Abstract
The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.
Highlights
The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale
Considerations: how consistently the XFEL pulses are produced and shaped; how efficiently these pulses are focused into a sample interaction region; how biomolecules are injected to optimise its illumination rate and quality; the extent and variability of radiation damage in each illumination event, which varies between biomolecules and pulse profiles; how quickly and reliably the faint diffraction signals are recorded; and how to recover statistically-robust structural information from these noisy and incomplete signals
For certain conditions and samples, this averaging may require an infeasibly large number of measurements. This could be informed by a realistic simulation tool, which may support the development of adaptive schemes that are better than indiscriminate averaging. To address these needs of XFEL-based imaging science, we have developed a realistic framework named simS2E that simulates biomolecular imaging at the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument[3] at the European XFEL4,5
Summary
The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. Considerations: how consistently the XFEL pulses are produced and shaped; how efficiently these pulses are focused into a sample interaction region; how biomolecules are injected to optimise its illumination rate and quality; the extent and variability of radiation damage in each illumination event, which varies between biomolecules and pulse profiles; how quickly and reliably the faint diffraction signals are recorded; and how to recover statistically-robust structural information from these noisy and incomplete signals Whereas each of these considerations has been studied in isolation, we still lack a thorough and realistic framework to understand their inter-dependencies, mutual constraints and myriad opportunities for global optimisation across this multi-component experiment. The need for such a framework has been identified by the single particle imaging community as one of the key steps needed to move forward this entire field[2]
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