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  • 1.
    Caleman, Carl
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, Hamburg, Germany.
    Jönsson, Olof
    KTH Royal Inst Technol, Dept Appl Phys, S-10691 Stockholm, Sweden.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala Univ, Dept Phys & Astron, Box 516, Uppsala, Sweden.
    Ultrafast dynamics of water exposed to XFEL pulses2019In: Optics Damage and Materials Processing by EUV/X-ray Radiation VII / [ed] Juha, L Bajt, S Guizard, S, SPIE - International Society for Optical Engineering, 2019, article id 1103507Conference paper (Refereed)
    Abstract [en]

    These proceedings investigate the ionization and temperature dynamics of water samples exposed to intense ultrashort X-ray free-electron laser pulses ranging from 10(4) - 10(7) J/cm(2), based on simulations using a non-local thermodynamic plasma code. In comparison to earlier work combining simulations and experiments, a regime where a hybrid simulations approach should be applicable is presented.

  • 2.
    Jönsson, H. Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    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.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Scott, Howard A.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Simulations of Radiation Damage as a Function of the Temporal Pulse Profile in Femtosecond X-ray Protein Crystallography2015In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, p. 256-266Article in journal (Refereed)
    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.

  • 3.
    Jönsson, Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala university.
    Scott, Howard A.
    Lawrence Livermore National Laboratory, Livermore, California, USA.
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Hamburg, Germany.
    Aplin, Steve J.
    Center for Free-Electron Laser Science, DESY, Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography2018In: High Energy Density Physics, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed)
    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.

  • 4.
    Jönsson, Olof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Scott, Howard A.
    Lawrence Livermore Natl Lab, Livermore, CA 94550 USA.
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany;Univ Hamburg, Dept Phys, Luruper Chaussee 149, DE-22761 Hamburg, Germany;Univ Hamburg, Ctr Ultrafast Imaging, Luruper Chaussee 149, DE-22761 Hamburg, Germany.
    Aplin, Steve J.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    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.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
    FreeDam: A webtool for free-electron laser-induced damage in femtosecond X-ray crystallography2018In: HIGH ENERGY DENSITY PHYSICS, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed)
    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.

  • 5.
    Sanchez-Gonzalez, A.
    et al.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Barillot, T. R.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Squibb, R. J.
    Univ Gothenburg, Dept Phys, SE-41296 Gothenburg, Sweden..
    Kolorenc, P.
    Charles Univ Prague, Fac Math & Phys, Inst Theoret Phys, CR-18000 Prague, Czech Republic..
    Agåker, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Averbukh, V.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Bearpark, M. J.
    Univ London Imperial Coll Sci Technol & Med, Dept Chem, London SW7 2AZ, England..
    Bostedt, C.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Bozek, J. D.
    SOLEIL Synchrotron, PLEIADES Beamline, LOrme Merisiers, F-91192 Gif Sur Yvette, France..
    Bruce, S.
    Univ Texas, Texas Ctr High Energy Dens Sci CHEDS, Austin, TX 78712 USA..
    Montero, S. Carron
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Coffee, R. N.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Cooper, B.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Cryan, J. P.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Dong, Minjie
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Eland, J. H. D.
    Univ Oxford, Dept Chem, Oxford OX1 3QZ, England..
    Fang, L.
    Univ Texas, Texas Ctr High Energy Dens Sci CHEDS, Austin, TX 78712 USA..
    Fukuzawa, H.
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan..
    Guehr, M.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Ilchen, M.
    European XFEL GmbH, D-22761 Hamburg, Germany..
    Johnsson, A. S.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Liekhus-S, C.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Stanford Univ, Dept Phys, Stanford, CA 94305 USA.;Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA..
    Marinelli, A.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Maxwell, T.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Motomura, K.
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan..
    Mucke, Melanie
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Natan, A.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Stanford Univ, Dept Phys, Stanford, CA 94305 USA.;Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA..
    Osipov, T.
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA..
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Pernpointner, M.
    Heidelberg Univ, Theoret Chem, D-69120 Heidelberg, Germany..
    Petrovic, V. S.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Stanford Univ, Dept Phys, Stanford, CA 94305 USA.;Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA..
    Robb, M. A.
    Univ London Imperial Coll Sci Technol & Med, Dept Chem, London SW7 2AZ, England..
    Sathe, C.
    Lund Univ, MAX IV Lab, SE-22100 Lund, Sweden..
    Simpson, E. R.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Underwood, J. G.
    UCL, Dept Phys & Astron, London WC1E 6BT, England..
    Vacher, Morgane
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ London Imperial Coll Sci Technol & Med, Dept Chem, London SW7 2AZ, England..
    Walke, D. J.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Wolf, T. J. A.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA..
    Zhaunerchyk, V.
    Univ Gothenburg, Dept Phys, SE-41296 Gothenburg, Sweden..
    Rubensson, Jan-Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Berrah, N.
    Western Michigan Univ, Dept Phys, Kalamazoo, MI 49008 USA..
    Bucksbaum, P. H.
    SLAC Natl Accelerator Lab, PULSE Inst, Menlo Pk, CA 94025 USA.;Stanford Univ, Dept Phys, Stanford, CA 94305 USA.;Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA..
    Ueda, K.
    Tohoku Univ, Inst Multidisciplinary Res Adv Mat, Sendai, Miyagi 9808577, Japan..
    Feifel, R.
    Univ Gothenburg, Dept Phys, SE-41296 Gothenburg, Sweden..
    Frasinski, L. J.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Marangos, J. P.
    Univ London Imperial Coll Sci Technol & Med, Blackett Lab, London SW7 2AZ, England..
    Auger Electron and Photoabsorption Spectra of Glycine in the Vicinity of the Oxygen K-edge Measured with an X-FEL2015In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 48, no 23, article id 234004Article in journal (Refereed)
    Abstract [en]

