No description available.

Myosins are molecular motor proteins involved in cell movement, vesicle and organelle transport by moving along the cytoskeletal actin filaments. They include a myosin heavy chain and at least one myosin light chain (LC). The latter are typically bilobal proteins like calmodulin, where each lobe comprises a pair of EF-hand Ca2+-binding motifs. The LCs bind to ~25-residue IQ motifs that loosely conform to an IQXXXRGXXXR consensus sequence, and impart rigidity that is crucial for myosin function. The highly motile amoeba Dictyostelium discoideum expresses seven class I myosins, two of which (MyoD and MyoB) recruit the specific LCs MlcD and MlcB, with MlcB being the first observed single-lobe LC. However, the LCs for the remaining D. discoideum class I myosins are unknown. Identifying and characterizing these LCs is one focus of this thesis, with an overall goal of understanding their role in myosin function and regulation. Nuclear magnetic resonance spectroscopy, site-directed mutagenesis, and computational modeling were used to determine the solution structure of apo-MlcB and identify the MyoB IQ motif-binding site. Apo-MlcB differs from the typical closed conformation of an EF-hand Ca2+-binding protein in the apo-state as helix 1 in its structure is splayed from the remaining helices. The MyoB IQ motif-binding surface is not altered by Ca2+, involves residues from helices 1 and 4, and from residues in the N-terminal canonical EF-hand Ca2+-binding loop, and represents a unique mode of IQ recognition by a myosin LC. Calmodulin was identified as the LC for MyoA and MyoE while another single-lobe LC, MlcC, bound to two of three IQ motifs in MyoC. The solution structure of MlcC was more similar to the C-terminal lobe of apo-calmodulin than to apo-MlcB. Chemical shift perturbation studies suggest that like apo-CaM, MlcC undergoes a global MyoC IQ motif-induced conformational change. Computational modeling of the MlcC-MyoC IQ complex indicates that this is a feasible mode of IQ recognition. The structures of MlcB and MlcC, with their different modes of IQ motif binding, provide novel insights into IQ motif binding specificity and begin to illustrate their role in myosin function and regulation. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2013-01-29 11:42:03.428

In this thesis we review and build on the common methods used to analyze null geodesics in Schwarzschild de Sitter space. We present a general technique which allows finding measurable intersection angles of null trajectories analytically, and as one of its applications we establish a general relativistic aberration relationship. The tools presented are used to analyze some standard setups of gravitational deflection of light and gain a clear understanding of the role that the cosmological constant, Λ, plays in gravitational lensing phenomena. Through reviewing some recent papers on the topic with the present results in mind, we attempt to explain the major sources of disagreement in the ongoing debate on the subject, which started with Rindler and Ishak’s original paper, regarding the influence of Λ on lensing phenomena. To avoid ambiguities and room for misunderstanding we present clear definitions of the quantities used in the present analysis as well as in other papers we discuss. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2013-09-30 21:18:26.762

This thesis describes a number of compositions in which the objective was to investigate whether, and how far, the organisation of light can function as an extension of musical expression in the non-figurative visual realm. I explore the extent to which sound and light are compatible as media, in the sense of both being able to communicate a common set of ideas. The thesis begins by placing the discussion in a historical context, with an overview of the history of analogies between sound and light from Antiquity to the 19th century, as well as the history of Light Art. The second part of the thesis describes synaesthesia as a historically developed aesthetic concept and as a field of research that reveals interesting facts about the neuronal processing of stimulations from the senses. The third part forms the core of the research. It leads from a general historic discussion to more specific problems that emerged in my own work with sound and light. Light is a medium strongly characterised by purity; at first, light therefore seemed an inappropriate medium in which to offer plausible translations of different degrees of sonic noise. However, because of the importance that the inclusion of noise has taken in music since the 20th century, this would have meant a severe handicap in looking for a homological relationship between sound and light in artistic contexts. From a discussion of the broad implications the idea of dirt has in social and cultural contexts, the focus is eventually reduced to the aesthetic problem at hand. By means of a classification of three different sorts of noise, a more differentiated understanding becomes possible of the various functions that noise can have. Corresponding forms of ‘dirty light’ eventually become conceivable and artistically applicable. In the fourth part, six compositions and one audiovisual installation are discussed. Each of these works explores different relationships between the visual and sonic component. When appropriate, the various concepts of ‘dirty light’ that have been derived in the third part are reflected in the form of concrete examples. After discussing each work individually, certain practical problems are addressed that surfaced repeatedly under different performance circumstances. In the fifth part I pose the question of how far events that are conceived to be musical have to be based on sonic events. Common definitions of music that describe sonic events as its exclusive concern are questioned and a number of examples of music are discussed where the sonic outcome is hardly audible or even completely silent. I propose a notion that conceives music as a larger field of activity in which visual manifestations form an integral part. The seven audiovisual works form the practical component of this dissertation. As a result of this research a more differentiated understanding of the nature of the coupling of sound and light has emerged, alongside a comprehension of the at times strongly differing views on the general nature of cross-disciplinary works.

