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

## Predictive models for chromatin folding: connecting sequence to structure

Author:
Date created:
2018-04-13
Abstract:

The DNA packaged inside a nucleus shows complex structures stabilized by a host of DNA-bound factors. This combination of DNA and bound factors is known as chromatin. Both the distribution of bound factors and the contacts between different locations of the DNA can be now measured on a genome-wide scale. Nevertheless, to what extent is the likelihood of contact between sites in the genome encoded by the spatial sequence of bound factors? Current approaches at addressing this question primarily use simulations of heterogeneous polymers to generate structures using the locations of bound factors. In contrast, here we develop novel predictive models for connecting chromatin sequence to structure using statistical physics, information theory and machine learning. Since our methods do not require costly polymer simulations they can quickly predict the effect on structure due to changes in the distribution of bound factors. In addition, our methods are formulated in a manner that allows us to solve the inverse problem: namely, given just structural data, predict the likely sequence of bound factors. We show that the models developed can make biologically meaningful predictions, highlighting key features of the mechanisms through which the three-dimensional conformation of DNA is coordinated by the interactions between DNA-bound factors.

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

## Observation of critical spin dressing

Author:
Date created:
2018-03-26
Abstract:

It has long been proposed that spin dressing could be employed to realize a highly effective helium-3 nuclear precession co-magnetometer for a neutron electric dipole moment (nEDM) search. The proposal is to apply an intense, continuous, and far off-resonant oscillating magnetic field, called a dressing field, in such a way that the apparent Larmor precession frequencies of the helium-3 and the neutron are modified. Under appropriateconditions a desirable situation known as critical spin dressing (CSD) is anticipated: the neutron and the helium-3 nucleus (or more generally, any two spin species) are expected to behave as if they had the same gyromagnetic ratio and hence should precess at the same rate in a static magnetic field. Spin dressing has been studied in the context of the neutron, helium-3, and a variety of other systems. Critical spin dressing, however, has not previously been demonstrated. In this thesis I report the first experimental demonstration of pulsed CSD in which simultaneous spin dressing of 1H and 19F nuclei is achieved and studied. I also demonstrate that CSD can be performed using variety of different dressing field waveforms, a consideration that until now has received little or no attention. Examples of parameters studied include the role of phase and amplitude modulation on spin dressing. Of particular note is a significant improvement in reproducibility achieved by alternating the phase of successive cycles of the dressing field waveform by pi radians. Such innovations may prove useful in an eventual nEDM search where demands on precession stability are anticipated to be extreme. To enable my study of CSD I developed a simple and robust apparatus. The central innovation was the first use of Magneto-Impedance (MI) sensors to detect weak magnetic fields associated with the precession of nuclear magnetic moments. The thesis thus begins with summaries of experiments to characterise and validate the use of MI sensors for ultra-low field (ULF) nuclear magnetic resonance. I then describe a refined version of the ULF NMR apparatus, and the manner in which it is used to investigate CSD.

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

## In-situ measurement of the jet energy scale and studies of jet structure at ATLAS

Author:
Date created:
2017-12-07
Abstract:

This thesis presents results for the determination of the ATLAS jet energy scale (JES) using the Missing $E_{\mathrm T}$ Projecting Fraction (MPF) method along with studies to better understand and validate the MPF. Hadronic jets are the most commonly observed objects in proton-proton collisions, and are therefore a part of most final states for processes which are studied at the Large Hadron Collider (LHC). The abundance of jets makes a precise knowledge of the JES essential to the success of the ATLAS physics program. This thesis uses the MPF in events where either a photon or a Z boson is produced back-to-back with a jet to provide an uncertainty on the response of the calorimeter which is below 1\% for jets between 30 GeV and 1 TeV. Studies measuring the impact of the underlying event on the MPF's ability to measure the response of the hadronic recoil are also presented, which validate the previously held assumption that the MPF is insensitive to these effects. In addition, studies into the relation between the measured recoil response and the desired jet response are presented. This includes measures of the flow of energy across the jet boundary during the showering process and the effect on the total measured response of low energy/low response particles near the fringe of the recoil. These measurements show up to a 10% difference between the jet response and the recoil response for jets reconstructed with the anti-k_t algorithm with midrange size parameters (0.4-0.7). These differences however show little dependence on physics modeling choices (less than 1%), on which the Monte Carlo jet calibration is based. These results put the MPF technique on a firmer ground, and they will reduce future JES uncertainties for jets with energies below 100 GeV.

