Optical tweezers have been widely used by biophysicists to measure forces in single molecular processes, such as the force of a motor molecule walking and the force of a DNA molecule winding and unwinding. In these and similar force measurements, the usual assumption is that the force applied to a particle inside the tweezers is proportional to the displacement of the particle away from the trap center like Hookean springs, which would imply that the force field is conservative. However, the Gaussian beam model has indicated that the force field generated by optical tweezers is actually nonconservative, yet no experiments have measured or accounted for this effect. We introduce an experimental method -- the local drift method -- that can measure the force field in optical tweezers with high precision without any assumptions about the functional form of the force field. The force field is determined by analyzing the Brownian motion of a trapped particle. We successfully applied this method to different sizes of particles and measured the three dimensional force field with 10 nm spatial resolution and femtonewton precision in force. We find that the force field is indeed nonconservative. The nonconservative contribution increases radially away from the optical axis for both small and large particles. The curl vector field -- a measurement of the nonconservative force field -- reverses direction from counter-clockwise for small particles in the Rayleigh regime to clockwise for large particles in the ray optics regime, consistent with the different scattering force profiles in the two distinct scattering regimes. Together with the thermal fluctuations of the trapped particle, the nonconservative force can cause a complex flux of energy into the system. Optically-confined Brownian motion is further used to probe nanostructures such as a biopolymer network. This technique -- thermal noise imaging -- uses a Brownian particle as a "natural scanner" to explore a biopolymer network by moving the Brownian particle through the network with optical tweezers. The position fluctuations of the probe particle reflect the location of individual filaments as excluded volumes. The resolution of thermal noise imaging is directly coupled to the size of the probe particle. A smaller probe is capable of exploring smaller pore sizes formed by dense network. Previously, a 200 nm polystyrene particle had been used to probe an agar network. In this work, 100 nm gold probe particles are used to enhance the resolution. A 100 nm particle explore a network with mesh 2³ times smaller and therefore enhance the network resolution by 2³ times. A 100 nm particle also improves the imaging speed by a factor of 2 because of its faster diffusion. Three-dimensional thermal noise images of agarose filaments are obtained and a resolution of 10 nm for the position of the filaments is achieved. In addition, a gold particle is trapped with significantly less power than a polystyrene particle of the same size, indicating the possibility for using even smaller gold particles to further improve the resolution. / text

Superconductivity is a remarkable quantum phenomenon in which a macroscopic number of electrons form a condensate of Cooper pairs that can be described by a single quantum wave function. According to the celebrated Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity, there is a minimum length scale (the coherence length) below which the condensate has a rigid quantum phase. The fate of superconductivity in a system with spatial dimensions smaller than [the coherence length] has been the subject of intense interest for decades and recent studies of superconductivity in ultra-thin epitaxial metal films have revealed some surprising behaviors in light of BCS theory. Notably, it was found that superconductivity remains robust in thin lead films with thicknesses orders of magnitude smaller than the coherence length (i.e. in the extreme two dimensional limit). Such studies raise the critical question: what happens to superconductivity as all dimensions are reduced toward the zero dimensional limit? By controlling the lateral size of ultra thin 2D islands, we systematically address this fundamental question with a detailed scanning tunneling microscopy/spectroscopy study. We show that as the lateral dimension is reduced, the strength of the superconducting order parameter is also reduced, at first slowly for dimensions larger than the bulk coherence length, and then dramatically at a critical length scale of ~ 40nm. We find this length scale corresponds to the lateral decay length of the order parameter in an island containing regions of different heights and different superconducting strength. Overall, our results suggest that fluctuation corrections to the BCS theory are important in our samples and may need to be systematically addressed by theory. / text

Bose-Einstein condensates (BECs), with their superfluid behavior, quantized vortices, and high-level of control over trap geometry and other system parameters provide a compelling environment for studies of quantum fluid dynamics. Recently there has been an influx of theoretical and numerical progress in understanding the superfluid dynamics associated with two-dimensional quantum turbulence, with expectations that complementary experiments will soon be realized. In this dissertation I present progress in the development of an experimental toolkit that will enable such experimental studies of two-dimensional quantum turbulence. My approach to developing this toolkit has been twofold: first, efforts aimed at the development of experimental techniques for generating large disordered vortex distributions within a BEC; and second, efforts directed towards the design, implementation, and characterization of a quantum vortex microscope. Quantum turbulence in a superfluid is generally regarded as a disordered tangle of quantized vortices in three dimensions, or a disordered planar distribution of quantized vortices in two dimensions. However, not all vortex distributions, even large disordered ones, are expected to exhibit robust signatures of quantum turbulence. Identification and development of techniques for controlled forcing or initialization of turbulent vortex distributions is now underway. In this dissertation, I will discuss experimental techniques that were examined during the course of my dissertation research, namely generation of large disordered distributions of vortices, and progress towards injecting clusters of vortices into a BEC. Complimentary to vortex generation is the need to image these vortex distributions. The nondeterministic nature of quantum turbulence and other far-from-equilibrium superfluid dynamics requires the development of new imaging techniques that allow one to obtain information about vortex dynamics from a single BEC. To this end, the first vortex microscope constructed as part of my dissertation research enabled the first in situ images of quantized vortices in a single-component BEC, obtained without prior expansion. I have further developed and characterized a second vortex microscope, which has enabled the acquisition of multiple in situ images of a lattice of vortex cores, as well as the acquisition of single in situ images of vortex cores in a BEC confined in a weak hybrid trap. In this dissertation, I will discuss the state-of-the-art of imaging vortices and other superfluid phenomena in the University of Arizona BEC lab, as indicated by the examined performance of the quantum vortex microscope.

Micro-Electro-Mechanical Systems (MEMS) micromirrors have been developed for more than two decades along with the development of MEMS technology. They have been used into many application fields: optical switches, digital light projector (DLP), adoptive optics (AO), high definition (HD) display, barcode reader, endoscopic optical coherence tomography (OCT) and confocal microscope, and so on. Especially, MEMS mirrors applied into endoscopic OCT and confocal microscope are the intensive research field. Various actuation mechanisms, such as electrostatic, electromagnetic, electro bimorph thermal, electrowetting, piezoelectric (PZT) and hybrid actuators, are adopted by different types of micromirrors. Among these actuators, the electrostatic is easily understood and simple to realize, therefore, it is broadly adopted by a large number of micromirrors. This thesis reports the design, fabrication, and characterization of a 2-D Silicon-on-insulation (SOI) MEMS micromirror with sidewall (SW) electrodes for endoscopic OCT or confocal microscope imaging. The biaxial MEMS mirror with SW electrodes is actuated by electrostatic actuators. The dimension of mirror plate is 1000micron×1000micron, with a thickness of a 35micron. The analytical modeling of SW electrodes, fabrication process, and performance characteristics are described. In comparison to traditional electrostatic actuators, parallel-plate and comb-drive, SW electrodes combined with bottom electrodes achieve a large tilt angle under a low drive voltage that the comb-drive does and possess fairly simple fabrication process same as that of the parallel-plate. A new fabrication process based on SOI wafer, hybrid bulk/surface micromachined technology, and a high-aspect-ratio shadow mask is presented. Moreover, the fabrication process is successfully extended to fabricate 2×2 and 4×4 micromirror arrays. Finally, a biaxial MEMS mirror with SW electrodes was used into Confocal MACROscope for imaging. Studied optical requirements in terms of two optical configurations and frequency optimization of the micromirror, the biaxial MEMS mirror replaces the galvo-scanner and improves the MACROscope. Meanwhile, a new Micromirror-based Laser Scanning Microscope system is presented and allows 2D images to be acquired and displayed.

It is my hope that this thesis may serve as a guide for future students wishing to build a microscope from scratch. The design and construction of a scanning, confocal fluorescence microscope equipped with shaped microwave excitation is detailed. The use of the microscope is demonstrated by coherently manipulating single Nitrogen-Vacancy centres in diamond. Further the instrument is used to investigate a dual Halbach array magnet system.

