http://uu.diva-portal.org/smash/person.jsf?pid=authority-person:11435
Caleman, C orcid.org/0000-0003-2638-1940
Caleman, Carl
Caleman, C.
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), Article ID 144307.
Open this publication in new window or tab >>Femtosecond bond breaking and charge dynamics in ultracharged amino acids
Grånäs, Oscar
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
Timneanu, Nicusor
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
Eliah Dawod, Ibrahim
Ragazzon, Davide
Trygg, Sebastian
Souvatzis, Petros
Edvinsson, Tomas
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
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
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.
urn:nbn:se:uu:diva-395440 (URN)10.1063/1.5116814 (DOI)000500356200030 ()31615216 (PubMedID)
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
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
Makita, M.
Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
Vartiainen, I.
Mohacsi, I.
Paul Scherrer Inst, CH-5232 Villigen, Switzerland;LOrme Merisiers, Synchrotron SOLEIL, F-91190 Saint Aubin, France.
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Deutsch Elektronen Synchrotron DESY, CFEL, D-22667 Hamburg, Germany.
Diaz, A.
Jönsson, Olof
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. KTH Royal Inst Technol, Dept Appl Phys, SE-10691 Stockholm, Sweden.
Juranic, P.
Medvedev, N.
Czech Acad Sci, Inst Phys, Prague 18221 8, Czech Republic;Czech Acad Sci, Inst Plasma Phys, Prague 18200 8, Czech Republic.
Meents, A.
Deutsch Elektronen Synchrotron DESY, CFEL, D-22667 Hamburg, Germany.
Mozzanica, A.
Opara, N. L.
Paul Scherrer Inst, CH-5232 Villigen, Switzerland;Univ Basel, C CINA Biozentrum, CH-4058 Basel, Switzerland.
Padeste, C.
Panneels, V.
Saxena, V.
Deutsch Elektronen Synchrotron DESY, CFEL, D-22667 Hamburg, Germany;Bhat, Inst Plasma Res, Gandhinagar 382428, India.
Sikorski, M.
SLAC Natl Accelerator Lab, Linac Coherent Light Source, Menlo Pk, CA 94025 USA.
Song, S.
Vera, L.
Willmott, P. R.
Beaud, P.
Milne, C. J.
Ziaja-Motyka, B.
Deutsch Elektronen Synchrotron DESY, CFEL, D-22667 Hamburg, Germany;Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
David, C.
2019 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 602Article in journal (Refereed) Published
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.
NATURE PUBLISHING GROUP, 2019
Condensed Matter Physics Physical Chemistry
urn:nbn:se:uu:diva-376819 (URN)10.1038/s41598-018-36216-3 (DOI)000456554600041 ()30679456 (PubMedID)
EU, FP7, Seventh Framework Programme, 290605Swedish Research Council, 2013-3940
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?
Östlin, Christofer
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.
2019 (English)In: Structural Dynamics, E-ISSN 2329-7778, Vol. 6, article id 044103Article in journal (Refereed) Published
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.
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
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
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
Saak, Clara-Magdalena
Unger, Isaak
Brena, Barbara
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, Deutsches Elektronen-Synchrotron, DE-22607 Hamburg, Germany.
Björneholm, Olle
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
urn:nbn:se:uu:diva-391082 (URN)10.1039/C9CP02063B (DOI)000476603700022 ()31259327 (PubMedID)
Swedish Research Council, VR 2017-04162Swedish Research Council, VR 2018-00740Swedish Research Council, VR 2013-03940
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
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.
KTH Royal Inst Technol, Dept Appl Phys, S-10691 Stockholm, Sweden.
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.
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)
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.
SPIE - International Society for Optical Engineering, 2019
Proceedings of SPIE, ISSN 0277-786X, E-ISSN 1996-756X ; 11035
non-thermal processes, warm dense matter, ultrafast heating, X-ray lasers
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 on Optics Damage and Materials Processing by EUV/X-Ray Radiation VII, APR 01-03, 2019, Prague, CZECH REPUBLIC
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
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
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.
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.
Caleman, C
2018 (English)In: High Energy Density Physics, ISSN 1574-1818, Vol. 26, p. 93-98Article in journal (Refereed) Published
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.
FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
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
Lawrence Livermore Natl Lab, Livermore, CA 94550 USA.
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.
DESY, Ctr Free Electron Laser Sci, Notkestr 85, DE-22607 Hamburg, Germany.
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.
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.
Radiation damage, Non-local thermodynamic equilibrium, X-ray free-electron laser, Serial femtosecond X-ray crystallography
urn:nbn:se:uu:diva-387471 (URN)10.1016/j.hedp.2018.02.004 (DOI)000428964400014 ()
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
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
Ghahremanpour, Mohammad M.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
van Maaren, Paul J.
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, DE-22607 Hamburg, Germany.
Hutchison, Geoffrey R.
Univ Pittsburgh, Dept Chem, Pittsburgh, PA 15260 USA.
Van der Spoel, David
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
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.
urn:nbn:se:uu:diva-371548 (URN)10.1021/acs.jctc.8b00430 (DOI)000450695200011 ()30281307 (PubMedID)
Swedish Research Council, 2013-5947Swedish Research Council, SNIC2016/34-44
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
Ghahremanpour, Mohammad Mehdi
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626Article in journal (Refereed) Published
urn:nbn:se:uu:diva-380336 (URN)10.1021/acs.jctc.8b00430 (DOI)
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
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
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.
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 .
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.
XFEL, Single-particle imaging, Coulomb explosion, ultrafast, GROMACS, simulation.
urn:nbn:se:uu:diva-329340 (URN)10.1039/C7CP07267H (DOI)000431825300006 ()
Swedish Research Council, 2013-3940Swedish Foundation for Strategic Research Carl Tryggers foundation
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology
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
ORCID iD: orcid.org/0000-0003-2638-1940
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