Use cases

Use Case 14 – Temporal shape of XFEL pulses and radiation damage of a biomolecule in single particle imaging

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Single particle imaging is an emerging tool to determine the structure of biological molecules, without the need of crystallization. Among other things, the method is limited by radiation damage. For each sample that interacts with the X-rays from an XFEL, the dynamics will be different, since the pulses will not have the same temporal shape. In this work, we study the effects of the temporal shape on the resulting radiation damage. This is done by combining SimEx and molecular dynamics as described in GROMACS. This will in the end make it possible for us to quantify the resolution limits.

Main contributors

  • Juncheng E, European XFEL, development of the integration of GROMACS and SimEx.
  • Ibrahim Dawod, European XFEL/Uppsala university, development of the integration of GROMACS and SimEx.


Watch the video showcasing the workflow here

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SimEx on Github

Contact person

Ibrahim Dawod (Uppsala University / European XFEL)

Junchen E (European XFEL)

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