Abstract

X-ray free-electron laser pulses initiate a complex series of changes to the electronic and nuclear structure of matter on femtosecond timescales. These damage processes include widespread ionization, the formation of a quasi-plasma state and the ultimate explosion of the sample due to Coulomb forces. The accurate simulation of these dynamical effects is critical in designing feasible XFEL experiments and interpreting the results. Current molecular dynamics simulations are, however, computationally intensive, particularly when they treat unbound electrons as classical point particles. On the other hand, plasma simulations are computationally efficient but do not model atomic motion. Here we present a hybrid approach to XFEL damage simulation that combines molecular dynamics for the nuclear motion and plasma models to describe the evolution of the low-energy electron continuum. The plasma properties of the unbound electron gas are used to define modified inter-ionic potentials for the molecular dynamics, including Debye screening and drag forces. The hybrid approach is significantly faster than damage simulations that treat unbound electrons as classical particles, enabling simulations to be performed on large sample volumes.

Highlights

  • The theory and modelling of the interaction of matter with intense X-ray pulses [1,2,3] has played an important role in the recent rise of X-ray free-electron lasers (XFELs) as a powerful new X-ray source for structural biology

  • We apply our model to evaluate the dependence of observed S-S bond lengths in nano-crystalline sample of lysozyme illuminated with three XFEL pulses that have the same total fluence but different pulse widths

  • We considered incident XFEL pulses with a total fluence of

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Summary

Introduction

The theory and modelling of the interaction of matter with intense X-ray pulses [1,2,3] has played an important role in the recent rise of X-ray free-electron lasers (XFELs) as a powerful new X-ray source for structural biology. Under the right experimental conditions, XFEL crystallography can be radiation-damage free for all practical purposes [4,5,6]. XFEL pulses are, violently destructive and the absence of radiation damage effects can not be taken for granted. Damage modelling still plays a key role in understanding when radiation damage can by mitigated by a suitable choice beam conditions [7,8,9]. XFELs are advantageous for time-resolved protein crystallography experiments [10,11].

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