excited state of typical alkali atoms. I characterize extensively the output of the source by measuring the second-order correlation function, quantifying two-photon indistinguishability, performing quantum state tomography of entangled states, and showing different statistics of the source. The unprecedented long coherence time of the photon pairs has also made possible the encoding of quantum information in the time domain of the photons. I present a theoretical proposal of multi-dimensional quantum information with such long-coherence-time photons and analyze its performance with realistic parameter settings. I implement this proposal with the quantum light source I have built, and show for the first time that a qutrit can be encoded in the time domain of the single photons. I demonstrate the coherence is preserved for the qutrit state, thus ruling out any classical probabilistic explanation of the experimental data. Such an encoding scheme provides an easy access to multi-dimensional systems and can be used as a versatile platform for many quantum information and quantum computation tasks.

This thesis analyzes different light localization phenomena in waveguide arrays. We report on the observation of quasi-Bloch oscillations, a new type of dynamic localization in the spatial evolution of light in curved, coupled optical waveguides. The delocalization and final relocalization of an optical beam in a waveguide array is shown by spatially resolving the optical intensity at various propagation distances. Through comparison to different structures, quasi-Bloch oscillations are shown to be robust beyond the nearest-neighbor tight-binding approximation.

This thesis analyzes different light localization phenomena in waveguide arrays. We report on the observation of quasi-Bloch oscillations, a new type of dynamic localization in the spatial evolution of light in curved, coupled optical waveguides. The delocalization and final relocalization of an optical beam in a waveguide array is shown by spatially resolving the optical intensity at various propagation distances. Through comparison to different structures, quasi-Bloch oscillations are shown to be robust beyond the nearest-neighbor tight-binding approximation.

We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.

We applied single-molecule fluorescence (SMF) methods to probe the properties of individual fluorescent probes, and to characterize the proteins of interest to which these probes were attached. One remarkable advantage of SMF spectroscopy is the ability to investigate heterogeneous subpopulations of the ensemble, which are buried in ensemble averaging in other measurements. Other advantages include the ability to probe the entire dynamic sequences of a single molecule transitioning between different conformational states. For the purpose of having an extended observation of single molecules, while maintaining the native nanoscale surroundings, we developed an improved vesicle preparation method for encapsulating scarce biological samples. SMF investigations revealed that molecules trapped in vesicles exhibit nearly ideal single-emitter behavior, which therefore recommends the vesicle encapsulation for reproducible and reliable SMF studies. Hyperactive Signal-Transducer-and-Activator-of-Transcription 3 (STAT3) protein contributes significantly to human cancers, such as leukemia and lymphoma. We have proposed a novel therapeutic strategy by designing a cholesterol-based protein membrane anchor (PMA), to tether STAT3 to the cell membrane and thus inhibit unwanted transcription at the cell nucleus. We designed in vitro proof-of-concept experiments by encapsulating STAT3 and PMAs in phospholipid vesicles. The efficiency and the stability of STAT3 anchoring in the lipid membrane were interrogated via quantitative fluorescence imaging and multiparameter SMF spectroscopy. Our in vitro data paved the way for the in vivo demonstration of STAT3 inhibition in live cells, thus demonstrating that PMA-induced protein localization is a conceptually viable therapeutic strategy. The recent discovery of intrinsically disordered proteins (IDPs) highlights important exceptions to the traditional structure-function paradigm. SMF methods are very suited for probing the properties of such highly heterogeneous systems. We studied in detail the effects of electrostatics on the conformational disorder of an IDP protein, Sic1 from yeast, and found that the electrostatic repulsion is a major factor controlling the dimensions of Sic1. Based on our data we also conclude that a rod-like shape seems a better candidate than a random Gaussian chain to describe and predict the behavior of Sic1.

