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

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Variance in Initiation Factors Does Not Strongly Affect the Replication Profile of Budding Yeast DNA

Author: 
Date created: 
2015-08-19
Abstract: 

DNA replication starts at many sites (origins) throughout eukaryotic DNA. To fully understand the replication program in higher organisms, one needs to understand the behaviour of these origins. In Saccharomyces cerevisiae (budding yeast), the spatial organization of the origins is simple: The origins are confined to known specific sites on the genome. The temporal behaviour of origins in budding yeast is more complex: They fire stochastically with a broad distribution of firing times. Several key proteins take part in the DNA replication process. The MCM2-7 hexamer in particular forms a helicase that unwinds DNA locally, allowing access for other proteins to replicate the separated DNA. Past analysis of the budding yeast replication program suggested the Multiple Initiator Model (MIM), which hypothesizes that the number of these MCMs loaded at an origin predicts the firing time of that origin. Part of the MIM formalism assumes that the number of loaded MCMs is large; in this case the relative fluctuations between cells will be small and are ignored. However, a recent experiment measuring the number of loaded MCMs has revealed that the number is low, and thus, cell-to-cell fluctuations may be larger than expected. The purpose of this thesis is to investigate the impact of large relative fluctuations in the number of MCMs on the MIM. To measure this effect, we built the "MIM simulator," a modular program that simulates the replication process. Although a naive argument suggests that the MIM should fail when the number of MCMs is low, the impact of these fluctuations is mitigated by the contributions from neighbouring origins. We conclude that inferences made with the MIM remain accurate in the case that the number of MCMs is lower than first assumed.

Document type: 
Thesis
File(s): 
Supervisor(s): 
John Bechhoefer
Malcolm Kennett
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.

Improvements to Modelling of Raman Scattering Intensity for Molybdenum Disulfide

Author: 
Date created: 
2015-07-28
Abstract: 

Single layer molybdenum disulfide (MoS2) has attracted significant interest as a semiconducting two-dimensional material. In this work, ultrathin layers of MoS2 were exfoliated on geland wax substrates. Raman studies of the ultrathin layers of MoS2 were carried out to characterize the thickness. During Raman measurement, an anomaly occurs: the strongest Raman intensity appears at a finite thickness of the MoS2, a phenomenon also seen in graphite. A previous work [Y. Y. Wang et al., Appl. Phys. Lett. 92, 043121 (2008)] theoretically explained this unexpected phenomenon but with some questionable details. To improve their model, the complex index of refraction was properly used in the optical equations, and the assumption of optical interference of Raman signals from an infinitesimal source was added. This modified model successfully predicted the experimental results when applied to graphite and was then applied to MoS2. The simulations indicated that a constant complex index of refraction for MoS2 of 6.5-1.7i provided the best fit to published experimental results for MoS2 on SiO2/Si. This helped to estimate the thickness of ultrathin layers on gel. Seven layers MoS2 on gel showed the strongest Raman intensity according to this simulation.

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

Switchable resonant hyperpolarization transfer from phosphorus-31 nuclei to silicon-29 nuclei in natural silicon

Author: 
Date created: 
2015-05-01
Abstract: 

Silicon has been the backbone of the microelectronics industry for decades. As spin-based technologies continue their rapid development, silicon is emerging as a material of primary interest for a number of these applications. There are several techniques that currently exist for polarizing the spin-1/2 silicon-29 nuclei, which account for 4.7% of the isotopic makeup of natural silicon (the other two stable isotopes, silicon-28 and silicon-30, have zero nuclear spin). Polarized silicon-29 nuclei may find use in quantum computing (QC) implementations and magnetic resonance (MR) imaging. Both of these applications benefit from the extremely long T1 and T2 of the silicon-29 nuclear spins. However, the lack of interactions between the silicon-29 nuclei and their surroundings that allow for these long relaxation times also means that it is difficult to find a source of spin-polarization that effectively couples to the silicon-29 spin ensemble. We identify and exploit a field-dependent, frequency-matched resonant transfer process between phosphorus-31 donor and silicon-29 nuclear spins in natural silicon to efficiently hyperpolarize the bulk silicon-29 to over 6%. This all-optical technique requires no microwave irradiation, and the coupling can be switched off to recover the ultra-long nuclear spin relaxation lifetimes of silicon-29. This switchable hyperpolarization technique significantly enhances the usefulness of silicon-29 spins in QC and MR imaging applications.

