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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ItemFlexible electrodes for neural recording, stimulation and neurochemical sensing( 2020)This thesis focuses on the development of implantable neural interfaces to perform multifunctional neural recording, neural stimulation and biochemical sensing. Neural interfacing devices using penetrating electrodes have emerged as an important tool in both neuroscience research and medical applications. These implantable electrodes enable communication between man-made devices and the nervous system by detecting and/or evoking neuronal activities. Recent years have seen a rapid development of electrodes fabricated using flexible, ultrathin microwires/microfibers. Compared to the arrays fabricated with rigid materials and larger cross sections, these microwires/microfibers have been shown to reduce foreign body response after implantation, with improved signal-to-noise ratio for neural recording and enhanced resolution for neural stimulation. Carbon fibers (CFs) are considered for implant into particular tissue types since they have small size, cause less tissue damage, and are flexible. CF recording electrodes have shown promise as recording electrodes and have the properties necessary to form sensing electrodes. Micron-scale electrodes such as CFs are expected to evoke localized neural responses due to localized electric fields. CFs are traditionally used with fast-scan cyclic voltammetry to study rapid neurotransmitter changes in vivo and in vitro, as they allow real-time detection of catecholamines with high sensitivity and selectivity. However, they possess narrow usable voltage range, which limits their application for neural stimulation. Additionally, surface fouling occurs with certain neurochemicals potentially obstructing further neurotransmitter adsorption onto the electrode surface. Therefore, they need to be coated with other materials to boost their electrochemical properties for neural stimulation. In this thesis, diamond and diamond-like materials, in particular nitrogen doped ultrananocrystalline diamond (NUNCD) hybrid and boron doped carbon nanowall (B-CNW) are considered as coatings for CFs to enhance properties towards neural interface applications. A focus is finding acceptable properties for recording, stimulation and neurochemical sensing. Novel fabrication techniques were developed to deposit the films onto the surface of CFs. Firstly, the surface of CFs was amine-functionalised and covalent bonds were formed with oxygen terminated nanodiamonds. Films were grown on the treated/seeded fibers using plasma-assisted chemical vapor deposition. To fabricate single fiber electrodes, individual fibers were insulated with capillary glass with 100 micrometer of fiber exposed. The physical and chemical properties of NUNCD hybrid and B-CNW were characterized and studied. The results from electrochemical characterization, in conjunction with both in vitro and in vivo assessments, suggest that these electrodes offer a highly functional alternative to conventional electrode materials for both recording and stimulation, yielding safe charge injection capacities up to 25.08 +-12.37 mC/cm2. To test the capability of electrodes for neural stimulation in vitro, explanted wholemount rat retina was used. The electrodes could elicit localized stimulation responses in the explanted retina. These electrodes with micron -scale cross sections have the potential to improve the spatial resolution for stimulation while minimizing axon bundle activation. In vivo and in vitro single-unit recording showed that the electrodes could detect signals with high signal-to-noise ratios up to 8.7. NUNCD hybrid coated CFs were able to electrochemically detect dopamine with high sensitivity and selectivity. Such electrodes are needed for the next generation of miniaturized, closed-loop implants that can self-tune therapies by monitoring both electrophysiological and biochemical biomarkers.
