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In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL. [ABSTRACT FROM AUTHOR]

In this work, we analyze the application of X-ray diffraction imaging techniques to follow ultrafast structural transitions in solid materials using the example of an X-ray pump–X-ray probe experiment with a single-crystal silicon performed at a Linac Coherent Light Source. Due to the spatially non-uniform profile of the X-ray beam, the diffractive signal recorded in this experiment included contributions from crystal parts experiencing different fluences from the peak fluence down to zero. With our theoretical model, we could identify specific processes contributing to the silicon melting in those crystal regions, i.e., the non-thermal and thermal melting whose occurrences depended on the locally absorbed X-ray doses. We then constructed the total volume-integrated signal by summing up the coherent signal contributions (amplitudes) from the various crystal regions and found that this significantly differed from the signals obtained for a few selected uniform fluence values, including the peak fluence. This shows that the diffraction imaging signal obtained for a structurally damaged material after an impact of a non-uniform X-ray pump pulse cannot be always interpreted as the material's response to a pulse of a specific (e.g., peak) fluence as it is sometimes believed. This observation has to be taken into account in planning and interpreting future experiments investigating structural changes in materials with X-ray diffraction imaging. [ABSTRACT FROM AUTHOR]