Probabilistic Ray-Tracing Aided Positioning at mmWave frequencies

We consider the following positioning problem where several base stations (BS) try to locate a user equipment (UE): The UE sends a positioning signal to several BS. Each BS performs Angle of Arrival (AoA) measurements on the received signal. These AoA measurements as well as a 3D model of the environment are then used to locate the UE. We propose a method to exploit not only the geometrical characteristics of the environment by a ray-tracing simulation, but also the statistical characteristics of the measurements to enhance the positioning accuracy.Comment: Accepted at the conference Indoor Positioning and Indoor Navigation (IPIN) 202

Perceptually Driven Interactive Sound Propagation for Virtual Environments

Sound simulation and rendering can significantly augment a user‘s sense of presence in virtual environments. Many techniques for sound propagation have been proposed that predict the behavior of sound as it interacts with the environment and is received by the user. At a broad level, the propagation algorithms can be classified into reverberation filters, geometric methods, and wave-based methods. In practice, heuristic methods based on reverberation filters are simple to implement and have a low computational overhead, while wave-based algorithms are limited to static scenes and involve extensive precomputation. However, relatively little work has been done on the psychoacoustic characterization of different propagation algorithms, and evaluating the relationship between scientific accuracy and perceptual benefits.In this dissertation, we present perceptual evaluations of sound propagation methods and their ability to model complex acoustic effects for virtual environments. Our results indicate that scientifically accurate methods for reverberation and diffraction do result in increased perceptual differentiation. Based on these evaluations, we present two novel hybrid sound propagation methods that combine the accuracy of wave-based methods with the speed of geometric methods for interactive sound propagation in dynamic scenes.Our first algorithm couples modal sound synthesis with geometric sound propagation using wave-based sound radiation to perform mode-aware sound propagation. We introduce diffraction kernels of rigid objects,which encapsulate the sound diffraction behaviors of individual objects in the free space and are then used to simulate plausible diffraction effects using an interactive path tracing algorithm. Finally, we present a novel perceptual driven metric that can be used to accelerate the computation of late reverberation to enable plausible simulation of reverberation with a low runtime overhead. We highlight the benefits of our novel propagation algorithms in different scenarios.Doctor of Philosoph

Computer Generation of Integral Images using Interpolative Shading Techniques

Research to produce artificial 3D images that duplicates the human stereovision has been ongoing for hundreds of years. What has taken millions of years to evolve in humans is proving elusive even for present day technological advancements. The difficulties are compounded when real-time generation is contemplated. The problem is one of depth. When perceiving the world around us it has been shown that the sense of depth is the result of many different factors. These can be described as monocular and binocular. Monocular depth cues include overlapping or occlusion, shading and shadows, texture etc. Another monocular cue is accommodation (and binocular to some extent) where the focal length of the crystalline lens is adjusted to view an image. The important binocular cues are convergence and parallax. Convergence allows the observer to judge distance by the difference in angle between the viewing axes of left and right eyes when both are focussing on a point. Parallax relates to the fact that each eye sees a slightly shifted view of the image. If a system can be produced that requires the observer to use all of these cues, as when viewing the real world, then the transition to and from viewing a 3D display will be seamless. However, for many 3D imaging techniques, which current work is primarily directed towards, this is not the case and raises a serious issue of viewer comfort. Researchers worldwide, in university and industry, are pursuing their approaches in the development of 3D systems, and physiological disturbances that can cause nausea in some observers will not be acceptable. The ideal 3D system would require, as minimum, accurate depth reproduction, multiviewer capability, and all-round seamless viewing. The necessity not to wear stereoscopic or polarising glasses would be ideal and lack of viewer fatigue essential. Finally, for whatever the use of the system, be it CAD, medical, scientific visualisation, remote inspection etc on the one hand, or consumer markets such as 3D video games and 3DTV on the other, the system has to be relatively inexpensive. Integral photography is a ‘real camera’ system that attempts to comply with this ideal; it was invented in 1908 but due to technological reasons was not capable of being a useful autostereoscopic system. However, more recently, along with advances in technology, it is becoming a more attractive proposition for those interested in developing a suitable system for 3DTV. The fast computer generation of integral images is the subject of this thesis; the adjective ‘fast’ being used to distinguish it from the much slower technique of ray tracing integral images. These two techniques are the standard in monoscopic computer graphics whereby ray tracing generates photo-realistic images and the fast forward geometric approach that uses interpolative shading techniques is the method used for real-time generation. Before this present work began it was not known if it was possible to create volumetric integral images using a similar fast approach as that employed by standard computer graphics, but it soon became apparent that it would be successful and hence a valuable contribution in this area. Presented herein is a full description of the development of two derived methods for producing rendered integral image animations using interpolative shading. The main body of the work is the development of code to put these methods into practice along with many observations and discoveries that the author came across during this task.The Defence and Research Agency (DERA), a contract (LAIRD) under the European Link/EPSRC photonics initiative, and DTI/EPSRC sponsorship within the PROMETHEUS project

The slicing extent technique for fast ray tracing

A new technique for image generation using ray tracing is introduced. The “Slicing Extent Technique” (SET) partitions object space with slicing planes perpendicular to all three axes. Planes are divided into two dimensional rectangular cells, which contain pointers to nearby objects. Cell size and the space between slices varies, and is determined by the objects’ locations and orientations. Unlike oct-tree and other space-partitioning methods, SET is not primarily concerned with dividing space into mutually exclusive volume elements (‘voxels’) and identifying objects within each voxel. Instead, SET is based on analysis of projections of objects onto slicing planes. In comparison to the existing space subdivision methods for ray tracing, SET avoids tree traversal and exhibit no anomalous behavior. There is no reorganization when new objects arrive. Preprocessing to create slices is inexpensive and produces a finely tuned filter mechanism which supports rapid ray tracing

Induced seismicity and environmental change at the geysers geothermal area in California.

Intensive exploitation of the reservoir at The Geysers geothermal area, California, induces myriads of small-magnitude earthquakes that are monitored by a dense, permanent seismometer network that covers most of the reservoir. However, majority of the seismic stations, which belong to the UNOCAL network are poorly calibrated. Station polarities, and sensor orientations for the 8 three-component stations of this network were determined by using accurate focal mechanism solutions from a temporary network and using a simple method of observing the waveform from known earthquake locations. Using data from the UNOCAL network, tomographic inversions were performed for the three-dimensional Vp and Vp/Vs-ratio structure of the reservoir for February 1993, October 1996 and August 1998, adding to the inversions for April 1991 and December 1994 that had already been performed by other investigators. The extensive low -Vp/Vs anomaly known to characterise the reservoir grew progressively in strength from a maximum of 9% to a maximum of 12.4% at sea level during the seven-year study period. The anomaly growth is attributed to the depletion of pore liquid water in the reservoir and its replacement with steam. This causes Vp to decrease by increasing compressibility, and Vs to increase because of the reduction in pore pressure and the drying of argillaceous minerals, e.g., illite, which increases the shear modulus. All these effects serendipitously combine to lower the Vp/Vs ratio, resulting in an exceptionally strong overall effect that provides a convenient tool for monitoring reservoir depletion in the seismogenic zone. Variations in the separate Vp and Vs fields indicate that water depletion was the most important process in the central part of the exploited reservoir, and that pressure reduction and mineral drying were the dominant effects more northwesterly and southeasterly. Relative relocation of micro earthquakes was also performed using the same network. Four regions were studied. Although most multiplets relocated into tighter clusters and the reduction in the RMS of the relative relocations was good, further work is needed to substantiate these initial findings

Visualising software in cyberspace

The problems of maintaining software systems are well documented. The increasing size and complexity of modern software serves only to worsen matters. Software maintainers are typically confronted with very large and very complex software systems, of which they may have little or no prior knowledge. At this stage they will normally have some maintenance task to perform, though possibly little indication of where or how to start. They need to investigate and understand the software to some extent in order to begin maintenance. This understanding process is termed program comprehension. There are various theories on program comprehension, many of which put emphasis on the construction of a mental model of the software within the mind of the maintainor. These same theories hypothesise a number of techniques employed by the maintainer for the creation and revision of this mental model. Software visualisation attempts to provide tool support for generating, supplementing and verifying the maintainer’s mental model. The majority of software visualisations to date have concentrated on producing two dimensional representations and animations of various aspects of a software system. Very little work has been performed previously regarding the issues involved in visualising software within a virtual reality environment. This research represents a significant first step into this exciting field and offers insight into the problems posed by this new media. This thesis provides an identification of the possibilities afforded byU3D graphics for software visualisation and program comprehension. It begins by defining seven key areas of 3D software visualisation, followed by the definition of two terms, visualisation and representation. These two terms provide a conceptual division between a visualisation and the elements of which it is comprised. This division enables improved discussion of the properties of a 3D visualisation and particularly the idenfification of properties that are desirable for a successful visualisation. A number of such desirable properties are suggested for both visualisations and representations, providing support for the design and evaluation of a 3D software visualisation system. Also presented are a number of prototype visualisations, each providing a different approach to the visualisation of a software system. The prototypes help demonstrate the practicalities and feasibility of 3D software visualisation. Evaluation of these prototypes is performed using a variety of techniques, the results of which emphasise the fact that there is substantial potential for the application of 3D graphics and virtual reality to software visualisation

Applying single-molecule localisation microscopy to achieve virtual optical sectioning and study T-cell activation

Single-molecule localisation microscopy (SMLM) allows imaging of fluorescently-tagged proteins in live cells with a precision well below that of the diffraction limit. As a single-molecule technique, it has also introduced a new quantitative approach to fluorescence microscopy. In the Part A of this thesis, the design and building of three SMLM instruments, the implementation of a custom-developed image analysis package and the characterisation of the photo-physical properties of the photo-activable fluorescent protein used in this thesis (mEos), are discussed. Then, a new post-processing method for SMLM analysis is characterised: axial optical sectioning of SMLM images is demonstrated by thresholding fitted localisations using their fitted width and amplitude to reject fluorophores that emit from above or below a virtual ‘light-sheet’, a thin volume centred on the focal plane of the microscope. This method provides qualitative and quantitative improvements to SMLM. In the Part B of this thesis, SMLM is applied to study T cell activation. Although the T cell receptor plays a key role in immunity, its stoichiometry in the membrane of resting T cells is still a matter of debate. Here, single-molecule counting methods are implemented to compare the stoichiometry of TCRs fused with mEos2 in resting T cells to monomeric and dimeric controls. However, because of the stochasticity of mEos2 photo-physics, results are inconclusive and new counting techniques based on structural imaging are discussed. In addition to TCR triggering, T cells require the co-stimulatory triggering of the CD28 transmembrane receptor to become fully activated. However, some immobilised anti-CD28 antibodies, referred to as super-agonists (SA), can directly activate T cells without triggering the TCR. In this thesis, single-molecule tracking techniques are used to investigate the molecular mechanism of CD28 super-agonism in live T cells. The results indicate that the diffusion of CD28 is slowed by SA binding. This effect is further discussed in light of the kinetic-segregation model proposed for TCR triggering. Quantitative SMLM as implemented and further developed in this work offers new tools to investigate the molecular mechanisms initiating T cell activation, ultimately facilitating the discovery of novel approaches to target these pathways for therapeutic purposes.This work was supported by the Wellcome Trust [studentship number 093756/B/10/Z]

The WEAVE fibre positioner: calibration, commissioning, and first-light

This thesis details the final assembly and calibration procedures for the WEAVE fibre positioner, from October 2019 to first-light in September 2022. The positioner was successfully mounted to the William Herschel Telescope (WHT) in May 2022. I present the first-light results of WEAVE for each of its three observing modes and discuss whether the positioner has met its design expectations. Chapter one describes the evolution of astronomical spectroscopy and the scientific motivations behind the construction of WEAVE. This is followed by the instrument design specification and sub-systems required to meet them. Chapter two will focus on the positioner in detail and include the evolution of our quality control methods. An account of the calibration procedures, in both the lab environment and on the elevation testing rig, is given in chapter three. The test rig revealed flexure behaviour in the positioner's structure, which was modified to correct for this. The calibration work was repeated with improved techniques, to predict changes in the positioner's metrology with elevation. This chapter then presents the results of the fibre movement testing, including the current placement timings To maximise the scientific output from WEAVE, I applied a series of adjustments to a subset of target fields, identifying methods that will improve the survey output using the fibre assignment program, Configure, and highlight potential selection effects. Chapter five presents the first-light results and the steps taken to achieve this. It required extensive measurements of the optical distortion map across the FoV, which were carefully mapped using astrometry of the night-sky across our focal plane. I then compare these results with the observational requirements from WEAVE's conception, to define its overall success. Chapter 6 provides an overview of the work completed in this thesis and describes potential upgrades to the instrument in the future

Expression and structural studies of multidomain proteins and complexes

It is generally accepted that there is a level of organization in proteins that overlaps the classical definitions of tertiary and quaternary structure, i.e. sequentially consecutive residues in polypeptide chains fold into distinct compact regions called domains. Many multidomain proteins are flexible and are not amenable to X-ray crystallography or are too big for multi dimensional nuclear magnetic resonance techniques, while other proteins form oligomeric structures from subunits. It is possible using small-angle X-ray and neutron scattering, coupled with molecular modelling techniques, to locate the relative positions of these domains or subunits relative to each other within the full protein structure. This PhD thesis has looked at a variety of native and recombinant oligomeric proteins and domains and attempts have been made to produce low resolution structures of their oligomerisation or their multidomain structures. Expression systems used include a Pseudomonas aeruginosa over-expression system and the baculovirus expression system. One multidomain protein was studied, namely factor I of the complement system. Two forms of factor I were studied, a native form purified from human plasma, and a recombinant form produced in insect cells. Scattering modelling was used to elucidate a bilobal domain arrangement in factor I, in which the different types of carbohydrate present on the two different forms could be modelled. The quaternary structures of two complexes were determined, namely the homo- oligomeric complexes of the Ps. aeruginosa amidase regulatory protein, AmiC, and the Mycobacterium leprae Holliday junction protein, RuvA. It was determined that in solution AmiC exists as a monomer-trimer equilibrium, and that RuvA adopts an octameric structure, both when lice and when complexed with DNA, within which the Holliday junction is buried in the RuvA-DNA complex