School of Physics - Theses
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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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ItemElectronic damage to single biomolecules in femtosecond X-ray imaging( 2013)Knowledge of the structure of large, complex molecules is of vital interest in understanding their function in biological systems. Standard X-ray crystallographic methods of structure determination are unsuitable for a large class of biomolecules for which it is difficult, or impossible to form high-quality crystals. The technique of coherent diffractive imaging (CDI) provides a route toward the determination of large molecular structures without crystallisation. CDI uses a Fourier transform mapping between fields in the sample and detector planes; this implies attainable resolution is limited by the angle to which signal can be measured. Unfortunately, biological molecules scatter weakly; in order to obtain signal to the required angle an extremely bright new source of X-rays is required. These new sources, the X-ray free-electron lasers (XFELs), have brightnesses approaching that sufficient to resolve biological molecules to atomic resolution. This increased brightness has an unfortunate side effect, the number of unwanted photoionisation events in the target molecule is vastly increased. This leads to an imbalance of charge that results in the eventual destruction of the molecule. In this thesis, I show that the intense illumination from an XFEL produces a time-dependent electron density in the target molecule. This effect targets the inner shell electrons in the molecule, and hence preferentially degrades the high-resolution information. I further show that the time-dependent electron density in the molecule can be treated as a partially coherent secondary source of X-rays, violating the coherence assumption inherent to CDI. This damage-induced degree of partial coherence is determined from simulated experimental conditions. It is demonstrated that this degree of partial coherence due to damage can be used to infer information about the physical processes underlying the interaction between the molecule and the X-ray field. This information can be transferred between similar molecules in an XFEL experiment to compensate for damage processes. Assumptions made about the partial coherence of the scattered X-ray field are used to recover the structure of a biomolecule in simulation using an adjusted CDI iterative scheme. Structure refinement and electron density recovery schemes are also investigated.
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ItemQuantitative studies of x-ray optical coherence( 2010)The continued development of synchrotron sources, especially over the previous two decades, has allowed the new field of coherent X-ray optics to flourish. Rapid advancement in the field is set to continue, with the recent completion of the new X-ray free electron laser (XFEL) source at the Stanford Linear Accelerator Centre. Unlike visible wavelength lasers, XFEL and synchrotron sources are not fully coherent, meaning that coherence based imaging techniques are not at present fully optimised for use with these sources. A pre-requisite for the optimisation of coherence based imaging techniques, is the full characterisation of the coherence properties of the incident beam used in these techniques. The task of characterising the coherence properties of an optical wavefield was first investigated by Zernicke in 1938. His use of Young’s double slit experiment remains to this day a popular means of performing a basic measurement of the coherence properties of a wavefield. A limitation of such measurement techniques arises because the coherence properties of an incident wavefield are fully described in terms of a four-dimensional correlation function. This means that a one-dimensional measurement such as a Young’s double slit type experiment fails to provide sufficient information about the wavefield to fully characterise the beam. Over the past 15 years, there has been a development of non-interferometric methods of coherence measurement which seek to obtain a full characterisation of the four-dimensional correlation function. The author develops a non-interferometric iterative method for mapping the correlation function, which is based upon the analysis of the partially coherent wavefield in terms of its coherent modes. A computational method for numerically extracting the coherent modes of a partially coherent wavefield is presented, which is followed by the development of an iterative scheme for experimentally determining the form of these modes. The iterative scheme is then quantitatively evaluated for both experimental and simulated data, and its performance represents a significant advancement towards the goal of achieving a fully general characterisation of optical coherence.