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

No description available.

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.

The thermal velocity fluctuations of microscopic particles mediate the transition from microscopic statistical mechanics to macroscopic long-time diffusion. Prior to this work, detection methods lacked the sensitivity necessary to resolve motion at the length and time scales at which thermal velocity fluctuations occur. This dissertation details two experiments which resulted in velocity measurement of the thermal motion of dielectric microspheres suspended by an optical trap in gases and liquids. First, optical tweezers were used to trap glass microspheres in air over a wide range of pressures and a detection system was developed to track the trapped microspheres' trajectories with MHz bandwidth and <100 fm/rt(Hz) position sensitivity. Low-noise trajectory measurements allowed for observation of fluctuations in the instantaneous velocity of a trapped particle with a signal to noise ratio (SNR) of 26 dB, and provided direct verification of the equipartition theorem and of the Maxwell-Boltzmann velocity distribution for a single Brownian particle. Next, the detection technology was further optimized and used to track optically trapped silica and barium titanate glass microspheres in water and acetone with >50 MHz bandwidth and <3 fm/rt(Hz) sensitivity. Brownian motion in a liquid is influenced by hydrodynamic, time-retarded coupling between the particle and the fluid flow its motion generates. Our measurements allowed for instantaneous velocity measurement with an SNR of up to 16 dB and confirmed the Maxwell Boltzmann distribution for Brownian motion in a liquid. The measurements also revealed several unusual features predicted for Brownian motion in the regime of hydrodynamic coupling, including faster-than-exponential decay of the velocity autocorrelation function, correlation of the thermal force and non-zero cross-correlation between the particle's velocity and the thermal force preceding it. / text

Single atoms are promising candidates for physically implementing quantum bits, the fundamental unit of quantum information. We have built an apparatus for cooling, trapping and imaging single rubidium atoms in microscopic optical tweezers. The traps are formed from a tightly focused off-resonant laser beam, which traps atoms using the optical dipole force. The traps have a diameter of ~1 &mu;m and a depth of ~1 mK. The novelty of our approach is the use a digital mirror device (DMD) to generate multiple independently movable tweezers from a single laser beam. The DMD consists of an array of micro-mirrors that can be switched on and off, thus acting as a binary amplitude modulator. We use the DMD to imprint a computer-generated hologram on the laser beam, which is converted in to the desired arrangement of traps in the focal plane of a lens. We have developed fast algorithms for calculating binary holograms suitable for the DMD. In addition, we use this method to measure and correct for errors in the phase of the wavefront caused by optical aberrations, which is necessary for producing diffraction-limited focal spots. Using this apparatus, we have trapped arrays of up to 20 atoms with arbitrary geometrical arrangements. We exploit light-assisted collisions between atoms to ensure there is at most one atom per trapping site. We measure the temperature of the atoms in the traps to be 12 &mu;K, and their lifetime to be 1.4 s. Finally, we demonstrate the ability to select individual atoms from an array and transport them over a distance of 14μm with laser cooling, and 5 &mu;m without.

