# Physics - Theses, Dissertations, and other Required Graduate Degree Essays

## A 3D computational model of cervical epithelial tissue: Exploring how cell characteristics and mutations affect homeostasis and tissue composition

Author:
Date created:
2019-12-06
Abstract:

Cervical cancer is the fourth most common cancer among women. Early diagnosis of precancerous lesions in the cervix is important to prevent development of invasive cervical cancer. At the same time, misdiagnosis can result in unnecessary surgery. Computational simulations open up a new approach to study how cell mutations disrupt the steady state of a healthy epithelial tissue and what mutations can lead to development of preneoplastic lesions. I modified a previously used 3D individual cell-based model to simulate a dynamic healthy stratified cervical epithelium and tested it by comparing my results with diagnostic data from healthy cervical biopsies. I explored how changes in several cell characteristics modified and affected the steady state to better understand the impact. In addition, I did simulations where a mutated stem cell was introduced into a healthy steady epithelium to study its effect on tissue homeostasis and how uncontrolled division of mutated cells leads to a cervical intraepithelial neoplasia 3 (CIN3) pre-neoplastic lesion. My simulation results showed good resemblance to biopsy data given to us by BC Cancer Research Center. These results yield insight into how different cell characteristics contribute to regulating tissue structure and how different kinds of cell mutations can lead to cervical pre-neoplastic lesions with different degrees of severity. This understanding can help in diagnosing cervical biopsies and possibly predict the potential severity of the lesion.

Document type:
Thesis
File(s):
Supervisor(s):
Eirikur Palsson
Department:
Science: Department of Physics
Thesis type:
(Thesis) M.Sc.

## Muon spin rotation/relaxation studies of the Kondo-Insulator SmB6

Author:
Date created:
2019-12-05
Abstract:

The intermediate-valence compound SmB6 is a well-known Kondo insulator, in which the hybridization of itinerant 5d electrons with localized samarium (Sm) 4f electrons leads to the opening of an insulating gap in the bulk. Yet in contrast to expectations for a Kondo insulator, SmB6 exhibits a low-temperature resistivity plateau due to the presence of metallic surface states, as well as low-temperature bulk magnetism of unknown origin. The presence of low-temperature bulk magnetism in SmB6 is also seemingly at odds with recent studies that suggest SmB6 is a topological insulator, with time-reversal symmetry protected metallic surface states emerging from a fully insulating hybridized bulk band structure. This thesis is an investigation of the bulk magnetic properties of SmB6 via magnetic susceptibility and muon spin rotation/relaxation (μSR) measurements. Similar measurements were also performed on 0.5% Fe-doped SmB6 for which Fe substitutes for Sm. The study of 0.5% Fe-doped SmB6 was undertaken to gain insight into the effect of magnetic impurities on the low-temperature magnetic properties of SmB6. Single crystals of pure SmB6 and the 0.5% Fe-SmB6 were grown by an Al-flux method. The bulk magnetic susceptibility measurements for both samples show a Curie-Weiss behaviour above 100 K, indicative of the presence of paramagnetic Sm-4f moments. A magnetic-field dependent upturn in thetemperature dependence of the magnetic susceptibility observed below 15 K in pure SmB6 is attributed to the presence of paramagnetic impurities and/or Sm vacancies. This is corroborated by an enhancement of the low-temperature upturn in the 0.5% Fe-SmB6 sample. The μSR results collectively provide evidence for the existence of bulk magnetic excitations at temperatures below 20 K. In particular, evidence is provided for the existence of a bulk magnetic excitation on the order of 1 meV, compatible with the existence of magnetic in-gap states and in particular a low-energy spin exciton. In addition, underlying low energy (100 neV) weak magnetic fluctuations are observed to persist down to at least 0.024 K. Similar forms of magnetism are observed in the candidate topological Kondo insulator YbB12, suggesting a common origin. Even so, intrinsic defects cannot be ruled out as a potential source of the low-temperature magnetism in SmB6.

