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Sökning: WFRF:(Andreasson Jakob)

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1.
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2.
  • Andreasson, Jakob, et al. (författare)
  • Automated identification and classification of single particle serial femtosecond X-ray diffraction data
  • 2014
  • Ingår i: Optics Express. - 1094-4087. ; 22:3, s. 2497-2510
  • Tidskriftsartikel (refereegranskat)abstract
    • The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of America
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3.
  • Andreasson, Jakob, 1975 (författare)
  • Avoided crossing of rattler modes in thermoelectric materials
  • 2008
  • Ingår i: Nature materials. ; 7, s. 811-815
  • Tidskriftsartikel (refereegranskat)abstract
    • Engineering of materials with specific physical properties has recently focused on the effect of nano-sized ‘guest domains’ in a‘host matrix’ that enable tuning of electrical, mechanical, photo-optical or thermal properties. A low thermal conductivity is aprerequisite for obtaining effective thermoelectric materials, and the challenge is to limit the conduction of heat by phonons, withoutsimultaneously reducing the charge transport. This is named the ‘phonon glass–electron crystal’ concept and may be realized inhost–guest systems. The guest entities are believed to have independent oscillations, so-called rattlermodes,which scatter the acousticphonons and reduce the thermal conductivity. We have investigated the phonon dispersion relation in the phonon glass–electroncrystal material Ba8Ga16Ge30 using neutron triple-axis spectroscopy. The results disclose unambiguously the theoretically predictedavoided crossing of the rattler modes and the acoustic-phonon branches. The observed phonon lifetimes are longer than expected,and a new explanation for the low L is provided.
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4.
  • Andreasson, Jakob, 1975, et al. (författare)
  • Electron-lattice interactions in the perovskite LaFe0.5Cr0.5O3 characterized by optical spectroscopy and LDA plus U calculations
  • 2009
  • Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X .- 2469-9950 .- 2469-9969. ; 80:7, s. 075103-
  • Tidskriftsartikel (refereegranskat)abstract
    • We use resonance Raman scattering (incident photon energies between 1.8 and 4.13 eV), LDA+U calculations, spectroscopic ellipsometry, and oblique IR reflectivity to characterize the strong electron-phonon interactions in the disordered perovskite LaFe0.5Cr0.5O3. When the photon energy coincides with a Cr to Fe Mott-Hubbard transfer gap around 2.4 eV the electron-phonon interaction is manifested by a Franck-Condon effect with exceptional first-and higher order scattering of a local oxygen breathing mode. At higher incident energies we observe a superposition of Franck-Condon scattering and Frohlich interaction induced infrared active longitudinal optical two-phonon scattering activated mainly by O to Fe charge transfer. Our results establish LaFe0.5Cr0.5O3 as a model compound for research on electron-phonon interactions in strongly correlated complex systems and show that Franck-Condon scattering in complex solids is not limited to Jahn-Teller active compounds.
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5.
  • Andreasson, Jakob, 1975, et al. (författare)
  • Electron-phonon interactions in perovskites containing Fe and Cr studied by Raman scattering using oxygen-isotope and cation substitution
  • 2008
  • Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X .- 2469-9950 .- 2469-9969. ; 78:23, s. 235103-
  • Tidskriftsartikel (refereegranskat)abstract
    • We use temperature-dependent inelastic light scattering to study the origin of the strong multiphonon scattering of a local oxygen breathing mode present in the mixed B-site orthorhombic (space group Pnma) perovskite LaFe0.5Cr0.5O3 but absent in isostructural LaFeO3 and LaCrO3. It is seen that the multiphonon scattering is critically sensitive to the presence of both Fe and Cr ions on the B site. These results support our interpretation that the multiphonon scattering is activated by local electron-phonon interactions according to the Franck-Condon picture following an Fe-Cr charge transfer. Further, O-18 substitution is performed on the x=0, 0.04, and 0.5 compounds and clearly shows that all modes appearing above the first-order phonon-scattering region in these compounds originate from higher-order oxygen stretching vibrations. In particular this is the case for the strong second-order scattering dominating the scattering response in LaFeO3. Accordingly we propose that these modes are generated by infrared-active longitudinal optical (IR LO) two-phonon and combination scattering activated by Frohlich interaction. For x=0.02 and 0.04 the characteristic IR LO two-phonon and Franck-Condon multiphonon-scattering profiles mix. We also study the influence of isovalent cation substitution and Sr doping in AFe(0.5)Cr(0.5)O(3) (A=La, Nd, and Gd) and La1-ySryFe0.5Cr0.5O3-delta (y=0, 0.16, and 0.5) on the strong electron-phonon coupling present in LaFe0.5Cr0.5O3. The Franck-Condon effect in LaFe0.5Cr0.5O3, is not significantly affected by isovalent A-site substitution, despite the increasing orthorhombic distortion associated with decreasing A-site ionic radii. On the contrary, aliovalent Sr doping causes a rapid decrease in the Franck-Condon scattering. This shows that the strong electron-phonon coupling in these compounds is highly sensitive to local lattice and electronic decoherence but insensitive to global lattice distortions. Finally, a preliminary assignment of the A(g) and B-2g phonon modes in AFe(0.5)Cr(0.5)O(3) (A=La, Nd, and Gd) is made based on the present observations and published results for LaCrO3 and AMnO(3). The modes associated with oxygen octahedral tilt and bending vibrations are heavily influenced by the magnitude of the orthorhombic distortion.
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6.
  • Andreasson, Jakob, 1975 (författare)
  • Electron-Phonon Interactions in Transition Metal Oxides Studied by Resonance Raman Scattering
  • 2008
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • In this thesis, studies of strong electron-phonon interactions in a number of transition metal oxides are presented. Two different electron-phonon interaction mechanisms are identified; Franck-Condon scattering and infrared active longitudinal optical (IR LO) two-phonon activation. The main experimental technique used is temperature dependent resonance Raman scattering and the electron-phonon interactions are studied by the resonant effects they cause on the first and higher order Raman active phonon scattering.The mixed transition metal oxide LaFe$_{0.5}$Cr$_{0.5}$O$_{3}$ with orthorhombic perovskite structure has been studied in detail using resonance Raman scattering with incident photon energies between $\hbar\omega$=1.83 ($\lambda$=676 nm) and $\hbar\omega$=4.13 eV ($\lambda$=300 nm) and variable temperatures. It is established that the characteristic Franck-Condon multi-phonon scattering of a local oxygen breathing mode appears as the photon energy is tuned to the Fe-Cr charge transfer gaps. This interpretation is supported by results obtained from LaFe$_{1-x}$Cr$_{x}$O$_{3}$ (0$\leq$x$\leq$1) which show that the Franck-Condon resonance is critically sensitive to the presence of both Fe and Cr ions in the structure and by Sr-doping in La$_{1-x}$Sr$_{x}$Fe$_{0.5}$Cr$_{0.5}$O$_{3-\delta}$ which shows that the Franck-Condon resonance is sensitive to local effects. In addition to the Franck-Condon effect, Fr\"ohlich interaction induced IR LO two-phonon scattering is observed in the perovskites LaFeO$_{3}$ using $\lambda$=515 nm ($\hbar\omega$=2.41 eV) and LaFe$_{0.5}$Cr$_{0.5}$O$_{3}$ using $\lambda$=334 nm ($\hbar\omega$=3.71 eV). Interestingly, these different resonance effects can be made to mix either by an introduction of a small amount of Cr in LaFeO$_{3}$ or by incident photon energy tuning in LaFe$_{0.5}$Cr$_{0.5}$O$_{3}$The results in the perovskites are complemented by observations in the spin ladder compound Sr$_{14}$Cu$_{24}$O$_{41}$ where an IR LO two-phonon resonance is activated for incident photon energies around the 1.8 eV charge transfer gap. In the spin ladder compound this resonance is linked to the formation of a charge density wave in the copper-oxide ladder layers below T=200 K.In combination, these observations illustrate the complexity of electron-phonon interactions in transition metal oxides and further establish resonance Raman scattering (in particular the higher order phonon scattering) as a sensitive probe of electron-phonon interactions and the relation between local and global effects in correlated material systems.
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7.
  • Andreasson, Jakob, 1975, et al. (författare)
  • Franck-Condon higher order lattice excitations in the LaFe(1-x)Cr(x)O3 (x=0, 0.1, 0.5, 0.9, 1.0) perovskites due to Fe-Cr charge transfer effects
  • 2007
  • Ingår i: Physical Review B. ; 75, s. 104302-
  • Tidskriftsartikel (refereegranskat)abstract
    • First and higher order lattice excitiations in the B-site disordered perovskites LaFe(1-x)Cr(x)O3 (x = 0, 0.1, 0.5, 0.9, 1) and La(0.835)Sr(0.165)Fe(0.5)Cr(0.5)O(3-d) are investigated using temperature dependent and polarised inelastic light scattering [lambda = 515 nm (2.41 eV) and 676 nm (1.83 eV)] on oriented crystallites.A peak at approximately 2.4 eV in the imaginary part of the dielectric function of LaFe(0.5)Cr(0.5)O3 is assigned to a charge transfer from Fe 3+ (d5) to Cr 3+ (d3) ions and coupled the appearance of an intense Ag-like mode at approximately 700 cm-1 in the Raman data. This excitation is identified as a symmetric oxygen breathing mode activated by the Fe-Cr charge transfer through an orbital coupling mechanism. Higher order scattering (up to 7th order) of the intrinsic Raman active symmetric breathing mode is also explained by an orbital mediated, electron-phonon coupling, similar to the Franck-Condon effect observed in the Jahn-Teller active perovskite structured manganite LaMnO3. These results show that the Franck-Condon mechanism is a more common mechanism for resonant higher order scattering in solids than previously believed and propose the LaFe(1-x)Cr(x)O(3) system as a model system for electron-phonon coupling and higher order Raman scattering in solids.
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8.
  • Andreasson, Jakob, et al. (författare)
  • Franck-Condon higher order lattice excitations in the LaFe1-xCrxO3 (x=0, 0.1, 0.5, 0.9, 1.0) perovskites due to Fe-Cr charge transfer effects
  • 2007
  • Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75
  • Tidskriftsartikel (refereegranskat)abstract
    • First and higher order lattice excitations in the B-site disordered perovskites LaFe1-xCrxO3 (x=0, 0.1, 0.5, 0.9, and 1) and La0.835Sr0.165Fe0.5Cr0.5O3-delta are investigated using temperature dependent and polarized inelastic light scattering [lambda=515 nm (2.41 eV) and 676 nm (1.83 eV)] on oriented crystallites. A peak at approximately 2.4 eV in the imaginary part of the dielectric function of LaFe0.5Cr0.5O3 is assigned to a charge transfer from Fe3+ (d(5)) to Cr3+ (d(3)) ions, coupled with the appearance of an intense A(g)-like mode at approximately 700 cm(-1) in the Raman data. This excitation is identified as a symmetric oxygen breathing mode activated by the Fe-Cr charge transfer through an orbital coupling mechanism. Higher order scattering (up to seventh order) of the intrinsic Raman active symmetric breathing mode is also explained by an orbital-mediated electron-phonon coupling, similar to the Franck-Condon effect observed in the Jahn-Teller active-perovskite-structured manganite LaMaO(3). These results show that the Franck-Condon mechanism is a more common mechanism for resonant higher order scattering in solids than previously believed and propose the LaFe1-xCrxO3 system as a model system for electron-phonon coupling and higher order Raman scattering in solids.
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9.
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10.
  • Andreasson, Jakob, et al. (författare)
  • Saturated ablation in metal hydrides and acceleration of protons and deuterons to keV energies with a soft-x-ray laser
  • 2011
  • Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 83:1, s. 016403-
  • Tidskriftsartikel (refereegranskat)abstract
    • Studies of materials under extreme conditions have relevance to a broad area of research, including planetary physics, fusion research, materials science, and structural biology with x-ray lasers. We study such extreme conditions and experimentally probe the interaction between ultrashort soft x-ray pulses and solid targets (metals and their deuterides) at the FLASH free-electron laser where power densities exceeding 1017 W/cm2 were reached. Time-of-flight ion spectrometry and crater analysis were used to characterize the interaction. The results show the onset of saturation in the ablation process at power densities above 1016 W/cm2. This effect can be linked to a transiently induced x-ray transparency in the solid by the femtosecond x-ray pulse at high power densities. The measured kinetic energies of protons and deuterons ejected from the surface reach several keV and concur with predictions from plasma-expansion models. Simulations of the interactions were performed with a nonlocal thermodynamic equilibrium code with radiation transfer. These calculations return critical depths similar to the observed crater depths and capture the transient surface transparency at higher power densities.
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11.
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12.
  • Andreasson, Rolf, et al. (författare)
  • Solvability of Monge-Ampère equations and tropical affine structures on reflexive polytopes
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Given a reflexive polytope with a height function, we prove a necessary and sufficient condition for solvability of the associated Monge-Ampère equation. When the polytope is Delzant, solvability of this equation implies the metric SYZ conjecture for the corresponding family of Calabi-Yau hypersurfaces. We show how the location of the singularities in the tropical affine structure is determined by the PDE in the spirit of a free boundary problem and give positive and negative examples, demonstrating subtle issues with both solvability and properties of the singular set. We also improve on existing results regarding the SYZ conjecture for the Fermat family by showing regularity of the limiting potential.
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13.
  • Andrikopoulos, Prokopis C., et al. (författare)
  • Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations
  • 2020
  • Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 22:12, s. 6538-6552
  • Tidskriftsartikel (refereegranskat)abstract
    • Flavin mononucleotide (FMN) belongs to the large family of flavins, ubiquitous yellow-coloured biological chromophores that contain an isoalloxazine ring system. As a cofactor in flavoproteins, it is found in various enzymes and photosensory receptors, like those featuring the light-oxygen-voltage (LOV) domain. The photocycle of FMN is triggered by blue light and proceeds via a cascade of intermediate states. In this work, we have studied isolated FMN in an aqueous solution in order to elucidate the intrinsic electronic and vibrational changes of the chromophore upon excitation. The ultrafast transitions of excited FMN were monitored through the joint use of femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy encompassing a time window between 0 ps and 6 ns with 50 fs time resolution. Global analysis of the obtained transient visible absorption and transient Raman spectra in combination with extensive quantum chemistry calculations identified unambiguously the singlet and triplet FMN populations and addressed solvent dynamics effects. The good agreement between the experimental and theoretical spectra facilitated the assignment of electronic transitions and vibrations. Our results represent the first steps towards more complex experiments aimed at tracking structural changes of FMN embedded in light-inducible proteins upon photoexcitation.
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14.
  • Aquila, Andrew, et al. (författare)
  • Time-resolved protein nanocrystallography using an X-ray free-electron laser
  • 2012
  • Ingår i: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716
  • Tidskriftsartikel (refereegranskat)abstract
    • We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
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15.
  • Assalauova, Dameli, et al. (författare)
  • An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
  • 2020
  • Ingår i: IUCrJ. - 2052-2525. ; 7, s. 1102-1113
  • Tidskriftsartikel (refereegranskat)abstract
    • An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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16.
