School of Physics - Theses
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ItemQuantum technology for 3D imaging of single molecules( 2018)Biochemical processes are conducted by interactions of individual molecules that comprise cells. It is the transient physical shape of proteins that dictates their specific functionality. However, imaging individual instances of single molecular structures is one of the notable challenges in structural biology. Presently available protein structure reconstruction techniques, Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and cryogenic Electron microscopy (cryo-EM), cannot provide images of individual molecules. Despite their power and their complementary capabilities, said techniques produce only average molecular information. They achieve this by sampling large ensembles of molecules in nearly identical conformational states. As a result, individual instances of a generic, inhomogeneous or unstable atomic structures presently remain beyond reach. We seek to address this problem in a novel way by leveraging quantum technologies. In quantum computing, qubits are usually arranged in grids and coupled to one another in a highly organised manner. However, what if a qubit was coupled to an organic cluster of nuclear spins instead, e.g. that of a single molecule? What can be done with such a system in the context of quantum control and 3D imaging of individual molecular systems? What are its ultimate limits and possibilities? We explore those questions in stages throughout the chapters of this thesis. We begin in Chapter 2 by investigating dipole-dipole interactions present between the nuclear spins in a target molecule, on one side, and between an electron-spin based qubit and each of the nuclear target spins on the other. We consider the Nitrogen Vacancy (NV) centre in diamond as an example of a suitable qubit with an active community interest as a biocompatible nano-magnetometer. Our intention is to lay down foundations that will help us advance from magnetometry to 3D molecular imaging. Our inspiration comes from drawing parallels between the single molecule sensing in the qubit-target system and the clinical Magnetic Resonance Imaging (MRI). An MRI machine directly images a single, specific sample in its native state regardless of its characteristics. That is precisely what we would like to achieve on the molecular level. In Chapter 3, we develop a framework that allows a spin qubit to serve as a platform for 3D atomic imaging of molecules with Angstrom resolution. It uses an electron spin qubit simultaneously as a detector and as a gradient field provider for MRI-style imaging. We develop a theoretical quantum control methodology that allows dipole-dipole decoupling sequences used in solid-state NMR to be interleaved with the gradient field provided by the qubit. In Chapter 4, we propose group-V donors in silicon as a novel qubit platform for bioimaging. Actively researched for quantum computing purposes, such qubits have not been considered in the biological context. A prime example of this class of qubits is the phosphorus donor in silicon (Si:P). We show how its specific set of properties, including long coherence times, large wave function and low operational temperatures can be leveraged for the purposes of atomic level imaging. Finalising the work in Chapter 5, we simulate the imaging process for one transmembrane protein of the influenza virus embedded in a lipid membrane. This demonstration highlights the potential of silicon spin qubits in the future development of in situ single molecule imaging at sub-Angstrom resolution.
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ItemPractical Aspects of the Preparation of NV Centers In Diamond for Quantum Applications and Magnetometry( 2018)This thesis present the result of four experimental projects, that revolve around the practical aspects of using NV centers for quantum applications. The core of the this work deals with the coherence time of NV centers and how it is affected by damage introduced into the diamond lattice by ion implantation where we have discovered that while the emission of the NV center is sensitive to the damage the coherence time is not. The other topics of this work cover a novel method to deposit isolated nano diamond using aerosols and a method to secure the nano diamonds into silicon substrates using self-assembled mono layers. Finally, the work concludes with a proposal to use the magnetic field produced by spin vortices to increase the coherence time of NV centers where some preliminary result of the spin vortices fabrication are presented.
