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

Receive updates for this collection

Estimating deceiving signatures and their role in the observation of the VBF production mode in the Higgs-Boson decay into two W bosons

File(s): 
Date created: 
2022-01-11
Supervisor(s): 
Bernd Stelzer
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
Abstract: 

The Higgs boson is the most recently discovered fundamental particle and its precise characterization is an important test of the Standard Model. For these measurements, the decay into two W bosons is crucial because of the large branching ratio, the sensitivity to vector-boson couplings and the theoretical implications on WW scattering. The proton-proton collisions at the LHC with a centre-of-mass energy of √s = 13 TeV provide an excellent environment to study the Higgs boson. The data recorded by the ATLAS experiment between 2015 and 2018 is analyzed. With an integrated luminosity of 139/fb, it allows to measure precisely the two dominant production modes, gluon fusion (ggF) and vector-boson fusion (VBF). Only collisions with one electron and one muon in the final state are considered and cuts are applied to select signal-like events. For the VBF process, the selection is further refined with the help of a deep neural network. Then, the purified dataset is analyzed with a statistical model constructed from MC simulation and a data-driven background estimate of misidentified leptons. The cross sections times branching ratio are measured to be 12.4 ± 1.5 pb for the ggF and 0.79 +0.19 −0.16 pb for the VBF processes. For the first time, the VBF process is observed in this decay channel with a significance of 6.6 standard deviations. Also measurements of eleven Simplified Template Cross Sections are performed and found to be consistent with the Standard Model. This precise measurement could only be achieved because the treatment of events with misidentified leptons was improved significantly. These deceiving signatures are estimated with the data-driven Fake Factor Method. An auxiliary measurement is performed to extract fake factors in a phase space with a Z boson recoiling against a jet that is misidentified as lepton. This measurement is presented together with the relevant experimental improvements. As a result of this work, the uncertainties could be reduced to an extent that they do not significantly affect the measurement of the Higgs-boson cross section. Even though the Fake Factor Method is experimentally well-established, a consistent derivation for a phase space with many leptons does not exist. In this thesis, it is shown for the first time that the Fake Factor Method can be derived exactly from the Matrix Method for an arbitrary number of misidentified leptons. In addition, the uncertainty estimate is considered and cases are derived in which the fake estimate does not exhibit Gaussian uncertainties.

Document type: 
Thesis

Stochastic thermodynamics of Gaussian information engines

File(s): 
Date created: 
2021-08-06
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.
Abstract: 

Stochastic thermodynamics is an emerging field of research that has received considerable attention in the past two decades. Among its most visible applications is to understand the connections between information and thermodynamics. Recent theoretical advances in this field have established that the second law of thermodynamics, suitably modified to account for information, sets the limits of information-to-energy conversion; however, these limits are generally derived for systems that are ideal and assume that all of the system’s energy can be extracted. Real systems on the other hand face constraints that may prevent them, both in principle as well as in practice, from achieving the predicted theoretical limits. Prompted by recent advances in experimental capabilities which allow for a high degree of control of mesoscopic systems, we explore the limits of information-to-work conversion in a simple “textbook example” colloid-based information engine that is implementable in the lab. We use this engine to explore the limits of information-to-work conversion when the engine is restricted to operate in a mode where long-term energy storage is prioritized. We find that restricting the engine to this mode of operation severely limits its ability to convert information to work compared to when the engine is optimized for raw energy extraction, without regards for whether the energy is stored or not. Nevertheless, in certain cases, it is possible to design the feedback control to have a work input which guarantees the engine stores energy at the highest achievable rate. We therefore find that information engines sometimes convert information to work most effectively when there is a mixture of external work input and information processing. Additionally, real engines face the conundrum of measurement noise. This complicates the feedback control and introduces biases in the estimates of the relevant thermodynamic quantities. To eliminate this bias, we use either a filter or we introduce feedback delays. Both strategies successfully eliminate the bias in the estimates; however, we find that using the filter has an additional benefit in that it allows us to compute a trajectory-level estimate of the information-processing costs. These results inform our theoretical understanding of the limits of real systems that convert information to work and provides the first measure of the information-processing costs for continuous variables.

Document type: 
Thesis

Analyzing the effect that non-uniform receptor distribution and secretion of chemo attractants has on cell chemotaxis

Author: 
File(s): 
Date created: 
2021-12-10
Supervisor(s): 
Eirikur Palsson
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.
Abstract: 

Cell-cell signaling is a fundamental process of organisms during development, throughout their lifetime and in the course of cancer growth. In mammary tumors, tumor cells interact with macrophages via short-ranged signaling (paracrine) involving the growth factors EGF and CSF-1. This paracrine signaling enhances tumor cell invasion into surrounding tissues and blood vessels. Here I examined the roles that asymmetric receptor distribution, ligand secretion and gradient detection at the cellular level play in cancer cell invasion. Although there are already mathematical cell models that simulate cell movements in multicellular systems, none have included asymmetric distribution at the cell level. We incorporated non-uniform receptor density, ligand secretion and gradient detection in a 3-D individual cell-based model, that had been used to simulate the EGF/CSF-1 paracrine signaling in a tumor environment Our model can be used for any multicellular systems, where cells secrete and chemotax towards ligand gradients. Our model was optimized to reduce the computational cost of including non-uniform distributions at the sub-cellular level, when simulating thousands of interacting cells.I demonstrated that even when simulating thousands of cells, at scales much larger than the cell, non-uniformities at the single cell scale can significantly change the results. My simulations showed that non-uniform gradient detection dramatically enhanced the invasion of both tumor cells and macrophages and that non-uniform secretion significantly altered the invasion patterns of those cells. With no-flux boundary condition at the bottom, non-uniform secretion at either the front or back of the cell delayed the tumor cell invasion. However, secretion at the front enhanced macrophage invasion, while secretion at the back delayed it. Ultimately, fewer tumor cells invaded when secretion was at the front compared to uniform secretion and secretion at the back. These simulations helped us understand how the boundary conditions can potentially have a large impact on invasion profiles. They suggest that in vitro experiments with artificial boundary conditions may behave quite differently than the in vivo experiments that do not have no-flux boundary conditions. Overall, my simulations provide insight into how non-uniform receptor density, ligand secretion and gradient detection modify cell migration patterns. These simulations also suggest that it is very important to incorporate non-uniformities at the cell level when modelling chemically interacting multicellular systems.

Document type: 
Thesis

Energy and information flows in strongly coupled rotary machines

Author: 
File(s): 
Date created: 
2021-11-10
Supervisor(s): 
David Sivak
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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

Anomalous relaxation in colloidal systems

Author: 
File(s): 
Date created: 
2021-04-21
Supervisor(s): 
John Bechhoefer
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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

Modelling the transcriptional regulation of androgen receptor in prostate cancer

Author: 
File(s): 
Date created: 
2016-04-26
Supervisor(s): 
Eldon Emberly
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) M.Sc.
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

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

Author: 
File(s): 
Date created: 
2021-04-13
Supervisor(s): 
Karen Kavanagh
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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

Modelling and engineering artificial burnt-bridge ratchet molecular motors

Author: 
File(s): 
Date created: 
2021-04-23
Supervisor(s): 
Nancy Forde
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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

Nanostructure and ion dynamics of novel ionenes via scattering and simulation

Author: 
File(s): 
Date created: 
2021-04-08
Supervisor(s): 
Barbara Frisken
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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

Mechanisms for directed transport and organization at subcellular scales

Author: 
File(s): 
Date created: 
2020-12-18
Supervisor(s): 
Eldon Emberly
Department: 
Science: Department of Physics
Thesis type: 
(Thesis) Ph.D.
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