  • Barty, A., et al. (författare)
  • Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements
  • 2012
  • Ingår i: Nature Photonics. - 1749-4885 .- 1749-4893. ; 6:1, s. 35-40
  • Tidskriftsartikel (refereegranskat)abstract
    • X-ray free-electron lasers have enabled new approaches to the structural determination of protein crystals that are too small or radiation-sensitive for conventional analysis1. For sufficiently short pulses, diffraction is collected before significant changes occur to the sample, and it has been predicted that pulses as short as 10 fs may be required to acquire atomic-resolution structural information1, 2, 3, 4. Here, we describe a mechanism unique to ultrafast, ultra-intense X-ray experiments that allows structural information to be collected from crystalline samples using high radiation doses without the requirement for the pulse to terminate before the onset of sample damage. Instead, the diffracted X-rays are gated by a rapid loss of crystalline periodicity, producing apparent pulse lengths significantly shorter than the duration of the incident pulse. The shortest apparent pulse lengths occur at the highest resolution, and our measurements indicate that current X-ray free-electron laser technology5 should enable structural determination from submicrometre protein crystals with atomic resolution.
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17.
  • Bielecki, Johan, 1982, et al. (författare)
  • Electrospray sample injection for single-particle imaging with x-ray lasers
  • 2019
  • Ingår i: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:5
  • Tidskriftsartikel (refereegranskat)abstract
    • The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.
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18.
  • Budelmann, D., et al. (författare)
  • Antiferromagnetic and superconducting proximity effects in YBa2Cu3O7-delta/PrBa2Cu3O7-delta superlattices
  • 2003
  • Ingår i: Physical Review B Condensed Matter. - 0163-1829 .- 1095-3795. ; 67, s. 140507-
  • Tidskriftsartikel (refereegranskat)abstract
    • We investigate the interplay between the antiferromagnetic and superconducting order parameters in YBa2Cu3O7-delta/PrBa2Cu3O7-delta superlattices by inelastic light scattering. The ratio of superconducting to antiferromagnetic order is varied through different modulations 4/6, 4/9, and 4/12 of (Y/Pr)Ba2Cu3O7-delta layers. This allows us to identify the proximity effect of the superconducting order parameter into the antiferromagnetic barrier as signified, e.g., by the sharpening of the two-magnon excitation. This proximity effect as well as gap feature and phonon anomalies reveals the delicate interplay between superconducting and antiferromagnetic order parameters.
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19.
  • Chapman, Henry N, et al. (författare)
  • Femtosecond X-ray protein nanocrystallography.
  • 2011
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
  • Tidskriftsartikel (refereegranskat)abstract
    • X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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20.
  • Cryan, James P., et al. (författare)
  • Auger Electron Angular Distribution of Double Core-Hole States in the Molecular Reference Frame
  • 2010
  • Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 105:8, s. 083004-
  • Tidskriftsartikel (refereegranskat)abstract
    • The Linac Coherent Light Source free electron laser is a source of high brightness x rays, 2×1011 photons in a ∼5  fs pulse, that can be focused to produce double core vacancies through rapid sequential ionization. This enables double core vacancy Auger electron spectroscopy, an entirely new way to study femtosecond chemical dynamics with Auger electrons that probe the local valence structure of molecules near a specific atomic core. Using 1.1 keV photons for sequential x-ray ionization of impulsively aligned molecular nitrogen, we observed a rich single-site double core vacancy Auger electron spectrum near 413 eV, in good agreement with ab initio calculations, and we measured the corresponding Auger electron angle dependence in the molecular frame.
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21.
  • Cryan, J P, et al. (författare)
  • Molecular frame Auger electron energy spectrum from N2
  • 2012
  • Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:5, s. 055601-
  • Tidskriftsartikel (refereegranskat)abstract
    • Here we present the first angle-resolved, non-resonant (normal) Auger spectra for impulsively aligned nitrogen molecules. We have measured the angular pattern of Auger electron emission following K -shell photoionization by 1.1 keV photons from the Linac Coherent Light Source (LCLS). Using strong-field-induced molecular alignment to make molecular frame measurements is equally effective for both repulsive and quasi-bound final states. The capability to resolve Auger emission angular distributions in the molecular frame of reference provides a new tool for spectral assignments in congested Auger electron spectra that takes advantage of the symmetries of the final diction states. Based on our experimental results and theoretical predictions, we propose the assignment of the spectral features in the Auger electron spectrum.
