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Title: A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

Journal Article · · Scientific Reports
DOI: https://doi.org/10.1038/srep24791 · OSTI ID:1253731
 [1];  [2];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [3];  [3]
  1. European XFEL GmbH, Hamburg (Germany); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  2. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  3. European XFEL GmbH, Hamburg (Germany)
  4. Russian Academy of Sciences, Moscow (Russia)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); he Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Polish Academy of Sciences, Krakow (Poland)
  7. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Univ. of Hamburg, Hamburg (Germany)
  8. National Univ. of Singapore (Singapore)
+ Show Author Affiliations

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1253731
Journal Information:
Scientific Reports, Journal Name: Scientific Reports Vol. 6; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (20)

The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters journal January 2020
Theoretical evidence for the sensitivity of charge-rearrangement-enhanced x-ray ionization to molecular size text January 2019
The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters journal January 2020
Roadmap of ultrafast x-ray atomic and molecular physics journal January 2018
Theoretical evidence for the sensitivity of charge-rearrangement-enhanced x-ray ionization to molecular size journal July 2019
Ab initio calculation of electron-impact-ionization cross sections for ions in exotic electron configurations journal August 2018
XMDYN and XATOM : versatile simulation tools for quantitative modeling of X-ray free-electron laser induced dynamics of matter journal April 2016
Experimental 3D coherent diffractive imaging from photon-sparse random projections journal March 2019
Incorporating particle symmetry into orientation determination in single-particle imaging journal August 2018
Simulations of ultrafast x–ray laser experiments conference June 2017
Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers conference September 2017
Searching for 3D structural models from a library of biological shapes using a few 2D experimental images journal September 2018
Roadmap of ultrafast x-ray atomic and molecular physics text January 2019
Simulations of single-particle imaging of hydrated proteins with x-ray free-electron lasers text January 2017
Simulations of ultrafast x–ray laser experiments text January 2017
Ab initio calculation of electron-impact-ionization cross sections for ions in exotic electron configurations text January 2018
Roadmap of ultrafast x-ray atomic and molecular physics text January 2018
Experimental 3D coherent diffractive imaging from photon-sparse random projections text January 2019
Theoretical evidence for the sensitivity of charge-rearrangement-enhanced x-ray ionization to molecular size text January 2019
Theoretical evidence for the sensitivity of charge-rearrangement-enhanced x-ray ionization to molecular size text January 2019

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Related Subjects

42 ENGINEERING
X-rays
atomic and molecular interactions with photons
single-molecule biophysics