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

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Studies of Synthetic Molecular Motors

Author: 
Date created: 
2013-04-18
Abstract: 

To better understand the underlying principles by which biological motors operate, recent work has focused both on understanding their operational principles, and on designing new molecular motors ab initio. Here, by studying and designing motors which use Brownian motion and track asymmetry to bias the direction of motion, I gained insight into the underlying principles by which such motors operate. "Molecular spiders" [JACS. 128, 12693 (2006)] are one example of synthetic biomolecular walkers able to generate biased motion by coupling the chemical asymmetry arising from substrate binding and cleavage to bias their mechanical stepping.These DNA-based motors diffuse to their substrate track where productive binding between a molecular spider’s DNAzyme leg and a ssDNA substrate facilitates cleavage of the substrate. Once cleaved, the decreased binding affinity between the DNAzyme and resulting product allows the motor to diffuse along the track and form new interactions with uncleaved substrate molecules. Toinvestigate the origin of biased motion of molecular spiders, I have performed Monte Carlo simulations. Using my simulations, I also investigated their performance as molecular motors, and determined how to optimize their motor properties by modifying tunable experimental parameters in spider design. These studies assisted us in the design and construction of a novel protein-based synthetic motor, the "Lawnmower", which uses a burnt–bridges type of mechanism, the same as spiders, to autonomously and diffusively move forward. The lawnmower has trypsin proteases as blades, linked to a quantum dot hub, that interact with a one-dimensional peptide substrate track via binding to and cleavage of the substrates. Experimentally, it is confirmed with kinetic assays that ourlawnmower is an active motor and that there are an average number of 8 blades on each motor. I also outlined the synthesis and characterization of a highly modified DNA-peptide construct, which acts as the track for the lawnmower. For this, I employed PCR to generate a densely labeled DNA and click chemistry for peptide conjugation to the functionalized DNA. As an additional motors-relatedproject, I present the synthesis of a long one-dimensional DNA track with periodically repeating elements that provide specific binding sites for the "Tumbleweed" molecular motor.

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

First determination of the 8Li valence neutron asymptotic normalization coefficient using the 7Li(8Li,7Li)8Li reaction

Date created: 
2013-03-19
Abstract: 

Solar neutrino experiments have often been plagued with large uncertainties. With the recent results from the Borexino Collaboration, for the first time the total uncertainty in the 7Be solar neutrino flux measurement is smaller than the uncertainty of standard solar model (SSM) predictions. Improvement in neutrino experiments must be followed by refinements to the SSM; to do so requires reduced uncertainties on the parameters used in SSM calculations. One such value is the astrophysical S-factor describing the 7Be(p,gamma)8B reaction, S_{17}(0). We report here a determination of the asymptotic normalization coefficient (ANC) of the valence neutron in 8Li from a measurement of the angular distribution of the single neutron transfer between 8Li and 7Li via the 7Li(8Li,7Li)8Li reaction at 11 MeV. Using isospin symmetry the 8B ANC has also been calculated and used to infer a value for S_{17}(0) of 20.2 +/- 4.4 eV b.

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

Contribution of non-linear structure to the kinetic Sunyaev-Zeldovich power spectrum

Author: 
Date created: 
2013-02-06
Abstract: 

In the last two decades, a satisfactory standard cosmological model has been established. On the other side, a wealth of new precise data from various astronomical observations is becoming available, leading to increased interest in details of the CMB foreground physics. In this thesis we investigate a very promising foreground effect, the kinetic Sunyaev-Zeldovich (kSZ) effect, and calculate its contribution to the CMB power spectrum. The kSZ effect is due to the interaction of CMB photons with a moving structure between the observer and the surface of last scattering, such as a cluster of galaxies, that contains ionized gas and moves with a certain peculiar velocity. The strength of the effect is determined by both the non-linear density distribution of matter inside clusters and the peculiar velocity which is governed by the linearly perturbed matter density around them. We analyze the relative importance of the the linear and non-linear contributions to the kSZ considering only gravitational interactions. We find that the non-linear contribution significantly change the power spectrum in very small scales, thus we believe including baryonic physics which also governing the nonlinear evolution of the structures is necessary. The effect of baryons is to redistribute matter toward the centres of halos, which can be dramatic when baryon component is allowed to cool. We calculate this deviation as well as its impact on the kSZ CMB power spectrum.

