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- Jönsson, Olof, 1985-
(författare)
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Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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| 2. |
- Jönsson, H. Olof, 1985-
(författare)
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Femtosecond Dynamics in Water and Biological Materials with an X-Ray Laser
- 2016
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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.
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