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

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Energy and information flows in strongly coupled rotary machines

Author: 
Date created: 
2021-11-10
Abstract: 

Living systems at the molecular scale are composed of many coupled components with interactions varying in nature and strength. Microscopic biological systems operate far from equilibrium and are subject to strong fluctuations. These conditions pose significant challenges to efficient, precise, and rapid free-energy transduction, yet nature has evolved numerous molecular machines that do just this. We present a model of strongly coupled stochastic rotary motors inspired by FoF1-ATP synthase and study its behavior. Rather than aiming for the most accurate model of ATP synthase, the model is meant to be a starting point to explore the effect of less-than-tight coupling between components. To this end, we aim to give the model a minimum level of complexity while keeping biological considerations in mind. Energy and information flows are studied numerically and through analytically tractable limiting cases. The limiting cases provide bounds on the system’s performance. We find that the output power of a work-to-work converter consisting of two coupled subsystems in the presence of energy barriers can be maximized at intermediate-strength coupling rather than at tight coupling. This phenomenon is backed up by a simple theory that predicts the power maximizing coupling strength, and agrees well with numerical results. We observe several characteristics that show up at the coupling strength that maximizes output power: a maximum in power transmitted from Fo to F1, a maximum in information flow, and equal subsystem entropy production rates. Finally, we derive a bound on the machine’s input and output power, which accounts for the energy and information passed between subsystems. We conclude that intermediate-strength coupling is a realistic option for biological systems passing on energy and information to downstream processes.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Anomalous relaxation in colloidal systems

Author: 
Date created: 
2021-04-21
Abstract: 

The Mpemba effect refers to a phenomenon where a sample of hot water may cool and begin to freeze more quickly than a cool or warm water sample prepared under identical conditions. Although the effect has been known since the time of Aristotle, it is named after the Tanzanian teenager Erasto Mpemba, who discovered the effect in the 1960s. Although Mpemba and Osborne showed the effect in laboratory experiments, it has always been mysterious, its underlying mechanism a topic of hot debate. In this thesis, we experimentally show the Mpemba effect in a colloidal system with a micron-sized silica bead diffusing in a bath. The bead is subjected to an external double-well potential created by a feedback-based optical tweezer. When a system is quenched from an initially hot equilibrium state to a cold equilibrium state, the evolution of the system between the initial and the final state is a strongly nonequilibrium process. As a nonequilibrium state cannot, in general, be characterized by a single temperature, we adopt the notion of a “distance” measure as a proxy for temperature. We show Mpemba effects in an asymmetric double-well potential. Our experimental results agree quantitatively with predictions based on the Fokker-Planck equation. Using understanding gained from the Mpemba effect, we design an experiment to investigate the opposite effect and present the first experimental evidence for this inverse Mpemba effect. Contrary to the cooling effect, the inverse effect is related to a phenomenon where a system that is initially cold heats up faster than an initially warm system. By understanding the underlying mechanism of these anomalous effects, we demonstrate strong Mpemba and inverse Mpemba effects, where a system can cool or heat exponentially faster to the bath temperature than under typical conditions. Finally, we ask whether asymmetry in the potential is necessary and show experimentally that an anomalous cooling effect can be observed in a symmetric potential, leading to a higher-order Mpemba effect.

Document type: 
Thesis
File(s): 
Supervisor(s): 
John Bechhoefer
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Modelling the transcriptional regulation of androgen receptor in prostate cancer

Author: 
Date created: 
2016-04-26
Abstract: 

Transcription of genes and production of proteins are essential functions of a normal cell. If disturbed, misregulation of crucial genes leads to aberrant cell behaviour and in some cases, leads to the development of diseased states such as cancer. One major transcriptional regulation tool involves the binding of transcription factor onto enhancer sequences that will encourage or repress transcription depending on the role of the transcription factor. In prostate cells, misregulation of the androgen receptor(AR), a key transcriptional regulator, leads to the development and maintenance of prostate cancer. Androgen receptor binds to numerous locations in the genome, but it is still unclear how and which other key transcription factors aid and repress AR-mediated transcription. Here I analyzed the data that contained the transcriptional activity of 4139 putative AR binding sites (ARBS) in the genome with and without the presence of hormone using the STARR-seq assay. Only a small fraction of ARBS showed significant differential expression when treated with hormone. To understand the underlying essential factors behind hormone-dependent behaviour, we developed both machine learning and biophysical models to identify active enhancers in prostate cancer cells. We also identify potentially crucial transcription factors for androgen-dependent behaviour and discuss the benefits and shortcomings of each modelling method.

