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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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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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.