The objective of this thesis is to present the development of Raman microscopy for biochemical imaging of living cells. The main aim was to construct a Raman micro-spectrometer with the ability to perform time-course spectral measurements for the non-invasive study of biochemical processes in individual cells. The work can be divided into two parts: first, the development and characterization of the instrument; and second, completion of two experiments that demonstrate the suitability of Raman technique for studies of live cells. Instrumental development includes the design of optics and software for automated measurement. The experiments involve data collection and development of mathematical methods for analysis of the data. Chapter One provides an overview of techniques used in cell biology, with a special focus on Raman spectroscopy. It also highlights the importance of experiments on living cells, especially at the single cell level. Chapter Two explains the theoretical background of Raman spectroscopy. Furthermore, it presents the Raman spectroscopy techniques suitable for cell and biological studies. Chapter Three details the instrumentation and software development. The main parts of the confocal Raman micro-spectrometer, as designed for studying living cells, are: inverted microscope, 785 nm laser and high quality optics, environmental enclosure for maintaining physiological conditions during measurements of cells, and fluorescence wide-field microscopy facility for validation and confirmation of biochemical findings by Raman studies. Chapter Four focuses on the evaluation of the performance of the Raman setup and explains calibration and analysis methods applied to the data. Chapter Five and Six describe experiments performed on living cells. Chapter Five focuses on studies of the immunological synapse formed between primary dendritic and T cells indicating the polarisation of actin. Chapter Six describes time-course experiment performed on cancerous cells in the early phases of the apoptosis process, which enabled detection of the DNA condensation and accumulation of unsaturated lipids. Chapter Seven summarizes the work and gives concluding remarks.

Rydberg atoms are often proposed as the basis of quantum computing and quantum information protocols. One of the central reasons for this is that they provide a strong and long-ranged interaction that can be coherently switched on and off. This thesis details two techniques which use the exaggerated properties of Rydberg atoms to manipulate both the quantum state of the atom itself and that of the external light field. The first proposal initially focuses on the creation of many-body quantum states from two-level atoms trapped in a two-dimensional lattice. This approach uses the van der Waals interaction present between alkali metal atoms in highly excited Rydberg s-states. The approximate solution of the corresponding Hamiltonian is detailed in the regime where the laser driving is the largest energy scale of the system. The states which are most likely achieved using an oscillating laser detuning are then determined. These states are then taken as the basis for the creation of deterministic single-photons, whose properties are shown to rely on the interplay between interatomic spacing and the geometry of the lattice. The second technique described uses the coupling between a Rydberg atom and a moving electron to manipulate the atomic state. In this system, the atom is initially excited to a Rydberg s-state and trapped at a finite distance from an electron waveguide. Two analytical methods are used to show that the final state of the atom depends strongly on the direction and modulus of the electron momentum. A complementary numerical simulation shows that the atoms may be left in a polarised state, suggesting the possibility of using this setup to ‘switch on’ permanent electric dipoles in the atoms. This investigation leads naturally to a system where multiple interacting atoms are trapped close to the waveguide, allowing various many-body states to be accessed.

