Thesis (M. Sc.)--University of Alberta, 2010. / Title from pdf file main screen (viewed on Jan. 27, 2010). A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science, Department of Physics, University of Alberta. Includes bibliographical references.

Mechanical unfolding of -1 frameshift signals such as RNA pseudoknots have aimed to test the hypothesis that the stability of the pseudoknot is directly correlated to the frameshifting efficiency. Here we report unfolding of the Beet Western Yellow Virus (BWYV) pseudoknot by optical tweezers experiments complemented by computer simulations using steered molecular dynamics (SMD). Seven pseudoknot scenarios were studied: the wild-type pseudoknot in the presence and absence of Mg<super>2+</super>, the wild-type pseudoknot at high pH (deprotonated C8), and C8U, C8A, A24G, G19U, and G19UC mutant constructs. The mutants were selected to probe three key structural features of the BWYV pseudoknot, a triple-stranded helix at the base of stem 1, the stem junction region of stem 1 and stem 2, and a unique quadruple base-pair interaction involving a protonated cytosine in position 8 (C8). These regions are thought to control ribosomal frameshifting by different strategies such as thermodynamic stability, kinetic influences, and dynamics involving contacts with the ribosome. In addition, the mutants have been shown to either abolish frameshifting ability of the pseudoknot (C8 mutant cases and A24G), or actually increase the frameshifting efficiency (as seen with G19U and G19UC). We find three major conclusions from the stretching of the pseudoknot constructs with optical tweezers. First, stretching in the absence of Mg<super>2+</super> results in no observed unfolding transitions. We interpret this to mean that magnesium is indispensible for the stable folding of the pseudoknot. Second, we found that frameshifting efficiency is not correlated with the force required to unfold the pseudoknots. However, we observe the unfolding of stem 1 in all of the pseudoknots stretched, where stem 2 unfolding is below our noise level. For this reason, we cannot rule out the possibility that an estimate of the thermodynamic stability of the entire pseudoknot would correlate with frameshifting efficiency. And third, we found that each pseudoknot mutant that resulted in reduced frameshifting efficiency also exhibited more off-equilibrium unfolding transitions that the wild-type pseudoknot under comparable loading rates. We conclude from these studies that the resistance of a pseudoknot to unfolding is controlled by both thermodynamic and kinetic parameters. We then suggest new technologies that would allow for greater resolution in order to correlate pseudoknot unfolding behavior with -1 programmed ribosomal frameshifting events.

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Optical tweezers have allowed us to harness the momentum of light to trap, move, and manipulate microscopic particles with Angstrom-level precision. Position and force feedback systems grant us the ability to feel the microscopic world. As a tool, optical tweezers have allowed us to study a variety of biological systems, from the mechanical properties of red blood cells to the quantised motion of motor-molecules such as kinesin. They have been applied, with similar impact, to the manipulation of gases, atoms, and Bose-Einstein condensates. There are, however, limits to their applicability. Historically speaking, optical tweezers have only been used to trap relatively simple structures such as spheres or cylinders. This thesis is concerned with the development of a fabricational and optical manipulation protocol that allows holographical optical tweezers to trap photonic membranes. Photonic membranes are thin, flexible membranes, that are capable of supporting nanoplasmonic features. These features can be patterned to function as metamaterials, granting the photonic membrane the ability to function as almost any optical device. It is highly desirable to take advantage of these tools in a microfluidic environment, however, their extreme aspect ratios mean that they are not traditionally compatible with the primary technology of microfluidic manipulation: optical tweezers. In line with recent developments in optical manipulation, an holistic approach to optical trapping is used to overcome these limitations. Full six-degree-of-freedom control over a photonic membrane is demonstrated through the use of holographical optical tweezers. Furthermore, a photonic membrane (PM)-based surface-enhanced Raman spectroscopy sensor is presented which is capable of detecting rhodamine dye from a topologically undulating sample. This work moves towards marrying these technologies such that photonic membranes, designed for bespoke applications, can be readily deployed into a microfluidic environment. Extending the range of tools available in the microfluidic setting helps pave the way toward the next set of advances in the field of optical manipulation.