    We report the first measurement of the near oxygen K-edge auger spectrum of the glycine molecule. Our work employed an x-ray free electron laser as the photon source operated with input photon energies tunable between 527 and 547 eV. Complete electron spectra were recorded at each photon energy in the tuning range, revealing resonant and non-resonant auger structures. Finally ab initio theoretical predictions are compared with the measured above the edge auger spectrum and an assignment of auger decay channels is performed.

  • 6.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Advances in Biomolecular Imaging with X-ray Free-Electron Lasers2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Utilizing X-rays to solve molecular structures has proven to be an immensely powerful and im- portant scientific technique. The invention of X-ray crystallography has allowed for countless breakthroughs in chemistry, biology and material science and remains the number one method used for structural determination today. Of particular interest is the structures of biomolecules, such as proteins, due to their medical relevance. Unfortunately, the need for crystals of sufficient size constitutes the biggest drawback to this approach. This is troubling since many of the im- portant biomolecules, in particular membrane proteins, have proven to be difficult or sometimes even impossible to crystalize. When limited to a small nanocrystal or even a single particle, con- ventional crystallography is no longer adequate to probe the structure at high enough resolution. Recent developments, most notably the introduction of X-ray free-electron lasers (XFELs), have opened up new possibilities for circumventing these limitations. The high intensities and ultra- short pulse lengths provided by XFELs allows for diffractive imaging of smaller crystals through Serial Femtosecond Crystallography (SFX) and can even be extended to single molecules, Single Particle Imaging (SPI). These methods are still in their infancies, and much research and refine- ment is needed before they can be properly established.

    The current work covers fundamental studies of X-ray interaction with biomatter carried out to aid and improve upon SFX and SPI. Three papers based on computer simulation studies are presented, related to mainly two central aspects faced when imaging molecules with XFELs. Pa- per I explores a novel approach using explosion mapping to facilitate spatial orientation of single particles, which is necessary to reconstruct the three dimensional structure from two dimensional diffraction patterns. Paper II concerns radiation damage of the sample in SFX experiments using a plasma model and studies the impact of different pulse profiles on these processes. Lastly, pa- per III outlines the details of an online database available to researchers worldwide that contains simulated data on damage development in samples exposed to an XFEL pulse.

    In the first study, molecular dynamics was adopted to map the XFEL-induced Coulomb explo- sions in SPI for biomolecules. Four proteins were investigated, each with three different levels of hydration, and it was found that explosion patterns for both carbon and sulfur ions are re- producible for all twelve systems. However, water bound to the protein surface seems to have a shielding effect on carbons, causing their trajectories to be favored toward the exposed parts of the sample. This complicates the adoption for orientation determination as the water content would have to be known. Sulfurs, on the other hand, showed no signs of water dependence and consistently produced similar explosion patterns regardless of hydration level. We speculate that this is because of their higher mass and ionization cross section and conclude that mapping of heavier ions could provide valuable information for spatial orientation.