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

## Origin of perpendicular magnetic anisotropy in Co/Ni multilayers and their use in STT-RAM

Author:
Date created:
2017-12-08
Abstract:

Magnetic properties of (111)-textured SAF/Cu/FL multilayer film structures were optimized by varying individual layer thickness and sputtering conditions. The SAF is a synthetic antiferromagnet consisting of Co/Ni multilayers coupled antiferromagnetically across a Ru spacer layer, and the FL is a free layer consisting of a single Co/Ni multilayer. The Co and Ni thicknesses were varied to obtain larger perpendicular magnetic anisotropy. The perpendicular magnetic anisotropy, saturation magnetization, damping and zero-frequency line broadening of the Co/Ni multilayers strongly depend on the number of bilayers. With increasing Cu seed-layer thickness, the texture of the Co/Ni multilayers improves while the grain size and film roughness increase. The increase in grain size results in the reduction of the direct exchange coupling between magnetic grains, which enhances the coercivity of the SAF and the FL. Experimentally measured coercivities of the SAF and FL are compared with calculations obtained from a coherent rotation model. The effect of the role of the Co/Cu interface in the magnetoresistance, is also discussed. Spin-transfer-torque induced switching is investigated in 200 nm diameter circularly shaped, perpendicular magnetized nanopillars. The SAF layer is used as a reference layer to minimize the dipolar field on the free layer. The use of Pt and Pd was avoided to lower the spin-orbit scattering in magnetic layers and intrinsic damping in the free layer, and therefore, reduce the critical current required for spin-transfer-torque switching. In zero magnetic field the critical current required to switch the free layer from the parallel to antiparallel (antiparallel to parallel) alignment is 5.2 mA (4.9 mA). Given the volume of the free layer, VFL = 1.01×10-22 m3, the switching efficiency, Ic/(VFL 0Hc), is 5.28×1020 A/Tm3, twice as efficient as any previously reported device with a similar structure. Variation in perpendicular magnetic anisotropy of (111) textured Au/N×[Co/Ni]/Au films as a function of number of bilayer repeats N is studied. The experimental measurements show that the perpendicular magnetic anisotropy of Co/Ni multilayers first increases with N for N ≤ 10 and then moderately decreases for N> 10. The model we propose reveals that the decrease of the anisotropy for N < 10 is predominantly due to the reduction in the magnetoelastic and magnetocrystalline anisotropies. A moderate decrease in the perpendicular magnetic anisotropy for N > 10 is due to the reduction in the magnetocrystalline and the surface anisotropies.

Document type:
Thesis
File(s):
Senior supervisor:
Erol Girt
Bret Heinrich
Department:
Science: Department of Physics
Thesis type:
(Thesis) Ph.D.

## Electrical transport in semiconductor nanowires

Author:
Date created:
2017-08-28
Abstract:

Semiconductor nanowires are promising building blocks for future nanoscale electronic devices. A fundamental control of the impurity and free-carrier concentration as well as the understanding of charge injection and extraction is required. This thesis describes numerical and experimental studies on the electrical transport in semiconductor nanowires. We present a numerical study on geometric scaling of space-charge-limited current, which is often observed in semiconductor nanowires due to carrier depletion and reduced electrostatic screening. The model highlights the effects of the surroundings for nanowires and shows that the dielectric properties of the semiconductor have a negligible effect on the space-charge-limited transport for small dimensions. The results of numerical calculations agree with a simple capacitance formalism which assumes a uniform charge distribution along the nanowire, and experimental measurements for InAs nanowires confirm these results. We discuss the elemental composition and electrical transport characteristics of nominally-undoped and Ga-doped ZnO nanowires, a promising candidate for optoelectronic applications in the UV range. We estimate an upper limit of the Ga impurity concentration with atom-probe tomography and present the electrical transport characteristics measured with a nanoprobe technique and with lithographically-defined contacts allowing back-gated measurements. An increase in apparent resistivity by two orders of magnitude and drop in the effective carrier concentration and mobility was found. Little change in resistivity was observed with Ga doping, which indicates that the concentration of native or background dopants was higher than the Ga doping concentration. We investigate the electrical properties of undoped, Si-doped and Mg-doped InN nanowires directly on degenerate n-type and p-type Si substrates, with a nanoprobe technique. The resulting transport characteristics are weakly rectifying for InN grown on n+-Si with similar ratios for all InN dopant types. On p+-Si, Mg-doped InN nanowires show a strong rectification behaviour with opposite voltage polarity compared to n+-Si, while undoped and Si-doped nanowires show nearly symmetric transport. These characteristics are analyzed in terms of the properties of broken gap band offsets at the Si/InN heterojunction.

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

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

Author:
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

Author:
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

Author:
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.