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

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Models for protein localization in bacteria and chromatin structure in eukaryotes

Date created: 
2014-03-17
Abstract: 

In the fi rst part of this thesis, we focus on the problem of how proteins localize within the cytoplasm of bacteria. Experimentally, it is found that proteins that have attractive interactions are able to localize to one or both of the poles in cylindrical bacteria. We put forward a model that only relies on the aggregating tendency of proteins and the occlusion by the bacterial nucleoid. Monte-Carlo simulations enabled us to find the stable and metastable localization patterns, allowing us to explore the phase space of parameters in our model. Our findings explains the di fferent patterns observed for PopZ localization in Escherichia coli and Caulobacter crescentus as well as misfolded proteins. We find the kinetics of expressing proteins has a crucial role: unipolar patterning is an energetically favorable state while other polar patterns can be achieved at higher rates of protein expression. Using sets of di fferent GFP tagged aggregating proteins we are able to experimentally test this prediction and alter the localization from unipolar to bipolar simply by increasing the rate of expression. In the second part, we consider the structuring of the DNA within the eukaryotic nucleous and its associated proteins. A new high-throughput experimental technique, Hi-C, is able to measure the looping frequencies between all parts of the genome. We transform the measured data and are able to extract a distance independent free energy by subtracting out the background free energy of interactions due to the polymer nature of DNA. Our mean- field model quanti ties the interaction strengths between chromatin factors and loops along the chromosomes in a protein pairwise interaction matrix J. Since the Hi-C data carries di erent biases, using our approach we are able to assess the best sets of corrections that lead to the free energy having the most mutual information with the underlying chromatin profi les. Further to this, we use Principal Component Analysis (PCA) to identify the frequent modes of genome wide looping. Hence, we are able to correlate these with known domain structures such as boundaries between active and silent regions of the genome.

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

Material Composition Analysis Using Time-Domain Terahertz Spectroscopy

Author: 
Date created: 
2014-04-22
Abstract: 

In this work, we apply terahertz time-domain spectroscopy to measure the thickness and composition of dielectric samples consisting of multiple constituents. We accomplish this in two stages. First, a two-component model is introduced that allows us to estimate the volume fractions of two constituents in addition to the sample thickness. Here the sample is assumed to be a homogeneous mixture, with its permittivity given by the Bruggeman effective medium theory (EMT). We apply the procedure to paper samples to extract thickness and moisture content. We perform Monte-Carlo simulations with a realistic noise model to understand the parameter correlations and predict the expected uncertainties. The simulation results are consistent with the observed repeatability measurements performed on paper samples. We show that our measurements can compete with existing thickness and moisture sensors currently deployed in the industry. Second, a three-component model is presented to determine the volume fractions of three constituents, along with the thickness. We also develop two different scattering models to account for the effects of scattering from inhomogeneities. We validate our model by measuring pulp samples compressed to different thicknesses thus having variable densities. Again, our measurements match well with the independently measured parameter values. Monte-Carlo simulations suggest avenues of improvement of the performance of the system.

Document type: 
Thesis
File(s): 
Senior supervisor: 
John Steven Dodge
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Microwave Spectroscopy of Magnetically Trapped Atomic Antihydrogen

Date created: 
2014-04-03
Abstract: 

We have every reason to believe that equal amounts of matter and antimatter were produced in the early universe. Moreover, theory predicts that the laws of physics make no distinction between the two. In this light, the fact that the observable universe is overwhelmingly dominated by matter is inexplicable. ALPHA is an international project located at CERN involving approximately 40 physicists from 15 different institutions in 7 countries. The primary goal of the collaboration is to study the antihydrogen atom at the highest level of precision possible, and thereby enable comparisons between hydrogen and antihydrogen. Through these comparisons it hopes to improve our understanding of the distinction between matter and antimatter, and perhaps shed some light on the puzzle of why we live in a matter dominated universe. The hyperfi ne energy intervals of ground-state hydrogen and antihydrogen represent an opportunity for a precision comparison. A discrepancy between the energy levels of these two atomic systems would indicate a major revolution in physics, and in our understanding of the universe. This thesis describes and interprets the fi rst proof-of-principle spectroscopic measurements performed on magnetically trapped antihydrogen atoms. The experiments were performed by the ALPHA collaboration using microwave radiation tuned to induce transitions between hyperfi ne levels of ground state antihydrogen atoms. Our observations con firm that positron spin resonance transitions between hyper fine levels of ground state antihydrogen are consistent with expectations for hydrogen to within 4 parts in 10^3. The hyper fine splitting of ground state antihydrogen atoms is also constrained to 1420 +/- 85 MHz.