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

Bringing the Higgs Boson to Rest

Date created: 
2013-01-31
Abstract: 

Within the Standard Model of particle physics, the Higgs boson can decay to a pair of W bosons which decay leptonically. Despite its relatively large branching ratio, this is a challenging channel in which to search for the Higgs boson since we cannot detect neutrinos directly with the ATLAS detector. The matrix element method is a first principles approach that allows for better separation of signal and background by responding to subtle differences in the measured event kinematics. A straightforward implementation of the method is to assume that the Higgs boson is produced at rest in the transverse plane. However, this is often not the case due to next-to-leading order effects like initial state radiation. In order to improve the sensitivity of the matrix element analysis, we developed an estimator for the transverse momentum of the Higgs boson that allows us to boost it into its transverse rest frame. Using a regression tree algorithm to estimate the transverse kinematics of the Higgs boson on an event-by-event basis, we observe a 15% improvement in sensitivity. The application of this technique to Higgs boson property measurements, such as the determination of its spin, is also explored.

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

Cross Section Measurement and Search for New Physics with Top Quark Pair Events Involving a Tau Lepton in ATLAS

Date created: 
2013-03-15
Abstract: 

In 2011, the ATLAS detector recorded an integrated luminosity of over 5 fb−1 of proton-proton collisions delivered by the LHC at a centre-of-mass √s=7 TeV. The first of two analyses is a test of the standard model and the world’s most precise measurement of the top quark pair production cross section for final states which include a hadronically decaying tau lepton. The second analysis uses the same dataset to search for a charged Higgs boson, also resulting in the world’s best limits for the search channel. In the cross section measurement, 2.1fb−1 of ATLAS proton-proton collision data is used to measure the top quark pair production cross section in events containing an isolated electron or muon and a tau lepton decaying hadronically. After initial event requirements, the leading background comes from top quark pairs with jets faking tau leptons. A fit to a tau lepton identification variable is used to determine the signal yield. The measured cross section 186±13(stat.)+20-19(syst.)±7(lumi.)pb, is in good agreement with the standard model prediction. Several extensions to the standard model predict the existence of at least one charged Higgs boson, H±. According to these extensions, the top quark can decay into a bottom quark and a light charged Higgs boson in addition to the standard model decay to a bottom quark and aW boson. In the second analysis, event yield ratios between different final states are measured using 4.6fb−1 of ATLAS data. This is compared to simulation to search for a violation of lepton universality. This ratio-based method reduces the impact of systematic uncertainties in the analysis. No significant deviations from the standard model predictions are observed. With the assumption that the charged Higgs boson branching ratio to a tau lepton and a neutrino is 100%, upper limits in the range 3.2%–4.4% can be placed on the top quark to charged Higgs branching ratio for 90≤mH±≤140 GeV. After combination with results from a search for charged Higgs bosons in t¯t decays using the thad+jets final state, upper limits on this branching ratio can be set in the range 0.8%–3.4%, for 90≤mH±≤140 GeV.

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

Chiral symmetry breaking in high-temperature superconductors and birefringent cold atoms, helicity modulus in layered bosons and phase diagram of superconductor-insulator transition

Date created: 
2012-06-26
Abstract: 