In the atmosphere, cloud droplets can remain in a supercooled liquid phase at temperatures as low as -40 °C. Above this temperature, cloud droplets freeze via heterogeneous ice nucleation whereby a rare and poorly understood subset of atmospheric particles catalyze the ice phase transition. As the phase state of clouds is critical in determining their radiative properties and lifetime, deficiencies in our understanding of heterogeneous ice nucleation poses a large uncertainty on our efforts to predict human induced global climate change. Experimental challenges in properly simulating particle-induced freezing processes under atmospherically relevant conditions have largely contributed to the absence of a well-established model and parameterizations that accurately predict heterogeneous ice nucleation. Conversely, the sparsity of reliable measurement techniques available struggle to be interpreted by a single consistent theoretical or empirical framework, which results in layers of uncertainty when attempting to extrapolate useful information regarding ice nucleation for use in atmospheric cloud models. In this dissertation a new framework for describing heterogeneous ice nucleation is developed. Starting from classical nucleation theory, the surface of an ice nucleating particle is treated as a continuum of heterogeneous ice nucleating activity and a particle specific distribution of this activity g is derived. It is hypothesized that an individual particle species exhibits a critical surface area. Above this critical area the ice nucleating activity of a particle species can be described by one g distribution, 𝑔, while below it 𝑔 expresses itself expresses externally resulting in particle to particle variability in ice nucleating activity. The framework is supported by cold plate droplet freezing measurements for dust and biological particles in which the total surface area of particle material available is varied. Freezing spectra above a certain surface area are shown to be successfully fitted with 𝑔 while a process of random sampling from 𝑔 can predict the freezing behavior below the identified critical surface area threshold. The framework is then extended to account for droplets composed of multiple particle species and successfully applied to predict the freezing spectra of a mixed proxy for an atmospheric dust-biological particle system. The contact freezing mode of ice nucleation, whereby a particle induces freezing upon collision with a droplet, is thought to be more efficient than particle initiated immersion freezing from within the droplet bulk. However, it has been a decades’ long challenge to accurately measure this ice nucleation mode, since it necessitates reliably measuring the rate at which particles hit a droplet surface combined with direct determination of freezing onset. In an effort to remedy this longstanding deficiency a temperature controlled chilled aerosol optical tweezers capable of stably isolating water droplets in air at subzero temperatures has been designed and implemented. The new temperature controlled system retains the powerful capabilities of traditional aerosol optical tweezers: retrieval of a cavity enhanced Raman spectrum which could be used to accurately determine the size and refractive index of a trapped droplet. With these capabilities, it is estimated that the design can achieve ice supersaturation conditions at the droplet surface. It was also found that a KCl aqueous droplet simultaneously cooling and evaporating exhibited a significantly higher measured refractive index at its surface than when it was held at a steady state temperature. This implies the potential of a “salting out” process. Sensitivity of the cavity enhanced Raman spectrum as well as the visual image of a trapped droplet to dust particle collisions is shown, an important step in measuring collision frequencies of dust particles with a trapped droplet. These results may pave the way for future experiments of the exceptionally poorly understood contact freezing mode of ice nucleation.

This thesis describes the construction of an Optical Tweezer apparatus to be used in conjunction with a confocal Raman spectrometer. The tweezer utilizes an infrared (λ=1064 nm) laser directed into an inverted microscope with NA=1.4 oil immersion 100x objective lens that strongly focuses the laser light into a sample to function as a single-beam gradient force trap. The long term goal of this research program is to develop a single molecule Raman tweezers apparatus that allows one to control the position of a Raman nanoplasmonic amplifier. This thesis describes the construction of the Raman tweezer apparatus along with several Raman spectra obtained from optically trapped samples of polystyrene fluorescent orange, amine-modified latex beads. In addition, I explored the Raman spectra of bulk cytochrome c mixed with or injected onto Ag aggregates for SERs enhancement.

Optical manipulation covers a wide range of techniques to guide and trap cells using only the forces exerted by light. Another optical tool is photoporation, the technique of injecting membrane-impermeable molecules using light, which has become an important alternative to other injection techniques. Together they provided sterile tools for manipulation and molecule delivery at the single-cell level. In this thesis, the properties of low Reynolds fluid flows are exploited to guide cells though a femtosecond Bessel beam. This design allows for high-throughput optical injection of cells without the need to individually target cells. A method of 'off-chip' hydrodynamic focusing was evaluated and was found to confine 95.6% of the sample within a region which would receive a femtosecond dose compared to 20% without any hydrodynamic focusing. The system was tested using two cell lines to optically inject the membrane-impermeable dye, propidium iodide. This resulted in an increase of throughput by an order of magnitude compared to the previous microfluidic design (to up to 10 cells per second). Next optical trapping and photoporation were combined to create a multimodal workstation. The system provides 3D beam control using spatial light modulators integrated into a custom user interface. The efficiency of optical injection of adherent cells and trapping capabilities were tested. The development of the system provides the groundwork for exploration of the parameters required for photoporation of non-adherent cells. Finally optical trapping is combined with temporally focused multiphoton illumination for scanless imaging. The axial resolution of the system was measured using different microscope objectives before imaging cells stained with calcein. Both single and a pair of recently trypsinised cells were optically trapped and imaged. The position of the trapped cells was manipulated using a spatial light modulator in order to obtain a z-stack of images without adjusting the objective position.