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Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and condensed matter physics.
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2015 (English)In: Optics Express, ISSN 1094-4087, E-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.

Place, publisher, year, edition, pages
2015. Vol. 23, no 2, 1213-1231 p.
Keyword [en]
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: urn:nbn:se:uu:diva-242136DOI: 10.1364/OE.23.001213ISI: 000349166100061OAI: oai:DiVA.org:uu-242136DiVA: diva2:782467
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2015-01-21 Created: 2015-01-21 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
Open this publication in new window or tab >>Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
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:nbn:se:uu:diva-294553 (URN)
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
2. Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
Open this publication in new window or tab >>Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                   

We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.

The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.

Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.

The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2017. 78 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1592
Keyword
X-ray free-electron laser; Serial Femtosecond Crystallography; Radiation Damage; Plasma Simulations; Ultrafast Lasers; X-ray Imaging; Diffraction Theory; Ultrafast Phenomena; Hit Detection; Plasma Emission Spectra; Serial Femtosecond Crystallography; Protein Structure; Protein Crystallography; Metalloprotein; Non-thermal Heating; Water; Ferredoxin; NLTE Simulation; XFEL; FEL; SFX
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-331936 (URN)978-91-513-0134-1 (ISBN)
Public defence
2017-12-15, Polhemssalen, Lägerhyddsvägen 1, Uppsala, 09:15 (English)
Opponent
Supervisors
Funder
Swedish Foundation for Strategic Research , ICA10-0090Swedish Research Council, 2013-3940The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-11-22 Created: 2017-10-25 Last updated: 2017-11-22

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Caleman, CarlTimneanu, NicusorJönsson, H. Olof

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