Optical interferometry offers a powerful tool for the study of the mechanical motion of micro- and nano-electromechanical systems (MEMS and NEMS). By examining the modulation of reflected light the displacement can be measured with sub-nanometre precision. Recent work with fibre interferometers carried out by other groups has studied the motion of nanomechanical systems down to temperatures as low as 1 K. Dissipation measurements in the last few years of a number of devices fabricated from high-stress amorphous silicon nitride have shown a marked increase in quality factors when compared to similar low-stress devices. The high quality factors and small masses of these devices have attracted a great deal of interest within the nanomechanical and optomechanical communities. Measurements of dissipation in nanomechanical resonators carried out in Nottingham to date have used the magnetomotive effect to detect nanomechanical motion. This has required that a layer of metal be applied to the high-stress silicon nitride, modifying the mechanical properties. In this thesis we present an overview of the design and construction of an optical detection system designed to study MEMS and NEMS devices from room temperature to liquid helium temperatures. Optical detection is able to measure the displacement of purely dielectric structures and as such is an ideal method with which to measure dissipation in these high-Q silicon nitride resonators, complementing the other nanomechanical measurement techniques available within Nottingham. Using this system, measurements have been made on a number of micro- and nano-electromechanical systems fabricated using processes developed during this work. Confocal images of these devices obtained using the fibre interferometer show a spatial resolution of 0.75 um, a value close to the diffraction limit of the system. Micromechanical quartz tuning forks have been measured to confirm the frequency response of the interferometer, with a value for the piezo-electro-mechanical coupling constant of 2.18 +/- 0.06 uC/m obtained that is in very good agreement with the values published in the literature. Nanomechanical measurements of 200 um square high-stress silicon nitride membranes have revealed thermoelastic damping to be the limiting dissipation mechanism for these resonators at room temperature. Using elastic theory it is possible to quantify the fQ floor predicted by thermoelastic damping seeing good agreement with experimental data. At lower temperatures inter-membrane coupling was observed, with acoustic vibrations from neighbouring membranes coupling into and being amplified by the membrane under observation. Discrepancies in quality factor between the observed and unobserved membranes are most likely due to optomechanical damping of the observed membrane by the laser. This inter-membrane coupling offers a powerful technique for the indirect observation of the flexural modes of nearby membranes without optically damping the response.

This work is centred on the development of Raman spectroscopy methods for investigating supported lipid bilayers (SLBs). These nanoscale, biological structures have found wide application as models of cellular membranes in many areas of scientific research. They consist of phospholipid molecules that self-organise into bilayer structures containing phase-separated microdomains, which play an important role in many biological processes. SLBs are well-defined and stable under a variety of conditions, allowing characterisation with a broad range of physical methods. However, many of these techniques provide purely a visualisation of the surface or disturb the bilayer with labelling. Raman spectroscopy can offer a non-invasive chemical and structural analysis of SLBs and microdomains. A Raman microspectroscopy (RMS) system with integrated atomic force microscope (AFM) has been developed and characterised for studying SLBs. This experimental setup combines the benefits of Raman spectroscopy with the high spatial resolution of confocal microscopy. Furthermore, the incorporation of AFM makes it possible to directly correlate chemical information and spatial features. Experiments are carried out to determine the capabilities of this system for investigating SLBs. A variety of substrates are considered for this application and only prolonged expose to high laser powers is found to have any effect on the Raman spectrum of lipids. However, a single SLB cannot be detected with RMS, so focus turns to employing scatteringenhancing techniques. Surface-enhanced Raman spectroscopy (SERS) substrates formed by nanosphere lithography (NSL) are developed to be used with the combined AFM-Raman system. Simultaneous topographical imaging and highsensitivity chemical mapping of molecular monolayers deposited across these substrates reveals the distribution and magnitude of electric field enhancement that they can provide. These measurements are supported by calculations and finite element method (FEM) simulations. Then similar experiments are performed on substrates covered with a bilayer of fatty acid molecules. Considering the close similarities between these molecules and phospholipids, this demonstrates the potential of combined AFM and SERS with NSL substrates for detecting SLBs and imaging the phase-separated microdomains they form. Finally, functionalised AFM probes are developed for tip-enhanced Raman spectroscopy (TERS) using dielectrophoresis (DEP). This phenomenon is generated within a conductive AFM setup to guide nanoparticles towards an AFM probe to cluster and grow at its tip apex. This growth is monitored with force spectroscopy and a variety of imaging parameters. The probes are then analysed with scanning electron microscopy (SEM) and energy-dispersive x-ray spectroscopy (EDX) to confirm the accumulation of nanoparticles on the tip both physically and chemically. The TERS activity of these functionalised probes is investigated with the combined AFM-Raman system, which demonstrates an enhancement of scattering when the tip apex of the probe and the laser are aligned.

Optical Tomography is a medical imaging modality that can be used to non- invasively image functional changes within the body. As near-infrared light is highly scattered by biological tissue, the process of image reconstruction is ill-posed and, in general is also under-determined. As such, model based iterative image reconstruction methods are used. These methods require an accurate model of light propagation through tissue, also known as the forward model. The diffusion approximation (DA) to the radiative transport equation is one of the most widely used forward models. It is based on the assumption that scattering events dominate over absorption events resulting in a diffuse light distribution. This is valid in cases with low absorption coefficients or large geometries (greater than a few scattering lengths). In many cases, however, such as in small animal imaging where the source-detector separation is small, this assumption is not valid and so a higher-ordered approximation is required. In this thesis, a three-dimensional frequency domain forward model based on the simplified spherical harmonics (SPN) approximation to the radiative transport equation is introduced. By comparison with a Monte- Carlo model, the SPN approximation is shown to be more accurate than the DA, especially in regions near to the sources and detectors and the increase in accuracy is greater in cases with stronger absorption. This is particularly important for bioluminescent imaging of small animals which involve both small geometries and strong absorption. Due to the asymptotic nature of the 3 SPN approximation, the highest ordered model was not necessarily the most accurate, but all models with N>1 were more accurate than the DA. The SPN based forward model has also been implemented into an image reconstruction algorithm. Despite the fact that the SPN approximation does not combine the scattering coefficient and anisotropy factor into a single variable, as is the case in the DA, it was found that it is not possible to reconstruct them uniquely. The SPN based models were shown to be able to reconstruct optical maps with greater accuracy than the DA. However, due to the increased number of unknowns to be recovered, the SP7 based reconstructed images contained significant artefact and cross-talk. Finally, a SPN-Diffusion hybrid model was developed in which the SPN model was used in the regions near to the source and the DA elsewhere. This model provides the increase of accuracy of the SPN models in the regions where the DA is insufficient, whilst retaining the computational efficiency of the DA. It was shown that the hybrid model leads to increased accuracy not only in the regions solved using the SPN model, but also in the DA based regions where as in a pure DA model, the errors near the source were propagated throughout the domain. It is also shown that the hybrid model can be solved in half the time of the full SPN model.

This dissertation presents a novel underwater machine vision technique which uses the optical properties of water to extract range information from colour images. By exploiting the fact that the attenuation of light in water is a function of frequency, an intensity-range transformation is developed and implemented to provide monocular vision systems with a three-dimensional scene reconstruction capability. The technique can also be used with images that have no salient, contrasting features and there are no restrictions on surface shapes. From a generalized reflectance map based on the optical properties of water, the closed form intensity-range transformation is derived to convert intensity images from various spectral bands into a range map wherein the value of each "pixel" is the range to the imaged surface. The technique is computationally efficient enough to be performed in real time and does not require specialized illumination or similar restrictive conditions. A calibration procedure is developed which enables the transformation to be practically implemented. An alternate approach to estimating range from multispectral data based on expanding the medium's transfer function and using these terms as elements in sensitivity vectors is also presented and analyzed. Mathematical analysis of the intensity-range transformation and associated developments is provided in terms of its performance in noise and sensitivity to various system parameters. Its performance as a function of light scattering is studied with the aid of computer simulation. Results from transforming actual underwater images are also presented. The results of this analysis and the demonstrated performance of the intensity-range transformation endorse it as a practical enhancement to underwater machine vision systems. / Graduate