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

Investigation of core-shell nanowires via electron-beam-induced current

Author: 
Date created: 
2021-04-13
Abstract: 

Core-shell semiconductor nanowires (NWs) have gained increasing attention since the last decade for their advances in multiple applications. This core-shell geometry is advantageous because of the relatively short distance required for excited electron-hole pairs (EHPs) to travel before being collected and the potential to eliminate surface recombination in the core. It is essential to fully understand the electrical properties, including the minority carrier diffusion length, depletion width, and doping level for optimization of growth and improving the optoelectronic performance. For this purpose, a characterization technique with high lateral and vertical spatial resolution, is needed. In this thesis, two types of coreshell NWs, both with n-type GaAs NW cores but with shells of either a metal, Fe, or p-type GaAs, were investigated using electron-induced-beam current (EBIC) measurements. Epitaxial Fe shells were grown onto GaAs NWs via electrodeposition, potentially acting as spin injectors or detectors. The radial Fe/GaAs barrier height was found to be 0.69 ± 0.03 eV, by comparing the experimental I-V characteristics to simulated results using various barrier heights. Both the axial and radial EBIC currents as a function of beam position exhibit oscillations that were reproducible. These oscillations were attributed to defects or oxides at the Fe/GaAs interface as recombination centers, showing the capability of extracting highly-spatially-resolved information from the radial junction via EBIC. In addition, axial and radial EBIC scans were carried out on unprocessed, free standing core-shell GaAs NW tunnel diodes, showing high sensitivity to the three-dimensional shape of the structure. The carrier kinetics in both the n-type core and the p-type shell were determined by analyzing radial EBIC profiles as a function of beam energy and beam direction. These profiles are highly sensitive to changes in depletion widths and minority carrier diffusion lengths due to geometric effects. Due to the complex core-shell geometry of our NWs, numerical calculations (Monte Carlo simulations) were employed to estimate the minority carrier diffusion length and depletion width. By comparing the radial profiles to simulations, minority carrier diffusion lengths were found to be 15 ± 5 nm and 50 ± 10 nm in the shell and the core, respectively. The relatively short hole diffusion length in the core, can be attributed to bulk point defects originating from low-temperature growth (400 ℃).

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

Modelling and engineering artificial burnt-bridge ratchet molecular motors

Author: 
Date created: 
2021-04-23
Abstract: 

Nature has evolved many mechanisms for achieving directed motion on the subcellular level. The burnt-bridge ratchet (BBR) is one mechanism used to accomplish superdiffusive motion over long distances via the successive cleavage of surface-bound energy-rich substrate sites. The BBR mechanism is utilized throughout Nature: it can be found in bacteria, plants, mammals, arthropods (for example Crustaceans and Cheliceratans), as well as non-life forms such as influenza. Motivated to understand how fundamental engineering principles alter BBR kinetics, we have built both computer models and synthetic experimental systems to understand BBR kinetics. By exploring the dynamics of BBRs through simulation we find that their motor-like properties are highly dependent on the number of catalytic legs, the distance that the legs can reach from the central hub, and the hub topology. We further explore how design features in the underlying landscape affect BBR dynamics. We find that reducing the landscape from two- to one-dimensional increases superdiffusivity but leads to a loss in processivity. We also find that landscape elasticity affects all motor-like dynamical properties of BBRs: there are different optimal stiffnesses for distinct dynamical characteristics. For a spherical-hub BBR, speed, processivity, and persistence length are optimized at high, intermediate and soft stiffnesses, respectively, while rolling is also optimized at a high surface stiffness. Towards our development of a novel micron-sized protein-based BBR in the lab, we develop a new surface chemistry passivation technique and apply it to the surface of nanowires, turning an array of waveguiding nanowires into a high-throughput biosensing assay. In a separate assay, our protein-based BBR, which we call the lawnmower, is implemented in two dimensions on glass cover slips prepared with our surface chemistry (which serves as the lawn). We find the lawnmower dynamics reproduce key observations found in other similar systems, such as saltatory motion and broadly varying anomalously diffusive behaviour. The successful implementation of the lawnmower marks the first demonstration of an artificial protein-based molecular motor.