    In the second study, radiation damage in terms of ionization and atomic displacement within a nanometer-sized crystal illuminated by an XFEL pulse was explored with a non-local thermody- namic equilibrium plasma code. Different temporal distributions of the same number of photons was employed to assess its impact of damage dynamics. The results show that the pulse profile is substantially important. A front-loaded pulse is more beneficial for imaging purposes since the bulk of the photons encounters an undamaged sample. If the majority of photons instead arrive late, early photons will already have initiated the crystal decay causing further contribution to the diffraction pattern to be degraded.

    In the third study, the free-electron laser damage simulation database (FreeDam) was estab- lished. It presents simulated time-resolved data for average ionization, ion and electron temper- atures and atomic displacement for various materials and XFEL parameters. Simulations were carried out using the same code as in paper II, and the data is freely available online.

    This thesis is aimed to provide one of the stepping stones toward atomic resolution imaging of nanocrystals and single particles with free-electron lasers. If realized, these techniques could well turn out to be one of the greatest scientific achievements of the 21th century.

    List of papers
    1. Reproducibility of Single Protein Explosions Induced by X-ray Lasers
    Open this publication in new window or tab >>Reproducibility of Single Protein Explosions Induced by X-ray Lasers
    Show others...
    2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed) Published
    Abstract [en]

    Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

    Keywords
    XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-329340 (URN)10.1039/C7CP07267H (DOI)000431825300006 ()
    Funder
    Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation
    Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2019-04-28Bibliographically 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
    Show others...
    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: 2019-04-28
    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
    Show others...
    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: 2019-04-28
  • 7.
    Östlin, Christofer
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Simulations of Biomolecular Fragmentation and Diffraction with Ultrafast X-ray Lasers2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Studies of biomolecules have recently seen substantial developments. New X-ray lasers allow for high-resolution imaging of protein crystals too small for conventional X-ray crystallography. Even structures of single particles have been determined at lower resolutions with these new sources. The secret lies in the ultrashort high-intensity pulses, which allow for diffraction and retrieval of structural information before the sample gets fragmented. However, the attainable resolution is still limited, in particular when imaging non-crystalline samples, making further advancements highly desired. In this thesis, some of the resolution-limiting obstacles facing single particle imaging (SPI) of proteins are studied in silico.

    As the X-ray pulse interacts with injected single molecules, their spatial orientation is generally unknown. Recovering the orientation is essential to the structure determination process, and currently nontrivial. Molecular dynamics simulations show that the Coulomb explosion due to intense X-ray ionization could provide information pertaining to the original orientation. Used in conjunction with current methods, this would lead to an enhanced three-dimensional reconstruction of the protein.

    Radiation damage and sample heterogeneity constitute considerable sources of noise in SPI. Pulse durations are presently not brief enough to circumvent damage, causing the sample to deteriorate during imaging, and the accuracy of the averaged diffraction pattern is impaired by structural variations. The extent of these effects were studied by molecular dynamics. Our findings suggest that radiation damage in terms of ionization and atomic displacement promotes a gating mechanism, benefiting imaging with longer pulses. Because of this, sample heterogeneity poses a greater challenge and efforts should be made to minimize its impact.

    X-ray lasers generate pulses with a stochastic temporal distribution of photons, affecting the achievable resolution on a  pulse-to-pulse basis. Plasma simulations were performed to investigate how these fluctuations influence the damage dynamics and the diffraction signal. The results reveal that structural information is particularly well-preserved if the temporal distribution is skewed such that most photons are concentrated at the beginning.

    While many obstacles remain, the prospect of atomic-resolution SPI is drawing ever closer. This thesis is but one of the stepping stones necessary to get us there. Once we do, the possibilities are limitless.

