<p> Vacuum sublimated thin films of metallophthalocyanines (where metal = Cu, Fe, Zn, and Mn) and metal-free phthalocyanine were prepared at different deposition temperatures. The optical properties have been studied in the wavelength range of 340 nm to 2500 nm for samples deposited at room temperature up to 250 &deg;C. Atomic force microscopy was used to obtain images of the surface morphology. Absorption coefficient spectra obtained verify the &pi; to &pi;* transition in the region 526 nm to 735 nm for the Q band, throughout all samples studied. The independence of deposition temperature or grain size in peak positions in absorption coefficient throughout all samples has been shown. The ratio of intensity of the two absorption coefficient peaks in the Q band has been calculated, showing a change in MnPc intensity ratio with changing deposition temperature. The intensity of the highest peak in the Q band has been compared for different metallophthalocyanines and across different deposition temperatures. CuPc deposited at 250 &deg;C has been shown to have the highest peak magnitude of absorption coefficient, with a value of 3.9&times;10⁵ cm^&ndash;1.</p><p>

When a material has inhomogeneities at a lengthscale comparable to the wavelength of light, interference can give rise to structural colors: colors that originate from the interaction of the material's microstructure with light and do not require absorbing dyes. In this thesis we study a class of these materials, called photonic glasses, where the inhomogeneities form a dense and random arrangement. Photonic glasses have angle-independent structural colors that look like those of conventional dyes. However, when this work started, there was only a handful of colors accessible with photonic glasses, mostly hues of blue. We use various types of colloidal particles to make photonic glasses, and we study, both theoretically and experimentally, how the optical properties of these glasses relate to their structure and constituent particles. Based on our observations from glasses of conventional particles, we construct a theoretical model that explains the scarcity of yellow, orange, and red photonic glasses. Guided by this model, we develop novel colloidal systems that allow a higher degree of control over structural color. We assemble glasses of soft, core-shell particles with scattering cores and transparent shells, where the resonant wavelength can be tuned independently of the reflectivity. We then encapsulate glasses of these core-shell particles into emulsion droplets of tunable size; in this system, we observe, for the first time, angle-independent structural colors that cover the entire visible spectrum. To enhance color saturation, we begin experimenting with inverse glasses, where the refractive index of the particles is lower than the refractive index of the medium, with promising results. Finally, based on our theoretical model for scattering from colloidal glasses, we begin an exploration of the color gamut that could be achieved with this technique, and we find that photonic glasses are a promising approach to a new type of long-lasting, non-toxic, and tunable pigment.

Nitrogen-vacancy (NV) centers in diamond have recently emerged as a promising new system for quantum information and nanoscale sensing applications. They have long coherence times at room temperature and can be positioned in proximity to the diamond surface, enabling magnetometry with high spatial resolution and coherent coupling to other quantum systems. This thesis presents three experiments in which single NV centers were used to sense magnetic fields at the nanometer scale. In the first experiment, the coherent evolution of a single NV spin is coupled to the motion of a magnetized mechanical resonator tens of nanometers from the NV. Coherent manipulation of the spin is used to sense the driven and Brownian motion of the resonator under ambient conditions, with picometer-scale sensitivity to motion. Future applications of this technique include the detection of the zero-point fluctuations of a mechanical resonator, the realization of strong spin-phonon coupling at a single quantum level, and the implementation of quantum spin transducers. In the second experiment, a single NV electronic spin is used to measure the quantum dynamics of distant individual nuclear spins from within a surrounding spin bath. The demonstrated sensing technique dramatically increases the potential size of NV based quantum registers for quantum information applications, and provides a new method for nanoscale magnetic resonance imaging of single nuclear spins. In the third experiment, single NV electronic spins are used to probe magnetic Johnson noise in the vicinity of conductive silver films. Measurements of polycrystalline silver films over a range of distances (20-200 nanometers) and temperatures (10-300 Kelvin) are consistent with the classically expected behavior of the magnetic fluctuations. However, Johnson noise is found to be dramatically suppressed next to single-crystal films, indicative of a substantial deviation from Ohm's law arising from the ballistic motion of the electrons in the metal. These result demonstrate that our technique provides a general, non-invasive probe of local electron transport in samples of arbitrary size and dimensionality, which can be used to explore materials response to localized impurities and the interplay between transport, interactions and disorder at the nanoscale. / Physics