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

Cosmological constraints on new scalar gravitational interactions

Author: 
Date created: 
2015-01-09
Abstract: 

Scalar-Tensor theory is a framework for modified gravity that encompasses many well-studied alternatives to General Relativity. Of particular interests are theories which possess a screening mechanism, which allows for the satisfaction of the bounds of solar system and laboratory scale tests of gravity, while giving rise to novel effects on cosmological scales. Among these are Large-Curvature f(R) as well as Chameleon, Symmetron and Dilaton gravity. All of these models can be described in terms of a recently introduced parametrization of Scalar-Tensor Theory, which involves two free functions of time alone. These models have been implemented by modifying the existing code MGCAMB. In this thesis, we discuss our implementation of these models. We present the results of Fisher forecasts for the constraints on the parameters of the 4 aforementioned models, taking the Large Synoptic Survey Telescope (LSST) and Planck as representative surveys. We also use the Principal Components Analysis approach, forecasting constraints for bins of the two functions upon discretization.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Levon Pogosian
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Can localized impurities exert global effects on lipid model membranes?

Date created: 
2015-04-23
Abstract: 

The currently accepted model for cell membrane organization involves "lipid rafts"', which differ in composition from the surrounding lipid sea. The existence of these nano-scale heterogeneities is supported by observation of coexisting ordered and disordered lipid phases in lipid model membranes. Fluorescence is a popular family of techniques that can provide dynamic and structural information about membranes. With any probe method, characterization of the effects of fluorescent probe addition on the systems they are used to study is important for the interpretation of experimental data. Comparison can be made between labelled and unlabelled samples using a non-perturbing method, such as deuterium nuclear magnetic resonance spectroscopy (2H NMR). This thesis used 2H NMR to study the effects of an equipartitioning probe, Laurdan, and a non-equipartitioning probe, naphthopyrene, on a well-studied three-component lipid membrane system (35:35:30 dioleoyl-sn-glycero-3-phosphocholine (DOPC)/dipalmitoyl-sn-glycero-3-phosphocholine-D62 (DPPC-D62)/cholesterol) with a miscibility phase transition. In phase-separated membranes, 0.03-0.6\% naphthopyrene disordered lipid chains of DPPC-D62 in the liquid-disordered phase, but not of those in the liquid-ordered phase. 0.1-2% Laurdan did not affect the DPPC-D62 in either phase in these membranes. Above the miscibility transition temperature (22 degrees Celsius), there is a single homogeneous liquid phase that is not perturbed by the addition of either probe. Laurdan is particularly well suited to the study of phase separation in lipid membranes. It partitions equally well into ordered and disordered lipid phases and displays a polarity-dependent emission spectral shift. Laurdan general polarization (GP) parameter, which characterizes said spectral shift, has been used to characterize membrane fluidity. Two-photon excitation microscopy Laurdan GP images were acquired for membranes with 0.2-2% Laurdan, and Laurdan GP values were found to be strongly correlated with \dnmr methylene order parameters of DPPC-D62 in the liquid-ordered phase. Finally, photo-induced phase separation is known to occur in fluorescence microscopy experiments; however, our 2H NMR experiments showed that naphthopyrene can alter membrane properties in the absence of light. The fact that trace amounts of probe (e.g., 0.03-0.6% naphthopyrene) affect lipid molecular order has biological implications: biomolecules present in very small amounts are known to have important functions in cells.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Jenifer Thewalt
Department: 
Science:
Thesis type: 
(Thesis) Ph.D.