    List of papers
    1. Reproducibility of Single Protein Explosions Induced by X-ray Lasers
    Open this publication in new window or tab >>Reproducibility of Single Protein Explosions Induced by X-ray Lasers
    Show others...
    2018 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed) Published
    Abstract [en]

    Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

    Keywords
    XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-329340 (URN)10.1039/C7CP07267H (DOI)000431825300006 ()
    Funder
    Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation
    Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2019-04-28Bibliographically approved
    2. Is Radiation Damage the Limiting Factor in Single Particle Imaging with X-ray Free-Electron Lasers?
    Open this publication in new window or tab >>Is Radiation Damage the Limiting Factor in Single Particle Imaging with X-ray Free-Electron Lasers?
    2019 (English)In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, article id 044103Article in journal (Refereed) Published
    Abstract [en]

    The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors of coherent diffractive imaging of single particles and that X-ray pulses need to be as short as possible. Based on molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

    Keywords
    X-ray free electron laser, XFEL, X-ray diffraction, Ultrafast imaging, Coherent diffractive imaging, CDI, Single particle imaging, Computer simulation, Molecular dynamics, GROMACS, Radiation damage, Coulomb explosion
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-382432 (URN)10.1063/1.5098309 (DOI)000492051300004 ()31463335 (PubMedID)
    Funder
    Swedish Research CouncilSwedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Swedish National Infrastructure for Computing (SNIC), snic2016-7-61
    Available from: 2019-04-25 Created: 2019-04-25 Last updated: 2019-11-15Bibliographically approved
    3. Sample Heterogeneity in Single Particle Imaging Using X-ray Lasers
    Open this publication in new window or tab >>Sample Heterogeneity in Single Particle Imaging Using X-ray Lasers
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    X-ray free-electron laser, XFEL, Coherent diffractive imaging, CDI, Molecular dynamics, Single particle imaging, X-ray diffraction, Sample heterogeneity, Noise
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-382437 (URN)
    Funder
    Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
    Available from: 2019-04-25 Created: 2019-04-25 Last updated: 2019-04-28
    4. 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
    Show others...
    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: 2019-04-28
    5. 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
    Show others...
    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: 2019-04-28
  • 8.
    Östlin, Christofer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Mandl, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Martin, Andrew
    School of Science, RMIT University, Melbourne, Australia .
    Caleman, C
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Hamburg, Germany.
    Sample Heterogeneity in Single Particle Imaging Using X-ray LasersManuscript (preprint) (Other academic)
  • 9.
    Östlin, Christofer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Hamburg, Germany .
    Martin, Andrew
    School of Science, RMIT University, Melbourne, Australia.
    Is Radiation Damage the Limiting Factor in Single Particle Imaging with X-ray Free-Electron Lasers?2019In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, article id 044103Article in journal (Refereed)
    Abstract [en]

    The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors of coherent diffractive imaging of single particles and that X-ray pulses need to be as short as possible. Based on molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

  • 10.
    Östlin, Christofer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Timneanu, Nicusor
    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.
    Jönsson, H. Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Martin, Andrew V.
    University of Melbourne, School of Physics, ARC Centre of Excellence for Advanced Molecular Imaging.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Center for Free-Electron Laser Science, DESY, Notkestraße 85, DE-22607 Hamburg, Germany .
    Reproducibility of Single Protein Explosions Induced by X-ray Lasers2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 18, p. 12381-12389Article in journal (Refereed)
    Abstract [en]

    Single particle imaging (SPI) using X-ray pulses has become increasingly attainable with the advent of high-intensity free electron lasers. Eliminating the need for crystallized samples enables structural studies of molecules previously inaccessible by conventional crystallography. While this emerging technique already demonstrates substantial promise, some obstacles need to be overcome before SPI can reach its full potential. One such problem is determining the spatial orientation of the sample at the time of X-ray interaction. Existing solutions rely on diffraction data and are computationally demanding and sensitive to noise. In this in silico study, we explore the possibility of aiding these methods by mapping the ion distribution as the sample undergoes a Coulomb explosion following the intense ionization. By detecting the ions ejected from the fragmented sample, the orientation of the original sample should be possible to determine. Knowledge of the orientation has been shown earlier to be of substantial advantage in the reconstruction of the original structure. 150 explosions of each of twelve separate systems – four polypeptides with different amounts of surface bound water – were simulated with molecular dynamics (MD) and the average angular distribution of carbon and sulfur ions was investigated independently. The results show that the explosion maps are reproducible in both cases, supporting the idea that orientation information is preserved. Additional water seems to restrict the carbon ion trajectories further through a shielding mechanism, making the maps more distinct. For sulfurs, water has no significant impact on the trajectories, likely due to their higher mass and greater ionization cross section, indicating that they could be of particular interest. Based on these findings, we conclude that explosion data can aid spatial orientation in SPI experiments and could substantially improve the capabilities of the novel technique.

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