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ItemHigh field phenomenology in linear accelerators for the compact linear collider( 2018)The Compact Linear Collider (CLIC) is a 3 TeV linear electron-positron collider which is proposed to operate with loaded accelerating gradients up to 100 MV/m. These high gradients are accompanied by high field phenomena which limit the operation of the accelerating structures. Achieving reliable operation at these accelerating gradients requires an in-depth understanding of these phenomena and their effects on CLIC. This thesis investigates the phenomenology of high fields in CLIC accelerating structures through tests performed at the CERN's high gradient testing facilities. The commissioning of a novel RF test stand will be presented. Using a unique RF pulse weaving method in combination with RF pulse compression, the new test stand offered the ability to test multiple accelerating structures in situ and at repetition rates up to 200 Hz. This offered a significant increase in the high gradient testing capacity at CERN. Using the new test stand, as well as existing infrastructure, four unique accelerating structures underwent conditioning to high gradients. These accelerating structures included a CLIC baseline design prototype, a structure with high order mode damping material, and two structures fabricated through novel machining and joining technologies. Three of the four structures were able to reliably operate at unloaded accelerating gradients of at least 100 MV/m with low breakdown rates. Concurrent to the high gradient testing of accelerating structure, was an investigation into the radiation within the testing facilities, which was known to be the result of field emission capture. A series of measurements and simulations characterised the radiation produced during high power testing. A particular focus for the investigation was how the field emission capture varies with phase velocity. A model to describe the dependency of the capture of field emitted electrons on the phase velocity is presented. Measurements on the X-band test stands at CERN demonstrated that the capture increased ~20% for a 1 MHz increase in the RF driver frequency. These results were corroborated using a three dimensional RF and particle simulation.
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ItemBackground estimation studies for hadronically decaying tau leptons at the ATLAS experiment( 2018)This project aims to develop a data-driven technique for the estimation of the dominant background contribution in the inclusive search for new physics signals where equally charged lepton pairs are featured in the final state and where an hadronically decaying tau lepton can be found in a pair. The studies presented in this thesis were performed with data collected by the ATLAS experiment. A data driven technique has been developed for the abundant background of jets originated from the hadronisation of quarks or gluons which are mis-identified as hadronically decaying tau leptons. Mis-identification weighting factors have been measured for the extrapolation of this background into the signal region of the analysis and have been validated using a selection independent with respect to the the signal region. Systematic uncertainties have also been estimated. The work presented in this thesis will be incorporated in a general extrapolation technique within the ATLAS experiment aiming to be used by all ATLAS searches featuring hadronic tau decays in the final state.
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ItemPathways towards graphene based electrical DNA sequencing: a study of nucleobase adsorption on exposed channel graphene field effect transistors( 2018)The field of genetics has grown rapidly since the isolation of the double helix complex, DNA, that provides the genetic code behind all known life. The development of methods that allow this code to be read, and more recently edited, already underpins a large number of technologies that span from forensics to medical applications. The promise of genetic technologies demand faster and cheaper methods of DNA sequencing. As the genetic code is stored at the molecular level, new rapid sequencing techniques have focused on finding methods for reliable and selective single molecule detection. The recent isolation of graphene, an electrically conductive two dimensional carbon lattice, has been proposed as an ideal candidate for a new generation of sensors that can operate at single molecule concentrations. As these early proposals are based on theoretical modeling of a large range of graphene based sensor designs they are unable to account for the imperfect reality of fabricated graphene sensors. To that end this thesis focuses on providing experimental evidence for the suitability of graphene as the material for developing single molecule sensitive and selective sensors. Graphene field effect transistors are fabricated on silicon dioxide substrates and then characterized in an ultra high vacuum enviroment at the Australian Synchrotron Soft x-ray beam line where controlled amounts the of DNA nucleobases can be deposited. Utilizing soft x-ray and electrical measurements we show device sensitivities compatible with single molecule detection and distinct nucleobase dependent responses, opening a pathway towards functionalization and label-free selectivity for future genetic sequencing devices.
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ItemSimulations of source recovery and completeness in galaxy surveys at high redshift( 2018)The search for and characterisation of galaxies at high-redshift is a very active topic in Astrophysics. Thanks to advances in observations from space, the redshift frontier is approaching the epoch of formation of first generation objects. Thus, these samples of galaxies can give us insight into the processes that govern galaxy formation and evolution. One of the key observables used to characterise galaxy populations throughout the cosmic history is their luminosity function (number of galaxies per unit luminosity per unit volume), which requires knowledge and characterisation of the completeness and selection functions of a survey, in addition to the catalogue of discovered objects. In this thesis, we present a search for high-redshift galaxies (redshift z > 6) in two in the Hubble Space Telescope surveys, the Brightest of Reionizing Galaxies Survey (BoRG), and the Reionization Lensing Cluster Survey (RELICS) using a photometric selection technique (the Lyman break dropout selection). We aim at using the resulting galaxy candidates to estimate a new measurement of the luminosity function at z ~ 10. To achieve that, we develop GLACiAR, an open Python-based tool available on GitHub, which is designed to estimate the completeness and selection functions in galaxy surveys. The code is tailored for multiband imaging datasets aimed at searching for high-redshift galaxies through the Lyman Break technique, but it can be applied broadly. The code generates artificial galaxies that follow Sérsic profiles with different indexes and with customisable size, redshift and spectral energy distribution properties, adds them to input images, and measures the recovery rate. We finally apply GLACiAR to quantify the completeness and redshift selection functions for J-dropouts sources (redshift z ~ 10 galaxies). Our comparison with a previous completeness analysis on the same dataset shows overall agreement, but also highlights how different modelling assumptions for artificial sources can impact completeness estimates.
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ItemTop down fabricated silicon nanowires with quantum functionalities( 2018)This Ph.D thesis is concerned with the design, fabrication and mea- surement of silicon-on-insulator based nanowire devices that exhibit quantum effects in their operation. The devices were all formed us- ing top-down fabrication techniques in conjunction with ion implan- tation doping and/or silicidation. Devices studied include ring structures that exhibit Aharonov-Bohm oscillations, Esaki diodes and hybrid superconducting / semicon- ducting devices that reveal interesting magnetic-field dependent transport features at cryogenic temperatures. The research was performed within the Centre of Excellence for Quantum Computation and Communication Technology (CQC2T) with an over- arching aim of developing devices and fabrication protocols that can be useful for creating some of the future building blocks needed in quantum information hardware and quantum sensor development. In a combined research effort with our collaborators at Namlab in Dresden, Germany, a top down fabrication approach for phosphorous or erbium/oxygen implanted sili- con nanowires with diffused nickel contacts was developed. Several different device designs where realised such as conventional 4-terminal structures, Hall-bars and ring structures. The main focus was on design and fabrication of 0-dimensional systems, so called quantum dots, accomplished by confining a small nanowire segment in between two silicided segments (NixSiy). These devices allow study of fundamental physics of impurities in confined systems and quantisation effects like single electron tunneling (SET) for future quantum computation applications. Further insights in NixSiy was gained by investigating fully silicided 4-terminal ring structures at cryogenic temperatures. Periodic oscillations in the magneto-resistance data taken with a constant AC current of I = 1 μA were found. A fast Fourier transformation (FFT) confirmed the assumption that those features are caused by the changing flux through the enclosed ring area of the device, as predicted by the Aharonov-Bohm Effect. A second peak could be identified with the Altshuler-Aronov- Spivak oscillations. A comparison of both peak heights allowed the phase coherence length lφ to be estimated which was in good agreement with values presented in the literature. In addition to the oscillations in the magneto-resistance data, a resistance drop around zero magnetic field was present which could be identified with the effect of weak anti-localisation. A fit-function was used to model the collected data and de- termine important values of the system such as the spin orbit breaking length ls.o. and phase breaking length lφ which confirm the already existing values in this work and literature. Additional ring structures where characterised, degenerately implanted (either p- or n-type) and top down fabricated, to determine similarities and differences towards the silicided ones. 4-terminal AC characterisation measurements with a constant current of I = 1 μA at cryogenic temperatures revealed no Aharonov-Bohm effect. Neverthe- less, periodic and symmetric features in the magneto-resistance data for temperatures below the critical temperature of aluminum, Tcrit = 1.19 K, have been found for both devices. The features observed in the magneto-resistance data are sensitive to temper- ature and magnetic fields (parallel B|| and perpendicular B⊥) and disappear