Document type:
Thesis
File(s):
Supervisor(s):
Jeff Sonier
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Modifying spin diffusion in a nondegenerate ultracold gas

Author:
Date created:
2019-12-09
Abstract:

Diffusion plays a major role in describing how particles and heat move in any nonequilibrium system. The diffusion of quantum properties is not as well understood as the diffusion of classical properties, especially at low temperatures or high densities. Exploring the diffusion of the quantum property known as spin is beneficial for explaining quantum effects that arise at low temperatures or high densities, and this knowledge acquired could assist in the development of new ultra-low-power devices. This thesis examines spin diffusion at various temperatures and densities using the highly-tunable experimental platform of ultracold atoms. Around one million rubidium-87 atoms are cooled to nanokelvin temperatures to create an ultracold gas, where quantum interactions between atoms can significantly modify spin diffusion compared to classical diffusion. One-dimensional spin diffusion is observed for an initial two-domain spin profile. Remarkably, diffusion of this spin profile is slowed at temperatures above quantum degeneracy, where the ultracold gas is largely classical but with quantum collisions. We demonstrate that this slowing of spin diffusion is due to the presence of spin coherence between spin domains, and that the removal of coherence speeds up spin diffusion to classical timescales. Spin diffusion is further modified by applying a linear differential potential that can speed, slow, or stop spin diffusion of a two-domain spin profile. Differential potentials spatially alter the precession of spins, which then alters the spin-rotating quantum collisions that modify spin diffusion. For a linear differential potential with a specific sign and magnitude, stabilized spin domains in an ultracold gas are observed for 40 times longer than classical diffusion timescales. In addition to modifying spin diffusion with coherence and differential potentials, we demonstrate arbitrary control of one-dimensional spin diffusion using temporally varying differential potentials and three-domain spin profiles. These spin diffusion modifying techniques could be useful for manipulating spin in other nonequilibrium systems, and set the stage for simulating spin-based devices in ultracold atoms.

Document type:
Thesis
File(s):
Supervisor(s):
Jeffrey McGuirk
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Application of position sensitive detector in nuclear well logging tools

Author:
Date created:
2020-01-23
Abstract:

Nuclear well-logging tools play an essential role in helping petroleum engineers and geoscientists to understand properties of formations and give a quantitative evaluation of the hydrocarbon reservoir. As the exploration of oil and gas shifts to thinner and more heterogeneous reservoirs, there is a high demand for new tools with better vertical resolution. This thesis proposes using a position-sensitive detector (PSD) to replace the conventional detectors in nuclear well-logging tools to improve their vertical resolution. With the Monte Carlo method, the performance of a PSD and its applications in a density logging tool and a natural gamma-ray tool were studied. The results show that with a PSD, the vertical resolutions of both tools are significantly improved. Particularly, the density tool with a PSD can evaluate the density correctly when the thickness of a layer is only 5 cm, which is dramatically better than the 16 cm for a conventional density tool. Besides, because the proposed density tool has distinct depth of investigations (DOI) at different positions of the PSD, the tool can provide a two-dimensional density image, which indicates the structure of the formation. As to a natural gamma-ray well-logging tool with a PSD, its vertical resolution depends on the position resolution of the PSD, which is different from the conventional tool whose vertical resolution is determined by the crystal's length. Based on this change, the statistical fluctuation of the gamma-ray measurement can be reduced by increasing the crystal's length of the PSD without affecting its vertical resolution. In short, this work confirms the feasibility of using the PSD in nuclear well-logging tools in theory and indicates that the logging tools with the PSD have a promising potential application in determining the properties of thin-bedded strata.

Document type:
Thesis
File(s):
Supervisor(s):
Dugan O'Neil
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Development and characterization of a magnetic particle imaging scanner

Author:
Date created:
2019-11-22
Abstract:

Magnetic particle imaging (MPI) is a tracer-based imaging modality with a variety of promising bio-medical applications including cancer diagnosis, cell tracking, and vascular imaging. It can potentially provide fast and sensitive mapping of superparamagnetic nanoparticle (SPN) distributions, and is expected to yield sub-millimeter resolution. These distributions are inferred from SPN responses to applied static and time-varying magnetic fields. The non-linear response of SPN magnetization to the time-varying component of the field induces time-dependent signals at harmonics of the fundamental in a detection coil. Signal localization is obtained by applying a strongly inhomogeneous static field that is arranged such that its amplitude is zero in certain Field Free Regions' (FFRs). SPNs located near a FFR contribute significantly to the detected signal. The remaining SPNs contribute much less to the detected signal because they are exposed to a strong static magnetic field and their magnetization response is saturated. A map depicting the distribution of SPNs is then generated by systematically displacing the FFR over a desired Field Of View (FOV). Conventional approaches to MPI use the same current-driven time-varying magnetic fields to manipulate the FFR and to excite the SPNs. The resulting size of the FOV and the temporal resolution are proportional to the FFR-manipulation field amplitude and frequency, respectively. This fact, combined with restrictions imposed by health-related risks associated with high amplitude rapidly-varying magnetic fields represents a significant challenge to the field. In this thesis, I describe and demonstrate an alternative approach to MPI in which particle excitation and FFR manipulation are decoupled from one another. The additional degree of freedom enabled by this decoupling suggests new strategies for studying and exploiting contrast mechanisms, optimizing image quality and resolution, and device-size scaling. The prototype instrument I describe uses rotating arrays of permanent magnets to scan a Field Free Point (FFP) through the FOV, and current-driven oscillating magnetic fields to elicit non-linear magnetization responses from SPNs. Narrow-band phase-sensitive detection of these responses at one or more harmonics of the excitation field provides a rich source of information from which images can be reconstructed. Images generated from data acquired using this instrument are presented, demonstrating native resolutions of order one millimetre if the magnitude of the detected signal is employed. The resolution of these images can be improved at the expense of contrast using high harmonic components of the detected electromotive force. I also introduce a new imaging protocol, which we refer to as phase-weighting', which substantially improves the spatial resolution of MP images through the use of phase information that is ultimately associated with SPN relaxation. Phase-weighted MP images with resolutions of order a few hundred micrometers, inferred from the width of the underlying point spread function, are obtained and presented. This represents a substantial advance in the state-of-the art within the field of MPI.

Document type:
Thesis
File(s):
Supervisor(s):
Mike Hayden
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Optical and magnetic properties of the T radiation damage centre in 28Si

Author:
Date created:
2019-09-16
Abstract:

While many defects in silicon provide long-lived spin qubits, it remains difficult to use them as the base for a spin-photon interface, because many have no optical transition at all, and those which do typically suffer from poor radiative efficiencies or have inconvenient optical transition energies. A number of silicon defects with transition wavelengths in the telecommunication bands are already known to exist, prominently from the set of centres known as radiation damage centres, produced when exposing the silicon lattice to radiation damage. Of special interest is the T centre, a paramagnetic defect thought to be made of two carbon atoms and one hydrogen atom. The ground state of the neutral defect has an uncoupled electron spin, and the bound exciton associated with the centre has a strong luminescence transition at 1326 nm. In this first study of T centres in 28Si, we revealed the expected but nonetheless remarkable linewidth improvement over natural Si due to the removal of isotopic broadening, which provides an improved bound on the true single-centre linewidth in natural Si. From pulsed laser transient spectroscopy, we measured a lifetime of 0.94(1) μs for the bound exciton state. Using photoluminescence excitation techniques, we attributed the dominant broadening mechanism to thermal excitations to a higher excited state and showed that resonant optical saturation of the transition results in a dipole moment of 0.27(3) Debye and a radiative efficiency of 13(4) %. We also estimated the T centre concentration of one sample from its absorption spectrum, and gave energy values for a series of transitions to higher energy excitonic states. Furthermore, experiments with an external magnetic field confirmed that the excited state Zeeman splitting is anisotropic and reveal that the ground state electron has an anisotropic hyperfine interaction with the hydrogen atom with a coupling constant on the order of 3 MHz. We demonstrated that initialization, readout and control over both the electron spin and the nuclear spin are possible using optical excitation and magnetic resonance, and measured T1 relaxation times greater than 16 s as well as T2 coherence times of 2.1(1) ms for the electron spin and 1.1(2) s for the hydrogen nuclear spin.

