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

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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.

2H-NMR Study of Model Membranes: Investigating the Effect of Sterol Structure on the Chain Ordering and Phase Behavior of Lipid Mixtures

Author: 
Date created: 
2014-11-18
Abstract: 

We employed deuterium nuclear magnetic resonance spectroscopy (2H-NMR) to investigate the effect of sterol structure on lipid membrane organization. Cholesterol is the major sterol component of mammalian cell plasma membranes. It strongly affects the properties of phospholipid membranes. For example, incorporating cholesterol in liquid crystalline membranes increases lipid acyl chain order, and induces the liquid ordered phase which is considered to have biological importance. We first measured the chain ordering in pure bilayers of 1-cholesterylhemisuccinoyl-2-palmitoyl(d31)-sn-glycero-3-phosphocholine (CholPC), a sterol-modified phospholipid with a cholesterol moiety covalently attached to the phospholipid glycerol backbone in place of one of the lipid acyl chains. We then compared CholPC’s chain ordering with that of 1-palmitoyl-2-palmitoyl-d31-sn-glycero-3-phosphocholine (DPPC-d31)/cholesterol and found that constrainded cholesterol’s ability to order adjacent acyl chains is greatly reduced. Several sterols, broadly similar in structure to cholesterol but with specific chemical modifications, are prevalent in plant or fungal cell plasma membranes. We used 2H-NMR to study the influence of sterol structure on its effectiveness in modifying the acyl chain order of a 1-palmitoyl(d31)-2-oleoyl-sn-glycero-3-phosphocholine (POPC-d31) membrane. Spectra of POPC-d31 multilamellar vesicles containing campesterol, β-sitosterol, brassicasterol or stigmasterol were taken at 25oC for sterol concentrations up to 45 mol% and compared to previous observations obtained using cholesterol, 7-dehydrocholesterol (7-DHC) or ergosterol. Among the sterol structural modifications we compared, the C22 double bond reduced the sterol’s ordering ability the most, followed by a C24 ethyl or methyl substituent. Finally we used 2H-NMR to study the effect of sterol structure on the propensity of sterols to induce phase separation in equimolar DPPC/POPC/sterol membranes containing 7-DHC, brassicasterol or stigmasterol. The results were compared to previous observations obtained for membranes containing cholesterol or ergosterol, which highlighted the significance of sterol structure on phase separation promoting properties. Such comparative studies are prerequisites to establishing the underlying principles of sterol/phospholipid interactions.

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

Evidence for Standard Model Higgs boson decays to tau lepton pairs in the ATLAS detector supported by a search in the fully hadronic final state

Author: 
Date created: 
2014-12-04
Abstract: 

This thesis presents the results of a search for Standard Model Higgs bosons decaying to tau lepton pairs, where both tau leptons decay hadronically. The search is performed using the proton-proton collision data collected in 2012 by the ATLAS detector at the Large Hadron Collider at CERN. The search is complicated by a significant source of background events from non-resonant multijet processes and by di-tau events from Z boson decays that share similar features with the Higgs signal. The multijet background is estimated from a control region in data, and the Z→ττ background is estimated from Z→μμ events in data where the muons are replaced by simulated tau leptons. Other minor backgrounds are estimated from simulation. A multivariate analysis using boosted decision trees is optimized to search for Higgs events produced via gluon-gluon fusion and vector boson fusion at a Higgs mass of 125 GeV. A cut-based analysis is also developed and presented in support of the multivariate analysis. An excess of events over the expected background is observed with a statistical significance of 2.9 standard deviations. When combined with excesses observed by searches in the fully leptonic and semi-leptonic final states, the statistical significance reaches 4.5 standard deviations. The combined excess is compatible with and provides direct evidence for the coupling of the recently discovered Higgs boson to fermions.

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

Towards silicon-based quantum Dits: optical study of group-V donors 75As:28Si and 121Sb:28Si

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

Silicon-based quantum information processing devices show great promise, being one of the most advanced candidates for the basis of the quantum computer. The spin state of phosphorus atoms in isotopic silicon has been demonstrated to have the longest solid-state coherence times. In this thesis, I describe experiments characterizing the other group-V shallow donors arsenic and antimony in silicon, in the context of developing quantum information processing technology. A sample of isotopic silicon containing these dopants was commissioned. I report here the results of photoluminescence excitation spectroscopy, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy, and pulsed NMR experiments. I found that antimony is not a suitable candidate in this context by virtue of being unpolarizable by our technique; however, arsenic is sufficiently polarizable. I report a measured coherence time of 2.0 s for the neutral arsenic nuclear spin.

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

Tissue-specific and trait-associated variation of human DNA methylation

Author: 
Date created: 
2014-08-14
Abstract: 

Epigenetics refers to a host of different mechanisms that regulate the expression levels of genes in an organism that do not rely on direct changes to the DNA sequence. These marks are heritable and sensitive to external signals. One epigenetic mechanism is DNA methylation, which consists on the attachment of a methyl group to a CpG dinucleotide. With the use of microarrays, DNA methylation studies typically interrogate the methylation status of hundreds of thousands of CpG sites in cohorts that range from tens to hundreds of individuals. In this thesis we identify tissue-specific and trait-specific patterns of methylation and highlight biological features associated with them. We also quantify the extent to which DNA methylation can optimally encode information about certain human traits.

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