Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
Refine search result
1 - 7 of 7
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    André, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Dawod, Ibrahim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular DynamicsManuscript (preprint) (Other academic)
    Abstract [en]

    We have developed a hybrid Monte Carlo and classical molecular dynamics code to follow the ultrafast atomic dynamics in biological macromolecules induced by a femtosecond X-ray laser. Our model for fragmentation shows good qualitative agreement with ab-initio simulations of small molecules, while being computationally faster.  We applied the code for macromolecules and simulated the Coulomb explosion dynamics due to the fast ionization in six proteins with different physical properties. The trajectories of the ions are followed and projected onto a detector, where the particular pattern depends on the protein, providing a unique footprint. We utilize algorithms such as principal component analysis  and t-distributed stochastic neighbor embedding to classify the fragmentation pattern. The results show that the classification algorithms are able to separate the explosion patterns into distinct groups. We envision that this method could be used to provide additional class information, like particle mass or shape, in structural determination experiments using X-ray lasers.

  • 2.
    Cardoch, Sebastian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study2022In: ACS Nanoscience Au, E-ISSN 2694-2496, Vol. 2, no 2, p. 119-127Article in journal (Refereed)
    Abstract [en]

    A nanopore is a tool in single-molecule sensing biotechnology that offers label-free identification with high throughput. Nanopores have been successfully applied to sequence DNA and show potential in the study of proteins. Nevertheless, the task remains challenging due to the large variability in size, charges, and folds of proteins. Miniproteins have a small number of residues, limited secondary structure, and stable tertiary structure, which can offer a systematic way to reduce complexity. In this computational work, we theoretically evaluated sensing two miniproteins found in the human body using a silicon nitride nanopore. We employed molecular dynamics methods to compute occupied-pore ionic current magnitudes and electronic structure calculations to obtain interaction strengths between pore wall and miniprotein. From the interaction strength, we derived dwell times using a mix of combinatorics and numerical solutions. This latter approach circumvents typical computational demands needed to simulate translocation events using molecular dynamics. We focused on two miniproteins potentially difficult to distinguish owing to their isotropic geometry, similar number of residues, and overall comparable structure. We found that the occupied-pore current magnitudes not to vary significantly, but their dwell times differ by 1 order of magnitude. Together, these results suggest a successful identification protocol for similar miniproteins.

    Download full text (pdf)
    fulltext
  • 3.
    Cardoch, Sebastian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Trost, Fabian
    Scott, Howard A.
    Chapman, Henry N.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions2023In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 107, no 1, article id 015205Article in journal (Refereed)
    Abstract [en]

    Saturable absorption is a nonlinear effect where a material's ability to absorb light is frustrated due to a high influx of photons and the creation of electron vacancies. Experimentally induced saturable absorption in copper revealed a reduction in the temporal duration of transmitted x-ray laser pulses, but a detailed account of changes in opacity and emergence of resonances is still missing. In this computational work, we employ nonlocal thermodynamic equilibrium plasma simulations to study the interaction of femtosecond x rays and copper. Following the onset of frustrated absorption, we find that a K–M resonant transition occurring at highly charged states turns copper opaque again. The changes in absorption generate a transient transparent window responsible for the shortened transmission signal. We also propose using fluorescence induced by the incident beam as an alternative source to achieve shorter x-ray pulses. Intense femtosecond x rays are valuable to probe the structure and dynamics of biological samples or to reach extreme states of matter. Shortened pulses could be relevant for emerging imaging techniques.

    Download full text (pdf)
    fulltext
  • 4.
    Dawod, Ibrahim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    André, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    E, Juncheng
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany. Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics2024In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 160, no 18Article in journal (Refereed)
    Abstract [en]

    We describe a method to compute photon–matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.

    Download full text (pdf)
    fulltext
  • 5.
    Dawod, Ibrahim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Patra Kumar, Kajwal
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Jönsson, H. Olof
    Department of Applied physics, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
    Sellberg, Jonas A.
    Department of Applied physics, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
    Martin, Andrew V.
    School of Science, RMIT University, Melbourne, Victoria 3000, Australia.
    Binns, Jack
    School of Science, RMIT University, Melbourne, Victoria 3000, Australia.
    Grånäs, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Mancuso, Adrian P.
    European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany. Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia. Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK .
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85 DE-22607 Hamburg, Germany.
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Anisotropic melting of ice induced by ultrafast non-thermal heatingManuscript (preprint) (Other academic)
    Abstract [en]

    Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.