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22.
  • Daurer, Benedikt J., et al. (författare)
  • Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
  • 2017
  • Ingår i: IUCrJ. - : INT UNION CRYSTALLOGRAPHY. - 2052-2525. ; 4, s. 251-262
  • Tidskriftsartikel (refereegranskat)abstract
    • This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of similar to 40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from similar to 35 to similar to 300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 * 10(12) photons per mu m(2) per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
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23.
  • Dicke, B., et al. (författare)
  • Transferring the entatic-state principle to copper photochemistry
  • 2018
  • Ingår i: Nature Chemistry. - : NATURE PUBLISHING GROUP. - 1755-4330 .- 1755-4349. ; 10:3, s. 355-362
  • Tidskriftsartikel (refereegranskat)abstract
    • The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex-with a specifically designed constraining ligand geometry-that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.
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24.
  • Dicke, B., et al. (författare)
  • Transferring the entatic-state principle to copper photochemistry
  • 2018
  • Ingår i: Nature Chemistry. - : Springer Science and Business Media LLC. - 1755-4349 .- 1755-4330. ; 10:3, s. 355-362
  • Tidskriftsartikel (refereegranskat)abstract
    • The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex-with a specifically designed constraining ligand geometry-that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.
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25.
  • Ekeberg, Tomas, et al. (författare)
  • Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
  • 2016
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.
  •  
26.
  • Ekeberg, Tomas, 1983-, et al. (författare)
  • Three-dimensional structure determination with an X-ray laser
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus. 
  •  
27.
  • Emminger, Carola, et al. (författare)
  • Analysis of temperature-dependent and time-resolved ellipsometry spectra of Ge
  • 2021
  • Konferensbidrag (refereegranskat)abstract
    • The dielectric function of Ge measured with static and time-resolved spectroscopic ellipsometry is analyzed using linear filtering techniques to investigate the temperature dependence of the direct band gap, as well as the temporal evolvement of critical points obtained from femtosecond pump-probe ellipsometry measurements.
  •  
28.
  • Emminger, Carola, et al. (författare)
  • Coherent acoustic phonon oscillations and transient critical point parameters of Ge from femtosecond pump‐probe ellipsometry
  • 2022
  • Ingår i: Physica Status Solidi - Rapid Research Letters. - : Wiley. - 1862-6254 .- 1862-6270. ; 16:7
  • Tidskriftsartikel (refereegranskat)abstract
    • The complex pseudodielectric function of Ge and Si from femtosecond pump-probe spectroscopic ellipsometry with 267, 400, and 800 nm pump-pulse wavelengths is analyzed by fitting analytical lineshapes to the second derivatives of the pseudodielectric function with respect to energy. This yields the critical point parameters (threshold energy, lifetime broadening, amplitude, and excitonic phase angle) of E1 and E1+Δ1 in Ge and E1 in Si as functions of delay time. Coherent longitudinal acoustic phonon oscillations with a period of about 11 ps are observed in the transient critical point parameters of Ge. From the amplitude of these oscillations, the laser-induced strain is found to be on the order of 0.1% for Ge measured with the 800 nm pump pulse, which is in reasonable agreement with the strain calculated from theory.
  •  
29.
  • Espinoza, Shirly, et al. (författare)
  • Characterization of the high harmonics source for the VUV ellipsometer at ELI Beamlines
  • 2020
  • Ingår i: Journal of Vacuum Science and Technology B. - : American Institute of Physics (AIP). - 2166-2746 .- 2166-2754. ; 38:2
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, the authors present the characterization experiments of a 20 fs vacuum ultraviolet beam from a high harmonic generation source. The beam hits a silicon sample and passes a triple reflection gold polarizer located inside an ultrahigh vacuum chamber. The polarizer’s Malus curve was obtained; the total acquisition time for each point of the curve was 30 s. This aims to be the first vacuum ultraviolet time-resolved user station dedicated to ellipsometry. The high harmonic beam is generated by a 12 mJ, 1 kHz, 20 fs, in-house-developed laser and detected by a back-illuminated charge-coupled device. 
