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Publications (10 of 76) Show all publications
Bielecki, J., Hantke, M. F., Daurer, B. J., Reddy, H. K. N., Hasse, D., Larsson, D. S. D., . . . Maia, F. R. N. (2019). Electrospray sample injection for single-particle imaging with x-ray lasers. Science Advances, 5(5), Article ID eaav8801.
Open this publication in new window or tab >>Electrospray sample injection for single-particle imaging with x-ray lasers
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2019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 5, article id eaav8801Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-387970 (URN)10.1126/sciadv.aav8801 (DOI)000470125000080 ()31058226 (PubMedID)
Available from: 2019-05-03 Created: 2019-06-27 Last updated: 2019-06-27Bibliographically approved
Pietrini, A., Bielecki, J., Timneanu, N., Hantke, M. F., Andreasson, J., Loh, N. D., . . . Nettelblad, C. (2018). A statistical approach to detect protein complexes at X-ray free electron laser facilities. Communications Physics, 1, 92:1-11, Article ID 92.
Open this publication in new window or tab >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
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2018 (English)In: Communications Physics, E-ISSN 2399-3650, Vol. 1, p. 92:1-11, article id 92Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
Projects
eSSENCE
Available from: 2018-12-07 Created: 2018-12-17 Last updated: 2019-05-06Bibliographically approved
Lundholm, I. V., Sellberg, J. A., Ekeberg, T., Hantke, M. F., Okamoto, K., van der Schot, G., . . . Maia, F. R. N. (2018). Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging. IUCrJ, 5, 531-541
Open this publication in new window or tab >>Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
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2018 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 5, p. 531-541Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-360034 (URN)10.1107/S2052252518010047 (DOI)000444010100003 ()
Projects
eSSENCE
Available from: 2018-09-01 Created: 2018-09-09 Last updated: 2019-07-01Bibliographically approved
Gorkhover, T., Ulmer, A., Ferguson, K., Bucher, M., Maia, F. R. N., Bielecki, J., . . . Bostedt, C. (2018). Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles [Letter to the editor]. Nature Photonics, 12, 150-153
Open this publication in new window or tab >>Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
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2018 (English)In: Nature Photonics, ISSN 1749-4885, E-ISSN 1749-4893, Vol. 12, p. 150-153Article in journal, Letter (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-345590 (URN)10.1038/s41566-018-0110-y (DOI)000426153800014 ()
Projects
eSSENCE
Available from: 2018-02-26 Created: 2018-03-09 Last updated: 2019-07-01Bibliographically approved
Jönsson, O., Östlin, C., Scott, H. A., Chapman, H., Aplin, S. J., Timneanu, N. & Caleman, C. (2018). FreeDam – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography. High Energy Density Physics, 26, 93-98
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: 2019-04-28
Jönsson, O., Östlin, C., Scott, H. A., Chapman, H., Aplin, S. J., Timneanu, N. & Caleman, C. (2018). FreeDam: A webtool for free-electron laser-induced damage in femtosecond X-ray crystallography. HIGH ENERGY DENSITY PHYSICS, 26, 93-98
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
Radiation damage, Non-local thermodynamic equilibrium, X-ray free-electron laser, Serial femtosecond X-ray crystallography
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-387471 (URN)10.1016/j.hedp.2018.02.004 (DOI)000428964400014 ()
Funder
Swedish Research Council, 20133940Swedish Foundation for Strategic Research , ICA10-0090The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Swedish National Infrastructure for Computing (SNIC), 2016-7-61
Available from: 2019-06-24 Created: 2019-06-24 Last updated: 2019-06-24Bibliographically approved
Östlin, C., Timneanu, N., Jönsson, H. O., Ekeberg, T., Martin, A. V. & Caleman, C. (2018). Reproducibility of Single Protein Explosions Induced by X-ray Lasers. Physical Chemistry, Chemical Physics - PCCP, 20(18), 12381-12389
Open this publication in new window or tab >>Reproducibility of Single Protein Explosions Induced by X-ray Lasers
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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
Beyerlein, K., Jönsson, O., Alonso-Mori, R., Aquila, A., Bajt, S., Barty, A., . . . Caleman, C. (2018). Ultrafast non-thermal heating of water initiated by an X-ray laser. Proceedings of the National Academy of Sciences of the United States of America, 115(22), 5652-5657
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
Daurer, B. J., Okamoto, K., Bielecki, J., Maia, F. R. N., Mühlig, K., Seibert, M. M., . . . Larsson, D. S. D. (2017). Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ, 4, 251-262
Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
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2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-323439 (URN)10.1107/S2052252517003591 (DOI)000400460500008 ()28512572 (PubMedID)
Projects
eSSENCE
Available from: 2017-04-07 Created: 2017-11-14 Last updated: 2019-07-01Bibliographically approved
Jönsson, H. O., Caleman, C., Andreasson, J. & Timneanu, N. (2017). Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission. IUCrJ, 4(6), 778-784
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7328-0400

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