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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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ItemOptimizing diamond for a better neural interface( 2016)This thesis focuses on the optimization of the biological and electrochemical properties of diamond for a better neural interface. Neural interfaces create links between the nervous system and the outside world and are promising for restoring and enhancing the function of neural tissues lost or damaged due to neural diseases or injuries. Neural interfaces built by diamond aim to function reliably and effectively for a long period of time. In comparison with existing materials used for neural interfaces, diamond has some attractive properties in terms of its well-known chemical and mechanical stability. However, the biological and electrochemical properties of the stimulation and recording electrodes can also determine the success of the devices. The electrodes are required to provide safe, sufficient charge injection for stimulation and exhibit low impedance for high quality recording. The biocompatibility requirements of the electrode materials are also demanding, in order to form close contact with the targeted neurons to decrease the charge injection threshold and to increase the signal amplitude for recording. Unfortunately, the reported diamond electrochemical properties are unsuitable for neural stimulation and recording. Furthermore, the investigation of neuron growth on diamond surfaces is limited. In this thesis, I consider the use of diamond, in particular nitrogen doped ultrananocrystalline diamond (N-UNCD), for neural interfaces by assessing its biocompatibility using in vitro cell culture, and by measuring its electrochemical properties. Both the biocompatibility and electrochemical properties of the as-grown N-UNCD were shown to require improvement before it can be used as a neural interface material. To optimize the diamond surfaces for neural interfaces, I propose and discuss several different strategies. The first set of strategies involve the use of five different surface treatments that are often used as part of sterilization procedures. The resulting change of neuron response and electrochemical properties of N-UNCD was studied, combining the characterization of the physical and chemical properties of N-UNCD. A two-step sterilization method, short oxygen plasma treatment followed by hydrogen peroxide sterilization, was found to be the most useful. Then, I investigated the effect of low-power oxygen plasma on the biological and electrochemical properties of N-UNCD. N-UNCD substrates with low surface roughness and activated by oxygen plasma for 3 hours, were found to show optimal biocompatibility and electrochemical properties for neural interfaces. Finally, the fabrication of diamond electrodes with optimized surface properties for neural interfaces was investigated. A microelectrode pair was fabricated composed of two microelectrodes before and after surface optimization, with the aim of demonstrating the different efficacies for in vitro neural stimulation and recording. Prolonged oxygen plasma treatment was shown to improve the charge injection capacities of electrodes on the Bionic Vision Australia High-Acuity device, beneficial for its application in Epi-retinal stimulation. A diamond electrode array was finally fabricated with low surface roughness. This low roughness diamond electrode array after long time oxygen plasma activation is expected to work as a neural interface with high efficacy and long-term stability.
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ItemCharacterization of silicon and diamond semiconductor devices in the low temperature regime( 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 [1]. 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 [2], especially for nanomechanics due to its strength and high Young's modulus [3]. 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 [6], but its superconducting behaviour at very low temperatures has not yet been demonstrated [7]. 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 [8], 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 [9], and it also shows strong luminescent properties when it is added to Si as a dopant [10]. As such, Er is also of interest as optoelectronic semiconductor material [11]. Since the recent demonstration that it is possible to optically address single erbium ions in the silicon lattice [12] 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.
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ItemAn all-diamond hermetic encapsulation for a high-acuity retinal prosthesis( 2014)Bionic vision through electrical stimulation of the retina is fast becoming a reality. To date, clinical trials have allowed blind patients to see a lover’s smile and navigate night scenes. (K Stingl et al, 2013) This kind of data has encouraged an abundance of research activity. Bionic Vision Australia, among others, is developing a retinal prosthesis to restore high visual acuity. One of its flagship technologies is a diamond electrode array, which will form part of the encapsulation for the implanted electronics. The remainder of the encapsulation also needs to be constructed from leak-proof, or hermetic, materials. The aim of this work was to design and test feasibility of a hermetic encapsulation that incorporated the diamond electrode array. An all-diamond hermetic encapsulation design was proposed, in which a diamond box-shaped capsule was bonded to the diamond array, with the electronics contained inside. Diamond capsules were made from polycrystalline diamond. Laser micromachining was found to be the optimal fabrication method. Hermetic joints were made in diamond using vacuum brazing with precious metal braze alloys. Several brazes were investigated for their ability to wet and form strong bonds with diamond. Bond interfaces were studied for morphology, chemical composition and hermeticity. Brazed diamond capsules were sealed at room temperature using laser microwelding. Welds were optimised for smooth surface morphology and hermeticity. The results demonstrated a hermetic all-diamond encapsulation. Combining the hermetic capsule, the brazing technique, and the welding technique with the diamond electrode array formed a retinal prosthesis technology that can protect against degradation for the lifetime of the patient.
