Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
The Importance of Radiation Damage for Molecular Reconstruction from FEL Diffraction Experiments
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
2018 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Serial Femtosecond X-ray crystallography (SFX) is a rapidly growing experimental technique by which the structure of a crystalline sample may be determined. The X- rays arrive at the sample in pulse trains of the order of femtoseconds. Each X-ray pulse train hits a unique crystal at a random orientation and produces a diffraction pattern on the detector and series of patterns is obtained, which is the reason for the denomination "serial". Here, the radiation damage done to a sample during an SFX experiment was studied by simulating diffraction patterns including damage. Throughout, a model reference structure in the form of a reflection list was used to simulate patterns. The aim was to minimise the effects of damage through a correction based on available damage data. Firstly, a simulation case with made-up damage data was performed. The made-up data was used to modify the structure factors such that they would appear damaged. After structural reconstruction, the same data was used to correct for the damage. This was done as a validation of the method pipeline. Secondly, a more realistic case, with actual simulated damage

data and a distribution of incident intensities was carried out. The expectation value of the distribution was used to correct for damage. It is found for both cases that the damage correction improves the agreement between simulated data and the original model. This is a first step toward successfully correcting for radiation damage which would be a big step forward for SFX. 

Place, publisher, year, edition, pages
2018. , p. 39
Series
UPTEC F, ISSN 1401-5757 ; 18005
Keywords [en]
Radiation damage, SFX, XFEL, Diffraction, Protein, Crystallography
National Category
Atom and Molecular Physics and Optics
Identifiers
URN: urn:nbn:se:uu:diva-340808OAI: oai:DiVA.org:uu-340808DiVA, id: diva2:1179962
External cooperation
Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
Educational program
Master Programme in Engineering Physics
Presentation
2017-12-04, Seminar room IV at Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany, Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany, Hamburg, Germany, 15:49 (English)
Supervisors
Examiners
Available from: 2018-02-05 Created: 2018-02-02 Last updated: 2018-02-05Bibliographically approved

Open Access in DiVA

fulltext(2242 kB)38 downloads
File information
File name FULLTEXT01.pdfFile size 2242 kBChecksum SHA-512
0dc351f3ae590dce92bcdf32949c2007d3786fd7ce10ffc09f80d9739a7120e8eb646d4f76592428bdecfd436802f3f5f38cb17646fafc5e23258d1b9da148cc
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Bjärnhall Prytz, Nicklas
By organisation
Molecular and Condensed Matter Physics
Atom and Molecular Physics and Optics

Search outside of DiVA

GoogleGoogle Scholar
Total: 38 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

urn-nbn

Altmetric score

urn-nbn
Total: 180 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf