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Publications (10 of 75) Show all publications
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)
Open this publication in new window or tab >>Femtosecond bond breaking and charge dynamics in ultracharged amino acids
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2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 14Article 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.

Place, publisher, year, edition, pages
American Institute of Physics, 2019
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-395440 (URN)10.1063/1.5116814 (DOI)
Available from: 2019-10-18 Created: 2019-10-18 Last updated: 2019-10-18
Makita, M., Vartiainen, I., Mohacsi, I., Caleman, C., Diaz, A., Jönsson, O., . . . David, C. (2019). Femtosecond phase-transition in hard x-ray excited bismuth. Scientific Reports, 9, Article ID 602.
Open this publication in new window or tab >>Femtosecond phase-transition in hard x-ray excited bismuth
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2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 602Article in journal (Refereed) Published
Abstract [en]

The evolution of bismuth crystal structure upon excitation of its A(1g) phonon has been intensely studied with short pulse optical lasers. Here we present the first-time observation of a hard x-ray induced ultrafast phase transition in a bismuth single crystal at high intensities (similar to 10(14) W/cm(2)). The lattice evolution was followed using a recently demonstrated x-ray single-shot probing setup. The time evolution of the (111) Bragg peak intensity showed strong dependence on the excitation fluence. After exposure to a sufficiently intense x-ray pulse, the peak intensity dropped to zero within 300 fs, i.e. faster than one oscillation period of the A(1g) mode at room temperature. Our analysis indicates a nonthermal origin of a lattice disordering process, and excludes interpretations based on electron-ion equilibration process, or on thermodynamic heating process leading to plasma formation.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2019
National Category
Condensed Matter Physics Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-376819 (URN)10.1038/s41598-018-36216-3 (DOI)000456554600041 ()30679456 (PubMedID)
Funder
EU, FP7, Seventh Framework Programme, 290605Swedish Research Council, 2013-3940
Available from: 2019-02-18 Created: 2019-02-18 Last updated: 2019-02-18Bibliographically 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
Saak, C.-M., Unger, I., Brena, B., Caleman, C. & Björneholm, O. (2019). Site-specific X-ray induced dynamics in liquid methanol. Physical Chemistry, Chemical Physics - PCCP, 21(28), 15478-15486
Open this publication in new window or tab >>Site-specific X-ray induced dynamics in liquid methanol
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2019 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 28, p. 15478-15486Article in journal (Refereed) Published
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-391082 (URN)10.1039/C9CP02063B (DOI)000476603700022 ()31259327 (PubMedID)
Funder
Swedish Research Council, VR 2017-04162Swedish Research Council, VR 2018-00740Swedish Research Council, VR 2013-03940
Available from: 2019-08-18 Created: 2019-08-18 Last updated: 2019-09-24Bibliographically 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
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
Ghahremanpour, M. M., van Maaren, P. J., Caleman, C., Hutchison, G. R. & Van der Spoel, D. (2018). Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. Journal of Chemical Theory and Computation, 14(11), 5553-5566
Open this publication in new window or tab >>Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 11, p. 5553-5566Article in journal (Refereed) Published
Abstract [en]

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1s-Gaussian or a ns-Slater (n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library (https://doi.org/10.5281/zenodo.1004711) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-371548 (URN)10.1021/acs.jctc.8b00430 (DOI)000450695200011 ()30281307 (PubMedID)
Funder
Swedish Research Council, 2013-5947Swedish Research Council, SNIC2016/34-44
Available from: 2018-12-21 Created: 2018-12-21 Last updated: 2018-12-21Bibliographically approved
Ghahremanpour, M. M., van Maaren, P. J., Caleman, C., Hutchison, G. R. & Van der Spoel, D. (2018). Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. Journal of Chemical Theory and Computation
Open this publication in new window or tab >>Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-380336 (URN)10.1021/acs.jctc.8b00430 (DOI)
Available from: 2019-03-26 Created: 2019-03-26 Last updated: 2019-04-01
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
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-2638-1940

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