Universal inhomogeneous magnetic-field response in the normal state of cuprate high-Tc superconductors

Date created: 
2015-04-20
Abstract: 

Tremendous effort continues to be devoted to elucidating the anomalous normal state of high-temperature cuprate superconductors. Experiments on underdoped cuprates have revealed a rich phase above the superconducting transition temperature (Tc) with the presence of electronic nematicity, charge-density-wave order, anomalous weak magnetic order, Cooper pairing, and superconducting fluctuations. A key finding has been the observation of nanoscale electronic inhomogeneity at the surface of Bi2Sr2CaCu2O8+δ by scanning tunneling microscopy (STM). Understanding the role played by the electronic inhomogeneity in the various observed phenomena requires answers to the following questions: (i) Is there a similar degree of electronic inhomogeneity in the bulk? (ii) Does the electronic inhomogeneity observed in Bi2Sr2CaCu2O8+δ have any relevance to other cuprate superconductors? To address these questions one needs a bulk technique that can distinguish between a spatially uniform and inhomogeneous system. The present thesis reports on the results of a muon spin rotation (µSR) study of the bulk of Bi2+xSr2-xCaCu2O8+δ , as well as pure and Ca-doped YBa2Cu3O7-δ, which together with prior measurements reveal a universal inhomogeneous magnetic-field response of hole-doped cuprates extending to temperatures far above Tc. In particular, the inhomogeneous line broadening above Tc is found to scale with the maximum value 〖T_c〗^max for each cuprate family, indicating that the inhomogeneity in the normal state is controlled by the same energy scale as Tc. Since the degree of chemical disorder is very different in the materials we have measured, the observed scaling constitutes strong evidence for an intrinsic electronic tendency toward inhomogeneity in the normal-state, from which bulk superconductivity emerges at lower temperatures.

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

A Study of Thickness Distribution and Crystal Structure of Sputter-deposited Silicon Thin Films

Author: 
Date created: 
2015-01-22
Abstract: 

Silicon thin films have a wide range of applications in different industries such as microelectronics and solar cells. Controlling the properties of the film such as thickness, uniformity and crystal structure during the deposition process is of crucial importance in the final performance of the device. In this work, the thickness distribution and crystal structure of silicon films deposited by the magnetron sputtering technique were studied. A computer model was developed to simulate the thickness distribution of sputter-deposited silicon films. The simulation results were compared to the measured film thickness profiles obtained by X-ray reflectometry measurements. The good agreement between the experimental and simulation results demonstrates that the model is consistent with the observed experimental results. The crystal structure of silicon films were examined by means of the X-ray diffraction measurements. Silicon has an as-deposited amorphous structure. To induce the crystallization at low temperatures, a copper layer was deposited on top of the silicon film. The crystallization of silicon was observed at 340°C which is considerably lower than the solid phase crystallization of amorphous silicon (~700°C). It is also shown that silicon crystallites tend to grow in the [111] direction. The full width at half maximum of the silicon (111) peak is less than 2 degrees which indicates a strong texture along this direction.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Erol Girt
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Off-Axis Electron Holography of Isolated Ferromagnetic Nanowires

Date created: 
2014-12-02
Abstract: 

The investigations carried out in this thesis involved the nanoscale characterization of isolated ferromagnetic nanowires (NWs) using off-axis electron holography (EH), high-resolution transmission electron microscopy, scanning transmission electron microscopy and energy dispersive spectroscopy. The research focused on two categories of NWs, single phase CoFeB NWs and multilayer CoFeB/Cu NWs, which were fabricated by pulsed-current electrodeposition in nanoporous alumina membranes as an array of NWs. EH has been used to investigate the local magnetic behavior of the isolated NWs in their remanent state. In addition, the uniformity in diameter, composition, crystal structure of individual NWs were investigated. Single phase CoFeB ferromagnetic NWs, with diameters ranging between 20 to 170 nm, were studied. Electron diffraction patterns indicated that the NWs were nanocrystalline, BCC CoFeB, with grain sizes up to 20 nm × 20 nm. Holograms from EH showed that the magnetization inside the NWs was uniform over most of their length, except at their edges. Since the NWs consisted of soft magnetic nanocrystals, the magnetic anisotropy was likely dominated by the shape anisotropy. Numerical simulations suggested that the stray field at the tips of the NWs was well reproduced by a truncated cone model, rather than a cylinder. The average magnetic induction was 1.4 ± 0.3 T. Multilayer NWs consisted of periodic magnetic layers of CoFeB alloys and non-magnetic layers of Cu. Individual NW compositions, crystallinity, and layer thicknesses were calibrated using scanning transmission electron microscopy and energy dispersive spectroscopy. These properties were found to be significantly different from their expected nominal values assumed for the arrays, based on single-phase growth rates. Diffraction patterns obtained from the NWs again showed that both the CoFeB and Cu layers were nanocrystalline (BCC CoFeB, FCC Cu) but that the CoFeB layers had a significant atomic fraction of Cu, despite the small concentration of Cu used in the electrolyte. Nevertheless, the average magnetic induction of individual CoFeB layers ranged between 0.5 and 1.5 T, depending upon the thickness of the layer, from 50 nm to 250 nm, and the direction of an external magnetic field applied in situ. The magnetization was axial for all external field directions when the CoFeB layer was thicker than the diameter (45 nm), while for thin CoFeB and Cu layers (< 10 nm), magnetic vortices were detected, associated with opposing magnetization in neighbouring layers. These observations provided important insight for the interpretation of previously reported effective-anisotropy fields of similar NW arrays.

