Several Monte Carlo simulations of single-molecule fluorescence systems are developed to help evaluate and improve ongoing experiments. In the first simulation, trapping of a single molecule in a nanochannel is studied. Molecules move along the nanochannel by diffusion and electrokinetic flow. Single-molecule fluorescence signals excited by two spatially offset laser beams are detected and the direction of the flow is adjusted to try to equalize the signals and center the molecule between the beams. An algorithm is evaluated for trapping individual molecules in succession by rapidly reloading the trap after a molecule photobleaches or escapes. This is shown to be effective for trapping fast-diffusing single-chromophore molecules in succession within a micron-sized confocal region while accommodating the limited electrokinetic speed and the finite latency of feedback imposed by experimental hardware. In the second simulation, trapping of a molecule in a two-dimensional fluidic device consisting of sub-micron-separated glass plates is studied. Two different illumination schemes for sensing the molecule's position are compared: (i) a single continuous laser spot circularly scanned at 40 KHz or 240 KHz in the plane of the device; and (ii) four pulsed laser spots arranged in a square and temporally alternated at 304 MHz In either case, the times of detected photons are used by algorithms to control the electrokinetic flow in two dimensions to compensate diffusion and achieve single-molecule trapping. However each scheme is found to have limitations, as circular scanning produces a modulation in the fluorescence signal and in the autocorrelation function, whereas the four-pulse scheme becomes ineffective if the fluorescence lifetime of the molecule is greater than the time between laser pulses, The third simulation investigates appropriate conditions for detection of single molecules flowing through an array of fluidic channels for an application to high-throughput screening for pharmaceutical drug discovery. For parallelized single-molecule detection, illumination is provided by a continuous laser focused to a line intersecting all channels and fluorescence is imaged to a single row of pixels of an electron-multiplying CCD with sufficient gain for single-photon detection. The simulation separately models each channel to determine laser, flow, and camera operating conditions suitable for efficient detection.

Thesis (doctoral)--University of Tartu,, 2006. / Thesis based on four papers.

Thesis (Ph. D.)--Oregon Graduate Center, 1976.

Ph.D. / Physics / This work presents results pertinent to the study of spatial diversity as a means for partially overcoming the deleterious effects of the clear-air turbulent atmosphere on direct detection and heterodyne optical communication systems. For photon counting receivers, an averaged threshold receiver is presented, which is seen to be simpler to implement and to provide consistently lower bit error rates than optimized memoryless receivers. The heterodyne results include the introduction of a partial tracking heterodyne array; a discussion, both theoretical and experimental, of IF signal magnitude probability distributions for static heterodyne arrays; and a theoretical treatment of the probability distribution for a single heterodyne element with angle-of-arrival tracking.

In recent years laser technology has increasingly developed with the use of fiber lasers and this has provided the possibility to implement different techniques in the defense industry. LADAR is at the forefront of these techniques. Fiber lasers constitute a perfect source for LADAR systems due to their excellent robustness, compact size and high-power generation capability. In this study we will explore the development of a pulsed fiber laser source for a LADAR system that can obtain high resolution 3D images in eye-safe region. A high power, all fiber integrated erbium system with strictly single mode operation in eye-safe region based on MOPA (master oscillator power amplifier) configuration with seed source and amplifier part was developed. Both the use of an actively mode locked laser with erbium doped fiber and fiber coupled modulated distributed feedback diode laser were investigated as seed sources for the amplifier part. Both erbium doped single clad fiber and erbium-ytterbium doped double clad gain fiber were used in this amplifier system. After amplification of the actively mode locked laser, 12 W of average optical power was obtained through single mode fiber with 1ns pulse duration at 10 MHz which corresponds to 1.2 kW peak power. For the fiber coupled DFB diode laser, 9.5W average power was obtained with around 8 ns duration pulses at 100 kHz and about 9.2 W average power was also obtained with around 700 ps duration pulses at 1 MHz through strictly single mode fiber at the output of the same amplifier system as was used in the actively mode locked seed source. In both cases calculated peak power was around 10 kW v which is estimated as the highest peak power for an all fiber integrated system with single mode operation. The development of such a fiber system with high power capability, compact size and free of misalignment is expected to be useful for LADAR application as well as other areas such as eye surgery, 3D silicon processing or any other material processing applications.

Many rare-earth-doped materials are suitable for laser operation and this thesis focuses on diode-pumped solid-state lasers employing crystals doped with the trivalent rare-earth ions neodymium (Nd3+), ytterbium (Yb3+) and erbium (Er3+). Especially, the quasi-three-level transitions in Nd and Yb have been studied as well as the eye-safe three-level transition around 1.5 µm in Er. Quasi-three-level laser transitions in neodymium-doped crystals such as Nd:YAG, Nd:YLF and Nd:YVO4 have received a great deal of interest because they allow for generation of blue light by frequency doubling. For solid-state blue laser sources, there exist numerous applications as in high-density optical data storage, colour displays, submarine communication and biological applications. Efficient lasing on quasi-three-level transitions at 900¬–950 nm in Nd-doped crystals is considerably more difficult to achieve than on the stronger four-level transitions at 1–1.1 µm. The problems with these quasi-three-level transitions are a significant reabsorption loss at room temperature and a small stimulated emission cross section. This requires a tight focusing of the pump light, which is achieved by end-pumping with high-intensity diode lasers. Nd:YAG lasers at the 946 nm transition have been built and a maximum power of 7.0 W was obtained. By inserting a thin quartz etalon in the laser cavity, the 938.5 nm laser line could be selected and an output power of 3.9 W was then obtained. By using nonlinear crystals, frequency-doubling of laser light at both 946 nm and 938.5 nm was achieved. Efficient generation of blue light at 473 nm has been obtained in periodically poled KTP, both in single-pass extra-cavity and intracavity configurations. More than 0.5 W was obtained at 473 nm by intracavity doubling. Intracavity second harmonic generation of the 938.5 nm transition gave slightly more than 200 mW at 469 nm. During recent years, Yb-doped double-tungstate crystals like KGW and KYW have shown efficient laser operation. A comparative, experimental study of the laser performance and thermal-lensing properties between standard b-cut Yb:KGW and Yb:KGW cut along a novel athermal direction is presented. The results show that the thermal lens is about two times weaker and less astigmatic in the athermal-direction-cut crystal, for the same absorbed power. Also, Er-Yb-doped KGW and KYW have been investigated and the fluorescence dynamics have been measured for the Yb (2F5/2), Er (4I13/2) and Er (4S3/2) levels around 1 µm, 1.5 µm and 0.55 µm, respectively. The influence of upconversion is a detrimental effect both in Nd-doped and Er-Yb-doped lasers. Analytical models starting from rate equations have been developed for these lasers including the influence of upconversion effects. The results of the general models have been applied to 946 nm Nd:YAG lasers and to Er-Yb-doped double-tungstate crystals in order to find the optimum doping concentrations for high gain for an eye-safe laser at 1.53 µm. / QC 20100901

Fiber lasers represent the state-of-the-art in laser technology and hold great promise for a wide range of applications because they have a minimum of exposed optical interfaces, very high efficiency, and are capable of exceptional beam quality. In the near future, the most important markets such as micromachining, automotive, biomedical and military applications will begin to use this technology. The scope of this thesis is to design and develop a short picosecond pulsed fiber laser using rare-earth doped fiber as a gain medium. The proposed master oscillator power amplifier (MOPA) will be used to generate pulses with high repetition rates. In this study, first we explain the basic theoretical background of nonlinear optics and fiber laser. Then, the numerical simulation will be introduced to explain how the laser system design and optimization. The simulation is based on nonlinear Schr&ouml / dinger equation with the method of split-step evaluation. The brief theoretical background and simulation results of the laser system will be shown. Finally, the experimental study of the developmental fiber laser system that comprises an oscillator, preamplifier and power amplifier will be discussed.

Two synthesis pathways were employed throughout this work to create a variety of unique carbon materials. The first of these routes involves the photo-dissociation of liquids by direct irradiation with ultrashort laser pulses; while the second entails the bombardment of polycrystalline chemical layers by a pulsed laser induced carbon plasma. The pulsed laser irradiation (PLI) of liquid benzene (C6H6) was found to result in the formation of amorphous carbon nanoparticles consisting of clusters of sp2-bonded aromatic rings bridged by sp hybridized polyyne functionalities. In a complimentary experiment, liquid toluene (C6H5CH3) was irradiated under similar conditions leading to the synthesis of a series of free floating methyl capped polyynes, with chain lengths ranging from C10 – C20. The synthesis of polyynes is an active and cutting edge topic in material science and chemistry. In a more complex experiment, solutions of ferrocene and benzene were irradiated by fs-laser pulses resulting in highly ordered mesoscale structures exhibiting four unique geometries; ribbons, loops, tubes, and hollow spherical shells. After a purification process, the higher order structures were destroyed and replaced with nanoparticles consisting of three distinct species including; pure iron, and two phases in which part of the ferrocene molecule was bound to either carbon or iron/carbon complexes. This material is extremely interesting because it exhibits properties similar to that of an electret and is also ferromagnetic over a large temperature range. In the final liquid phase laser irradiation experiment, a new hybrid deposition technique was originated and used to coat stainless steel electrodes with disordered mesoporous nanocrystalline graphite. This method involves the laser induced breakdown of benzene and the subsequent electrodeposition of the resulting carbon ions. Another focus in this work involved the synthesis of a special class of polymer-like carbon nanomaterials using a new method that augments traditional pulsed laser deposition. This technique involves the plasma processing of frozen materials with a pulsed laser initiated graphitic plasma. We call this technique "pulsed laser induced plasma processing" or "PLIPP". Various thin film compositions were created by processing alkane and alkene ices. Finally, in a slight departure from the previous experiments, the effects of carbon ion bombardment on water ice were examined in an effort to understand certain astrophysical processes.

The need for custom footwear among the consumers is growing every day. Serious research is being undertaken with regards to the fit and comfort of the footwear. The integration of scanning systems in the footwear and orthotic industries have played a significant role in generating 3D digital representation of the foot for automated measurements from which a custom footwear or an orthosis is manufactured. The cost of such systems is considerably high for many manufacturers due to their expensive components, complex processing algorithms and difficult calibration techniques. This thesis presents a fast and robust calibration technique for a low-cost 3D laser scanner. The calibration technique is based on determining the mathematical relationship that relates the image coordinates to the real world coordinates. The relationship is determined by mapping the known real world coordinates of a reference object to its corresponding image coordinates by multivariate polynomial regression. With the developed mathematical relationship, 3D data points can be obtained from the 2D images of any object placed in the scanner. An image processing script is developed to detect the 2D image points of the laser profile in a series of scan images from 8 cameras. The detected 2D image points are reconstructed into 3D data points based on the mathematical model developed by the calibration process. Following that, the output model is achieved by triangulating the 3D data points as a mesh model with vertices and normals. The data is exported as a computer aided design (CAD) software readable format for viewing and measuring. This method proves to be less complex and the scanner was able to generate 3D models with an accuracy of +/-0.05 cm. The 3D data points from the output model were compared against a reference model scanned by an industrial grade scanner to verify and validate the result. The devised methodology for calibrating the 3D laser scanner can be employed to obtain accurate and reliable 3D data of the foot shape and it has been successfully tested with several participants.

This thesis is concerned with sensitivity alterations of Fiber Bragg Grating (FBG), sensors through additive coatings produced by a combined Laser-Assisted Maskless Micro-deposition (LAMM) and electroless plating process. The coatings can also protect the brittle FBG used in harsh environments. The thesis encompasses design, fabrication procedures, modeling and comparison of experimental and modeling results to gain insight into the advantages and short-comings of the approach. Starting with the opto-mechanical modeling, a program is written in MAPLE to analyze the effect of different on-fiber metallic materials and coating thicknesses on the sensitivity of FBGs to temperature and axial force. On the basis of the proper material and thickness, the sensitivity of FBG at different thermal and loading strains are predicted. The optimal theoretical data suggests that if the thickness of the Ni layer is 30–50 μm, maximum temperature sensitivity is achieved. Some experiments are proposed to test the feasibility of the coated FBG sensors. LAMM is used to coat bare FBGs with a 1-2 μm thick conductive silver layer followed by the electroless nickel plating process to increase layer thickness to a desired level ranging from 1 to 80 μm. Our analytical and experimental results suggest that the temperature sensitivity of the coated FBG with 1 μm Ag and 33 μm Ni is increased almost twice compared to a bare FBG with sensitivity of 0.011±0.001 nm/°C. On the contrary, the force sensitivity is decreased; however, this sensitivity reduction is less than values reported in the literature.