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Publications (10 of 94) Show all publications
Svensson, P., Schwob, L., Grånäs, O., Unger, I., Björneholm, O., Timneanu, N., . . . Berholts, M. (2024). Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics. Physical Chemistry, Chemical Physics - PCCP, 26(2), 770-779
Open this publication in new window or tab >>Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics
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2024 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 2, p. 770-779Article in journal (Refereed) Published
Abstract [en]

The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2024
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-522697 (URN)10.1039/d3cp03800a (DOI)001090175100001 ()37888897 (PubMedID)
Funder
Swedish Research Council, 2019-03935Swedish Research Council, 2017-05128Swedish Research Council, 2018-00740Swedish Foundation for Strategic ResearchSwedish National Infrastructure for Computing (SNIC), 2022/1-36Swedish National Infrastructure for Computing (SNIC), 2022/22-597
Available from: 2024-02-08 Created: 2024-02-08 Last updated: 2024-02-08Bibliographically approved
Ekeberg, T., Assalauova, D., Bielecki, J., Boll, R., Daurer, B. J., Eichacker, L. A., . . . Maia, F. R. N. (2024). Observation of a single protein by ultrafast X-ray diffraction. Light: Science & Applications, 13(1), Article ID 15.
Open this publication in new window or tab >>Observation of a single protein by ultrafast X-ray diffraction
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2024 (English)In: Light: Science & Applications, ISSN 2095-5545, E-ISSN 2047-7538, Vol. 13, no 1, article id 15Article in journal (Refereed) Published
Abstract [en]

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

Place, publisher, year, edition, pages
Springer Nature, 2024
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-520488 (URN)10.1038/s41377-023-01352-7 (DOI)001142025600001 ()38216563 (PubMedID)
Funder
German Research Foundation (DFG), 152/772-1German Research Foundation (DFG), 152/774-1German Research Foundation (DFG), 152/775-1German Research Foundation (DFG), 152/776-1German Research Foundation (DFG), 152/777-1German Research Foundation (DFG), 390715994EU, European Research Council, 614507European Regional Development Fund (ERDF), CZ.02.1.01/0.0/0.0/15_003/0000447Swedish Research Council, 2017-05336Swedish Research Council, 2018-00234Swedish Research Council, 2019-03935Swedish Foundation for Strategic Research, ITM17-0455
Available from: 2024-01-12 Created: 2024-01-12 Last updated: 2024-01-30Bibliographically approved
Kierspel, T., Kadek, A., Barran, P., Bellina, B., Bijedic N, A., Brodmerkel, M. N., . . . Uetrecht, C. (2023). Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC. Analytical and Bioanalytical Chemistry, 415(18 SI), 4209-4220
Open this publication in new window or tab >>Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC
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2023 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, no 18 SI, p. 4209-4220Article in journal (Refereed) Published
Abstract [en]

MS SPIDOC is a novel sample delivery system designed for single (isolated) particle imaging at X-ray Free-Electron Lasers that is adaptable towards most large-scale facility beamlines. Biological samples can range from small proteins to MDa particles. Following nano-electrospray ionization, ionic samples can be m/z-filtered and structurally separated before being oriented at the interaction zone. Here, we present the simulation package developed alongside this prototype. The first part describes how the front-to-end ion trajectory simulations have been conducted. Highlighted is a quadrant lens; a simple but efficient device that steers the ion beam within the vicinity of the strong DC orientation field in the interaction zone to ensure spatial overlap with the X-rays. The second part focuses on protein orientation and discusses its potential with respect to diffractive imaging methods. Last, coherent diffractive imaging of prototypical T = 1 and T = 3 norovirus capsids is shown. We use realistic experimental parameters from the SPB/SFX instrument at the European XFEL to demonstrate that low-resolution diffractive imaging data (q < 0.3 nm−1) can be collected with only a few X-ray pulses. Such low-resolution data are sufficient to distinguish between both symmetries of the capsids, allowing to probe low abundant species in a beam if MS SPIDOC is used as sample delivery.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
SPI, X-ray, Native MS, Protein complex structure, Viral particles, Simulation, Modeling
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-500359 (URN)10.1007/s00216-023-04658-y (DOI)000963181300001 ()37014373 (PubMedID)
Funder
Swedish Research Council, 2018-00740Swedish Research Council, 2020-04825EU, Horizon 2020, 801406
Available from: 2023-04-14 Created: 2023-04-14 Last updated: 2024-01-26Bibliographically approved
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
Trost, F., Ayyer, K., Oberthuer, D., Yefanov, O., Bajt, S., Caleman, C., . . . Chapman, H. N. (2023). Speckle contrast of interfering fluorescence X-rays. Journal of Synchrotron Radiation, 30(1), 11-23
Open this publication in new window or tab >>Speckle contrast of interfering fluorescence X-rays
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2023 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 30, no 1, p. 11-23Article in journal (Refereed) Published
Abstract [en]

With the development of X-ray free-electron lasers (XFELs), producing pulses of femtosecond durations comparable with the coherence times of X-ray fluorescence, it has become possible to observe intensity–intensity correlations due to the interference of emission from independent atoms. This has been used to compare durations of X-ray pulses and to measure the size of a focusedX-ray beam, for example. Here it is shown that it is also possible to observe the interference of fluorescence photons through the measurement of the speckle contrast of angle-resolved fluorescence patterns. Speckle contrast is often used as a measure of the degree of coherence of the incident beam or the fluctuations of the illuminated sample as determined from X-ray diffraction patterns formed by elastic scattering, rather than from fluorescence patterns as addressed here. Commonly used approaches to estimate speckle contrast were found to suffer when applied to XFEL-generated fluorescence patterns due to low photon counts and a significant variation of the excitation pulse energy from shot to shot. A new method to reliably estimate speckle contrast under such conditions, using a weighting scheme, is introduced. The method is demonstrated by comparing the speckle contrast of fluorescence observed with pulses of 3 fs to 15 fs duration.