This thesis explored the theory, design, fabrication and characterization of AlGaAs Bragg reflection waveguides (BRW) towards the goal of a platform for monolithic integration of active and optically nonlinear devices. Through integration of a diode laser and nonlinear phase-matched cavity, the possibility of on-chip nonlinear frequency generation was explored. Such integrated devices would be highly useful as a robust, alignment free, small footprint and electrically injected alternative to bulk optic systems. A theoretical framework for modal analysis of arbitrary 1-D photonic crystal defect waveguides is developed. This method relies on the transverse resonance condition. It is then demonstrated in the context of several types of Bragg reflection waveguides. The framework is then extended to phase-match second-order nonlinearities and incorporating quantum-wells for diode lasers. Experiments within a slab and ridge waveguide demonstrated phase-matched Type-I second harmonic generation at fundamental wavelength of 1587 and 1600 nm, respectively; a first for this type of waveguide. For the slab waveguide, conversion efficiency was 0.1 %/W. In the more strongly confined ridge waveguides, efficiency increased to 8.6 %/W owing to the increased intensity. The normalized conversion efficiency was estimated to be at 600 %/Wcm^2. Diode lasers emitting at 980 nm in the BRW mode were also fabricated. Verification of the Bragg mode was performed through imaging the near- field of the mode. Propagation loss of this type of mode was measured directly for the first time at 14 cm^-1. The lasers were found to be very insensitive with characteristic temperature at 215 K. Two designs incorporating both laser and phase-matched nonlinearity within the same cavity were fabricated, for degenerate and non-degenerate down-conversion. Though the lasers were sub-optimal, a parametric fluorescence signal was readily detected. Fluorescence power as high as 4 nW for the degenerate design and 5 nW for the non-degenerate design were detected. The conversion efficiency was 4176 %/Wcm^2 and 874 %/Wcm^2, respectively. Neither design was found to emit near the design wavelength. In general, the signal is between 1600-1800 nm and the idler is between 2200-2400 nm. Improvements in laser performance are expected to drastically increase the conversion efficiency.

In this thesis, we demonstrate a new type of resonant, nonlinear, light-matter interaction facilitated by the unique electromagnetic vacuum density-of-state (DOS) structure of Photonic Band Gap (PBG) materials. Strong light localization inside PBG waveguides allows extremely strong coupling between laser fields and embedded two-level quantum dots (QD). The resulting Mollow splitting is large enough to traverse the precipitous DOS jump created by a waveguide mode cutoff. This allows the QD Bloch vector to sense the non-smoothness of the vacuum structure and evolve in novel ways that are forbidden in free space. These unusual strong-coupling effects are described using a "vacuum structure term" of the Bloch equation, combined with field-dependent relaxation rates experienced by the QD Bloch vector. This leads to alternation between coherent evolution and enhanced relaxation. As a result, dynamic high-contrast switching of QD populations can be realized with a single beam of picosecond pulses. During enhanced relaxation to a slightly inverted steady state at the pulse peak, the Bloch vector rapidly switches from anti-parallel to parallel alignment with the pulse torque vector. This then leads to a highly inverted state through subsequent coherent "adiabatic following" near the pulse tail, providing a robust mechanism for picosecond, femto-Joule all-optical switching. The simultaneous input of a second, weaker (signal) driving beam at a different frequency on top of the stronger (holding) beam enables rich modulation effects and unprecedented coherent control over the QD population. This occurs through resonant coupling of the signal pulse with the Mollow sideband transitions created by the holding pulse, leading to either augmentation or negation of the final QD population achieved by the holding pulse alone. This effect is applied to ultrafast all-optical logic AND, OR and NOT gates in the presence of significant (0.1 THz) nonradiative dephasing and (about 1%) inhomogeneous broadening. Further numerical studies of pulse evolutions inside the proposed devices demonstrate satisfactory population contrast within a PBG waveguide length of about 10 micro meter. These results provide the building blocks for low-power, ultrafast, multi-wavelength channel, on-chip, all-optical computing.