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

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Mechanisms for directed transport and organization at subcellular scales

Author: 
Date created: 
2020-12-18
Abstract: 

The timely and faithful segregation of genetic material is an essential cellular function that relies on the transport and stable positioning of subcellular components despite the disruptive influence of thermal fluctuations. In prokaryotes, a two-protein system (known as ParABS) has been identified as being responsible for the positioning of low-copy number plasmids and chromosomes prior to cell division. Multiple experimental observations, in vitro reconstitutions and computational modelling efforts support the idea that this system is powered by the ‘burnt-bridge’ Brownian ratchet mechanism. In this thesis we provide computational models that complement these studies to understand how this mechanism generates and sustains directional transport through the transduction of chemical energy into mechanical motion. In particular we study the effects of chemical kinetics, inter-protein interaction strength, system size and availability of proteins that drive this mechanism with an application to the rich protein dynamics observed in vivo. Finally, we simulate a coarse-grained model for a highly polyvalent ‘burnt-bridges’ Brownian ratchet capable of translocating either by rotation or translation and detail the system parameters that govern the transitions between these two distinct modes of motion. The models presented in this thesis provide key insights and make experimentally testable predictions which can be used for the engineering of novel synthetic motor systems.

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

Investigation of complex impurity centers in zinc oxide

Author: 
Date created: 
2021-04-08
Abstract: 

Zinc oxide is a potentially useful material in optoelectronics. It has a 3.3 eV direct bandgap which makes it a comparatively inexpensive candidate for replacing gallium nitride as a UV light emitter. Production of stable p-type ZnO is the biggest challenge for the introduction of this material to industry. Many attempts to produce stable p-type ZnO by doping single atom point defects have failed. The remaining dopant candidates are complex defects including two or more components. In this thesis, we mostly focus on the study of bound excitons corresponding to Li related defects. We show that the line at 3353.4 meV in the UV spectra of ZnO, previously assigned to tin, is a complex donor impurity including Sn and Li atoms. We performed annealing experiments, diffusing the Li content out of the lattice. The intensity of the 3353.4 meV line decreased as a result of annealing, which suggests the involvement of Li in this impurity. This process was reversed by the introduction of Li into the sample and the original intensity was restored. This was strong evidence of the involvement of Li in this impurity. We found a 0.4 eV ± 0.2eV activation energy for the ejection of Li from the complex using the annealing results. Density functional analysis of a complex consisting of Li and Sn in the nearest neighboring Zn sites results in much bigger activation energies for different mechanisms of ejection of Li. This evidence suggests that the impurity is more complicated than Li and Sn in nearest neighboring Zn sites. We tried to further investigate this impurity by introducing a different isotope of Li. Substitution of natural Li (96% 7Li) with 6Li showed a change of -0.022±0.008 in the energy position of the recombination energy of the D0X attributed to the line at 3353.4 eV. Our theoretical prediction of the shift suggested a lower limit of -0.031 for the expected shift. In addition, we observed new Li-related lines and showed they are due to bound excitons. We also investigated the effect of the environment in which Li doping is done on the emergence of these new lines.

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

Laser-assisted selective tuning of silicon nanophotonic structures

Author: 
Date created: 
2020-12-11
Abstract: 

Silicon photonic integrated circuits have advanced to the point where thousands of components can now be combined into functioning optical circuits. A variety of quantum technologies are based upon the integrated silicon photonics platform, including pure photonics approaches as well as those based upon emerging silicon spin-photon interfaces. Integrated photonic components, such as grating couplers, photonic crystal cavities, and waveguides, are subject to slight manufacturing variations. For quantum technology applications, such variations often need to be minimized and ideally eliminated through careful post-processing. The laser-assisted "spot oxidation" post-processing technique is able to locally and permanently shift the resonance wavelength of nanophotonic devices using a 532nm continuous wave laser. While global tuning techniques affect entire chips, spot-oxidation is of interest because it can locally correct for specific manufacturing variations among many components within a single chip in an automated way. Yet prior to this work it was unclear if spot oxidation could be made compatible with photonic structures with SiO2 top-cladding, which are more robust and attractive for commercial deployment. Here, we apply laser-assisted tuning to silicon-on-insulator (SOI) devices with SiO2 top-cladding in the telecommunication O-band. In this work, we successfully tune both photonic crystal nanobeam cavities and sub-wavelength grating couplers up to 1.04(5)nm and 9(1)nm, respectively. This will enable higher-yield photonic circuits, as well as allow us to permanently locally tune optical structures into resonance with optically active colour centres in silicon.