  •  
30.
  • Espinoza, Shirly, et al. (författare)
  • Transient dielectric functions of Ge, Si, and InP from femtosecond pump-probe ellipsometry
  • 2019
  • Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 115:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Transient dielectric functions with a 120 fs time resolution of Ge, Si, and InP were acquired from 1.7 to 3.5eV with a femtosecond pump-probe rotating-compensator ellipsometer. The intensity of the pump laser (with 1.55, 3.10, or 4.65eV photon energy) was adjusted to create an initial near-surface carrier density of 10(20)cm(-3). In Ge, there is a significant (similar to 15%) decrease in the E-1 and E-1+Delta(1) critical point absorption and a Kramers-Kronig consistent change in the refractive index because photoexcited electrons at L block these transitions and reduce their amplitudes. Only a small redshift of the E-1 critical point is observed, which we attribute to lattice heating and exchange-correlation effects. Minimal changes were found for Si and InP, where electrons near Delta and Gamma do not participate in interband transitions between 1.7 and 3.5eV.
  •  
31.
  • Espinoza, S., et al. (författare)
  • User oriented end-station on VUV pump-probe magneto-optical ellipsometry at ELI beamlines
  • 2017
  • Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 421, s. 378-382
  • Tidskriftsartikel (refereegranskat)abstract
    • A state of the art ellipsometer for user operations is being implemented at ELI Beamlines in Prague, Czech Republic. It combines three of the most promising and exotic forms of ellipsometry: VUV, pump-probe and magneto-optical ellipsometry. This new ellipsometer covers a spectral operational range from the NIR up to the VUV, with high through-put between 1 and 40 eV. The ellipsometer also allows measurements of magneto-optical spectra with a 1 kHz switchable magnetic field of up to 1.5 T across the sample combining ellipsometry and Kerr spectroscopy measurements in an unprecedented spectral range. This form of generalized ellipsometry enables users to address diagonal and off-diagonal components of the dielectric tensor within one measurement. Pump-probe measurements enable users to study the dynamic behaviour of the dielectric tensor in order to resolve the time-domain phenomena in the femto to 100 ns range.
  •  
32.
  • Glownia, James M., et al. (författare)
  • Time-resolved pump-probe experiments at the LCLS
  • 2010
  • Ingår i: Optics Express. - 1094-4087. ; 18:17, s. 17620-17630
  • Tidskriftsartikel (refereegranskat)abstract
    • The first time-resolved x-ray/optical pump-probe experiments at the SLAC Linac Coherent Light Source (LCLS) used a combination of feedback methods and post-analysis binning techniques to synchronize an ultrafast optical laser to the linac-based x-ray laser. Transient molecular nitrogen alignment revival features were resolved in time-dependent x-ray-induced fragmentation spectra. These alignment features were used to find the temporal overlap of the pump and probe pulses. The strong-field dissociation of x-ray generated quasi-bound molecular dications was used to establish the residual timing jitter. This analysis shows that the relative arrival time of the Ti:Sapphire laser and the x-ray pulses had a distribution with a standard deviation of approximately 120 fs. The largest contribution to the jitter noise spectrum was the locking of the laser oscillator to the reference RF of the accelerator, which suggests that simple technical improvements could reduce the jitter to better than 50 fs.
  •  
33.
  • Gorkhover, Tais, et al. (författare)
  • Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
  • 2018
  • Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 12:3, s. 150-153
  • Tidskriftsartikel (refereegranskat)abstract
    • Ultrafast X-ray imaging on individual fragile specimens such as aerosols 1 , metastable particles 2 , superfluid quantum systems 3 and live biospecimens 4 provides high-resolution information that is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely defined 4,5 . Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lateral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond timescale.