This work is a compilation of several research projects with them main theme being high-temperature superconductivity. We construct the field theory of underdoped cuprates beginning with a well-defined d-wave superconductor and adding the vortex degree of freedom using a singular gauge transformation. The symmetries of the theory both in the presence and absence of a quasi-particle mass are studied. Nodal quasi-particles are known to obey a relativistic Lorentz symmetry while their massless nature represent another symmetry which we will identify as a chiral SU(2) symmetry. It is shown that 2+1 quantum electrodynamics is the effective theory that describes underdoped cuprates in the zero- temperature pseudogap regime. We focus on the mechanism of dynamical mass generation in three dimensional quantum elec- trodynamics and theories with four-fermion interactions. This is a field that has been subject of extensive research in last two decades. However, our momentum-shell renormalization group ap- proach is new to the field and through that we are able to estimate the conditions for the mass generation mechanism and also work out the phase diagram of the theory for charge and inter- action strength. We discuss the applications of momentum-shell renormalization group to other four-fermionic theories in the absence of a gauge field. The justification for this is the fact that in the superconducting regime the system can be described by a massive gauge field theory coupled to relativistic quasi-particles which effectively represent a four-fermionic theory. Inspired by the field theory constructed for underdoped cuprates we discuss the superfluid re- sponse of the underdoped materials using an anisotropic bosonic model and compare it to experiment. The idea is to see how c-axis superfluid density measurements can help one set the parameters in our field theory for underdoped cuprates. The behaviours of the superfluid responses in both out- of-plane and in-plane measurements has been detailed as a function of temperature and density (doping) and it is shown that there is disagreement with the measured c-axis response using the iii conjectured bosonic Hamiltonian.

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

Measurement of the neutrino asymmetry in the beta decay of laser-cooled, polarized 37k

Author: 
Date created: 
2005
Abstract: 

The TRINAT collaboration began investigating fundamental symmetries searching for scalar contributions to the predominantly V - A structure of the weak interaction by measuring the /3 - v correlation parameter using the pure Fermi decay of magnetooptically trapped 38mK . This thesis describes the first physics measurement using polarized, laser-cooled 3 7 ~ , and represents the next generation of TRINAT experiments aimed at searching for right-handed currents predicted to restore parity at higher energy scales in some extensions to the Standard Model. Using a detector geometry similar to that of the scalar search, we have learned to implement optical pumping techniques to achieve very high (2 96%) nuclear polarizations of our radioactive atom sample. Furthermore, we have pioneered techniques to measure this observable - independent of the /3 decay observables - in situ on all the nuclei that are decaying. By observing the emitted /3+ and recoiling 37Ar in the back-to-back geometry, we have extracted a measurement of the neutrino asymmetry parameter: B, = -0.755 f 0.020 f 0.013, in agreement with the Standard Model (stat) (syst) prediction of -O.7692(15). This 3% measurement of the B, represents the first /3 decay physics measurement using a polarized, laser-cooled source. This is not yet competitive with other limits on right-handed current parameters; however, we have identified our dominant systematics and have learned how to minimize them so that the next time the experiment is performed, we expect to be able to reduce our uncertainty to the 0.5% level. Additionally, we have outlined how we may make use of a correlation unique to our setup to further enhance our sensitivity. We expect that future experiments will be able to have a significant impact in either finding new physics or helping to constrain the variety of models considered as viable extensions to the Standard Model.

Document type: 
Thesis
File(s): 
Department: 
Department of Physics - Simon Fraser University
Thesis type: 
Thesis (Ph.D.)

String theory, dual theories and D-branes

Author: 
Date created: 
2004
Abstract: 

In the context of the Anti-de Sitter / Conformal Field Theory correspondence we consider the Berenstein-Maldacena-Nastase (BMN) sector of the large-N Super Yang-Mills theory and demonstrate explicitly the correspondence of four-impurity operators therein to known states in string theory on the pp-wave background obtained as a Penrose limit of Ads space. In the corresponding gauge theory we calculate matrix elements of the dilatation operator in the BMN operator basis. These matrix elements are found to coincide with those of the light-cone string Hamiltonian, which is computed using the string field theory vertex in the pp-wave background. Our results are in agreement with others' results obtained using gauge-theory three-point functions. We next solve perturbative superstring theory on the Nappi-Witten background, obtaining the bosonic and fermionic spectra, and find that supersymmetry can be preserved in the Penrose limit. Our results indicate that the high-energy sector of little string theory, being holographically dual to the string theory which we solve, retains a supersymmetric spectrum. We perform a semiclassical analysis of strings in the Nappi- Witten metric and find that the relationship between energy and momentum coincides with the known result for a flat background. In the context of Vacuum String Field Theory (VSFT), we put forth some ideas as to how a distinction might be made between 'background7 D-branes, which are encoded explicitly in the formulation of split-string field theory, and 'string-field' D-branes, which correspond to solitonic lump solutions. We use the geometrical surface-state formulation of VSFT to investigate tachyon fluctuations about certain lump solutions, called sliver states, and thereby calculate their tensions. We perform this analysis both with and without a background B-field, and are able to reproduce the standard string-theory results for the ratios of D-brane tensions. We investigate tachyon fluctuations about another state known as the butterfly. As would be expected for a D-brane, the equation of motion derived for the tachyon field corresponds to the requirement that the quadratic term in the string-field action vanish on-shell. We begin a calculation of the tension of the butterfly and conjecture that this too will coincide with the standard D-brane expression.