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

Spectroscopy and phenomenology of unconventional superconductors

Author: 
Date created: 
2020-12-16
Abstract: 

The challenge of condensed matter physics is to understand how various states of matter emerge from periodic or amorphous arrangements of atoms. This is typically easier if there are no impurities in the material under investigation. However, many of the properties that make materials technologically useful stem from the very disorder and impurities that complicate their study. In this work we investigate three unconventional superconductors with the dirty BCS framework of superconductivity, with impurities treated in the selfconsistent t-matrix approximation. The three materials behave quite differently and allow us to explore and reveal a rich, subtle, and poorly appreciated range of effects that must be considered when studying superconducting materials and probing the limits of applicability of current theories of superconductivity. Microwave spectroscopy measurements of FeSe, a member of the iron-based family of superconductors, were performed at frequencies below 1 GHz using a novel helical resonator. The measurements show that the material is particularly clean, with an electronic mean free path that exceeds that of all known binary compounds. They also reveal the presence of a finite gap on both superconducting bands, strongly constraining which pairing states should be considered for FeSe. Nb-doped SrTiO3 has an extremely low carrier concentration and multiple electronic bands at the Fermi sruface. Microwave spectroscopy measurements, this time with a stripline resonator, reveal a single spectroscopic gap despite clear evidence for multiple superconducting bands. Elastic scattering introduced via Nb dopants is proposed as the mechanism by which the two bands homogenize into a single spectroscopic signature, as per Anderson’s theorem. The impurity hypothesis is tested with single-band fits to the superfluid density and is found to be in good agreement with measured data. Finally La2−xSrxCuO4, a member of the famous cuprate family of superconductors is explored in detail under the assumption that Born scattering with large amounts of impurities can explain a number of puzzling measurements that have caused controversy in the high-Tc community over the past few years. Many features of the experimental measurements can quantitatively be accounted for with very few free parameters and no fine tuning.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Broun
Erol Girt
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Study of magnetic interlayer coupling in synthetic antiferromagnets for use in MRAM devices

Author: 
Date created: 
2020-12-08
Abstract: 

In recent years, there has been an ever increasing level of effort focused on creating novel technologies based on spintronics. One of the most exciting of these technologies is spin transfer torque random access memory (STT-MRAM), which is a solid state non-volatile memory technology that is orders of magnitude better than flash memory in terms of speed and write endurance. One critical component of an STT-MRAM memory cell is the so-called fixed magnetic layer. The direction of magnetization of this layer must remain fixed so that it can act as a reference for the reading and writing of information to the cell. This layer is ideally composed of a synthetic antiferromagnet (SAF) with zero net magnetization because it can offer thermal stability, have its magnetization be less effected by external magnetic fields, and have reduced stray fields. One challenge with integrating a SAF into an STT-MRAM memory cell is that they are typically not thermally robust. Creating an STT-MRAM device generally requires at least one annealing step at temperatures between 200 and 300C. During this annealing process, the antiferromagnetic coupling (AFC) within the SAF changes dramatically and usually becomes ferromagnetic, thereby eliminating the SAF and all of its advantages. The work in this thesis centers around understanding exactly how and why this magnetic coupling changes during the annealing process, and how to prevent it so that a SAF fixed magnetic layer can be used in STT-MRAM devices. We start by depositing thin films containing two FeCoB layers coupled across several different non-magnetic spacer layers of varying thicknesses. We determine the magnitude and direction of the magnetic coupling between the two FeCoB layers both before and after annealing my analyzing ferromagnetic resonance (FMR) and magnetostatic measurements. Next, we study the role that boron has on the magnetic coupling by co-depositing it into the Ru spacer layer of samples with the structure NiFe/Ru/FeCo. From this, we conclude that the presence of boron within the FeCoB layer leads to increased diffusion of magnetic atoms into the non-magnetic spacer layer during the annealing process, which is responsible for the change in coupling seen in SAF structures. In order to prevent this, we insert diffusion barriers next to the FeCoB layers within a SAF. We find that with the diffusion barriers, we are able to create a thermally robust SAF structure that maintains AFC coupling even after annealing at temperatures of up to 350C.

