Abstract
X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.
Highlights
The idea of using X-ray free-electron lasers (XFELs) for the determination of protein structures was introduced at the turn of the century (Neutze et al, 2000)
In this paper we give a detailed presentation of our methodology for combining classical molecular dynamics (GROMACS) and non-thermal plasma simulations (CRETIN) to investigate the ultrafast phase transition of a protic ionic liquid to plasma, initiated and probed by an XFEL pulse
A typical experiment at an XFEL will use femtosecond X-ray pulses to record scattering from liquid samples, and, while the pulse propagates through the sample and quickly turns it into a plasma, the recorded diffraction pattern provides an average picture of the entire dynamics
Summary
The idea of using X-ray free-electron lasers (XFELs) for the determination of protein structures was introduced at the turn of the century (Neutze et al, 2000). With the glorious goal to perform high-resolution imaging of single protein molecules, considerable effort has been made to develop and build XFEL facilities that today are available to the scientific community. Even though high-resolution single-particle imaging using XFELs has not been achieved yet, XFEL sources have created numerous exciting new research directions. The XFEL pulses can have a peak brilliance that is several orders of magnitude higher than that at fourthgeneration synchrotron facilities. This feature allows for investigations of matter under extreme conditions, as any sample put in the beam will be highly ionized and heated while the X-ray pulse is still propagating through it (Beyerlein et al, 2018). Since biomolecules are sensitive to radiation damage, the high ionization due to the intense X-ray pulse leads to complications in the reconstruction process, limiting the achievable resolutions (Howells et al, 2009; de la Mora et al, 2020; Ostlin et al, 2019)
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