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

Epitaxial electrodeposition of Fe onto GaAs nanowires.

Author: 
Date created: 
2015-01-07
Abstract: 

Fe contacts with thickness ranging from 50 nanometers to 100 nanometers were selectively fabricated onto Au catalysed, Te-doped n-GaAs (111) nanowires via galvanostatic electrodeposition. An insulating polymer (SU-8) was used to fill in between the nanowires preventing deposition directly onto the GaAs substrate. Scanning transmission electron microscopy investigations combined with energy-dispersive X-ray analysis verified the existence of single-crystalline, epitaxial Fe/GaAs (110) on the sidewalls of typical nanowires. Electrical barrier heights (0.53 ± 0.02 eV) and ideality factors (1.7 to 1.9) were obtained from current-voltage measurements of individual nanowires in a scanning electron microscope.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Karen Kavanagh
Department: 
Science:
Thesis type: 
(Thesis) M.Sc.

Optimizing the Refractive Index Sensitivity of Extraordinary Optical Transmission Based Sensors

Author: 
Date created: 
2014-12-08
Abstract: 

Extraordinary optical transmission involves the resonant coupling of incident electromagnetic radiation with surface charge density oscillations called surface plasmons. The resulting propagating surface modes are known as surface plasmon polaritons. In extraordinary optical transmission the coupling mechanism is a periodic array of sub-wavelength holes perforating a thin metallic film. As light shines on the metal surface energy accumulates within the surface modes, tunnels through the holes, and is re-scattered into the far field on the opposite side of the film. The resonance condition depends intimately on the profile of the metal film, geometry of the hole array, and the optical properties of the metal film and adjacent dielectric. These surface modes are evanescently constrained to the metal-dielectric interface, and therefore make excellent probes of the local refractive index. This thesis describes a series of studies aimed at optimizing the refractive index response of nanohole arrays in thin gold films. I designed and optimized these sensors to detect the refractive index changes caused by antibodies secreted by live, microfluidically-trapped immune cells, binding to functionalized arrays. In calibration studies, the minimum detectable concentration of antibody in cell growth medium was 3 ± 1 μg/ml. In live cell studies, I was able to detect antibodies secreted from 200 trapped cells, detecting a peak shift of 10 nm above that of a control sample. Detection from lower numbers of cells was unreliable, likely due to competing reactions from non-specific binding. In the quest to improve the device sensitivity, the influence of the array geometry and the role of the nanohole array lattice on the transmission spectrum of square and hexagonal arrays were clarified. With these insights and improvements, the minimum bulk refractive index resolution (glucose solutions) increased from 2.5 ± 0.3 x10-3 to 1.5 ± 0.1 x10-3 units, ultimately limited by the optical system and the 1 nm resolution of the spectrometer used in the measurements. A superior data analysis technique based on an integrated response analysis of the entire transmission spectrum was introduced. Finally, I demonstrated a process to recycle the delicate nanohole arrays without destroying their physical and optical properties.

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