at higher magnetic fields (≈ 200 mT) or temperatures (≈ 1.2 K). This behaviour strongly sug- gests that the cause of the observed features can be found in magnetic flux quantisation related to Andreev reflections at the superconductor / metal interfaces. However, other effects like quantum phase slips can not be ruled out at this stage. Finally, the versatility of ion implantation and the chosen top down approach to fab- ricate sharp degenerately implanted p/n junctions, so called Esaki diodes, to observe electron tunneling or negative differential resistance was investigated. Multiple over- lay exposures and two ion implantation steps allowed the formation of a p/n junction nanowire diode. Room temperature I/V characterisation measurements of the de- generately implanted diode revealed a non linear behaviour which showed a negative differential resistance like behaviour for small forward biases. Those devices offer po- tential applications as building blocks for future complimentary metal semiconductor oxide (CMOS) compatible tunnel diodes. Main fabrication tools used where electron beam evaporation, electron beam lithog- raphy (EBL) and reactive ion etching (RIE). Characterisation involved room tem- perature and cryogenic magneto-resistance measurements with AC and DC signals of Hall-bar and van der Pauw devices as well as standard material characterisation such as Rutherford backscattering (RBS), Raman characterisation, atomic force microscopy (AFM), focused ion beam (FIB) and scanning electron microscopy (SEM). For testing purposes many devices have been fabricated to identify critical tool parameters for nanofabrication such as dose parametric tests for EBL.
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ItemCharacterisation of a cold-atom electron source for ultrafast diffractive imaging( 2018)The understanding of atomic structures and processes is continually improving with the great technological development in imaging techniques. Ultrafast electron and X-ray techniques are able to perform measurements at atomic lengths and timescales and both these techniques require the generation of high-brightness ultrashort-duration electron bunches. Electron imaging techniques directly use these short bright bunches and in X-ray free electron lasers (XFELs) the electron bunches are used to generate short bright bunches of X-rays. It is hoped that cold-atom electron and ion sources (CAEISs) will also be able to produce ultrashort high-brightness electron bunches that are brighter than conventional sources. CAEISs generate electrons via near-threshold ionisation from an ultracold atomic gas and have been shown to create electrons bunches with temperature as low as 10 K. Conventional photocathode sources have temperatures of thousands of Kelvin and, as brightness is inversely proportional to the temperature of the source, CAEISs have the potential to produce much brighter electron bunches. CAEISs are also capable of producing extremely cold ion bunches and show great promise as an ion source for ion milling and microscopy. This thesis describes a number of developments involved with the CAEIS project at the University of Melbourne, in particular pushing the boundaries of laser frequency stabilisation to allow for precise selection of atomic states for cooling and ionisation, and a new technique for measuring the brightness of charged particle bunches. Laser frequency stabilisation is an essential component of the CAEIS and many other applications including metrology, spectroscopy and laser cooling. Polarisation spectroscopy is a commonly used technique for laser frequency stabilisation but the full measurement and control bandwidth has not previously been demonstrated. Here it is shown that the bandwidth is sufficient to not only stabilise the frequency of the laser, but also to reduce the laser linewidth to much less than 1 kHz, two orders of magnitude better than previously reported. This demonstration provides a new approach for precisely accessing the high-lying Rydberg-levels of atoms, if used in conjunction with cavity based frequency locking methods, allowing for a greater exploration of the ionisation methods involved in a CAEIS. Brightness is the most comprehensive figure of merit for charged particle beams and a new technique for measuring beam brightness with sub-nanosecond time-resolution is presented. The technique achieves time-resolved brightness measurements by streaking one-dimensional pepperpot measurements across the detector. Time-resolved brightness measurements have the potential to reveal information related to the ionisation processes used in CAEISs and can show the efficacy of techniques used to counter the effects of space charge in the beams produced from a CAEIS. The performance of the CAEIS apparatus operating in its normal pulsed mode is compared to continuous operation with emphasis on the beam current and electron trajectory stability. The beam quality was also improved by identifying an astigmatism in the beam and correcting it with a 3D printed magnetic quadrupole lens. Virtually all the beam measurements presented here utilise image processing techniques that allow for multi-shot averaging despite instability in the electron beam trajectory. This iteration of a CAEIS was able to produce ultrashort-duration electron bunches and these have been used to demonstrate ultrafast electron diffraction from thin gold foils. This is an important step along the path to being able to perform ultrafast single-shot coherent diffractive imaging (CDI) and the next iteration of the CAEIS should have sufficient current to demonstrate diffraction that is both single-shot and ultrafast.
