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Figure 1
A graphical representation of ion diffusion in GroEL, where ion locations are chosen stochastically using the time-dependent temperature. Simulation parameters are: 8 keV, 5.0 × 1020 W cm−2 and 100 nm pulse diameter. Ionized hydrogen (white) moves much faster than ions of other elements. The accumulated diffraction pattern for each pulse time is shown below and these were generated by randomly assigning each atom an ionization state and a displacement according to the rate-equations model described in Appendix A[link]. The effect of shot noise is shown on the right-hand half of each diffraction image. Intensities are normalized with the same number of incident photons (1012) prior to calculating shot noise. There are correlations between the speckle structure at early and late pulse times due to the gating effect, as shown by the inset regions.

Volume 2| Part 6| October 2015| Pages 661-674
ISSN: 2052-2525