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

Lateral spin injection and detection via electrodeposited Fe/GaAs contacts

Author: 
Date created: 
2013-09-06
Abstract: 

Experimental studies of lateral spin injection and detection through electrodeposited Fe/GaAs tunnel contacts are reported in this thesis. An enhanced spin valve voltage is demonstrated via non-local lateral spin transport measurements compared to their vacuum-deposited counterparts. We have proposed a simple theoretical model to explain this result. Combined with experimental evidence for interfacial oxygen from atom probe tomography, we speculate that the enhancements occur due to a magnetic iron oxide layer forming at the Fe/GaAs interface during the electrodeposition. This layer acts as a tunnel barrier with a spin-dependent height. This discovery of greatly enhanced spin injection into GaAs via electrodeposited contacts introduces a promising new direction for the development of practical semiconductor spintronic devices. This thesis addresses three major challenges: i) The electrodeposition of Fe onto an epitaxial n-GaAs layer on a semi-insulating substrate to fabricate the tunnel contacts and lower-doped channel required for lateral spin injection. ii) Demonstration of spin accumulation and transport using patterned contacts in lateral configurations. iii) Understanding magnetic in-homogeneities and defects in the thin Fe film and correlating these to the observed enhanced spin injection. Continuous Fe film coverage was achieved over a desired area of the epitaxial GaAs by creating a uniform potential at the back of the sample. Nucleation and growth of Fe was observed within a range of applied current densities from 0.05 to 0.20 mA/mm^2, with the best Fe epitaxy occurring at 0.15 mA/mm^2. Modelling via a micromagnetic simulator showed that magnetic hysteresis curves from the electrodeposited Fe did not follow the standard behavior of a thin Fe film (single or polycrystalline). Instead, these Fe films demonstrated inhomogeneous magnetization controlled by strong local uniaxial anisotropies along both the <100> and <110> crystallographic directions. The presence of defects and coalescence boundaries responsible for these in-homogeneities were detected by transmission electron microscopy. Spin valve and Hanle measurements showed evidence of a local magnetostatic field, possibly originating from magnetic impurities at the electrodeposited Fe/epitaxial GaAs interface. We suggest that these magnetic impurities enhanced the tunneling probability and the spin accumulation within the GaAs channel while reducing the spin lifetime.

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

Physics of Birefringent Fermions

Date created: 
2012-12-07
Abstract: 

There has been much recent interest in Dirac fermions due to their physical realizationas low energy excitations in graphene. In this thesis we introduce birefringent relativisticfermions, for which the chiral symmetry usually present for Dirac fermions is broken, andthere can be more than one Fermi velocity. We first introduce a lattice model of spinlessfermions that can arise from a scheme to introduce an artificial magnetic field for coldatoms. This model has an unusual Hofstadter-like spectrum as a function of the flux perplaquette. When there is an average of half a flux quantum per plaquette, the model hasDirac points in its spectrum and exhibits low energy excitations with two different “speedsof light”, i.e. birefringent fermions. We investigate the effects of several perturbations onthe spectrum such as staggered potentials and topological defects and we study the orderedphases that can arise from interactions. We find that sufficiently strong nearest neighbourinteractions lead to a charge density wave phase but that next-nearest neighbour interactionsallow the possibility of other phases. We also study the response of birefringent fermionsto a magnetic field and discuss how both Landau levels and the Integer Quantum Hall effectfor regular Dirac fermions are modified for birefringent fermions.

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

Terahertz Conductivity Measurements of MnSi

Author: 
Date created: 
2013-12-18
Abstract: 

This thesis presents measurements of the dynamical conductivity of a MnSi lm via terahertz time domain spectroscopy. We determine the Drude scattering rate and plasma frequency at low temperatures, and compare these to theoretical predictions. From a comparison of the plasma frequency measurement with band theory, we determine a mass renormalization of m*/m~5.5. Above the critical temperature, ts to the Drude model yield negative values for the scattering lifetime, indicating the existence of a pseudogap. At low temperatures and low frequencies, the resistivity has the well-known Fermi liquid form with the ratio of the temperature dependent term to the frequency dependent term, b>1. At the lowest temperature we estimate b ~ 4, with a large systematic uncertainty that we characterize for later improvement. This result is consistent with Fermi liquid theory predictions for electron-electron scattering.

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

Lifetime Measurement of the 6.79 MeV Excited State of 15O to Help Constrain the 14N(p,gamma)15O Reaction Rate

Author: 
Date created: 
2013-12-11
Abstract: 

In main sequence stars such as our Sun, the source of energy comes from converting hydrogen into helium. There are two competing mechanisms via which this can happen: the pp chain and CNO cycle. The latter is a cycle of reactions involving carbon, nitrogen and oxygen which are catalysts for the conversion of hydrogen into helium. The slowest reaction 14N(p,γ)15O in the cycle will affect the energy generation timescale and the amount of helium ash produced via the CNO cycle. This has several astrophysical impacts. It affects the evolutionary timescale of main sequence stars from which the ages of globular clusters can be calculated, the nucleosynthesis of heavier elements in H burning shells of red giant stars, and the fraction of energy produced by the CNO cycle compared to the pp chain in our Sun which helps determine the interior composition of the Sun. For main sequence stars the CNO cycle dominates over the pp chain for core temperatures T < 0.02 GK. For the 14N(p,γ)15O reaction this corresponds to a low center of mass energy Ecm = 30 keV. This is lower than the low energy limit of the reaction rate measurable in the laboratory. This means that we need to extrapolate down to low energy using theory. The largest remaining uncertainty in the theoretical calculations is due to the lifetime τ of the 6.79 MeV state of 15O. In this work the lifetimes of three excited states of 15O were measured using the Doppler shift attenuation method (DSAM) populating the states via the 3He(16O,α)15O reaction at a beam energy of 50 MeV. The low lifetime limit measurable using the DSAM is ∼1 fs. The lifetime of the 6.79 MeV state is near that limit, making this measurement challenging. A 1.8 fs upper limit (68.3% C.L.) on this lifetime is reported here. In addition we measured the lifetimes of the 6.17 and 6.86 MeV state in 15O which were < 2.5 fs and 13.3+0.8−1.2 fs (68.3% C.L.) respectively.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dugan O'Neil
Barry Davids
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Theory of the electronic and magnetic structure and transport properties of single molecule magnets

Date created: 
2013-10-23
Abstract: 

Developing electronic components at the molecular scale is the ultimate goal in molecular electronics. Because of their large magnetic anisotropy barriers and associated stable magnetic moments, single molecule magnets (SMMs) bring a new dimension to this field and also raise the possibility of molecular magnetic information storage and quantum computation. Therefore the transport properties of transistors based on individual SMMs are attracting considerable experimental and theoretical interest at present. This thesis presents a theoretical investigation of the electron and spin transport and associated phenomena in SMM transistors (SMMTs). A tight binding model is developed as an alternative approach to the giant spin Hamiltonian and density functional theory (DFT) methodologies for studying SMMs. Unique aspects of this approach are that it captures more physics than the giant spin Hamiltonians do but is much simpler than DFT and it has more flexibility for modeling experimental behaviors. Because of its simplicity this model is helpful in developing a physical understanding of SMMs and their transport properties. The tight binding model yields the total Mn12 SMM spin, the spins of the individual Mn ions, the magnetic easy axis orientation, the size of the magnetic anisotropy barrier and the size of the HOMO-LUMO gap consistent with experiments. Based on this tight binding methodology, this thesis addresses the following transport problems of current interest: ligand-based transport resonances in SMMTs, gate controlled switching between Coulomb blockade and coherent resonant tunneling in SMMTs, identification of the orientation of the magnetic easy axis of a SMM, the spin filtering effect of the SMMTs, quantum dot spin valves based on SMMs which support ligand--based transport, and tunneling and cotunneling transport through Mn12 SMMs in the weak coupling regime.

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

Structural Study of Anion Exchange Polymer Electrolyte Membranes, mes-PBI, mes-PDMBI and the Blends Using X-ray Scattering Techniques and Molecular Dynamics Simulations

Date created: 
2014-01-08
Abstract: 

In this work, I studied the structure of novel anion exchange polymer membranes (AEMs) using X-ray scattering techniques combined with molecular simulations as a complementary method. I simulated a monomer and a chain of each sample consisting of 3 monomers using ChemSketch. Good agreement between our simulations for the monomers and results found in the literature was observed. Comparing WAXS data to the simulation results, I attribute some of the features observed in the scattering data for each sample to specific repeat units along the chain of each polymer. A side-to-side and a stacking distance were measured for the pure samples. I observed an increase of 0.22 A in side-to-side distance and 0.17 A in stacking distance for pairs of PBI-PDMBI and mesPBI-mesPDMBI, respectively. I attribute this increase in both cases to adding mesitylene group to the structure.

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

Non equilibrium dynamics of quantum Ising chains in the presence of transverse and longitudinal magnetic fields

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2013-08-26
Abstract: 

There has been much recent interest in the study of out of equilibrium quantum systems due to experimental advances in trapped cold atomic gases that allow systematic studies of these effects. In this work we study a quantum Ising model in the presence of transverse and longitudinal magnetic fields. The model lacks an analytical solution in the most general case and has to be treated numerically. We first investigate the static properties of the model, including the ground state energy and the zero temperature phase diagram, using the Density Matrix Renormalization Group (DMRG) method. We identify ordered and disordered phases separated by a quantum phase transition. We then consider the time evolution of the system following an abrupt quench of the fields. We study the response of the order parameter to the quenches within the ordered and disordered phases as well as quenches between the phases using the time-dependent DMRG method. The results are in qualitative agreement with experiments and the implemented numerical method in this work can be extended to allow for more general interactions.

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