  • 6.
    Galchenkova, Marina
    et al.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Dawod, Ibrahim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. European XFEL, Holzkoppel 4, DE-22869 Schenefeld, Germany.
    Sprenger, Janina
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Oberthur, Dominik
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    De Santis, Emiliano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    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, Chemical and Bio-Molecular Physics.
    Chapman, Henry N.
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany. Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany. Department of Physics, Universität Hamburg, 22761 Hamburg, Germany .
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Yefanov, Oleksandr
    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestraße 85, DE-22607 Hamburg, Germany.
    Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laserManuscript (preprint) (Other academic)
    Abstract [en]

    Radiation damage is a topic since the dawn of X-ray crystallography, and has gained new importance in the era of X-ray free-electron lasers (XFELs), due to their unprecedented brilliance and pulse duration. One of the driving questions has been how short the XFEL pulse has to be for the structural information to be ”damage free”. Here we compare data from Serial Femtosecond Crystallography (SFX) experiments conducted with a 3 fs and a 10 fs X-ray pulse. We conclude that even if the estimated displacement of atoms in the sample is an order of magnitude larger in the case of the 10 fs experiment, the displacement is still too small to affect the experimental data at a resolution relevant for structural determination.

  • 7.
    Trost, Fabian
    et al.
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Ayyer, Kartik
    Max Planck Inst Struct & Dynam Matter, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Prasciolu, Mauro
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Barthelmess, Miriam
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Yefanov, Oleksandr
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Dresselhaus, J. Lukas
    Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Li, Chufeng
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Bait, Sasa
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Carnis, Jerome
    DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Wollweber, Tamme
    Max Planck Inst Struct & Dynam Matter, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Mall, Abhishek
    Max Planck Inst Struct & Dynam Matter, D-22607 Hamburg, Germany..
    Shen, Zhou
    Max Planck Inst Struct & Dynam Matter, D-22607 Hamburg, Germany..
    Zhuang, Yulong
    Max Planck Inst Struct & Dynam Matter, D-22607 Hamburg, Germany..
    Richter, Stefan
    Friedrich Alexander Univ Erlangen Nurnberg, Dept Phys, Staudtstr 1, D-91058 Erlangen, Germany.;Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Grad Sch Adv Opt Technol SAOT, Paul Gordan Str 6, D-91052 Erlangen, Germany..
    Karl, Sebastian
    Friedrich Alexander Univ Erlangen Nurnberg, Dept Phys, Staudtstr 1, D-91058 Erlangen, Germany..
    Cardoch, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Patra Kumar, Kajwal
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Moeller, Johannes
    European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany.
    Zozulya, Alexey
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Shayduk, Roman
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Lu, Wei
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Brausse, Felix
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Friedrich, Bertram
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Boesenberg, Ulrike
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Petrov, Ilia
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Tomin, Sergey
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Guetg, Marc
    DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Madsen, Anders
    European Xray Free Electron Laser Facil, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Timneanu, Nicusor
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Caleman, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany..
    Roehlsberger, Ralf
    DESY, Notkestr 85, D-22607 Hamburg, Germany.;Helmholtz Inst Jena, Frobelstieg 3, D-07743 Jena, Germany.;GSI Helmholtzzentrum Schwerionenforschung, Planckstr 1, D-62491 Jena, Germany.;Friedrich Schiller Univ Jena, Inst Opt & Quantenelektron, Max Wien Pl 1, D-07743 Jena, Germany..
    von Zanthier, Joachim
    Friedrich Alexander Univ Erlangen Nurnberg, Dept Phys, Staudtstr 1, D-91058 Erlangen, Germany.;Friedrich Alexander Univ Erlangen Nurnberg, Erlangen Grad Sch Adv Opt Technol SAOT, Paul Gordan Str 6, D-91052 Erlangen, Germany..
    Chapman, Henry
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. DESY, Ctr Free Electron Laser Sci CFEL, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Hamburg Ctr Ultrafast Imaging, Luruper Chaussee 149, D-22761 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22761 Hamburg, Germany..
    Imaging via Correlation of X-Ray Fluorescence Photons2023In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 130, no 17, article id 173201Article in journal (Refereed)
    Abstract [en]

    We demonstrate that x-ray fluorescence emission, which cannot maintain a stationary interference pattern, can be used to obtain images of structures by recording photon-photon correlations in the manner of the stellar intensity interferometry of Hanbury Brown and Twiss. This is achieved utilizing femtosecondduration pulses of a hard x-ray free-electron laser to generate the emission in exposures comparable to the coherence time of the fluorescence. Iterative phasing of the photon correlation map generated a model-free real-space image of the structure of the emitters. Since fluorescence can dominate coherent scattering, this may enable imaging uncrystallised macromolecules.

1 - 7 of 7
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf