Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

Abstract

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Keywords: X-ray free-electron lasers; diffraction; scattering; simulations; single-particle imaging.

Figure 1

The temporal structure of the simulated X-ray pulse, the average number of bound electrons (Z _bound, dashed curves) and the average atomic displacements (solid curves) in the 2nip sample as a function of time for pulse durations of (a) 3 fs, (b) 9 fs and (c) 30 fs.

Figure 2

(Top left) The number of photons per pulse incident on the sample (N _ph,pulse) as a function of pulse duration. (Bottom left) The number of detected photons per diffraction pattern (N _ph,det). (Top right) The square of the average number of bound electrons in the sample molecule () in the middle of the pulse. (Bottom right) The scattering efficiency N _ph,det/N _ph,pulse. The decrease in N _e,bound as a consequence of ionization processes results in a reduced scattering efficiency with increasing pulse duration. Nevertheless, the total number of detected photons increases, since the longer pulses contain more photons.

Figure 3

(a) The coefficient of variation of oriented three-dimensional diffraction volumes for pulse durations of 3, 9 and 30 fs. (b) The coefficient of variation for a pulse duration of 9 fs and re-scaled coefficients for 3 fs. Triangles: every pattern has been multiplied by a constant factor of 3.3 to match the average photon count in the 9 fs patterns. Squares: every 3 fs pattern has been multiplied by an individual factor such that the average and r.m.s. photon counts match the 9 fs data.