uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Alternative names
Publications (10 of 79) Show all publications
Ho, P. J., Daurer, B. J., Hantke, M., Bielecki, J., Al Haddad, A., Bucher, M., . . . Bostedt, C. (2020). The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters. Nature Communications, 11, Article ID 167.
Open this publication in new window or tab >>The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters
Show others...
2020 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 11, article id 167Article in journal (Refereed) Published
Abstract [en]

Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments. X-ray free electron lasers provide high photon flux to explore single particle diffraction imaging of biological samples. Here the authors present dynamic electronic structure calculations and benchmark them to single-particle XFEL diffraction data of sucrose clusters to predict optimal single-shot imaging conditions.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2020
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-406723 (URN)10.1038/s41467-019-13905-9 (DOI)000510942100001 ()31919346 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilSwedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Wellcome trust, 204732/Z/16/Z
Available from: 2020-03-19 Created: 2020-03-19 Last updated: 2020-03-19Bibliographically approved
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
Show others...
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
Grånäs, O., Timneanu, N., Eliah Dawod, I., Ragazzon, D., Trygg, S., Souvatzis, P., . . . Caleman, C. (2019). Femtosecond bond breaking and charge dynamics in ultracharged amino acids. Journal of Chemical Physics, 151(14), Article ID 144307.
Open this publication in new window or tab >>Femtosecond bond breaking and charge dynamics in ultracharged amino acids
Show others...
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 14, article id 144307Article in journal (Refereed) Published
Abstract [en]

Historically, structure determination of nanocrystals, proteins, and macromolecules required the growth of high-quality crystals sufficiently large to diffract X-rays efficiently while withstanding radiation damage. The development of the X-ray free-electron laser has opened the path toward high resolution single particle imaging, and the extreme intensity of the X-rays ensures that enough diffraction statistics are collected before the sample is destroyed by radiation damage. Still, recovery of the structure is a challenge, in part due to the partial fragmentation of the sample during the diffraction event. In this study, we use first-principles based methods to study the impact of radiation induced ionization of six amino acids on the reconstruction process. In particular, we study the fragmentation and charge rearrangement to elucidate the time scales involved and the characteristic fragments occurring.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-395440 (URN)10.1063/1.5116814 (DOI)000500356200030 ()31615216 (PubMedID)
Funder
Swedish National Infrastructure for Computing (SNIC), SNIC 2019/8-30Swedish National Infrastructure for Computing (SNIC), SNIC 2018/3-221Swedish Research Council, 637-2013-7303Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research , ICA16-0037
Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2020-01-13Bibliographically approved
Östlin, C., Timneanu, N., Caleman, C. & Martin, A. (2019). Is Radiation Damage the Limiting Factor in Single Particle Imaging with X-ray Free-Electron Lasers?. Structural Dynamics, 6, Article ID 044103.
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
Caleman, C., Jönsson, O., Östlin, C. & Timneanu, N. (2019). Ultrafast dynamics of water exposed to XFEL pulses. In: Juha, L Bajt, S Guizard, S (Ed.), Optics Damage and Materials Processing by EUV/X-ray Radiation VII: . Paper presented at Conference on Optics Damage and Materials Processing by EUV/X-Ray Radiation VII, APR 01-03, 2019, Prague, CZECH REPUBLIC. SPIE - International Society for Optical Engineering, Article ID 1103507.
Open this publication in new window or tab >>Ultrafast dynamics of water exposed to XFEL pulses
2019 (English)In: 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, Published 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.

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2019
Series
Proceedings of SPIE, ISSN 0277-786X, E-ISSN 1996-756X ; 11035
Keywords
non-thermal processes, warm dense matter, ultrafast heating, X-ray lasers
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-396480 (URN)10.1117/12.2524199 (DOI)000489750600002 ()978-1-5106-2737-6 (ISBN)978-1-5106-2736-9 (ISBN)
Conference
Conference on Optics Damage and Materials Processing by EUV/X-Ray Radiation VII, APR 01-03, 2019, Prague, CZECH REPUBLIC
Funder
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2019-11-06 Created: 2019-11-06 Last updated: 2019-11-06Bibliographically 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
Show others...
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
Show others...
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
Show others...
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
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
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
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
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7328-0400

Search in DiVA

Show all publications