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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
Öppna denna publikation i ny flik eller fönster >>Heavy element incorporation in nitroimidazole radiosensitizers: molecular-level insights into fragmentation dynamics
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2024 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, nr 2, s. 770-779Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Royal Society of Chemistry, 2024
Nationell ämneskategori
Atom- och molekylfysik och optik
Identifikatorer
urn:nbn:se:uu:diva-522697 (URN)10.1039/d3cp03800a (DOI)001090175100001 ()37888897 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2019-03935Vetenskapsrådet, 2017-05128Vetenskapsrådet, 2018-00740Stiftelsen för strategisk forskning (SSF)Swedish National Infrastructure for Computing (SNIC), 2022/1-36Swedish National Infrastructure for Computing (SNIC), 2022/22-597
Tillgänglig från: 2024-02-08 Skapad: 2024-02-08 Senast uppdaterad: 2024-02-08Bibliografiskt granskad
Dawod, I., Cardoch, S., André, T., De Santis, E., E, J., Mancuso, A. P., . . . Timneanu, N. (2024). MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics. Journal of Chemical Physics, 160(18)
Öppna denna publikation i ny flik eller fönster >>MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics
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2024 (Engelska)Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 160, nr 18Artikel i tidskrift (Refereegranskat) Published
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.

Ort, förlag, år, upplaga, sidor
American Institute of Physics (AIP), 2024
Nationell ämneskategori
Atom- och molekylfysik och optik
Identifikatorer
urn:nbn:se:uu:diva-519450 (URN)10.1063/5.0197225 (DOI)001222371200003 ()
Forskningsfinansiär
Vetenskapsrådet, 2018- 00740Vetenskapsrådet, 2019-03935
Tillgänglig från: 2024-01-08 Skapad: 2024-01-08 Senast uppdaterad: 2024-06-18Bibliografiskt granskad
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.
Öppna denna publikation i ny flik eller fönster >>Observation of a single protein by ultrafast X-ray diffraction
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2024 (Engelska)Ingår i: Light: Science & Applications, ISSN 2095-5545, E-ISSN 2047-7538, Vol. 13, nr 1, artikel-id 15Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Springer Nature, 2024
Nationell ämneskategori
Biofysik
Identifikatorer
urn:nbn:se:uu:diva-520488 (URN)10.1038/s41377-023-01352-7 (DOI)001142025600001 ()38216563 (PubMedID)
Forskningsfinansiär
Deutsche Forschungsgemeinschaft (DFG), 152/772-1Deutsche Forschungsgemeinschaft (DFG), 152/774-1Deutsche Forschungsgemeinschaft (DFG), 152/775-1Deutsche Forschungsgemeinschaft (DFG), 152/776-1Deutsche Forschungsgemeinschaft (DFG), 152/777-1Deutsche Forschungsgemeinschaft (DFG), 390715994EU, Europeiska forskningsrådet, 614507Europeiska regionala utvecklingsfonden (ERUF), CZ.02.1.01/0.0/0.0/15_003/0000447Vetenskapsrådet, 2017-05336Vetenskapsrådet, 2018-00234Vetenskapsrådet, 2019-03935Stiftelsen för strategisk forskning (SSF), ITM17-0455
Tillgänglig från: 2024-01-12 Skapad: 2024-01-12 Senast uppdaterad: 2024-01-30Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Coherent diffractive imaging of proteins and viral capsids: simulating MS SPIDOC
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2023 (Engelska)Ingår i: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 415, nr 18 SI, s. 4209-4220Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Springer Nature, 2023
Nyckelord
SPI, X-ray, Native MS, Protein complex structure, Viral particles, Simulation, Modeling
Nationell ämneskategori
Biofysik
Identifikatorer
urn:nbn:se:uu:diva-500359 (URN)10.1007/s00216-023-04658-y (DOI)000963181300001 ()37014373 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2018-00740Vetenskapsrådet, 2020-04825EU, Horisont 2020, 801406
Tillgänglig från: 2023-04-14 Skapad: 2023-04-14 Senast uppdaterad: 2024-01-26Bibliografiskt granskad
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.
Öppna denna publikation i ny flik eller fönster >>Decreasing ultrafast x-ray pulse durations with saturable absorption and resonant transitions
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2023 (Engelska)Ingår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 107, nr 1, artikel-id 015205Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
American Physical SocietyAmerican Physical Society (APS), 2023
Nationell ämneskategori
Atom- och molekylfysik och optik Fusion, plasma och rymdfysik
Identifikatorer
urn:nbn:se:uu:diva-495128 (URN)10.1103/physreve.107.015205 (DOI)000923229600007 ()
Forskningsfinansiär
Vetenskapsrådet, 2019-03935Vetenskapsrådet, 2018-00740Deutsche Forschungsgemeinschaft (DFG), 390715994
Tillgänglig från: 2023-01-24 Skapad: 2023-01-24 Senast uppdaterad: 2024-01-15Bibliografiskt granskad
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.
Öppna denna publikation i ny flik eller fönster >>Imaging via Correlation of X-Ray Fluorescence Photons
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2023 (Engelska)Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 130, nr 17, artikel-id 173201Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
American Physical Society, 2023
Nationell ämneskategori
Atom- och molekylfysik och optik
Identifikatorer
urn:nbn:se:uu:diva-503245 (URN)10.1103/PhysRevLett.130.173201 (DOI)000979791600002 ()37172237 (PubMedID)
Forskningsfinansiär
Deutsche Forschungsgemeinschaft (DFG), EXC 2056Deutsche Forschungsgemeinschaft (DFG), 390715994Vetenskapsrådet, 2018-00740Vetenskapsrådet, 2019-03935
Tillgänglig från: 2023-06-14 Skapad: 2023-06-14 Senast uppdaterad: 2023-06-14Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Speckle contrast of interfering fluorescence X-rays
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2023 (Engelska)Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 30, nr 1, s. 11-23Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
International Union Of CrystallographyInternational Union of Crystallography (IUCr), 2023
Nyckelord
speckle contrast estimation, X-ray fluorescence, incoherent diffraction imaging, XPCS
Nationell ämneskategori
Atom- och molekylfysik och optik
Identifikatorer
urn:nbn:se:uu:diva-495130 (URN)10.1107/s1600577522009997 (DOI)000908417600002 ()36601922 (PubMedID)
Forskningsfinansiär
Deutsche Forschungsgemeinschaft (DFG), 390715994Vetenskapsrådet, 2019-03935Vetenskapsrådet, 2018-00740
Tillgänglig från: 2023-01-24 Skapad: 2023-01-24 Senast uppdaterad: 2024-01-15Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study
2022 (Engelska)Ingår i: ACS Nanoscience Au, E-ISSN 2694-2496, Vol. 2, nr 2, s. 119-127Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
American Chemical Society (ACS), 2022
Nationell ämneskategori
Den kondenserade materiens fysik
Identifikatorer
urn:nbn:se:uu:diva-495139 (URN)10.1021/acsnanoscienceau.1c00022 (DOI)001027123700001 ()37101662 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2017-04627Vetenskapsrådet, 2018-00740Vetenskapsrådet, 2019-03935
Tillgänglig från: 2023-01-24 Skapad: 2023-01-24 Senast uppdaterad: 2023-10-09Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Imaging of femtosecond bond breaking and charge dynamics in ultracharged peptides
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2022 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, nr 3, s. 1532-1543Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
Royal Society of Chemistry (RSC), 2022
Nationell ämneskategori
Fysikalisk kemi
Identifikatorer
urn:nbn:se:uu:diva-468649 (URN)10.1039/d1cp03419g (DOI)000733885500001 ()34939631 (PubMedID)
Forskningsfinansiär
Vetenskapsrådet, 2018-05973Vetenskapsrådet, 2019-03935Vetenskapsrådet, 2018-00740Stiftelsen för strategisk forskning (SSF), ICA16-0037Swedish National Infrastructure for Computing (SNIC)
Tillgänglig från: 2022-02-28 Skapad: 2022-02-28 Senast uppdaterad: 2024-01-09Bibliografiskt granskad
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
Öppna denna publikation i ny flik eller fönster >>Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses
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2021 (Engelska)Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 28, nr 5, s. 1296-1308Artikel i tidskrift (Refereegranskat) 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.