Current far-field super-resolution techniques offer unprecedented spatial resolution, however, the identification and quantification of multiple molecules that cannot be spatially resolved remains challenging, mainly hampered by the lack of a comprehensive kinetic model for stochastic dye blinking, undercounting due to imperfect dye labeling of molecules, photobleaching, and limited multiplexing capabilities. Here I have developed and validated a quantitative multiplexing super-resolution approach, based on programmable autonomous blinking of a nucleic acid probe. I use the transient binding of short fluorescently labeled oligonucleotides (technique named DNA-PAINT) for simple and easy-to-implement multiplexed 2D and 3D super-resolution imaging inside fixed cells and achieve sub-10 nm spatial resolution in vitro using synthetic DNA structures. To achieve multiplexing we developed Exchange-PAINT that allows sequential imaging of multiple target molecules using only a single dye and a single laser source. For first time we experimentally have demonstrated super-resolution imaging of 10 synthetic DNA structures and 4 organelles imaging in cells by targeting 4 specific proteins. For single molecular counting we developed a method called quantitative PAINT or qPAINT, that enables counting by analyzing the predictable binding kinetics of the DNA imager strands with their targets molecules. We precisely benchmarked qPAINT using synthetic DNA nanostructures with a defined number of binding sites, and showed that qPAINT can count integer numbers of molecules with a precision of ~90 % over a large dynamic range (10 to 150 molecules). High counting precision and accuracy was maintained when imaging cell surface receptor clusters, mRNA molecules in fixed cells and protein clusters from nucleoporines that form the nuclear pore complex (NCP). We also applied this new approach for analyzing the complex interactions of 5 receptor tyrosine kinases (RTKs) simultaneously within their native cellular context in a breast cancer cell line and finally for in situ visualization of single-copy regions of the genome in mouse fibroblasts. / Systems Biology

Experiments with ultracold atoms in optical lattices provide outstanding opportunities to realize exotic quantum states due to a high degree of tunability and control. In this thesis, I present experiments that extend this control from global parameters to the level of individual particles. Using a quantum gas microscope for 87Rb, we have developed a single-site addressing scheme based on digital amplitude holograms. The system self-corrects for aberrations in the imaging setup and creates arbitrary beam profiles. We are thus able to shape optical potentials on the scale of single lattice sites and control the dynamics of individual atoms. We study the role of quantum statistics and interactions in the Bose-Hubbard model on the fundamental level of two particles. Bosonic quantum statistics are apparent in the Hong-Ou-Mandel interference of massive particles, which we observe in tailored double-well potentials. These underlying statistics, in combination with tunable repulsive interactions, dominate the dynamics in single- and two-particle quantum walks. We observe highly coherent position-space Bloch oscillations, bosonic bunching in Hanbury Brown-Twiss interference and the fermionization of strongly interacting bosons. Many-body states of indistinguishable quantum particles are characterized by large-scale spatial entanglement, which is difficult to detect in itinerant systems. Here, we extend the concept of Hong-Ou-Mandel interference from individual particles to many-body states to directly quantify entanglement entropy. We perform collective measurements on two copies of a quantum state and detect entanglement entropy through many-body interference. We measure the second order Rényi entropy in small Bose-Hubbard systems and detect the buildup of spatial entanglement across the superfluid-insulator transition. Our experiments open new opportunities for the single-particle-resolved preparation and characterization of many-body quantum states. / Physics

