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Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. (Molekyl- och den kondenserade materiens fysik)
2016 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Using high intensity ultrashort pulses from X-ray free electron lasers to investigate soft matter is a recent and successful development. The last decade has seen the development of new variant of protein crystallography with femtosecond dynamics, and single particle imaging with atomic resolution is on the horizon. The work presented here is part of the effort to explain what processes influence the capability to achieve high resolution information in these techniques. Non-local thermal equilibrium plasma continuum modelling is used to predict signal changes as a function of pulse duration, shape and energy. It is found that ionization is the main contributor to radiation damage in certain photon energy and intensity ranges, and diffusion depending on heating is dominant in other scenarios. In femtosecond protein crystallography, self-gating of Bragg diffraction is predicted to quench the signal from the latest parts of an X-ray pulse. At high intensities ionization is dominant and the last part of the pulse will contain less information at low resolution. At lower intensities, displacement will dominate and high resolution information will be gated first. Temporal pulse shape is also an important factor. The difference between pulse shapes is most prominent at low photon energy in the form of a general increase or decrease in signal, but the resolution dependance is most prominent at high energies. When investigating the X-ray scattering from water a simple diffusion model can be replaced by a molecular dynamics simulation, which predicts structural changes in water on femtosecond timescales. Experiments performed at LCLS are presented that supports the simulation results on structural changes that occur in the solvent during the exposure.

Place, publisher, year, edition, pages
Uppsala universitet, 2016.
National Category
Biophysics Atom and Molecular Physics and Optics
Research subject
Physics with specialization in Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-294553OAI: oai:DiVA.org:uu-294553DiVA: diva2:930559
Presentation
2016-06-14, 80121, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 15:19 (English)
Opponent
Supervisors
Available from: 2016-05-27 Created: 2016-05-24 Last updated: 2016-05-27Bibliographically approved
List of papers
1. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
Open this publication in new window or tab >>Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
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2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, 256-266 p.Article in journal (Refereed) Published
Abstract [en]

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 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs 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. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.

Keyword
X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
Available from: 2015-02-25 Created: 2015-02-25 Last updated: 2016-05-27Bibliographically approved
2. Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
Open this publication in new window or tab >>Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
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2015 (English)In: Optics Express, ISSN 1094-4087, Vol. 23, no 2, 1213-1231 p.Article in journal (Refereed) Published
Abstract [en]

In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

Keyword
Ultrafast lasers, UV, EUV, and X-ray lasers, X-ray imaging, Diffraction theory, Ultrafast phenomena
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-242136 (URN)10.1364/OE.23.001213 (DOI)000349166100061 ()
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2015-01-21 Created: 2015-01-21 Last updated: 2016-05-27Bibliographically approved
3. Ultrafast non-thermal heating of water
Open this publication in new window or tab >>Ultrafast non-thermal heating of water
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(English)Manuscript (preprint) (Other academic)
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-294554 (URN)
Available from: 2016-05-24 Created: 2016-05-24 Last updated: 2016-05-27

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Jönsson, H. Olof
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