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

Receive updates for this collection

Energy-speed-accuracy tradeoffs in a driven, stochastic, rotary machine

Date created: 
2017-08-03
Abstract: 

Molecular machines are stochastic systems capable of converting between different forms of energy such as chemical potential energy and mechanical work. The F1 subunit of ATP synthase couples the rotation of its central crankshaft with the synthesis or hydrolysis of ATP. This machine can reach maximal speeds of hundreds of rotations per second, and is believed to be capable of nearly 100% efficiency in near-equilibrium conditions, although a biased cycling machine is a nonequilibrium system and therefore must waste some energy in the form of dissipation. We explore the fundamental relationships among the accuracy, speed, and dissipated energy of such driven rotary molecular machines, in a simple model of F1. Simulations using Fokker-Planck dynamics are used to explore the parameter space of driving strength, internal energetics of the system, and rotation rate. A tradeoff between accuracy and work as speed increases is found to occur over the range of biologically rele- vant timescales. We search for a way to improve this tradeoff by applying approximations of dissipation minimizing protocols and find a reduction in both work and accuracy, yet accuracy drops less than the work does, leading to an overall decrease in the ratio of work to accuracy.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.

Lithography-free oxide isolation of GaAs nanowires using the VLS growth method

Author: 
Date created: 
2017-06-28
Abstract: 

Semiconductor nanowires show significant potential for incorporation into next generation technologies due to their unique electronic, optical and mechanical properties. In order to keep pace with the rapid development of new semiconductor technologies, quick and efficient device prototyping methods are required. In this work, a lithography-free approach for the fabrication of oxide-isolated nanowire devices is developed using a combination of atomic layer deposition and the vapour-liquid-solid method. Axial growth of Al2O3 and Ga2O3-coated GaAs nanowires is restarted using an annealing step which fractures the oxide surrounding the gold nanoparticle. The oxide fracture is observed to depend on the oxide composition and thickness, annealing temperature and nanoparticle radius. The compositionaland electronic properties of the regrown nanowires are investigated and a thermal expansion mismatch model is presented to describe the observed results.

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

Technological Improvements for Linear Ion Trap Experiments

Date created: 
2017-05-26
Abstract: 

Laser-cooled, trapped ions are a highly controlled experimental system that allows one to engineer novel quantum states of both fundamental and practical interest. For a string of ions in a linear radio frequency (RF) Paul trap, the linear-zigzag structural phase transition is an intriguing system to investigate quantum dynamics near the critical point of a prototype second-order phase transition, including the preparation of superposition states of different structural configurations. This thesis focuses on two technological improvements required for studying the linear-zigzag structural phase transition in the quantum regime. The first is the development of a compact and cost-effective RF synthesizer setup to provide multiple modulation sources for the laser manipulation of ion strings. The functionality and limitations of a prototype design, based on Direct Digital Synthesizer (DDS) development boards with a microcontroller interface, are evaluated and future improvements are identified. The second part of this thesis focuses on the stabilization of the secular trap frequencies in a linear Paul trap, which is necessary to obtain a stable critical point for the studies of the linear-zigzag transition. To this end, this thesis presents the implementation of a Ramsey spectroscopic technique to measure the secular frequencies and presents the preliminary results from the stability tests.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Paul Haljan
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.

Optical tweezers-based microrheological measurements using a high-speed camera

Date created: 
2017-05-18
Abstract: 

Collagen, the most abundant protein in the body, assembles into an extra-cellular fibrillar gel, which has both viscous and elastic properties. These properties can be determined by using optical tweezers to hold a micron-sized bead within the sample. Measurement of the bead’s thermally induced motion enables the determination of the frequency-dependent viscoelasticity. Rather than only probing response at a single location, holographic optical tweezers create multiple, independent traps, permitting simultaneous tracking of multiple embedded beads and characterization of their correlated motion. By using this technique in a collagen gel, we will be able to determine local and cross-correlated viscoelastic properties, which vary at different locations during its formation. Implications of this research lie in the fields of health and biomaterials. The aim of this work is to devise and validate protocols for using holographic optical tweezers to measure local and through-space viscoelasticity. Rather than using laser deflection to track particle motion, I use a high-speed camera and image analysis to track the simultaneous motion of multiple beads. This approach provides nanometer-scale resolution of particle position at sampling rates up to 2.5 kHz. I compare tracking data collected from the high-speed camera to those collected by the laser deflection method and find a discrepancy in the perceived motion of the bead. I perform many experimental tests to assess the root of this problem. Additionally, I numerically represent bead motion measurements if collected using both methods (laser-deflection method and high-speed camera method) and compare them to the idealized measurement results. In doing so, I learn about the limitations of each method, and how the viscous and elastic properties inferred from the data are affected by each measurement device. Finally, based on my numerical representations, I suggest a simple procedure to gain more accuracy in the viscous and elastic properties for both simple fluids (such as water) and complex fluids (such as collagen solutions) when using each method. This procedure can be used in future holographic optical tweezers-based experiments to obtain an accurate representation of the local and correlated properties of collagen.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Nancy Forde
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.

PT-Symmetric Hamiltonian H=p^2-(ix)^N: Welcome to the Complex World

Author: 
Date created: 
2017-03-21
Abstract: 

The Hermiticity from conventional quantum mechanics guarantees that the energy spectrum is real. However, if replace this mathematical condition by the physically transparent condition of parity-time reflection symmetry (PT-symmetry), the non-Hermitian Hamiltonian still guarantees that its entire energy spectrum is real if the Hamiltonian has unbroken PT-symmetry. If its PT-symmetry is broken, then two cases can happen - its entire energy spectrum is complex for the first case, or a finite number of real energy levels can still be obtained for the second case. This was “officially” discovered since 1998. After that, the developments in PT-symmetric quantum theory rapidly grew in the last 15 years - with more than 20 international conferences and symposia, and over 2000 research papers about PT-symmetry already published. Furthermore, at least 50 experiments to observe PT-symmetric system were published during the last 10 years. Those experiments told us that it was possible to experimentally measure complex eigenvalue and observe broken and unbroken PT-symmetry. Admittedly, PT-symmetric quantum theory is a young and new field - currently, still not many professors and researchers familiar with this subject. That is why this thesis comes in, and tries to serve a role to introduce this subject to wide audience from students to professors. In this thesis, the energy spectrum from the PT-symmetric Hamiltonian H = p^2 −(ix)^N with x ∈ C, N ∈ R and N ≥ 1 was studied in detail by using numerical and WKB approximation. What the corresponding eigenfunctions look like were also examined in numerical way. Lastly, a few interesting and weird phenomena from PT-symmetric non-relativistic classical mechanics were explored in brief. We hope that this study could not only demystify but also help people appreciate many aspects of PT-symmetry.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Andrei Frolov
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.

Evidence for the Production of the Standard Model Higgs Boson Produced via Vector Boson Fusion in the WW* Channel at the ATLAS Detector

Date created: 
2017-04-18
Abstract: 

In 2012, the ATLAS and CMS experiments at CERN's Large Hadron Collider announced they had each observed a new particle with a mass of about 125 GeV/c^2. Given the available data, the properties of this particle are consistent with the Higgs boson predicted by the Standard Model of particle physics (SM). The Higgs boson, as proposed within the SM, is the simplest manifestation of the Brout-Englert-Higgs mechanism. This discovery was driven by the gluon fusion (ggF) production mode, the dominant Higgs boson production mechanism at the LHC. The SM also predicts that the Higgs boson can be produced by the fusion of two weak vector bosons (VBF). Measuring VBF Higgs boson production is an important test of the SM but it is challenging to measure given its cross section is an order of magnitude smaller than that of ggF. After H->bb, H->WW* is the dominant decay channel for the SM Higgs boson at 125 GeV/c^2 and is therefore a promising channel to measure its properties. In addition, the VBF H->WW* search channel makes it possible to probe the exclusive coupling of the Higgs boson to the weak vector bosons. Precise measurements of these coupling strengths make it possible to constrain new models of physics beyond the SM. Despite its relatively large branching ratio, H->WW*->lnln is a challenging channel to search for the Higgs boson because of the neutrinos in the final state which are not directly detectable by the ATLAS detector. Consequently, it is not possible to fully reconstruct the mass of the WW system. Furthermore, there are several backgrounds that have the same signature in the detector as the signal. Top quark pair production is the largest background in this analysis. A multivariate analysis technique, based on an eight-variable boosted decision tree (BDT), is used to search for VBF H->WW*->lnln in the Run-I data and a subset of the Run-II data. This analysis provides the first evidence for VBF H->WW*->lnln with a significance of 3.2 standard deviations in Run-I and 1.9 standard deviations in Run-II. The measured signal strength relative to the rate predicted by the SM for VBF H->WW*->lnln is 1.3 +/- 0.5 using the Run-I data, and 1.7 +1.1/-0.9 using a fraction of the Run-II data.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bernd Stelzer
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Optical characterization of doped zinc oxide nanowires

Date created: 
2017-01-24
Abstract: 

ZnO is a promising semiconductor material with a direct band gap energy of 3.3 eV which makes it a good candidate for UV and visible range light emitting devices. Metalorganic chemical vapour epitaxy (MOVPE) provides the possibility of industrial scale growth of ZnO, with very fine control of impurity dopants. Despite the vast recent literature on ZnO, there are very few studies of systematic intentional doping. ZnO nanowires (NWs) can be grown easily on various substrates with high crystalline quality and low defect densities and tend to exhibit reduced substrate induced strain. This enables us to perform careful spectroscopic analysis of impurity related optical transitions and identify the physical nature of various dopant species. A detailed study of low temperature photoluminescence (PL) transitions in doped ZnO NWs, thin films, and bulk crystals grown by MOVPE and chemical vapour transport (CVT) methods is presented. The standard group III donors were first investigated. Donor bound exciton (D0X) transitions previously assigned to Ga, Al, and In were confirmed in intentionally doped samples. Group IV dopants such as carbon, and tin are interesting since they can act in principle as double donors or double acceptors. We report four new shallow D0X transitions (Z-lines), at 3360.8 (Z1), 3361.2 (Z2), 3361.7 (Z3) and 3361.9 (Z4) meV, which can be greatly enhanced by co-doping with carbon tetrachloride and hydrogen. These shallow donors appear to be due to carbon impurities complexed with other unknown defects in four distinct configurations. Carbon-doped samples also exhibit two distinct acceptors with binding energies of 133 ± 5 and 181 ± 5 meV. Doping concentration and temperature dependent PL studies of unintentionally doped and Sn-doped ZnO single crystals confirmed emission from the I10 D0X transition which was recently proven to contain Sn on a Zn site. Sb-doped ZnO NWs were grown in an attempt to produce p-type material as reported by some groups. Our PL studies including Magneto PL, have shown that rather than p-doped material, the addition of small amounts of Sb-dopant resulted in a new PL transition at 3364.3 meV, which turns out to be the shallowest D0X transition so far observed in ZnO.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Simon Watkins
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Precision microwave spectroscopy of the heavy fermion superconductor CeCoIn5

Date created: 
2016-11-21
Abstract: 

The heavy fermion superconductor CeCoIn5 demonstrates remarkable similarities to the high-Tc cuprates in many of its properties including proximity to antiferromagnetism, quasi-two-dimensionality, d-wave superconductivity, and departures from Fermi liquid behaviour in the normal state. It is also a “high-Tc” superconductor in the context of the heavy fermions. The experimental technique of microwave cavity perturbation has been used to measure the electrodynamics of a single crystal of CeCoIn5 over a range of temperatures, from 80 mK to 35 K, in a dilution refrigerator. Measurements at multiple frequencies required the development of an in-situ technique for the bolometric detection of the surface resistance. This has allowed conductivity spectra to be acquired, resulting in several important results. First, the resolution of an unexplained fractional power law in the penetration depth has been achieved by properly isolating the nodal quasiparticle contribution, revealing a previously unseen linear temperature dependence in CeCoIn5, as expected for a d-wave superconductor. Second, the temperature evolution of the microwave conductivity spectra implies that the effective mass of the quasiparticles continues to change below Tc, hinting that quantum criticality remains important even in the superconducting state. Third, conductivity spectra that are strikingly similar to those from YBa2Cu3O6+y suggest a strong connection in the underlying charge dynamics, as both CeCoIn5 and YBa2Cu3O6+y show a collapse in the quasiparticle scattering rate below Tc. Finally, the spectra indicate the presence of multiband effects.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Broun
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Mechanical Studies of Single Collagen Molecules Using Imaging and Force Spectroscopy