Diatomic molecules are considered good candidates for the study of strongly correlated systems and precision measurement searches due to their combination of complex internal states and strong long-range interactions. Cooling molecules down to ultracold temperatures is often a necessary step for fully utilizing the power of the molecule. This requires a trap for molecules and the ability to cool molecules to the mK regime and below. A magneto-optical trap (MOT) is a good tool for achieving mK temperatures. However, extra care is needed for molecules to form the necessary quasi-closed cycling transitions due to molecule's complicated energy structure. In our work with CaF, we use two repump lasers to block vibrational leakage and selection rules for the rotational degree of freedom to achieve about 10^{5} photon cycles. The two-stage buffer gas beam source is a general method to generate a cold and slow beam of molecules with a forward velocity of about 50 m/s. The compatibility of the buffer-gas source with a MOT is studied and we confirm that such beams can be nicely compatible with MOTs using various atomic species. In order to load molecules into a MOT from even such a slow beam, additional slowing is required due to the low capture velocity of a molecular MOT (< 10 m/s). We apply a frequency-broadened “white-light” slowing on CaF from a two-stage source, demonstrating slowing of CaF below 10 m/s. An AC MOT, which provides active remixing of dark substates, is also developed and Li atoms are slowed and trapped. These are crucial ingredients for co-trapping CaF molecules and Li atoms and study their collisional properties, which would lead to sympathetic cooling of molecules down to ultracold temperatures. The achievement of slowing and development of this system allowed for the detailed study of the CaF laser cooling system, as well as physical processes involved with AC MOTs and the proposed MOT for CaF. Crucial knowledge of this archetypal system provides significant progress toward manipulation and control of molecules similar to what has been achieved with atoms and what is necessary for searches for new physics with ultracold molecules. / Physics

The oxidizing capacity of the atmosphere regulates both the longwave and shortwave radiation budgets holding our planet in equilibrium. As planetary conditions continue to shi , insights into the oxidation pathways determining both greenhouse gas lifetimes and aerosol formation become paramount. In addition, oxidation and photochemistry act in conjunction to cleanse the troposphere of pollutants, which impact surface ozone levels and particulate ma er content. Both of these have implications for human health and quality of life. A few free radical species dominate the oxidation chemistry of the atmosphere – HOx, halogen radicals XOx (X≡Cl, Br, I), and NOx – with the hydroxyl radical playing a central role. In this thesis, I will discuss the development of laser-based spectroscopic techniques designed to target and quantify two chemical species: iodine monoxide and the hydroxyl radical. Due to their high reactivity and inhomogeneous chemical distributions, both IO and OH remain challenging to measure, with atmospheric lifetimes on the order of < 1 second and mean mixing ratios in the part per trillion (ppt) range. e spectroscopic methods discussed serve as the foundations upon which high sensitivity, high speci city instruments are developed for in situ chemical detection. In Chapter 2, I will discuss the eld validation of the Harvard IO instrument, which exploits a laser-induced uorescence (LIF) detection technique to quantify in situ mixing ratios of iodine monoxide. e Harvard IO instrument was deployed to Shoals MarineLab on Appledore Island, ME in August and September of 2011. An overview of the instrument will be detailed as well as results from the eld deployment and their implications for IO chemistry. Chapter 3 will continue in the vein of laser spectroscopy to discuss the development of a novel light source in the mid-infrared. I will explore the use of a nonlinear optical technique, Optical Parametric Generation (OPG), to create high-power pulsed radiation, which can be adapted to varied spectroscopic methods that require pulsed laser sources. e development of this light source allows for the detection of several trace species relevant to climate that exhibit fundamental vibrations in the overlapping spectral window. In Chapter 4, I will focus on extending the OPG laser system to target the vibrational bands of OH. e vibrational excitation serves as the rst step in a two-photon LIF (TP-LIF) detection technique for hydroxyl radicals in the troposphere. Several interferences, both known and unknown, plague the current measurements of OH, and TP-LIF provides an alternative detection scheme to signi cantly improve measurement accuracy. Finally, I will assess the implications for future measurements of OH and its coupling with halogen free radical species to mediate oxidation in the troposphere, which is essential to a be er understanding of the intersection between chemistry and climate. / Chemistry and Chemical Biology

This thesis presents a range of advances in the fabrication of femtosecond laser textured and hyperdoped silicon, a material platform with potential applications in photovoltaics, photodetectors, light-emitting diodes, lasers, and potentially other optoelectronic devices. After providing background and a review of the state of hyperdoped black silicon research in Chapter 1, we explore a range of fabrication approaches in Chapter 2, including laser texturing near and below the melting threshold of silicon, laser texturing and hyperdoping using scanned pulses, fabrication with thin films, control of the dopant concentration on textured substrates, and removal of surface material using chemical etching. In Chapter 3, we review the material microstructure of hyperdoped black silicon, including the morphology, the presence and origin of high-pressure material phases, and the incorporation of dopants from thin films. In Chapter 4, we explore the use of laser annealing to increase the crystallinity of hyperdoped black silicon, addressing a longstanding challenge in the field. We show that nanosecond laser annealing can be used on a wide variety of textures— from at least 10 micrometers in size to sub-micrometer in size—to produce high crystallinity and high optical absorptance simultaneously. Furthermore, we see that nanosecond laser annealing can reactivate the sub-bandgap absorptance after it has been deactivated by thermal annealing. We close Chapter 4 by exploring the use of fs laser pulses to anneal hyperdoped black silicon. Finally, in Chapter 5, we discuss advances in the thesis, outstanding challenges in the research field, and an outlook for applications. / Engineering and Applied Sciences - Applied Physics

Fluorescent-labeling imaging techniques have been widely used in live cell studies; however, the labeling processes can be laborious and challenging for non-transfectable cells and clinical cells, and labels can interfere with protein functions. In this thesis, we present the first demonstration of label-free detection and quantification of intracellular biomarker dynamics with a nanoscale localized-surface-plasmon fiber-tip-probe (LSP-FTP). Our results have established the FTP technique as a new tool to study the time dynamics of proteins and protein phosphorylations in single live cell, and could be generalized to study other types of primary cells in response to external triggers, including drugs. Chapter 2 focuses on the fabrication methods of fiber tip probes (FTPs). FTP is a lab-on-a-fiber probe wet-etched at nanoscale dimensions. The base material of FTPs may comprise any solid materials as long as they have matching etchants. FTPs take various configurations and may comprise of single-ended fiber, double-ended fiber, or an end-portion or mid-portion nanowire with various aspect ratios. Structures of FTPs can be tuned at nanoscale accuracy with extreme surface smoothness. These FTPs can be mass-fabricated and multiplexed at a single fabrication step and at low cost. Chapter 3 discusses the procedures and results on measuring intracellular biomarker dynamics in intact live cells. We demonstrated label-free detection of tumor suppressor p53 dynamics in single HeLa cells under ultraviolet radiation and under treatment with neocarzinostatin (NCS). Also, we employed the FTP technique to prove that \textbeta -Amyloid generation precedes Tau phosphorylation by continually monitoring intracellular levels of \textbeta -Amyloid and phosphorylated Tau in live human neuroblastoma cells (SY5Y). Chapter 4 discusses other potential applications of FTPs. An FTP with a nanodiamond at its tip can be used to measure various intracellular properties such as electromagnetic fields, temperature, or pressure. Manipulation of electron spins at nitrogen-vacancy centers in a nanodiamond allows these measurements. An FTP with a plasmonic particle at its tip can be used for surface-enhanced Raman spectroscopy (SERS) and potentially allow single molecular detection. A mechanical FTP with an end-portion nanowire (a few hundred micrometers long and sub-micron thick) functions as a cantilever sensor, and we can detect changes in its vibration modes induced by binding of analytes to a reaction entity immobilized relative to the nanowire. Free-standing FTP waveguides with a sub-micron portion in diameter can be used for efficient light coupling and device characterizations. / Chemical Physics

Optical interferometry is a technique for obtaining high-resolution imagery of a distant target by interfering light from multiple telescopes. Image restoration from interferometric measurements poses a unique set of challenges. The first challenge is that the measurement set provides only a sparse-sampling of the object’s Fourier Transform and hence image formation from these measurements is an inherently ill-posed inverse problem. Secondly, atmospheric turbulence causes severe distortion of the phase of the Fourier samples. We develop array design conditions for unique Fourier phase recovery, as well as a comprehensive algorithmic framework based on the notion of redundant-spaced-calibration (RSC), which together achieve reliable image reconstruction in spite of these challenges. Within this framework, we see that classical interferometric observables such as the bispectrum and closure phase can limit sensitivity, and that generalized notions of these observables can improve both theoretical and empirical performance. Our framework leverages techniques from lattice theory to resolve integer phase ambiguities in the interferometric phase measurements, and from graph theory, to select a reliable set of generalized observables. We analyze the expected shot-noise-limited performance of our algorithm for both pairwise and Fizeau interferometric architectures and corroborate this analysis with simulation results. We apply techniques from the field of compressed sensing to perform image reconstruction from the estimates of the object’s Fourier coefficients. The end result is a comprehensive strategy to achieve well-posed and easily-predictable reconstruction performance in optical interferometry. / Engineering and Applied Sciences - Engineering Sciences