Analysis of Diffracted Intensities from Finite Protein Crystals with Incomplete Unit Cells

Developments in experimental techniques in micro electron diffraction and serial X-ray crystallography provide the opportunity to collect diffraction data from protein nanocrystals. Incomplete unit cells on the surfaces of protein crystals can affect the distribution of diffracted intensities for crystals with very high surface-to-volume ratios. The extraction of structure factors from diffraction data for such finite protein crystals sizes is considered here. A theoretical model for the continuous diffracted intensity distribution for data merged from finite crystals with two symmetry-related sub-units of the conventional unit cell is presented. This is used to extend a whole-pattern fitting technique to account for incomplete unit cells in the extraction of structure factor amplitudes. The accuracy of structure factor amplitudes found from this whole-pattern fitting technique and from an integration approach are evaluated

Experimental aspects of multiharmonic-order coherent diffractive imaging

We describe some experimental aspects required for the implementation of a few-order high-harmonic source for coherent diffractive imaging in the extreme-ultraviolet region. Polychromatic high-angle diffractive images have been successfully processed for both periodic and aperiodic inorganic samples using a modified Gerchberg-Saxton algorithm and maximum-entropy-method refinement and reconstructions yielding a resolution of 100 nm can now be achieved at harmonic wavelengths around 32 nm

High-harmonic-generation spectrum reconstruction from Young's double-slits interference pattern using the maximum entropy method

A method is proposed that uses maximum entropy analysis of a Young's two-slit interference pattern for the measurement of the spectrum of a high-harmonic-generation light source. The approach is tested using experimental data, and the results are found to be consistent with those obtained directly using a grazing incidence spectrometer

Measurements of long-range electronic correlations during femtosecond diffraction experiments performed on nanocrystals of buckminsterfullerene

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data

Partial coherence: a route to performing faster coherent diffraction imaging

Coherent diffraction imaging (CDI) typically requires that the light source should be highly coherent both laterally and longitudinally. Beamlines at synchrotrons usually install a monochromator and slits to achieve a highly coherent source, leading to a large reduction of beam flux. We demonstrate that lateral and longitudinal partial coherence can be successfully included in a CDI reconstruction algorithm simultaneously, reducing the associated exposure time by two orders of magnitude. For the experimental case we present this allows the acquisition of CDI data in just 5 seconds compared to 20 minutes for full coherence. This significantly reduces the requirements on the stability of the imaging system as well as providing a route to imaging samples in real-time

Diffraction imaging: The limits of partial coherence

Coherent diffraction imaging (CDI) typically requires that the source should be highly coherent both laterally and longitudinally. In this paper, we demonstrate that lateral and longitudinal partial coherence can be successfully included in a CDI reconstruction algorithm simultaneously using experimental x-ray data. We study the interplay between lateral partial coherence and longitudinal partial coherence and their relative influence on CDI. We compare our results against the coherence criteria published by Spence et al. [Spence et al., Ultramicroscopy 101, 149 (2004)] and show that for iterative ab initio phase-recovery algorithms based on those typically used in CDI and in cases where the coherence properties are known, we are able to relax the minimal coherence requirements by a factor of 2 both laterally and longitudinally, potentially yielding significant reduction in exposure time

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene

X-ray free-electron lasers (XFELs) deliver x-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third-generation synchrotron source. The power density of an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond time scale. Exploration of the interaction of intense coherent x-ray pulses and matter is both of intrinsic scientific interest and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. We report observations of the diffraction of extremely intense 32-fs nanofocused x-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power significantly differs from the one obtained using either third-generation synchrotron sources or XFEL sources operating at low output power and does not correspond to the diffraction pattern expected from any known phase of crystalline C60. We interpret these data as evidence of a long-range, coherent dynamic electronic distortion that is driven by the interaction of the periodic array of C60 molecular targets with intense x-ray pulses of femtosecond duration