abstract: Volumetric cell imaging using 3D optical Computed Tomography (cell CT) is advantageous for identification and characterization of cancer cells. Many diseases arise from genomic changes, some of which are manifest at the cellular level in cytostructural and protein expression (functional) features which can be resolved, captured and quantified in 3D far more sensitively and specifically than in traditional 2D microscopy. Live single cells were rotated about an axis perpendicular to the optical axis to facilitate data acquisition for functional live cell CT imaging. The goal of this thesis research was to optimize and characterize the microvortex rotation chip. Initial efforts concentrated on optimizing the microfabrication process in terms of time (6-8 hours v/s 12-16 hours), yield (100% v/s 40-60%) and ease of repeatability. This was done using a tilted exposure lithography technique, as opposed to the backside diffuser photolithography (BDPL) method used previously (Myers 2012) (Chang and Yoon 2004). The fabrication parameters for the earlier BDPL technique were also optimized so as to improve its reliability. A new, PDMS to PDMS demolding process (soft lithography) was implemented, greatly improving flexibility in terms of demolding and improving the yield to 100%, up from 20-40%. A new pump and flow sensor assembly was specified, tested, procured and set up, allowing for both pressure-control and flow-control (feedback-control) modes; all the while retaining the best features of a previous, purpose-built pump assembly. Pilot experiments were performed to obtain the flow rate regime required for cell rotation. These experiments also allowed for the determination of optimal trapezoidal neck widths (opening to the main flow channel) to be used for cell rotation characterization. The optimal optical trap forces were experimentally estimated in order to minimize the required optical power incident on the cell. Finally, the relationships between (main channel) flow rates and cell rotation rates were quantified for different trapezoidal chamber dimensions, and at predetermined constant values of laser trapping strengths, allowing for parametric characterization of the system. / Dissertation/Thesis / Demonstration of process flow in the microvortex chip / Cell rotation in a 50 microns wide (at the neck) trapezoidal chamber,at a flow rate of 95 microliters/min at approximately 0.25 rev/s / Cell rotation in a 70 microns wide (at the neck) trapezoidal chamber,at a flow rate of 7 microliters/min at approximately 0.125 rev/s / M.S. Bioengineering 2013

<div>In the 1970's, Arthur Ashkin developed a remarkable system called the ``optical tweezer'' which utilizes the radiation pressure of light to manipulate particles. Because of its non-invasive nature and controllability, optical tweezers have been widely adopted in biology, chemistry and physics. In this dissertation, two applications related to optical tweezers will be discussed. The first application is about the demonstration of multiple feedback controlled optical tweezers which let us conduct novel experiments which have not been performed before. For the second application, levitation of a silica nanodumbbell and cooling its motion in five degrees of freedom is executed.</div><div><br></div><div>To be more specific, the first chapter of the thesis focuses on an experiment using the feedback controlled optical tweezers in water. A well-known thought experiment called ``Feynman's ratchet and pawl'' is experimentally demonstrated. Feynman’s ratchet is a microscopic heat engine which can rectify the random thermal fluctuation of molecules to harness useful work. After Feynman proposed this system in the 1960’s, it has drawn a lot of interest. In this dissertation, we demonstrate a solvable model of Feynman’s ratchet using a silica nanoparticle inside a feedback controlled one dimensional optical trap. The idea and techniques to realize two separate thermal reservoirs and to keep them in contact with the ratchet is discussed in detail. Also, both experiment and simulation about the characteristics of our system as a heat engine are fully explored.</div><div><br></div><div>In the latter part of the dissertation, trapping silica nanodumbbell in vacuum and cooling its motion in five degrees of freedom is discussed. A levitated nanoparticle in vacuum is an extraordinary optomechanical system with an exceptionally high mechanical quality factor. Therefore, levitated particles are often utilized as a sensor in various research. Different from a levitated single nanosphere, which is only sensitive to force, a levitated nanodumbbell is sensitive to both force and torque. This is due to the asymmetry of the particle resulting it to have three rotational degrees of freedoms as well as three translational degrees of freedoms. In this dissertation, creating and levitating a silica nanodumbbell will be demonstrated. Active feedback cooling also known as cold damping will be employed to stabilize and cool the two torsional degrees of freedom of the particle along with the three center of mass DOF in vacuum. Additionally, both computational and experimental analysis is conducted on a levitated nanodumbbell which we call rotation-coupled torsional motion. The complex torsional motion can be fully explained with the effects of both thermal nonlinearity and rotational coupling. The new findings and knowledge of a levitated non-spherical particles leads us one step further towards levitated optomechanics with more complex particles.</div>