Document type:
Thesis
File(s):
Supervisor(s):
Stephanie Simmons
Department:
Science: Department of Physics
Thesis type:
(Thesis) M.Sc.

## Photoexcitation spectroscopy of insulating cuprates

Author:
Date created:
2019-12-18
Abstract:

The ultrafast optical response of noble metals and insulating cuprates have been studied and characterized to better understand the lifecycle of photoexcitations in these two drastically different materials systems. Through the use of a tunable two-colour optical pump-probe system combined with THz photoconductivity measurements we are able to resolve questions around the nature of ultrafast response in these materials and estimate physical parameters, including the electron-phonon coupling in Au and Cu, the Auger recombination coefficient in YBa2Cu3O6, and the effect of carriers on the charge-transfer gap in La2CuO4 and Sr2CuO2Cl2. In the noble metals, where electrons thermalize on timescales shorter than our laser pulses, we use the systemic ability to tune the energy of the pump photons to expand upon past measurements. We show that the two-temperature model may be applied under a wide variety of conditions, demonstrate the importance of considering the depth dependence of the photoexcitation profile in tunable pump-probe experiments, and find mathematical simplifications for the fluence dependence of the relaxation time of the photoexcitation system. We estimate the electron-phonon coupling g = (23 ± 1) PW m−3 K−1 for Au and g = (120 ± 10) PW m−3 K−1 for Cu. Single-crystal and thin-film samples of the insulating cuprates, Sr2CuO2Cl2, La2CuO4, and YBa2Cu3O6, were studied over a variety of pump-probe conditions. Prior measurements of insulating cuprates showed seemingly contradictory behaviour, where the magnitude of the response had a sublinear fluence dependence but the dynamics of the response were fluence independent. Through a series of experiments we identify a simple model which can explain both behaviours through strong Auger recombination combined with Shockley-Read-Hall (SRH) recombination. For YBa2Cu3O6 we find that the nonlinear response depends primarily on the carrier density throughout our measurement time window, and we estimate an Auger coefficient of Ch = 7.8 × 10−26 cm6/s, several orders of magnitude larger than in conventional semiconductors with comparable gap energies. For Sr2CuO2Cl2 and La2CuO4 we find that the nonlinear response also depends primarily on carrier density at early times, but that as time evolves contributions emerge from the bosons given off as the carriers relax.

Document type:
Thesis
File(s):
Supervisor(s):
J. Steven Dodge
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Cosmological tests of fundamental physics

Author:
Date created:
2019-06-11
Abstract:

The standard model of Cosmology, or the $\Lambda$CDM model, is able to describe remarkably well a plethora of observations with only six parameters. Nonetheless, several questions about its very nature have yet to be answered. Chief amongst them is the nature of Dark Energy, responsible for the observed acceleration of the Universe. While in the $\Lambda$CDM model Dark Energy is modelled via the cosmological constant $\Lambda$, its observed value cannot be reconciled with the predictions of quantum field theory, the framework at the basis of the standard model of particle physics. Modifications of General Relativity, known as modified gravity, offer an alternative approach to Dark Energy. The growth of large scale structure is modified in alternative gravity theories in ways that can be tested using cosmological data. We present a comprehensive analysis of a set of scalar-tensor theories of gravity that exhibit the chameleon screening mechanism. This mechanism hides the force mediated by the extra scalar from detection in local and solar system tests of gravity, while still leaving imprints in the cosmological observables. With the increasing precision of cosmological surveys, finer effects must be included in the theoretical predictions. This is the case for the total mass of neutrinos that affect the structure formation at the percent level in a way that could be degenerate with modified gravity. Being able to break this degeneracy requires ability to account for the mass of neutrinos while constraining modified gravity theories. We thus introduce a consistent treatment of massive neutrinos in the phenomenological $\mu-\gamma$ framework and update the popular code MGCAMB used to constrain modified gravity models. We have also introduced the option for MGCAMB to work with general background histories where Dark Energy evolves with time. It has been recently shown that a dynamical Dark Energy with density that increases with time is able to alleviate the tensions between different datasets within the $\Lambda$CDM model. Modified gravity theories provide a framework to explain such behaviour of Dark Energy and we perform a reconstruction of the Lagrangian of Generalized Brans-Dicke theories from the observed expansion history of the Universe. We then study the viability of the such theories and ways of testing them with future data. Another challenge for upcoming CMB experiments is the detection of the primordial gravitational wave background in the B-mode polarization signal. Such a background is predicted by Inflation, a period of exponential expansion in the early Universe, which is the paradigm behind the choice of the initial conditions in the $\Lambda$CDM model. CMB B-modes also offer a powerful way to test the existence of primordial magnetic fields in the early Universe. These can also arise from the inflationary mechanism or be generated during phase transitions in the early universe. We have developed a publicly available code, dubbed MagCAMB, that computes the CMB anisotropies generated by primordial magnetic fields. We also derived the tightest constrain to date on the primordial magnetic field amplitude using the CMB spectra from the Planck satellite and the B-mode measurements by the South Pole Telescope.

Document type:
Thesis
File(s):
Supervisor(s):
Levon Pogosian
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## DC SQUID Magnetometry

Author:
Date created:
2019-10-10
Abstract:

This thesis describes the measurement of the local magnetic field of a D-Wave Systems Washington generation processor using on-chip multiplexed unshunted DC SQUID magnetometers. These measurements are used in conjunction with passive and active field compensation to minimize the magnetic field present during the superconducting transition of the chip in order to limit the number of magnetic flux lines trapped on chip. This maximizes the operability of the superconducting quantum processor.

Document type:
Thesis
File(s):
Supervisor(s):
David Broun
Department:
Science: Department of Physics
Thesis type:
(Thesis) M.Sc.

## On the hunt for a near-infrared single photon emitter in silicon — Optical characterization of radiation damage defects in 28Si

Author:
Date created:
2019-08-22
Abstract:

Integrated silicon photonics allows for the routine control and detection of light down to the single photon regime with low loss and in a scalable way, but to date still has the reputation of lacking fast, efficient and indistinguishable optical emitters that can be easily coupled to photonic structures. The identification of such an emitter will further enable the realization of on-chip low-energy, speed-of-light processing, and could open up exciting prospects for quantum computing and quantum communications. A multitude of radiation damage centres in silicon show bright emission in or near the attractive telecommunication band wavelength range at temperatures up to tens of Kelvin, which is compatible with the state-of-the-art superconducting nanowire single-photon detectors. These centres have been thoroughly studied in natural silicon using a wide variety of techniques, but their detailed spectral properties remained hidden by inhomogeneous line broadening due to the mixed isotopes present in natural silicon. We characterize three defect centres showing potential as single photon emitters, the C centre (790 meV, or 1571 nm), the G centre (969 meV, or 1280 nm), and the W centre (1019 meV, or 1217 nm). Performing ultra-high-resolution spectroscopy on ensembles of these defects in highly isotopically enriched 28Si, where isotopic inhomogeneous line broadening is removed, reveals a dramatic reduction in spectral linewidth of up to two orders of magnitude. We also report for the first time a quartet structure of the G centre that is revealed in 28Si, and a G linewidth that is only twice the lower bound given by the excited state lifetime. These results have direct implications for the spectral widths and fine structure to be expected from individual emitters, even in natural silicon.

Document type:
Thesis
File(s):
Supervisor(s):
Michael Thewalt
Department:
Science: Department of Physics
Thesis type:
(Thesis) M.Sc.