Towards Realistic Simulations of Macromolecules Irradiated under the Conditions of Coherent Diffraction Imaging with an X-ray Free-Electron Laser

Abstract

Biological samples are highly radiation sensitive. The rapid progress of their radiation damage prevents accurate structure determination of single macromolecular assemblies in standard diffraction experiments. However, computer simulations of the damage formation have shown that the radiation tolerance might be extended at very high intensities with ultrafast imaging such as is possible with the presently developed and operating x-ray free-electron lasers. Recent experiments with free-electron lasers on nanocrystals have demonstrated proof of the imaging principle at resolutions down to 1.6 Angstroms. However, there are still many physical and technical problems to be clarified on the way to imaging of single biomolecules at atomic resolution. In particular, theoretical simulations try to address an important question: How does the radiation damage progressing within an imaged single object limit the structural information about this object recorded in its diffraction image during a 3D imaging experiment? This information is crucial for adjusting pulse parameters during imaging so that high-resolution diffraction patterns can be obtained. Further, dynamics simulations should be used to verify the accuracy of the structure reconstruction performed from the experimental data. This is an important issue as the experimentally recorded diffraction signal is recorded from radiation-damaged samples.

Electron and fluorescence spectra of a water molecule irradiated by an x-ray free-electron laser pulse

“…Most computational methods simulating radiation damage in coherent diffractive imaging experiments [47][48][49][50][51] are based on the independent-atom model. In this concept the x-ray ionization of a polyatomic molecule is treated as if the molecule consisted of isolated atoms.…”

X-ray multiphoton ionization dynamics of a water molecule irradiated by an x-ray free-electron laser pulse

“…Pioneered by the work of Neutze et al [4], radiation damage in samples was studied in terms of molecular dynamics simulation [14][15][16] or hydrodynamic expansion models [17,18]. These works are mainly based on an independent atom model to describe the electronic radiation damage.…”

Ab initiocalculation of electron-impact-ionization cross sections for ions in exotic electron configurations

“…However, currently available XFEL pulses are not short enough * Corresponding author: john.jasper.bekx@desy.de to elude electronic motion and the subsequently induced electronic damage [20]. Therefore, quantitative understanding of the radiation damage mechanisms, as well as their proper treatment and incorporation into simulations, is vital for the accuracy of the structure determination from experimental data [20][21][22][23][24][25]. Such incorporation of radiation damage into photon-matter interaction studies has been done, e.g., with the molecular dynamics code XMDYN [26,27].…”