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Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses
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. (Molecular dynamics and structure)ORCID iD: 0000-0002-2076-0918
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. , p. 78
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1592
Keywords [en]
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: urn:nbn:se:uu:diva-331936ISBN: 978-91-513-0134-1 (print)OAI: oai:DiVA.org:uu-331936DiVA, id: diva2:1152670
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: 2018-03-07
List of papers
1. 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, E-ISSN 1094-4087, Vol. 23, no 2, p. 1213-1231Article 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.

Keywords
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: 2017-12-05Bibliographically approved
2. 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, p. 256-266Article 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.

Keywords
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: 2018-06-26
3. FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
Open this publication in new window or tab >>FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
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2018 (English)In: High Energy Density Physics, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed) Published
Abstract [en]

Over the last decade X-ray free-electron laser (XFEL) sources have been made available to the scientific community. One of the most successful uses of these new machines has been protein crystallography. When samples are exposed to the intense short X-ray pulses provided by the XFELs, the sample quickly becomes highly ionized and the atomic structure is affected. Here we present a webtool dubbed FreeDam based on non-thermal plasma simulations, for estimation of radiation damage in free-electron laser experiments in terms of ionization, temperatures and atomic displacements. The aim is to make this tool easily accessible to scientists who are planning and performing experiments at XFELs.

Keywords
FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329499 (URN)
Available from: 2017-09-17 Created: 2017-09-17 Last updated: 2018-06-26
4. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
Open this publication in new window or tab >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
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2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, p. 225-238Article in journal (Refereed) Published
Abstract [en]

Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

Keywords
free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
Available from: 2015-02-23 Created: 2015-02-23 Last updated: 2017-12-04Bibliographically approved
5. Ultrafast non-thermal heating of water initiated by an X-ray laser
Open this publication in new window or tab >>Ultrafast non-thermal heating of water initiated by an X-ray laser
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 22, p. 5652-5657Article in journal (Refereed) Published
Abstract [en]

X-ray Free-Electron Lasers have opened the door to a new era in structural biology, enabling imaging of biomolecules and dynamics that were impossible to access with conventional methods. A vast majority of imaging experiments, including Serial Femtosecond Crystallography, use a liquid jet to deliver the sample into the interaction region. We have observed structural changes in the carrying water during X-ray exposure, showing how it transforms from the liquid phase to a plasma. This ultrafast phase transition observed in water provides evidence that any biological structure exposed to these X-ray pulses is destroyed during the X-ray exposure.The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-294554 (URN)10.1073/pnas.1711220115 (DOI)000433283700046 ()29760050 (PubMedID)
Funder
Swedish Foundation for Strategic Research Swedish Research Council, 2013-3940The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Swedish National Infrastructure for Computing (SNIC)Carl Tryggers foundation
Note

De två första författarna delar förstaförfattarskapet

Available from: 2016-05-24 Created: 2016-05-24 Last updated: 2018-08-20Bibliographically approved
6. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
Open this publication in new window or tab >>Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 6, p. 778-784Article in journal (Refereed) Published
Abstract [en]

Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Keywords
hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
National Category
Biophysics
Research subject
Physics with specialization in Biophysics
Identifiers
urn:nbn:se:uu:diva-331934 (URN)10.1107/S2052252517014154 (DOI)000414266200011 ()29123680 (PubMedID)
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), 2016-7-61Swedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)ÅForsk (Ångpanneföreningen's Foundation for Research and Development)
Available from: 2017-10-25 Created: 2017-10-25 Last updated: 2018-02-05Bibliographically approved

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