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Cardoch, Sebastian
Publications (7 of 7) Show all publications
Cardoch, S., Trost, F., Scott, H. A., Chapman, H. N., Caleman, C. & Timneanu, N. (2023). Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions. Physical review. E, 107(1), Article ID 015205.
Open this publication in new window or tab >>Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions
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2023 (English)In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 107, no 1, article id 015205Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Physical SocietyAmerican Physical Society (APS), 2023
National Category
Atom and Molecular Physics and Optics Fusion, Plasma and Space Physics
Identifiers
urn:nbn:se:uu:diva-495128 (URN)10.1103/physreve.107.015205 (DOI)000923229600007 ()
Funder
Swedish Research Council, 2019-03935Swedish Research Council, 2018-00740German Research Foundation (DFG), 390715994
Available from: 2023-01-24 Created: 2023-01-24 Last updated: 2024-01-15Bibliographically approved
Trost, F., Ayyer, K., Prasciolu, M., Fleckenstein, H., Barthelmess, M., Yefanov, O., . . . Chapman, H. (2023). Imaging via Correlation of X-Ray Fluorescence Photons. Physical Review Letters, 130(17), Article ID 173201.
Open this publication in new window or tab >>Imaging via Correlation of X-Ray Fluorescence Photons
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2023 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 130, no 17, article id 173201Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Physical Society, 2023
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-503245 (URN)10.1103/PhysRevLett.130.173201 (DOI)000979791600002 ()37172237 (PubMedID)
Funder
German Research Foundation (DFG), EXC 2056German Research Foundation (DFG), 390715994Swedish Research Council, 2018-00740Swedish Research Council, 2019-03935
Available from: 2023-06-14 Created: 2023-06-14 Last updated: 2023-06-14Bibliographically approved
Cardoch, S., Timneanu, N., Caleman, C. & Scheicher, R. H. (2022). Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study. ACS Nanoscience Au, 2(2), 119-127
Open this publication in new window or tab >>Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study
2022 (English)In: ACS Nanoscience Au, E-ISSN 2694-2496, Vol. 2, no 2, p. 119-127Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2022
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-495139 (URN)10.1021/acsnanoscienceau.1c00022 (DOI)001027123700001 ()37101662 (PubMedID)
Funder
Swedish Research Council, 2017-04627Swedish Research Council, 2018-00740Swedish Research Council, 2019-03935
Available from: 2023-01-24 Created: 2023-01-24 Last updated: 2023-10-09Bibliographically approved
Dawod, I., Patra Kumar, K., Cardoch, S., Jönsson, H. O., Sellberg, J. A., Martin, A. V., . . . Timneanu, N.Anisotropic melting of ice induced by ultrafast non-thermal heating.
Open this publication in new window or tab >>Anisotropic melting of ice induced by ultrafast non-thermal heating
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(English)Manuscript (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.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-519477 (URN)
Projects
In thesis
Funder
Swedish Research Council, 2017-05128, 2018-00740, 2019-03935Carl Tryggers foundation , CTS 18:392The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
André, T., Dawod, I., Cardoch, S., Timneanu, N. & Caleman, C.Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular Dynamics.
Open this publication in new window or tab >>Macromolecule classification using X-ray laser induced fragmentation simulated with hybrid Monte Carlo/Molecular Dynamics
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(English)Manuscript (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.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-519565 (URN)
Projects
In thesis
Funder
Swedish Research Council, 2018-00740, 2019-03935, 2021-05988
Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
Dawod, I., Cardoch, S., André, T., De Santis, E., E, J., Mancuso, A. P., . . . Timneanu, N.MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics.
Open this publication in new window or tab >>MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
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(English)Manuscript (preprint) (Other academic)
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 computed based on changes to their electronic occupations and the free electron cloud created due to 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, which reduces the number of non-bonded interactions required to compute. In combination with parallelization through domain decomposition, large-scale molecular dynamics and ionization induced by X-ray lasers can be followed. 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 show several examples of the applicability of the method and we quantify the sizes that the method is suitable for. For large systems, we investigate non-thermal heating and scattering of bulk water, which we compare to previous experiments. We simulate molecular dynamics of a protein crystal induced by an X-ray pump, X-ray probe scheme, and find good agreement of the damage dynamics with experiments. For single particle imaging, we simulate 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 X-ray probe setup to understand the evolution of radiation damage.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-519450 (URN)
Projects
In thesis
Funder
Swedish Research Council, 2018- 00740, 2019-03935
Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-09
Galchenkova, M., Dawod, I., Sprenger, J., Oberthur, D., Cardoch, S., De Santis, E., . . . Yefanov, O.Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laser.
Open this publication in new window or tab >>Radiation damage in a hemoglobin crystal studied with an X-ray free-electron laser
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(English)Manuscript (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.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-519591 (URN)
Projects
In thesis
Funder
Swedish Research Council, 2018-00740, 2019-03935
Available from: 2024-01-08 Created: 2024-01-08 Last updated: 2024-01-18
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