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

Determining the jet energy scale for ATLAS in the Z+Jet channel

Author: 
Date created: 
2020-11-10
Abstract: 

This thesis presents a determination of the jet energy scale for the ATLAS detector using in-situ measurements. This calibration is critical, as jets are found in many analyses, and the energy measurement of jets contributes significantly to the uncertainty in numerous ATLAS results. The energy of the jet is initially taken to be the detector measurement, but this is lower than the true energy because the detector is calibrated for electromagnetic particles, not jets. One can find a correction to this energy by balancing the jet's transverse momentum against a well-measured reference object. Directly calibrating the calorimeter-level jet to the particle-level is called Direct Balance; here, a different method called the Missing ET Projection Fraction (MPF) method is used instead, which balances the pt of the recoiling system against the reference object. The MPF's pile-up resistant nature makes it more suitable to use in the ATLAS environment. Results for the MPF method in the Z+Jet channel are presented. A relative calibration of data to Monte Carlo simulation is provided, including a complete systematic uncertainty analysis. The uncertainty on the in-situ calibration is reduced to around 1% for most transverse momenta.

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

Correlated percolation in the fracture dynamics on a network of ionomer bundles

Author: 
Date created: 
2020-12-17
Abstract: 

Motivated by predicting the lifetime of polymer electrolyte membranes (PEMs), we map the fracture dynamics of a network of ionomer bundles onto a correlated percolation model. A kinetic Monte Carlo method is employed to study these dynamics. The swelling pressure upon water uptake causes the breakage events of ionomer bundles, and the strength of the bundle-to-bundle correlations is characterized by the stress field and the stress redistribution scheme. Local load sharing (LLS) and equal load sharing (ELS) are the two most frequently studied stress transfer schemes. We adopt a stress transfer scheme that follows a power-law-type spatial decay in this thesis as an intermediate scheme between LLS and ELS. By tuning the magnitude of the stress field and the effective range of stress transfer, two fracture regimes, i.e., the random breakage (percolation-type) regime and the localization (correlated crack growth) regime, can be observed. A central property considered in this thesis is the frequency distribution of percolation thresholds. Based on this distribution, we introduce an order parameter to assess the crossover between these two fracture regimes. Moreover, the average percolation threshold is found to exhibit a peculiar variation, which has not been reported in previous correlated percolation studies.

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

Optical second harmonic generation in WTe2

Author: 
Date created: 
2020-12-14
Abstract: 

We study second harmonic generation (SHG) in an acentric Weyl semimetal, tungsten ditelluride (WTe2), and estimate its second-order electric susceptibility, χ(2). WTe2 is a layered material that has a natural cleavage plane perpendicular to the c-axis, but the crystal symmetry prohibits SHG emission when light is normally incident on the natural planar surface. Hence, we measure the SHG susceptibility in a laser scanning microscope, where it is easier to measure the SHG from the striated edges of the crystal. We determine the susceptibility from the variation of the SHG images with incident power, using a model that accounts for both the statistics of the SHG detection process and the surface inhomogeneities of the sample. A preliminary estimate shows that χ(2) in WTe2 is comparable to that of GaAs, a well studied nonlinear crystal with large second-order susceptibility.