Plasmonics have been used to enhance the interaction of light with metallic nanostructures and lanthanide-doped upconversion nanocrystals. This enhancement can be achieved by using specific structures, materials, and plasmonic resonators at the emission and absorption wavelengths of the particles. This dissertation is based on four projects, which are mainly about the interaction of light and matter in metallic nanostructures and the up-conversion of nanocrystals using plasmonic resonators. In metal-insulator-metal systems, the cavity's resonant length is determined by the plasmon wavevector and the phase of reflection from the end faces. In general, the resonance length is not a simple multiple of the half-wavelength due to the significant reflection phase. As a result, in order to have a better understanding of MIM cavity resonances, the reflection phase must be calculated correctly. In the first project, the reflection phase obtained by SPPs upon reflection off the slit end-faces is calculated analytically using a simple mode matching model for real metals showing both dispersion and loss. The technique is similar to previous works, with the exception that we use the unconjugated version of the orthogonality relation. The results show good agreement with the experimental data. By having a strong grasp of the SPP dispersion, this technique aids in the design of plasmonic devices for operation at a specific wavelength. Single-photon sources are optical sources capable of emitting a single photon. A single lanthanide ion within a plasmonic nano structure with a large emission enhancement is one technique to generate a single-photon source at 1550 nm, which is a low-loss band used in fibre optics. In the second project, plasmonic double nanohole resonators are fabricated using colloidal lithography. These structures have been used to enhance the emission from low-concentration erbium emitters. The results indicate that different levels of emissions exist based on the amount of Er contained inside the nanocrystals. These findings would be an excellent starting point for developing a single-photon source operating at a 1550 nm wavelength employing erbium. Because not only can it increase the emission rate from erbium emitters, but it also helps to find and isolate a single emitter, which gives a stable single photon source. Because the surface plasmon resonance is exponentially coupled to the surface, it exhibits excellent sensitivity to changes in the refractive index near the surface. This is the underlying principle of commercially available surface plasmon resonance biosensors. Due to the wide range of applications in water quality testing and biosensing, it is critical to developing highly sensitive sensors that are compatible with commercial sensors. In the third project, we develop a design for SRSP sensing using a rectangular stripe grating and a 10 nm thick gold film. The 10 nm gold layer is sufficiently thick to enable continuous films to be formed using standard deposition procedures. We demonstrate that by employing rigorous coupled-wave analysis, the surface sensitivity of these films to an adlayer is increased by 3.3 times in angle units and the resolution is increased by fourfold while working at the commercial SPR system wavelength of 760 nm. Before trapping a particle in double nanohole apertures, we must first locate the double nanohole on the sample (gold on glass with apertures) and compare the scanning electron microscopy images with the image on the camera in the optical setup using certain markers. In the fourth project, to make DNH aperture trapping easier, we provide a polarization and transmission dependency approach for localizing and orienting DNHs on a substrate. This method provides a time and cost-effective way to ease the experimental process. This technique may also be used to localize different aperture clusters and single holes. / Graduate

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This thesis explores the structures and dynamics of optically confined matter, ranging from single particle traps to complex optically bound colloidal arrays, investigating and quantifying the behaviour of each system. It begins with an introduction to optical manipulation techniques and a discussion of the development of the single beam gradient force trap, more commonly referred to as optical tweezers. Following this, the building of a single beam optical trap will be presented alongside a discussion of some of the key components in such a setup, before it is calibrated, allowing a demonstration of some of the techniques which are utilised later in the thesis. The optical trapping of aerosol droplets is an area of key importance in atmospheric chemistry, as optical tweezers provide a valuable and versatile tool for droplet manipulation and characterisation. Trapping single aerosol droplets is facilitated by using annular rather than conventional Gaussian beams, as will be demonstrated, with significant advantages in increasing the size range of trappable droplets, and improving their axial localisation. These improvements will be demonstrated experimentally with an in-depth comparison of Gaussian and annular beam trapping. These enhancements are also verified theoretically using a model developed by Burnham and McGloin, showing excellent agreement with experimental results. Ionic liquids, defined as organic salts with melting points below room temperature, are another area of great contemporary interest. They are highly tunable and so have been referred to as "designer solvents", and also have important applications as "green" solvents in organic chemistry. Trapping particles within these novel liquids allows a micro-rheological investigation of their properties to be conducted. This is demonstrated by determining the temperature dependent viscosity changes of these media, showing excellent agreement with previous macro-rheological studies. In addition, hydrodynamic effects such as Faxen's correction to viscous drag in proximity to a surface, and hydrodynamic coupling between pairs of colloids trapped in ionic liquids are demonstrated. Following these single and dual particle studies, this thesis continues with an investigation of the structures and dynamics of optically bound matter formed of larger numbers of particles. The behaviour of these optically bound structures is particularly sensitive to the number of particles involved, and so a counter-propagating evanescent field trap in conjunction with an inverted optical tweezers setup is utilised in order to controllably assemble these structures and study the factors affecting their behaviour. Initially one-dimensional chains of optically bound 3.5 um diameter silica particles are studied, allowing an implementation of Generalized Lorentz-Mie Theory (GLMT) to be developed through collaboration with Dr. Jonathan Taylor of The University of Glasgow. Experimental and theoretical insights allow further understanding of the processes involved in the formation of these structures. Having studied the behaviour of 3.5 um diameter silica particles in a counter-propagating evanescent wave trap, the effects of changing particle size and refractive index are presented by using smaller silica and melamine particles. These results are explained in terms of the increased importance of interference fringes in determining the arrangement of the optically bound structures of smaller particles, and due to the increased interaction of the melamine particles with the evanescent field as a result of the larger refractive index contrast between them and the trapping medium. The thesis then concludes with a study of the dynamics of the previously presented optically bound chains. Initially the diffusion of single particles in the evanescent field is compared to their freely-diffusing behaviour, quantifying the confining effect of the field. The addition of particles to the field then allows the diffusive behaviour to be studied as a function of particle number, and understood in terms of on-axis confinement by adjacent particles. The tilting of these optically bound chains relative to the inter-beam axis is also explored as a function of particle number, as is the rigidity of these chains. Finally a more complex, dynamic effect is presented, dubbed "Newton's Cradle", in which particles are ejected from the ends of the chains before returning and repeating this process. This behaviour is understood by utilising the previously developed GLMT simulations.