The fabrication of micro-tapered optical fibres for sensing applications

This thesis describes the processes used to manufacture optical fibre tapers and tapered long period gratings (TLPGs) using a CO2 laser. A semi-automated system for fabricating adiabatic and non-adiabatic tapers with repeatable physical dimensions has been developed. The tapers had waist diameters which were reproducible to within ± 0.5 μm. This system has also been used to fabricate TLPGs with periods ranging from 378 μm to 650 μm. Novel techniques to monitor the process of fabricating tapers were also explored. These techniques included; monitoring the transmission of the fibre using a spectrophotometer, using an in-line fibre Bragg grating (FBG) to measure the strain experienced by the optical fibre and the use of a near infra-red (NIR) camera to aid fibre alignment and laser power optimisation. The spectrophotometer allowed the optical properties of the tapers to be tailored for specific applications and the FBG provided strain data for process optimisation. The use of a NIR camera and an FBG as an in-line strain sensor are a novel use of these devices in a fibre tapering process. Tapers were also thin-film coated using sputtering techniques to form surface plasmon resonance sensors and their refractive index sensitivity was measured. A novel protein sensor based on gold nanoparticles deposited on a fibre taper is also reported, together with a lossy mode resonance taper sensor. The TLPGs which were fabricated, comprised of between 6 to 18 periods. The refractive index sensitivity of a 6 period TPLG was measured and was 372 nm/ RI. Their resonance bands had twice the bandwidth and exhibited a higher extinction, compared to UV-written long period gratings of a similar number of periods

ADAPTIVE OPTICS IMAGING OF THE TEMPORAL RAPHE IN NORMAL AND GLAUCOMATOUS SUBJECTS

Thesis (Ph.D.) - Indiana University, Optometry, 2015Adaptive optics scanning laser ophthalmoscopy (AOSLO) allows high-resolution in vivo imaging of the retina. It provides us a new way to observe and measure the RNFL in vivo. Especially, it opens a possibility of imaging the RNFL in the temporal raphe which can be affected in early glaucoma. The main objective of this thesis is to use an AOSLO to observe and measure the RNFL in the temporal raphe in both normal and glaucomatous subjects. To do this, we first improved the AOSLO imaging with the following efforts: 1) A novel adaptive optics (AO) image processing algorithm was developed to improve the contrast of AO images. 2) A clinical planning module was developed to enhance the data acquisition efficiency, especially for large-scale RNFL imaging. With the improved AOSLO imaging, we investigated the temporal raphe in young healthy subjects. Moreover, we evaluated changes of the RNFL in the temporal retina between patients with glaucoma and age-similar controls. The results shed light on the generalization that has been drawn about the retinal anatomy. We found that the temporal raphe was not a perfect horizontal dividing line. Its angle varied between individuals but was related to the optic disc position. The angle between the temporal raphe and the line that connects the fovea and the center of optic disc was about 170 degrees on average. The temporal raphe changed with aging and glaucoma. Aging increased the separation between nerve fiber bundles in superior and inferior retina, forming a larger gap in the temporal raphe in AO images. In glaucomatous subjects, this gap significantly increased even when the corresponding local visual-field loss was relatively mild. A bundle index, which integrates information about the density and relative reflectivity of nerve fiber bundles, also decreased in glaucomatous subjects. The thesis demonstrated that AOSLO imaging can elucidate the normal anatomy of the temporal raphe in vivo, and the AOSLO can serve as a tool for understanding individual differences of the temporal raphe. This thesis also opened the possibility of using the temporal raphe as a site for glaucoma research and clinical assessment

Design and configuration of laser tweezers microscopy for force measurements on single DNA molecules

In this study, a detailed description of the optical tweezers microscopy technique is presented, as well as the methodologies used to prepare the DNA molecule for mechanical measurements at the nanoscale. The main objective is to initiate and extend the experimental biophysical studies on the DNA-proteins interactions at the University of Texas at Brownsville (UTB). DNA-binding proteins control almost all aspects of cellular function, such as transcription; chromosome maintenance, replication and DNA repair depend on the interaction of proteins with DNA. In view of such an important role played by DNA–protein interactions, various techniques have evolved over the years to elucidate them. Each technique, with its own advantages and drawbacks, serves a very specific purpose. The optical tweezers has evolved as one of the powerful tools for studying the DNA–Protein complexes at a single molecule level. It allows to characterize the mechanisms involved in DNA–protein complex formation in different conditions with high resolution. It quantitatively identifies protein position along DNA molecules, DNA flexibility, curvature and conformational change after protein binding. This thesis describes the design and calibration of the optical tweezers. We measure relative displacements with nanometer accuracy and forces with an accuracy of 10%. The capability of the instrument is demonstrated by stretching a single molecule of DNA because of the elasticity of DNA has previously been well characterized. Every DNA sample used in this study has been engineered biochemically in order to accomplish proper linkage between the biological system and its supports. Breaking down the main problem leads us to four different aspects, optical tweezers, engineered molecules, coupling molecules/supports system, and the gathering of data. There are a variety of methods used to approach these problems. For the optical tweezers we will be mainly dealing with the calibration of objectives, lasers, stage control, trapping a bead and tracking the bead. Sample preparation involves polymerase chain reaction (PCR), spectrophotometer analysis, DNA electrophoresis, DNA purification process, DNA binding tests, Dot Blot Analysis, measuring of size of particles, zeta potentials, and multimode reader. We are able to confirm visually through the microscope a complete bond system by engaging all results from the experiments. We consider that our study will open up new and exciting research opportunities at UTB to study biological interactions at the level of single molecules. Also our system will be a very useful equipment to demonstrate to local students the physical principals of optics applied to biological systems

Optimization of an SRF Gun for High Bunch Charge Applications at ELBE

As a cutting-edge technology for photoinjectors, SRF guns are expected to provide CW electron beams with high bunch charge and low emittance, which is critical to the development of future FELs, ERLs and 4th/5th generation light sources. However, existing research has not explored the full potential of SRF guns as predicted by theory. Currently, the research activities at ELBE focus on solving technological challenges of a 3.5 cell SRF gun as well as applying it to high-bunch-charge experiments. This thesis aims to optimize the ELBE SRF gun and the relevant beam transport for future high-bunch-charge applications at pELBE, nELBE, TELBE and CBS experimental stations. Chapter 1 describes the demands of these applications on the SRF gun in detail. Chapter 2 outlines the development of a simulation tool based on ASTRA and Elegant, followed by the optimized gun parameters and the beam transport for the four experimental stations. Chapter 3 introduces beam diagnostic methods and data processing applied in this thesis. Chapter 4 presents results of experiments, including the pulse length measurement of the UV laser for generating electrons from the photcathode, the commissioning of ELBE SRF Gun II, a verification experiment on the LSC effect conducted at PITZ and a beam transport experiment with the bunch charge of 200 pC. Simulation results have determined the effect of each SRF gun parameter on the beam quality and have provided optimized settings according to the requirements in Chapter 1. Experimentally, the LSC effect was confirmed at PITZ, in agreement with simulations which indicated that LSC significantly influences beam quality. The performance of ELBE SRF Gun II was improved and a beam with a bunch charge of 200 pC and an emittance of 7.7 μm from ELBE SRF Gun II has been transported through ELBE without visible beam loss. The development of the simulation tool and beam diagnostics will serve further research at ELBE. Results of both simulations and experiments enrich the understanding of the existing SRF gun as well as the ELBE beamline and will guide continuing improvements. Already, ELBE SRF Gun II can deliver twice the bunch charge and lower emittance compared to the thermionic injector routinely used for ELBE. Ongoing modifications and development of the gun-cavity and photocathodes are expected to provide still further improvements. Progress on high-bunch-charge experiments at ELBE can be expected by applying the SRF gun

Set up of a light sheet fluorescence microscope for cellular studies

Light-sheet fluorescence microscopy (LSFM) has been present in cell biology laboratories for quite some time, mainly as custom-made systems, with imaging applications ranging from single cells (in the μm scale) to small organisms (mm). Such microscopes distinguish themselves for having very low phototoxicity levels and high spatial and temporal resolution, properties that render it ideal for 3D characterization of cell motility in migration and traction force studies. Cellular motion has proven to be essential in biological processes such as tumor metastasis and tissue development. Experimental setups make extensive use of microdevices (bioMEMS) that are providing higher degrees of empirical complexity. The following report details the process of setting-up a functional LSFM device for imaging cell motion in microfluidic devices. It begins with a brief summary of fluorescence imaging and current techniques, important to understand why single-plane illumination microscopy (SPIM) was chosen among other light-sheet methods. Then, the whole SPIM set-up process is described, containing explanations about the physical and material properties of the hardware used, the intricacies of the control system, and important procedures. These procedures include: calibration of the microscope, sample preparation in microdevices, and image acquisition from the software provided. Real fluorescence images acquired serve as evidence of the functionality of the instrument. The current limitations are highlighted, and pointers on how to improve or enhance the device are given. The report contains many diagrams, tables and pictures to aid in the understanding of important concepts. In the Annex, a comprehensive table listing the project costs by category is attached. This table includes links to the manufacturers and providers. The aim of this writing is to serve as an exhaustive guideline and be of reproducible use for researchers aiming to build SPIM systems for similar applications.Ingeniería Biomédic