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ItemPrinciples and applications of quantum decoherence in biological, chemical, and condensed matter systems( 2013)This thesis focuses on the use of the Nitrogen-Vacancy (NV) defect centre in diamond as a single spin sensor of nanoscale magnetic fields. The NV system has attracted considerable interest in recent years due to its unique combination of sensitivity, nanoscale resolution, room temperature operation, and stable fluorescence, together with the inherent biocompatibility of diamond; making it ideal for measuring coherent quantum processes in biological, chemical and condensed matter systems. Existing NV-based sensing techniques, however, are ultimately limited by sources of magnetic noise that act to destroy the very resource required for their operation: the quantum phase coherence between NV spin levels. We address this problem by showing that this noise is a rich source of information about the dynamics of the environment we wish to measure. We develop protocols by which to extract dynamical environmental parameters from decoherence measurements of the NV spin, and a detailed experimental verification is conducted using diamond nanocrystals immersed in a MnCl2 electrolyte. We then detail how sensitivities can be improved by employing sophisticated dynamic decoupling techniques to remove the decoherence effects of the intrinsic noise, whilst preserving that of the target sample. To characterise the effects of pulse errors, we describe the full coherent evolution of the NV spin under pulse-based microwave control, including microwave driven and free precession intervals. This analysis explains the origin of many experimental artifacts overlooked in the literature, and is applied to three experimentally relevant cases, demonstrating remarkable agreement between theoretical and experimental results. We then analyse and discuss two important future applications of decoherence sensing to biological imaging. The first involves using a single NV centre in close proximity to an ion channel in a cell membrane to monitor its switch-on/switch-off activity. This technique is expected to have wide ranging implications for nanoscale biology and drug discovery. The second involves using an array of NV centres to image neuronal network dynamics. This technique is expected to yield significant insight into the way information is processed in the brain. In both cases, we find the temporal resolution to be of millisecond timescales, effectively allowing for real time imaging of these systems with micrometre spatial resolution. We analyse cases in which environmental frequencies are sufficiently high to result in a mutual exchange of energy with the NV spin, and discuss how this may be used to reconstruct the corresponding frequency spectrum. This analysis is then applied to two ground-breaking experiments, showing remarkable agreement. Protocols for in-situ monitoring of mobile nanodiamonds in biological systems are developed. In addition to obtaining information about the local magnetic environment, these protocols allow for the determination of both the position and orientation of the nanocrystal, yielding information about the mechanical forces to which it is subjected. These techniques are applied in analysing a set of experiments in which diamond nanocrystals are taken up endosomally by human cervical cancer cells. Finally, we focus our attention on understanding the microscopic dynamics of the spin bath and its effect on the NV spin. Many existing analytic approaches are based on simplified phenomenological models in which it is difficult to capture the complex physics associated with this system. Conversely, numerical approaches reproduce this complex behaviour, but are limited in the amount of theoretical insight they can provide. Using a systematic approach based on the spatial statistics of the spin bath constituents, we develop a purely analytic theory for the NV central spin decoherence problem that reproduces the experimental and numerical results found in the literature, whilst correcting the limitations and inaccuracies associated with existing analytical approaches.
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ItemPhysics of low-dimensional nanostructures( 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.
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ItemThe theory of the nitrogen-vacancy colour centre in diamond( 2012)The nitrogen-vacancy (NV) colour centre in diamond is a model system for many quantum technologies including, metrology, information processing and communications. The NV centre is also highly suitable for employment in various nanotechnology applications, such as biological and sub-diffraction limit imaging, and in tests of fundamental physics, such as cavity quantum electrodynamics and the quantum entanglement of mesoscopic systems. The remarkable properties of the centre are however, not currently fully understood, with several unresolved issues limiting the performance of the centre in its many important applications. As the unresolved issues are interrelated and concern different aspects of the centre's properties, they may only be resolved by the development of a single self-consistent theory of the NV centre. The aim of this work has been to develop such a theory. The theory has been developed using a combination of the molecular model of deep level defects in semiconductors, group theoretical methods and ab initio calculations. The highly structured nature of the theory will enable its future use in the systematic identification of other colour centres that possess properties that exceed those of the NV centre.
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ItemNanoscale quantum sensing using nitrogen-vacancy centres in diamond( 2012)Devices that detect and spatially image magnetic fields are important in many areas of study including chemistry, electronics, materials science and biology. By extending the boundaries of what is currently achievable we may begin to explore areas previously inaccessible to science, such as wide-field imaging of neuron signaling or structural determination of single molecules. Here we present experimental progress towards the development of a nanoscale magnetic sensor operating under ambient conditions using the nitrogen-vacancy (NV) centre in diamond. This thesis describes the construction of a lab-built, confocal microscope capable of detecting single NV centres, with additional microwave control for coherent manipulation of the NV spin. The feasibility of using NV-diamond for real-time detection of the action potential generated by a neuron, and with high spatial resolution is experimentally demonstrated. The quantum coherence of single NV spins is monitored in various chemical solutions, and detection of nanoscale magnetic environments external to the diamond are demonstrated. This work sets the experimental foundation for using manufactured single quantum systems as sensitive probes of external chemical environments. In addition, the first measurements of single quantum coherent spins inside living cells are performed with NV centres in nanodiamonds. These studies on NV centres inside living cells demonstrate their promise as magnetic sensors for biology. Furthermore, alternative quantum sensing technologies emerge including rotational tracking of nanodiamonds and enhanced identification of fluorescent nanoparticles.