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ItemQuantum technology for 3D imaging of single moleculesPerunicic, Viktor ( 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.
ItemCharacterization of silicon and diamond semiconductor devices in the low temperature regimeEikenberg, Nina ( 2015)At ultra low temperatures, materials reveal interesting behaviours that become evident due to the freezing out of thermal vibrations. We report studies of two important group IV material systems using a newly-commissioned dilution refrigerator at temperatures of less than 50 mK, and under axial magnetic fields of up to 7 Tesla and 1 Tesla in the lateral plane. We realized these magnetic fields with a 3D vector magnet and calibrated the system using well-known test samples. The first material studied in detail was nitrogen enhanced grown ultranano- crystalline diamond (N-UNCD). Diamond displays a combination of many extreme physical properties such as a high thermal conductivity, the highest number density of atoms, and a wide optical band gap, and is in addition to these properties also biocompatible . The ultra-nanocrystalline form of diamond is composed of small, 3-5 nm diameter grains of diamond and shares many of the desirable properties of the single crystal form, but is much easier to produce in thin form and can be used in wide variety of applications , especially for nanomechanics due to its strength and high Young's modulus . When doped with boron, nano-crystalline diamond (B-NCD) displays superconducting properties below a critical temperature of less than a few Kelvin [4, 5]. The nitrogen doped form has found application in biomedical devices , but its superconducting behaviour at very low temperatures has not yet been demonstrated . We fabricated N-UNCD thin films using microwave-enhanced CVD growth and used optical lithography to create Hall bar designs. We found that the conductivity of N-UNCD decreased with decreasing temperature, and between 36 mK and 4.9 K, a negative magneto-resistance was observed. Fitting the temperature and magnetic field dependent data with the 3D weak localization model developed by Kawabata , we found that 3D weak localization indeed plays a main role in the conduction mechanism of N-UNCD films even at ultra low temperatures. The second project was on the characterization of erbium doped silicon (Si:Er) semiconductor devices. Erbium has long been known to be important for use in optical fibre amplification in silica , and it also shows strong luminescent properties when it is added to Si as a dopant . As such, Er is also of interest as optoelectronic semiconductor material . Since the recent demonstration that it is possible to optically address single erbium ions in the silicon lattice  interest in Si:Er has increased. We studied silicon doped with erbium using ion implantation and report on our attempts to create CMOS devices with Er doped channels. The implanted material was characterized by optical spectroscopy, deep level transient spectroscopy, and measured both electrically and magnetically at low temperatures in the dilution refrigerator. Deep level transient spectroscopy performed on devices with varying anneal temperatures showed the emergence of electronically active traps with the minimum trap density occurring at annealing temperatures above 700 °C. Our results reveal that a rapid thermal anneal at 900 °C activates the luminescence from the implanted erbium ions. This effect remains, even if the sample is subjected to subsequent high temperature treatments. MOS devices co-doped with Er and P were fabricated and characterised to the extent they could be, based on the processing issues that arose.
ItemPhysics of low-dimensional nanostructuresDrumm, Daniel Warren ( 2012)Nanoscale constructs are offering access to the quantum mechanical regime due to their constrained size. The unusual, and often counterintuitive, behaviours of such constructs are of considerable interest to those developing new devices across several fields, including (but not limited to) quantum computing, communications, in vivo applications such as the bionic eye and bio-sensors, standard electronics and computing, and magnetometry. The physics of zero-, one-, and two-dimensional nanostructures comprised of various dopants or arrays of dopants in either diamond or silicon are presented and discussed. In particular, the zero-dimensional Xe-related defects in diamond are considered theoretically, via density functional theory, lattice dynamics, and thermodynamics. Xe defects have also been characterised experimentally via the probe-enhanced Ra- man spectroscopy (PERS) technique. In silicon, a one-dimensional nanowire consisting of P donors is studied with density functional theory. This wire is monatomically thin in one direction, and two donors wide in the other, with the donors spaced at the currently realisable sheet density of 25%. The two-dimensional case of infinite monatomically thin sheets of P donors is considered, both with effective mass theory and density functional theory (which is again undertaken for the most common experimental sheet density, 25%). The effective mass theory model has been applied to several sheet densities, agrees well with literature calculations of sheets with in-plane disorder, is far more rapid in execution, and offers an analytic scaling theory to describe the dependence of several key results on the sheet density. The density functional theory approach is then extended to the quasi-two dimensional case of bilayers of monatomically thin P sheets, in order to address the approach to minimal two-dimensional confinement.