Author: 
Date created: 
2016-12-07
Abstract: 

Collagen is a key component of the extracellular matrix and is the most abundant protein in vertebrates. Collagen is found in almost every connective tissue of the body including skin, bone, tendon, cartilage, arteries and cornea, where it plays a crucial role in providing structural support. Collagen molecules self-assemble to form hierarchical structures, from single molecules to fibrils to fibers and tissues. Structural and mechanical changes at the molecular level may affect self-assembly of the molecules and the resulting tissue. Despite its significance, the mechanics of collagen and its flexibility at the molecular level remain contentious, and collagen has been variously described as a flexible polymer to a semi-rigid rod. In this thesis, I present my work developing and utilizing experimental and analytical tools to study the mechanical proprieties of molecular collagen. I carefully designed and controlled a wide variety of experimental conditions, such as different collagen types and sources, solution pH and salt concentrations, and analysed the results in search of potential reasons for inconsistency in reported results of collagen flexibility at the basic molecular level. Atomic force microscopy (AFM) imaging is used to study effect of environmental factors such as ionic strength and pH on molecular conformations and flexibility of single collagen molecules. In addition, molecular conformations of different types of collagen from different sources are compared using AFM imaging. I measure persistence length of collagen molecules, a measure of flexibility, arising due to the conformational sampling of collagen. My results link the bending energy of collagen molecules to how tightly the helix is wound. In order to analyse AFM images of collagen, I developed an image and statistical analysis algorithm, SmarTrace, optimized for my images of collagen. The program was validated using images of DNA with known persistence length, then applied to collagen molecules. Analysis of different types of collagen in two different solutions and type I collagen in solutions of different ionic strength and pH show that collagen's flexibility depends strongly on ionic strength and pH. In addition, it shows that different types of collagen show similar average conformational characteristics in a given solution environment. In addition, mechanical properties and force-response of single collagen and procollagen molecules are studied using optical tweezers. I discuss the challenges of stretching single collagen proteins, whose length is much less than the size of the microspheres used as manipulation handles, and show how instrumental design and biochemistry can be used to overcome these challenges. The result of this work is an improved understanding of the sensitivity of molecular flexibility, stability and response of collagen to environmental factors. This can shed light on identifying underlying mechanisms of collagen-related diseases as well as designing and producing improved engineered biomaterials with tunable properties.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Nancy Forde
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Design and Fabrication of Nanoscale Bismuth Hall Probes

Author: 
Date created: 
2016-12-09
Abstract: 

Scanning Hall probe microscopy is a quantitative magnetic imaging technique with high magnetic flux sensitivity and high spatial resolution. Hall sensors have untapped potential to match the sensitivity of superconducting quantum interference devices (SQUIDs), which are well-known in magnetic microscopy for their flux sensitivity. Furthermore, Hall probes can do so with better spatial resolution. My thesis supports this conclusion with a theoretical calculation while comparing the Hall probe technique to other kinds of magnetic imaging. I have explored further improvements in the overall design and materials of Hall probes. I have obtained and analyzed magnetotransport data for various concentrations of lead in bismuth films and Hall probes. Bismuth, a compensated metal, is a good alternative to semiconductor Hall probes. The presence of electron and hole carriers, though, reduces the Hall effect, and bismuth would be even better for Hall sensors if one kind of carrier were compensated. A doping between 0 and 0.1% lead in bismuth appears to be best for lead-doped bismuth Hall probe operation. I have also made significant progress in the design and fabrication of a more durable Hall probe shape, inspired by hard drive read heads. The novel design should enable operation closer to the sample surface, improving spatial resolution and making it easier to detect flux.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Broun
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.