Measuring atomic displacement inside crystals has been an important field of interest for decades especially in semiconductor industry for its effect on the crystal structure and symmetry, subsequently on the bandgap structure. There are three different image based, diffraction based, and electron holography based techniques using transmission electron microscope (TEM). These methods enable measuring atomic displacement inside specimen. However, among all TEM techniques offering nano-scale resolution measurements, convergent beam electron diffraction (CBED) patterns show the highest sensitivity to the atomic displacement. Higher order Laue zone (HOLZ) lines split by small variations of lattice constant allowing the atomic displacement measurement through the crystal. However it is a cumbersome measurement and it can only reveal the atomic displacement in two dimensions. Therefore, the atomic displacement information at each depth through the specimen thickness is still missing. This information can be obtained by recovering the phase information across the split HOLZ line. The phase profile across the split HOLZ line can be retrieved by the electron interferometry method. The phase of the diffracted beam is the required information to reconstruct the atomic displacement profile through the specimen thickness. In this work, we first propose a novel technique of self-interference of split HOLZ line based on the diffracted beam interferometry which recovers the phase information across the split HOLZ line. The experimental details of the technique have been examined to report the parameters in order to implement the method. Regarding the novelty of the technique and the lack of the of a reference phase profile to discuss the results, phase profile simulation was a main contribution. For simulating the phase profile across the split HOLZ line the Howie-Whelan formula supporting the kinematical theory of diffraction is used. Accordingly, the analytical approach to simulate the phase profiles across the split HOLZ line for three various suggested atomic displacements are studied. Also, the effect of some parameters such as the atomic displacement amplitude, the specimen thickness, and the g reflection is investigated on the phase profile. This study leads to an equation used for fitting the experimental results with the simulated phase profile. Consequently, self-interference of split HOLZ line (SIS-HOLZ) is studied as a method of reconstructing the phase profile across the split HOLZ line which carries the information of atomic displacement through the specimen thickness. / Graduate / 0548 / 0794 / mananrp@uvic.ca

Protein structure models obtained from X-ray crystallography are subject to radiation damage. The resulting specific alterations to protein structures can be mistaken for biological features, or may obscure actual protein mechanisms, leading to misidentification or obscuration of biological insight. The radiation chemistry behind this site-specific damage is not well understood. Radiation damage processes progress in proportion to the dose absorbed by the crystal in the diffraction experiment. Doses can be estimated using existing software, but these assume idealised experimental conditions. To simulate complex diffraction experiments, including treatment of imperfect X-ray beam profiles and inhomogeneous dose distributions, a new program, RADDOSE-3D, was developed. RADDOSE-3D can be integrated into beamline software to provide convenient, more accurate, comparative, and publishable dose figures, also facilitating informed data collection decisions. There is currently no method to automatically detect specific radiation damage in protein structure models in the absence of an 'undamaged' reference model. Radiation damage research therefore generally relies on detailed observation of a few model proteins. A new metric, B_Damage, is designed and used to identify and quantify specific radiation damage in the first large-scale statistical survey of 2,704 published protein models, which are examined for the effects of local environments on site-specific radiation damage susceptibility. A significant positive correlation between susceptibility and solvent accessibility is identified. Current understanding of radiation damage progression is mostly based on a few consecutive structure model 'snapshots' at coarse dose intervals. The low sampling rate considerably limits the ability to identify varying site susceptibility and its causes. Real space electron density data are obtained for crystals of different mutants of a RhoGDI protein with very high sequence identity, to determine sensitising and stabilising factors for radiation induced structural changes. Utilising a newly developed data collection and analysis protocol, these changes could be tracked with unprecedented time resolution.

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