Laser nano-patterning with near-field optical microscope (NSOM) and the associated energy transport analysis are achieved in this study. Based on combined experimental/theoretical analyses, it is found that laser nano-patterning with a NSOM probes strongly depend on the laser conditions and material properties of the target: the energy transport from the NSOM probes to the targets changes from pure optical to a combination of thermal and optical transport when the pulse duration of laser is increased from femtosecond to nanosecond. As a result, the mechanisms of nano-pattern formation on targets changes from nano-ablation to nano-oxidation/ recrystallization when the laser pulse duration is increased from femtosecond to nanosecond. Also, with the laser nano-patterning experiments, thermal damage of NSOM probes is observed which can be attributed to the low transport efficiency (10-4 – 10-6) and associated heating of the metal cladding of NSOM probes. The heating of NSOM probes are studied with developed time harmonic and transient thermoreflectance (TR) imaging. From time harmonic TR when the NSOM probes are driven with continuous laser, it is found that the location of heating of NSOM probes is ~20-30µm away from the NSOM tip. The strength of the heating is determined by the laser power (linear dependence), wavelength of the laser (stronger with short A), and aperture size of NSOM probes (stronger when aperture size < A/2). From the transient TR imaging when the NSOM probes are driven with pulsed laser, it is found that the peak temperature of the NSOM probe shifts much closer to the tip. The possible reason for the change in the location of peak temperature when continuous laser is changed to pulsed laser can be attributed to the competition between the heat generation and dissipation rates at different location of the probe: the tip experiences highest temperature with pulsed heating as the entire heating processes is adiabatic. The tip also experiences highest heat dissipation rate due to its large surface-to-volume ratio which overcomes the heat generation at the tip under quasi-steady state resulting in shift of the hot spot. The knowledge obtained in this study can be important in the future design of more efficient NSOM probes and other nano-optic devices.

The microstructure of the brain at the cellular level provides crucial information for the understanding of the function of the brain. A large volume of high-resolution brain image data from 3D microscopy is an essential resource to study detailed microstructures of the brain. Accordingly, we have worked on obtaining high-resolution image data of entire mouse brains using the Knife-Edge Scanning Microscope (KESM). Furthermore, to disseminate these high-resolution whole mouse brain data sets to the neuroscience research community, we developed a web-based brain atlas, the KESM Brain Atlas (KESMBA). To visualize the data sets in 3D while using only a standard web browser, we employed distance attenuation and Google Maps API. The KESMBA is a powerful tool to analyze and share the KESM mouse brain data sets, but the image loading was slow because of the number of raster image (PNG) tiles and the file size. Moreover, since Google Maps API is governed by a commercial license, it does not provide enough flexibility for customization, extension, and mirroring. To solve these issues, we designed and developed a new KESM mouse brain atlas that uses a vector graphics format called Scalable Vector Graphics (SVG) instead of PNG, and OpenLayers API instead of Google Maps API. The SVG-based KESMBA using OpenLayers allows faster navigation and exploration of the KESM data, and more overlay of layers with the 4 times reduced file size compared to PNG tiles. Due to the reduced file size, the SVG-based KESMBA using OpenLayers is 2.45 times faster than the original atlas. By enhancing the performance, the users can more easily access the KESM data. We expect the SVG-based KESMBA to accelerate new discoveries in neuroscience.

<p><font face="Times-Roman"> <p align="left">The growth of the Internet has led to many interesting developments for both educational and commercial purposes. In this project an attempt was made to use the Internet for a research purpose to facilitate the determination of the thermal stability of diffusion barriers. Another purpose of this thesis is to investigate the teaching and training use of the Internet through the development of online interactive tools and activities as well as materials. The training aspects are mentioned as it is hoped that this thesis can serve as a form of documentation of the use of the Internet, while the central part was the determination of thermal stability of TiN, TaN and TiW diffusion <font face="Times-Roman">barriers on Ag.</font></p> </font></p>

The image analysis techniques presented in the présent thesis have been developed as part of a European projeet dedicated to the development of an automatic membrane protein crystallization pipeline. A large number of samples is simultaneously produced and assessed by transmission electron microscope (TEM) screening. Automating this fast step implicates an on-fine analysis of acquired images to assure the microscope control by selecting the regions to be observed at high magnification and identify the components for specimen characterization.The observation of the sample at medium magnification provides the information that is essential to characterize the success of the 2D crystallization. The resulting objects, and especially the artificial membranes, are identifiable at this scale. These latter present only a few characteristic signatures, appearing in an extremely noisy context with gray-level fluctuations. Moreover they are practically transparent to electrons yielding low contrast. This thesis presents an ensemble of image processing techniques to analyze medium magnification images (5-15 nm/pixel). The original contribution of this work lies in: i) a statistical evaluation of contours by measuring the correlation between gray-levels of neighbouring pixels to the contour and a gradient signal for over-segmentation reduction, ii) the recognition of foreground entities of the image and iii) an initial study for their classification. This chain has been already tested on-line on a prototype and is currently evaluated.

A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation.