This thesis presents optical trapping of various single nanoparticles, and the method for integrating the optical trap system into a microfluidic channel to examine the trapping stiffness and to study binding at the single molecule level. Optical trapping is the capability to immobilize, move, and manipulate small objects in a gentle way. Conventional trapping methods are able to trap dielectric particles with size greater than 100 nm. Optical trapping using nanostructures has overcome this limitation so that it has been of interest to trap nanoparticles for bio-analytical studies. In particular, aperture optical trapping allows for trapping at low powers, and easy detection of the trapping events by noting abrupt jumps in the transmission intensity of the trapping beam through the aperture. Improved trapping efficiency has been achieved by changing the aperture shape from a circle; for example, to a rectangle, double nanohole (DNH), or coaxial aperture. The DNH has the advantage of a well-defined trapping region between the two cusps where the nanoholes overlap, which typically allows only single particle trapping due to steric hindrance. Trapping of 21 nm encapsulated quantum dot has been achieved which shows optical trapping can be used in technologies that seek to place a quantum dot at a specific location in a plasmonic or nanophotonic structure. The DNH has been used to trap and unfold a single protein. The high signal-to-noise ratio of 33 in monitoring single protein trapping and unfolding shows a tremendous potential for using the double nanohole as a sensor for protein binding events at a single molecule level. The DNH integrated in a microfluidic chip with flow to show that stable trapping can be achieved under reasonable flow rates of a few µL/min. With such stable trapping under flow, it is possible to envision co-trapping of proteins to study their interactions. Co-trapping is achieved for the case where we flow in a protein (bovine serum albumin – BSA) and co-trap its antibody (anti-BSA). / Graduate / 0544 / 0752 / oskuie@uvic.ca

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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.

This thesis presents a route towards a single photon source based on erbium-doped nanocrystals, fabricated with methods that use double nanohole optical tweezers. Single photon sources are an exciting quantum technology and erbium is good candidate as it emits in the low-loss fiber optic C-band, but it is a weak emitter. Double nanohole apertures can be designed with plasmonic resonances to enhance the local electric field. In this thesis, double nanohole optical tweezers are used to isolate and enhance the emission of erbium-doped nanocrystals, with the tuned geometry showing a factor of 50 additional enhancement over rectangular apertures. With the enhanced emission, nanocrystals with discrete levels of erbium emitters are detected and isolated in real-time, based on their level of emission. This real-time process demonstrates a major improvement over typical post-processing approaches. A novel method to anchor nanocrystals in a double nanohole using a photochemical thiol reaction was investigated which yielded 40% of nanoparticles anchoring within 2 μm of the DNH, with 5% inside. This is useful as otherwise the trapping laser must be maintained to keep the nanocrystal in the trap. Another challenge is coupling to an optical fiber, for which a method to combine trapping and coupling was explored. Colloidal pattern transfer is presented as a low-cost fabrication method for nanoaperture optical fiber tweezers, with fiber-based trapping demonstrated using 40 nm polystyrene nanospheres and hexagonal boron nitride. The preliminary results from these methods show great potential, and with further refinement they may lead towards a method to fabricate a low-cost fiber-coupled single photon source based on erbium-doped nanocrystals. / Graduate

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Optical trapping is a method which uses focused laser light to manipulate small objects. This optical manipulation can be scaled below the diffraction limit by using interactions between light and apertures in a metal film to localize electric fields. This method can trap objects as small as several nanometers. The ability to determine the properties of a trapped nanoparticle is among the most pressing issues to the utilization of this method to a broader range of research and industrial applications. Presented here are two methods which demonstrate the ability to determine the properties of a trapped nanoparticle. The first method incorporates Raman spectroscopy into a trapping setup to obtain single particle identification. Raman spectroscopy provides a way to uniquely identify an object based on the light it scatters. Because Raman scattering is an intrinsically weak process, it has been difficult to obtain single particle sensitivity. Using localized electric fields at the trapping aperture, the Raman integrated trapping setup greatly enhances the optical interaction with the trapped particle enabling the required sensitivity. In this work, the trapping and identification of 20 nm titania and polystyrene nanoparticles is demonstrated. The second method uses an aperture assisted optical trap to detect the response of a magnetite nanoparticle to a varying applied magnetic field. This information is then used to determine the magnetic susceptibility, remanence, refractive index, and size distribution of the trapped particle. / Graduate / 0544 / 0752 / stevenjones3.14@gmail.com

THz spectroscopy is an emerging technique for studying the dynamics and interactions of cells and biomolecules, but many practical challenges still remain in experimental studies. We present a prototype of simple and inexpensive cell-trapping microfluidic chip for THz spectroscopic study of live cells. Cells are transported, trapped and concentrated into the THz exposure region by applying an AC bias signal while the chip maintains a steady temperature at 37 degrees C by resistive heating. We conduct some preliminary experiments on E. coli and T-cell solution and compare the transmission spectra of empty channels, channels filled with aqueous media only, and channels filled with aqueous media with un-concentrated and concentrated cells.

Leakage of stored bulk phase CO₂ is one risk for sequestration in deep saline aquifers. As the less dense CO₂ migrates upward within a storage formation or in layers above the formation, the security of its storage depends upon the trapping mechanisms that counteract the migration. The trapping mechanism motivating this research is local capillary trapping (LCT), which occurs during buoyancy-driven migration of bulk phase CO₂ within a saline aquifer with spatially heterogeneous petrophysical properties. When a CO₂ plume rising by buoyancy encounters a region where capillary entry pressure is locally larger than average, CO₂ accumulates beneath the region. One benefit of LCT, applied specifically to CO₂ sequestration and storage, is that saturation of stored CO₂ phase is larger than the saturation for other permanent trapping mechanisms. Another potential benefit is security: CO₂ that occupies local capillary traps remains there, even if the overlying formation that provides primary containment were to be compromised and allow leakage. Most work on LCT has involved numerical simulation (Saadatpoor 2010, Ganesh 2012); the research work presented here is a step toward understanding local capillary trapping at the bench scale. An apparatus and set of fluids are described which allow examining the extent of local capillary trapping, i.e. buoyant nonwetting phase immobilization beneath small-scale capillary barriers, which can be expected in typical heterogeneous storage formation. The bench scale environment analogous to CO₂ and brine in a saline aquifer is created in a quasi-two dimensional experimental apparatus with dimension of 63 cm by 63 cm by 5 cm, which allows for observation of plume migration with physically representative properties but at experimentally convenient ambient conditions. A surrogate fluid pair is developed to mimic the density, viscosity and interfacial tension relationship found at pressure and temperature typical of storage aquifers. Porous media heterogeneity, pressure boundary conditions, migration modes of uprising nonwetting phase, and presence of fracture/breach in the capillary barrier are studied in series of experiments for their influences on LCT. A variety of heterogeneous porous media made of a range of sizes of loosely packed silica beads are used to validate and test the persistence of local capillary trapping mechanism. By adjusting the boundary conditions (fluid levels in reservoirs attached to top and to bottom ports of the apparatus), the capillary pressure gradient across the domain was manipulated. Experiments were conducted with and without the presence of fracture/potential leakage pathway in the capillary seal. The trapped buoyant phase remained secure beneath the local capillary barriers, as long as the effective capillary pressure exerted by the trapped phase (proportional to column height of the phase) is smaller than the capillary entry pressure of the barrier. The local capillary trapping mechanism remained persistent even under forced imbibition, in which a significantly higher hydraulic potential gradient, and therefore a larger gradient in capillary pressure, was applied to the system. The column height of buoyant fluid that remained beneath the local capillary barrier was smaller by a factor corresponding to the increase in capillary pressure gradient. Mimicking a breach of the caprock by opening valves at the top of the apparatus allowed buoyant mobile phase held beneath the valves to escape, but buoyant phase held in local traps at saturations above residual, and therefore potentially mobile, was undisturbed. This work provides systematic validation of a novel concept, namely the long-term security of CO₂ that fills local (small-scale) capillary traps in heterogeneous storage formations. Results from this work reveal the first ever unequivocal experimental evidence on persistence of local capillary trapping mechanism. Attempts to quantify the nonwetting phase saturation and extent of LCT persistence serve as the initial steps to potentially reduce the risks associated with long-term storage security. / text