Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
Abstract
Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 104to 107 J cm-2with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for differentmore »
- Authors:
-
- Uppsala Univ. (Sweden)
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Uppsala Univ. (Sweden); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science
- Publication Date:
- Research Org.:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1810658
- Report Number(s):
- LLNL-JRNL-819977
Journal ID: ISSN 1600-5775; 1029489; TRN: US2213068
- Grant/Contract Number:
- AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Synchrotron Radiation (Online)
- Additional Journal Information:
- Journal Name: Journal of Synchrotron Radiation (Online); Journal Volume: 22; Journal Issue: 2; Journal ID: ISSN 1600-5775
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 73 NUCLEAR PHYSICS AND RADIATION PHYSICS; x-ray free-electron laser; serial femtosecond crystallography; radiation damage; plasma simulations
Citation Formats
Jönsson, H. Olof, Tîmneanu, Nicuşor, Östlin, Christofer, Scott, Howard A., and Caleman, Carl. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. United States: N. p., 2015.
Web. doi:10.1107/s1600577515002878.
Jönsson, H. Olof, Tîmneanu, Nicuşor, Östlin, Christofer, Scott, Howard A., & Caleman, Carl. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography. United States. https://doi.org/10.1107/s1600577515002878
Jönsson, H. Olof, Tîmneanu, Nicuşor, Östlin, Christofer, Scott, Howard A., and Caleman, Carl. Wed .
"Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography". United States. https://doi.org/10.1107/s1600577515002878. https://www.osti.gov/servlets/purl/1810658.
@article{osti_1810658,
title = {Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography},
author = {Jönsson, H. Olof and Tîmneanu, Nicuşor and Östlin, Christofer and Scott, Howard A. and Caleman, Carl},
abstractNote = {Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 104to 107 J cm-2with photon energies from 2 to 12 keV, up to 100 fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. Overall, the different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.},
doi = {10.1107/s1600577515002878},
journal = {Journal of Synchrotron Radiation (Online)},
number = 2,
volume = 22,
place = {United States},
year = {Wed Feb 25 00:00:00 EST 2015},
month = {Wed Feb 25 00:00:00 EST 2015}
}
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Works referencing / citing this record:
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