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

Dissipation and control in microscopic nonequilibrium systems

Author: 
Date created: 
2020-11-24
Abstract: 

Quantifying the flow of energy, entropy, and information within and through nonequilibrium systems remains a central challenge in understanding the microscopic physics of biological systems. Over the past two and a half decades, parallel developments in the fields of theoretical stochastic thermodynamics and single-molecule experiments have made tremendous steps towards this end, advancing our understanding of the fundamental physical limitations and constraints faced by biological systems in vivo. Central in this focus are molecular machines: nanoscale protein complexes which interconvert between different forms of energy to perform useful functions to the cell. While single-molecule experiments on molecular machines have predicted impressively high efficiencies, much is still unknown about their performance in vivo. In this thesis we build upon these primitives, largely by making use of near-equilibrium phenomenological models to simplify and make tractable the problem of quantifying dissipation in molecular machines and predicting the operational modes which are imperative to minimizing their dissipation. By exploring the relevance of near-equilibrium models in the experimental investigation of a DNA hairpin, we find that such an approach can provide utility in understanding the strategies to reduce dissipation in nonequilibrium processes. However, single-molecule manipulations are significantly separated from the in vivo dynamics of molecular machines, and thus for the remainder of the thesis we expand upon this approach in various ways, generalizing the existing theoretical framework to more closely parallel the dynamics of molecular machines. By incorporating the inter-system feedback present in molecular machines, we find that familiar intuitions about how excess work and entropy production are related break down. Finally, we derive a phenomenological expression for the energy flows communicated within the components of a mechanochemical molecular machine. Ultimately, our analysis shows that intersystem feedback can lead to nonvanishing energy flows which are the manifestation of a Maxwell demon in the molecular machine itself.

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

In situ observations of hexagonal boron nitride growth on Cu (110)

Date created: 
2020-08-05
Abstract: 

Hexagonal boron nitride (h-BN) was grown on top of (0001) textured polycrystalline Ru or single crystalline Cu (110) inside a Low Energy Electron Microscope (LEEM). Ru samples were prepared via radiofrequency magnetron sputtering on Si (100), Cu (110) single crystals were prepared ex situ via mechanical and electro-chemical polishing. Samples were exposed to borazine precursor at temperatures of 600–750°C and pressures of 0.5 - 10×10−7 Torr. Exposure of Ru substrates resulted in rapid yet small grained h-BN growth covering the entire surface. Exposure of Cu (110) single crystals resulted in the nucleation of well-aligned trigonal h-BN islands when Cu (110) showed a particular hydrogen-induced surface reconstruction. These islands merged to ribbons along surface steps, and into larger, more irregularly shaped features. A ring in the low energy electron diffraction (LEED) pattern was observed with a preferential orientation aligned along Cu (0 1) directions of the underlying substrate. A second Cu (110) single crystal was prepared via multiple sputter-anneal cycles using argon and hydrogen ions resulting in an unreconstructed surface. Exposing this single crystal to borazine also resulted in trigonal h-BN islands, yet these islands did not merge nor appear to align with surface steps. Nucleation was determined by defects and decreased with increasing temperature. LEED patterns revealed two preferential orientations, each aligned with Cu (1 1) directions. Growth dynamic plots suggested a modification to the growth model for self-limited monolayer growth, as islands did not merge. Extracted growth rates did not depend on the substrate temperature in the range tested, but increased with pressure. On the other hand, the maximum coverage increased with temperature, but did not depend on pressure. Annealing this Cu (110) single crystal in H2 atmosphere resulted in a weak (2 x 1) reconstruction. These surfaces had a lower defect density, and borazine exposure at 700–750°C resulted in larger h-BN islands, revealing preferred dendritic growth along the Cu (0 1) and (1 0) directions. This resulted in T-shaped islands early on in the exposure, which later filled out into triangular shapes, indicating a strong influence of the substrate. Dark-field LEEM revealed that neighboring islands did not merge, regardless of whether they had the same orientation or not.

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