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

Nanostructure and ion dynamics of novel ionenes via scattering and simulation

Author: 
Date created: 
2021-04-08
Abstract: 

The creation of advanced solid polymer electrolytes is of critical importance for the development of many technologies, especially fuel cells and hydrogen electrolyzers. While hydrogen fuel cells are a top candidate to replace the internal combustion engine in many applications, they are currently too expensive for mainstream adoption due to the use of perfluorinated sulfonic acid-based (PFSA) polymer electrolytes, which are expensive, and require expensive platinum catalysts and titanium cell components. Utilizing hydrocarbon alkaline membranes can dramatically reduce costs, but such membranes that achieve chemical stability and ion conductivity comparable to PFSAs have proven elusive. It has been shown that polyatomic cations integrated into polymer backbones, when sterically protected, can provide high ion conductivity and excellent chemical stability. As these materials consist of cations directly integrated into rigid polymer backbones, the phase separation observed in high-performing polymers such as PFSA is not possible, and it is not clear how high conductivity is achieved. This thesis provides a comprehensive investigation into the nanostructure of such materials via a combination of X-ray scattering at controlled humidity and atomistic molecular dynamics simulations, which reveal a sponge-like nanostructure, near-complete percolation at low degrees of hydration, and no evidence of long-range phase separation. A preliminary analysis of the ion dynamics reveals an unexpectedly strong relationship between accessible volume and ion mobility, suggesting that ion mobility is almost completely defined by the accessible volume in these materials.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Barbara Frisken
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.

Mechanisms for directed transport and organization at subcellular scales

Author: 
Date created: 
2020-12-18
Abstract: 

The timely and faithful segregation of genetic material is an essential cellular function that relies on the transport and stable positioning of subcellular components despite the disruptive influence of thermal fluctuations. In prokaryotes, a two-protein system (known as ParABS) has been identified as being responsible for the positioning of low-copy number plasmids and chromosomes prior to cell division. Multiple experimental observations, in vitro reconstitutions and computational modelling efforts support the idea that this system is powered by the ‘burnt-bridge’ Brownian ratchet mechanism. In this thesis we provide computational models that complement these studies to understand how this mechanism generates and sustains directional transport through the transduction of chemical energy into mechanical motion. In particular we study the effects of chemical kinetics, inter-protein interaction strength, system size and availability of proteins that drive this mechanism with an application to the rich protein dynamics observed in vivo. Finally, we simulate a coarse-grained model for a highly polyvalent ‘burnt-bridges’ Brownian ratchet capable of translocating either by rotation or translation and detail the system parameters that govern the transitions between these two distinct modes of motion. The models presented in this thesis provide key insights and make experimentally testable predictions which can be used for the engineering of novel synthetic motor systems.

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

Investigation of complex impurity centers in zinc oxide

Author: 
Date created: 
2021-04-08
Abstract: 

Zinc oxide is a potentially useful material in optoelectronics. It has a 3.3 eV direct bandgap which makes it a comparatively inexpensive candidate for replacing gallium nitride as a UV light emitter. Production of stable p-type ZnO is the biggest challenge for the introduction of this material to industry. Many attempts to produce stable p-type ZnO by doping single atom point defects have failed. The remaining dopant candidates are complex defects including two or more components. In this thesis, we mostly focus on the study of bound excitons corresponding to Li related defects. We show that the line at 3353.4 meV in the UV spectra of ZnO, previously assigned to tin, is a complex donor impurity including Sn and Li atoms. We performed annealing experiments, diffusing the Li content out of the lattice. The intensity of the 3353.4 meV line decreased as a result of annealing, which suggests the involvement of Li in this impurity. This process was reversed by the introduction of Li into the sample and the original intensity was restored. This was strong evidence of the involvement of Li in this impurity. We found a 0.4 eV ± 0.2eV activation energy for the ejection of Li from the complex using the annealing results. Density functional analysis of a complex consisting of Li and Sn in the nearest neighboring Zn sites results in much bigger activation energies for different mechanisms of ejection of Li. This evidence suggests that the impurity is more complicated than Li and Sn in nearest neighboring Zn sites. We tried to further investigate this impurity by introducing a different isotope of Li. Substitution of natural Li (96% 7Li) with 6Li showed a change of -0.022±0.008 in the energy position of the recombination energy of the D0X attributed to the line at 3353.4 eV. Our theoretical prediction of the shift suggested a lower limit of -0.031 for the expected shift. In addition, we observed new Li-related lines and showed they are due to bound excitons. We also investigated the effect of the environment in which Li doping is done on the emergence of these new lines.

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

Laser-assisted selective tuning of silicon nanophotonic structures

Author: 
Date created: 
2020-12-11
Abstract: 

Silicon photonic integrated circuits have advanced to the point where thousands of components can now be combined into functioning optical circuits. A variety of quantum technologies are based upon the integrated silicon photonics platform, including pure photonics approaches as well as those based upon emerging silicon spin-photon interfaces. Integrated photonic components, such as grating couplers, photonic crystal cavities, and waveguides, are subject to slight manufacturing variations. For quantum technology applications, such variations often need to be minimized and ideally eliminated through careful post-processing. The laser-assisted "spot oxidation" post-processing technique is able to locally and permanently shift the resonance wavelength of nanophotonic devices using a 532nm continuous wave laser. While global tuning techniques affect entire chips, spot-oxidation is of interest because it can locally correct for specific manufacturing variations among many components within a single chip in an automated way. Yet prior to this work it was unclear if spot oxidation could be made compatible with photonic structures with SiO2 top-cladding, which are more robust and attractive for commercial deployment. Here, we apply laser-assisted tuning to silicon-on-insulator (SOI) devices with SiO2 top-cladding in the telecommunication O-band. In this work, we successfully tune both photonic crystal nanobeam cavities and sub-wavelength grating couplers up to 1.04(5)nm and 9(1)nm, respectively. This will enable higher-yield photonic circuits, as well as allow us to permanently locally tune optical structures into resonance with optically active colour centres in silicon.

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

Spectroscopy and phenomenology of unconventional superconductors

Author: 
Date created: 
2020-12-16
Abstract: 

The challenge of condensed matter physics is to understand how various states of matter emerge from periodic or amorphous arrangements of atoms. This is typically easier if there are no impurities in the material under investigation. However, many of the properties that make materials technologically useful stem from the very disorder and impurities that complicate their study. In this work we investigate three unconventional superconductors with the dirty BCS framework of superconductivity, with impurities treated in the selfconsistent t-matrix approximation. The three materials behave quite differently and allow us to explore and reveal a rich, subtle, and poorly appreciated range of effects that must be considered when studying superconducting materials and probing the limits of applicability of current theories of superconductivity. Microwave spectroscopy measurements of FeSe, a member of the iron-based family of superconductors, were performed at frequencies below 1 GHz using a novel helical resonator. The measurements show that the material is particularly clean, with an electronic mean free path that exceeds that of all known binary compounds. They also reveal the presence of a finite gap on both superconducting bands, strongly constraining which pairing states should be considered for FeSe. Nb-doped SrTiO3 has an extremely low carrier concentration and multiple electronic bands at the Fermi sruface. Microwave spectroscopy measurements, this time with a stripline resonator, reveal a single spectroscopic gap despite clear evidence for multiple superconducting bands. Elastic scattering introduced via Nb dopants is proposed as the mechanism by which the two bands homogenize into a single spectroscopic signature, as per Anderson’s theorem. The impurity hypothesis is tested with single-band fits to the superfluid density and is found to be in good agreement with measured data. Finally La2−xSrxCuO4, a member of the famous cuprate family of superconductors is explored in detail under the assumption that Born scattering with large amounts of impurities can explain a number of puzzling measurements that have caused controversy in the high-Tc community over the past few years. Many features of the experimental measurements can quantitatively be accounted for with very few free parameters and no fine tuning.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Broun
Erol Girt
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.