Ort, förlag, år, upplaga, sidor
International Union Of CrystallographyINT UNION CRYSTALLOGRAPHY, 2021
Nyckelord
radiation damage, molecular dynamics, non-local thermodynamic equilibrium, protic ionic liquids, X-ray free-electron lasers
Nationell ämneskategori
Atom- och molekylfysik och optik Acceleratorfysik och instrumentering
Identifikatorer
urn:nbn:se:uu:diva-456491 (URN)10.1107/S1600577521007657 (DOI)000693111600005 ()34475279 (PubMedID)
Konferens
11th International Workshop on X-Ray Radiation Damage to Biological Crystalline Samples, OCT 14-16, 2020, ELECTR NETWORK
Forskningsfinansiär
Vetenskapsrådet, 2018-00740Vetenskapsrådet, 2019-3935Carl Tryggers stiftelse för vetenskaplig forskning , CTS 18:392
Tillgänglig från: 2021-10-19 Skapad: 2021-10-19 Senast uppdaterad: 2024-01-15Bibliografiskt granskad
Projekt
Experiment avseende Klusterexplosion med röntgenlaser, SLAC National Accelerator Laboratory, Stanford university, USA, november 2009. [2009-07466_VR]; Uppsala universitetExperimenttid vid SLAC, Stanford university [2010-07395_VR]; Uppsala universitetFIXED: Fluorescens Icke-koherent eXtrem röntgenstrålning Emission och Diffraktion för bestämning av proteinstrukturer [2019-03935_VR]; Uppsala universitet; Publikationer
Dawod, I., Cardoch, S., André, T., De Santis, E., E, J., Mancuso, A. P., . . . Timneanu, N. (2024). MolDStruct: modelling the dynamics and structure of matter exposed to ultrafast X-ray lasers with hybrid collisional-radiative/molecular dynamics. Journal of Chemical Physics, 160(18)
Organisationer
Identifikatorer
ORCID-id: ORCID iD iconorcid.org/0000-0001-7328-0400

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