Document type: 
Thesis
File(s): 
Department: 
Department of Physics - Simon Fraser University
Thesis type: 
Thesis (Ph.D.)

Isotope effects on the fundamental band gap of lead sulfide

Author: 
Date created: 
2005
Abstract: 

Lead sulfide (PbS) is one of the oldest known semiconductors, occurring naturally as the mineral galena. One of its interesting properties is a strong increase of the band gap energy with increasing temperature, opposite in sign to almost all other semiconductors. We report on the isotope shift of the band gap energy between natural PbS (containing mostly 32S) and PbS made with enriched 34S, measured using low temperature photoluminescence spectroscopy. The observed isotope shift is also opposite to the normal expectation of larger band gap for the heavier mass. In addition, we report on improved measurements of the temperature dependence of the band gap energy measured using absorption spectroscopy, to study the expected connection between the isotope shift of the band gap energy and its shift with temperature.

Document type: 
Thesis
File(s): 
Department: 
Department of Physics - Simon Fraser University
Thesis type: 
Thesis (M.Sc.)

Aluminum gallium nitride / gallium nitride high electron mobility transistor fabrication and characterization

Author: 
Date created: 
2005
Abstract: 

In the last decade, All-,GaXN/GaN High Electron Mobility Transistors (HEMTs) have been intensively studied because their intrinsic electrical properties make them attractive for high power microwave device applications. Despite much progress, current slump continues to be a problem, limiting output power, reducing reliability, and complicating device modelling. In this work, a complete A~I-,G~,N/G~N HEMT fabrication procedure was developed, and electrical characteristics related to current slump, microwave modelling, and delay time analysis were explored. Low resistance ohmic contacts were achieved, enabling high channel current densities. Schottky contacts were developed with a new ion implant isolation architecture, enabling gate leakage currents 2 to 4 orders of magnitude lower than typical results from the literature. Through pulsed current-voltage measurements, the importance of bias stresses in the gate-source region was demonstrated for the first time. In contrast to the conventional "virtual gate" model, gate-source stresses were shown to be more important than gatedrain stresses when biased near threshold. Slow slump transients were studied by passivating transistor surfaces with ultrathin layers. These results excluded dielectric strain and electron injection reduction as viable passivation mechanisms. A novel model was proposed associating slow slump behaviour with trapping of many electrons at screw dislocation sites. The effect of slump on RF properties was examined through microwave measurements by extracting the parasitic source and drain resistances without special biasing. Besides significantly improving the accuracy of small-signal modelling, we were able to show the bias dependence of parasitic resistances which confirmed the effect of source-side bias stressing. The question of channel electron velocities in nitride transistors remains controversial. We determined an effective electron velocity of - 1.9 x 1 o7 cmls through two methods. We first extracted effective velocities through delay time analysis, and then through the small-signal model elements. To our knowledge, this was the first time an equivalent model extraction led to self-consistent electron velocity values for nitride transistors. Finally, our equivalent circuit model showed the correct interrelation between frequency response and access resistances. The cohesive picture of current slump, equivalent circuit model extraction, and delay time analysis gives a high degree of confidence in these results.

Document type: 
Thesis
File(s): 
Department: 
Department of Physics - Simon Fraser University
Thesis type: 
Thesis (Ph.D.)