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

The development of next-generation, nanoscale technologies that interface biological systems will pave the way towards new understanding of such complex systems. Nanowires – one-dimensional nanoscale structures – have shown unique potential as an ideal physical interface to biological systems. Herein, we focus on the development of nanowire-based devices that can enable a wide variety of biological studies. First, we built upon standard nanofabrication techniques to optimize nanowire devices, resulting in perfectly ordered arrays of both opaque (Silicon) and transparent (Silicon dioxide) nanowires with user defined structural profile, densities, and overall patterns, as well as high sample consistency and large scale production. The high-precision and well-controlled fabrication method in conjunction with additional technologies laid the foundation for the generation of highly specialized platforms for imaging, electrochemical interrogation, and molecular biology. Next, we utilized nanowires as the fundamental structure in the development of integrated nanoelectronic platforms to directly interrogate the electrical activity of biological systems. Initially, we generated a scalable intracellular electrode platform based on vertical nanowires that allows for parallel electrical interfacing to multiple mammalian neurons. Our prototype device consisted of 16 individually addressable stimulation/recording sites, each containing an array of 9 electrically active silicon nanowires. We showed that these vertical nanowire electrode arrays could intracellularly record and stimulate neuronal activity in dissociated cultures of rat cortical neurons similar to patch clamp electrodes. In addition, we used our intracellular electrode platform to measure multiple individual synaptic connections, which enables the reconstruction of the functional connectivity maps of neuronal circuits. In order to expand and improve the capability of this functional prototype device we designed and fabricated a new hybrid chip that combines a front-side nanowire-based interface for neuronal recording with backside complementary metal oxide semiconductor (CMOS) circuits for on-chip multiplexing, voltage control for stimulation, signal amplification, and signal processing. Individual chips contain 1024 stimulation/recording sites enabling large-scale interfacing of neuronal networks with single cell resolution. Through electrical and electrochemical characterization of the devices, we demonstrated their enhanced functionality at a massively parallel scale. In our initial cell experiments, we achieved intracellular stimulations and recordings of changes in the membrane potential in a variety of cells including: HEK293T, cardiomyocytes, and rat cortical neurons. This demonstrated the device capability for single-cell-resolution recording/stimulation which when extended to a large number of neurons in a massively parallel fashion will enable the functional mapping of a complex neuronal network. / Physics

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

Molecular interactions between cellular components such as proteins and nucleic acids govern the fundamental processes of living systems. Technological advancements in the past decade have allowed the characterization of these molecular interactions at the single-molecule level with high temporal and spatial resolution. Simultaneously, progress in computer simulation has enabled theoretical research at the atomistic level, assisting in the interpretation of experimental results. This thesis combines single-molecule force spectroscopy and simulation to explore inter- and intra-molecular interactions. Specifically, we investigate the interaction between RecA and DNA to elucidate the underlying molecular mechanism of the DNA homologous recombination process. We also evaluate the stability of the von Willebrand Factor (vWF) A2 domain to determine the molecular origins of von Willebrand Diseases (vWD). This thesis also describes the development and application of a new single-molecule technique that combines the centrifuge force microscope (CFM) with DNA self-assembled mechanical switches to enable massively parallel repeating force measurements of molecular interactions. / Engineering and Applied Sciences - Applied Physics

In 1992, B. Smith, L. Finzi and C. Bustamante were the first to directly observe the behaviour of a single DNA molecule with the help of video fluorescence microscopy. Their results greatly improved our understanding of the static and dynamic properties of a single isolated chain which represents the foundation of polymer physics. A series of experimental results and theoretical models followed the work of Smith et al. Current theoretical approaches to study polymers involve many techniques: thermodynamic analysis, field theory, scaling, renormalization group theory and computer simulations. In Chapter 2, we present a Molecular Dynamics study of the effect of strong lateral confinement on the properties of a tethered polymer pulled at constant velocity. Our results are compared with recent theoretical predictions and experimental results. One can also ask questions about the behaviour of dilute polymer solutions, or even concentrated solutions such as melts or gels, where the interactions among the polymers are important. For instance, gel electrophoresis (GE) is one of the most common analytical tools used in biology. Since the introduction of GE in 1937, molecular biology has grown substantially. Indeed, GE has shown to be an excellent separation method for DNA molecules since in free solution, the electrophoretic mobility of a DNA molecule is independent of its size. Because of that, most of the theoretical developments in the field have been aimed at improving DNA electrophoretic separation tools. In 1993, Zimm and Lumpkin proposed a new reptation model to explain gel electrophoresis of polyelectrolytes in irregular matrices. Following this work, we propose in Chapter 3 a more detailed model of this problem where the well-known memory effects of the standard reptation theory are taken into account. Our results are in qualitative agreement with available experimental results and disagree with those of Zimm and Lumpkin. In Chapter 4, we examine the reptation of a polymer in a static environment with quenched random energies that are correlated over a finite length scale lambda based on the algorithm detailed in Chapter 3. The results obtained differ from our previous model (Chapter 3) and are compared with those of Zimm and Lumpkin.

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Significant sub-systems were created and others enhanced providing a platform for an order of magnitude precision increase of the small 4He interval - 23P1→23P2 laser spectroscopy measurement, as well as other helium transitions. These measurements serve as tests of helium theory and quantum electro-dynamics in general. Many improvements to the original experiment are discussed and characterized. In particular, counting speed increased 10x, the signal level was doubled, a novel Doppler shift minimization technique was implemented, a control node re-architecture was realized along with many useful features, and the development environment was updated. An initial 28% precision improvement was achieved also providing a foundation for additional gain via a created smaller and more heavily windowed vacuum cavity and picomotor controls.