Place, publisher, year, edition, pages
International Union Of CrystallographyInternational Union of Crystallography (IUCr), 2023
Keywords
speckle contrast estimation, X-ray fluorescence, incoherent diffraction imaging, XPCS
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-495130 (URN)10.1107/s1600577522009997 (DOI)000908417600002 ()36601922 (PubMedID)
Funder
German Research Foundation (DFG), 390715994Swedish Research Council, 2019-03935Swedish Research Council, 2018-00740
Available from: 2023-01-24 Created: 2023-01-24 Last updated: 2024-01-15Bibliographically 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
Eliah Dawod, I., Timneanu, N., Mancuso, A. P., Caleman, C. & Grånäs, O. (2022). Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides. Physical Chemistry, Chemical Physics - PCCP, 24(3), 1532-1543
Open this publication in new window or tab >>Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides
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2022 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 3, p. 1532-1543Article in journal (Refereed) Published
Abstract [en]

X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

Place, publisher, year, edition, pages
Royal Society of Chemistry (RSC), 2022
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-468649 (URN)10.1039/d1cp03419g (DOI)000733885500001 ()34939631 (PubMedID)
Funder
Swedish Research Council, 2018-05973Swedish Research Council, 2019-03935Swedish Research Council, 2018-00740Swedish Foundation for Strategic Research, ICA16-0037Swedish National Infrastructure for Computing (SNIC)
Available from: 2022-02-28 Created: 2022-02-28 Last updated: 2024-01-09Bibliographically approved
Patra Kumar, K., Dawod, I. E., Martin, A. V., Greaves, T. L., Persson, D., Caleman, C. & Timneanu, N. (2021). Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses. Paper presented at 11th International Workshop on X-Ray Radiation Damage to Biological Crystalline Samples, OCT 14-16, 2020, ELECTR NETWORK. Journal of Synchrotron Radiation, 28(5), 1296-1308
Open this publication in new window or tab >>Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses
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2021 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 28, no 5, p. 1296-1308Article in journal (Refereed) Published
Abstract [en]

X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.

Place, publisher, year, edition, pages
International Union Of CrystallographyINT UNION CRYSTALLOGRAPHY, 2021
Keywords
radiation damage, molecular dynamics, non-local thermodynamic equilibrium, protic ionic liquids, X-ray free-electron lasers
National Category
Atom and Molecular Physics and Optics Accelerator Physics and Instrumentation
Identifiers
urn:nbn:se:uu:diva-456491 (URN)10.1107/S1600577521007657 (DOI)000693111600005 ()34475279 (PubMedID)
Conference
11th International Workshop on X-Ray Radiation Damage to Biological Crystalline Samples, OCT 14-16, 2020, ELECTR NETWORK
Funder
Swedish Research Council, 2018-00740Swedish Research Council, 2019-3935Carl Tryggers foundation , CTS 18:392
Available from: 2021-10-19 Created: 2021-10-19 Last updated: 2024-01-15Bibliographically approved
Candanedo, J., Caleman, C., Timneanu, N., Beckstein, O. & Spence, J. C. (2020). Dynamics of rare gas solids irradiated by electron beams. Journal of Chemical Physics, 152(14), Article ID 144303.
Open this publication in new window or tab >>Dynamics of rare gas solids irradiated by electron beams
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2020 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 14, article id 144303Article in journal (Refereed) Published
Abstract [en]

The remarkable success of x-ray free-electron lasers and their ability to image biological macromolecules while outrunning secondary radiation damage due to photoelectrons, by using femtosecond pulses, raise the question of whether this can be done using pulsed high-energy electron beams. In this paper, we use excited state molecular dynamics simulations, with tabulated potentials, for rare gas solids to investigate the effect of radiation damage due to inelastic scattering (by plasmons, excitons, and heat) on the pair distribution function. We use electron energy loss spectra to characterize the electronic excitations responsible for radiation damage.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2020
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-410959 (URN)10.1063/1.5134801 (DOI)000526884700001 ()32295352 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2020-05-28 Created: 2020-05-28 Last updated: 2022-12-09Bibliographically approved
Projects
Explosions of Clusters in Intense X-ray Pulses [2009-07466_VR]; Uppsala UniversityNanocrystal imaging using intense and ultrashort X-ray pulses [2010-07395_VR]; Uppsala UniversityFIXED: Fluorescent Incoherent X-ray Emission and Diffraction to determine protein structures [2019-03935_VR]; Uppsala University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7328-0400

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