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ItemDetermination of the CKM matrix element |Vcb| from exclusive B0 → D*lν decays with the Belle experiment( 2018)The magnitude of of the CKM matrix element |Vcb| is determined based on the exclusive semileptonic B0 → D*lν decay with data from the Belle experiment at KEKB. Two different parameterisations of the hadronic transition form factors are used in the extraction of the form factor parameters and F (1)|Vcb|ηEW . We find that the commonly used model dependent Caprini-Lellouch-Neubert form factor parameterisation yielded |Vcb| results 10% lower than the model independent Boyd-Grinstein-Lebed approach. The latter are in good agreement with the inclusive approach for the determination of |Vcb|, suggesting the long standing inclusive- exclusive tension may be solved. The branching fraction of B0 → D*lν decays and the lepton universality ratio B(B0 → D*eν)/B(B0 → D*μν) are also measured. Results compatible with the world average for the former, and with the SM for the latter are found. This thesis presents the most precise measurements of B0 → D*lν and exclusive |Vcb| ever performed.
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ItemWhole pattern analysis of serial protein X-ray crystallography diffraction data( 2018)Serial X-ray crystallography has quickly developed as an approach for the determination of crystal structures from proteins that do not form crystals of sufficient size or quality for conventional X-ray crystallography experiments. The opening of X-ray free-electron lasers sources has spurred developments in experimental and analytical techniques in this field and has motivated the use of similar approaches at microfocused synchrotron sources. In these experiments, final data-sets are typically formed from collections of diffraction images from single exposures of individual protein micro- and nano- crystals. Variations in crystal and beam characteristics and in crystal orientations may be expected from image to image. Data processing and analysis methods have developed in response to the unique requirements posed by the experimental approach of serial X-ray crystallography. This thesis presents and examines a new analysis approach for the extraction of structure factor amplitudes from serial X-ray crystallography data. Crystal size and crystal disorder can affect the distribution of intensities between Bragg peak positions in the regime of crystals as finite diffracting objects. This thesis examines the diffracted intensity distributions formed from the merging of data from such protein crystals. A general procedure for the extraction of structure factor amplitudes from these distributions is presented that is based on an approach of whole-pattern fitting analysis. This approach holds similarities to intensity extraction techniques used in powder diffraction, yet is given a higher dimensionality in this work due to the collection of diffraction data from individual protein crystals that is achieved in serial X-ray crystallography experiments. This thesis demonstrates that the modeling and whole-pattern fitting analysis of continuous diffracted intensities distributions can improve the accuracy of extracted structure factor amplitudes. Simulation studies are presented to examine the feasibility of whole-pattern fitting for the analysis of merged diffraction data from finite protein crystals under several conditions, including two simple models of crystal disorder. Significant stages in the treatment of serial X-ray crystallography data occurs prior to the extraction of structure factor amplitudes. These include the sorting of diffraction images, the indexing of images from unconstrained orientations and the merging of images to form a single data-set for the determination of the crystal structure. These steps are shown in this thesis for two separate serial X-ray crystallography experiments performed using synchrotron radiation. Finally, the application of the whole-pattern fitting analysis to an experimental data-set is presented and protein crystal structures are determined. A general framework for the processing, merging and analysis of serial X-ray crystallography data is presented in this thesis. The applicability of this analysis framework can be regarded to be most relevant for the nanoscale protein crystals, for which extended intensity distributions around Bragg locations may be expected. In such cases, a three-dimensional powder diffraction analysis approach as presented here may be valuable for the determination of new protein structures.