  •  
34.
  • Hantke, Max F., et al. (författare)
  • A data set from flash X-ray imaging of carboxysomes
  • 2016
  • Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Tidskriftsartikel (refereegranskat)abstract
    • Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
  •  
35.
  • Hantke, Max F., et al. (författare)
  • High-throughput imaging of heterogeneous cell organelles with an X-ray laser
  • 2014
  • Ingår i: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 8:12, s. 943-949
  • Tidskriftsartikel (refereegranskat)abstract
    • We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.
  •  
36.
  • Hantke, Max Felix, et al. (författare)
  • Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams
  • 2018
  • Ingår i: IUCrJ. - 2052-2525. ; 5, s. 673-680
  • Tidskriftsartikel (refereegranskat)abstract
    • Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the 'Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100-500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
  •  
37.
  • Hau-Riege, Stefan P., et al. (författare)
  • Sacrificial Tamper Slows Down Sample Explosion in FLASH Diffraction Experiments
  • 2010
  • Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 104:6, s. 064801-
  • Tidskriftsartikel (refereegranskat)abstract
    • Intense and ultrashort x-ray pulses from free-electron lasers open up the possibility for near-atomic resolution imaging without the need for crystallization. Such experiments require high photon fluences and pulses shorter than the time to destroy the sample. We describe results with a new femtosecond pump-probe diffraction technique employing coherent 0.1 keV x rays from the FLASH soft x-ray free-electron laser. We show that the lifetime of a nanostructured sample can be extended to several picoseconds by a tamper layer to dampen and quench the sample explosion, making <1 nm resolution imaging feasible.
  •  
38.
  • Holmlund, Joakim, 1968, et al. (författare)
  • Resonant two-phonon Raman scattering as a probe of hole crystal formation in Sr14?xCaxCu24O41
  • 2006
  • Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 74
  • Tidskriftsartikel (refereegranskat)abstract
    • The charge dynamics of the spin ladder compound Sr14-xCaxCu24O41 with x=0,6,13.6 has been investigated using wavelength- and temperature-dependent phonon Raman scattering on single crystals. In the unsubstituted, x=0, compound, a set of sharp two-phonon lines shows a strong increase in intensity below T similar to 200 K for light polarized along the ladder layer and with excitation energy close to the charge transfer gap similar to 1.9 eV. The temperature dependence of the strongly enhanced two-phonon bands below 200 K closely follows the recently reported formation of a standing charge density wave in the ladders [P. Abbamonte , Nature 431, 1078 (2004)]. Upon calcium substitution the polarized resonant Raman response rapidly decreases, signaling an increase of hole mobility in the ladder units. Temperature-dependent measurements of the x=13.6 sample indicate mobility of holes down to
  •  
39.
  • Holmlund, Joakim, 1968, et al. (författare)
  • Two-magnon Raman scattering from the Cu3O4 layers in (Sr-2,Ba-2)Cu3O4Cl
  • 2009
  • Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969 .- 1098-0121 .- 1550-235X. ; 79:8
  • Tidskriftsartikel (refereegranskat)abstract
    • (Sr-2,Ba-2)Cu3O4Cl2 are antiferromagnetic insulators which are akin to the parent compounds of the cuprate superconductors but with two distinct magnetic ordering temperatures related to two magnetic Cu-I and Cu-II spin sublattices. Here we present a study of these materials by means of Raman spectroscopy. Following the temperature and polarization dependence of the data, we readily identify two distinct features at around 3000 and 300 cm(-1) that are related to two-magnon scattering from the two sublattices. The estimated spin-exchange coupling constants for the Cu-I and Cu-II sublattices are found to be J(I)similar to 139-143(132-136) meV and J(II)similar to 14 (11) meV for Sr(Ba) compounds. Moreover, we observe modes at around 480 and 445 cm(-1) for the Sr and Ba containing samples, respectively, which disappears at the ordering temperature of the Cu-II. We argue that these modes may also be of magnetic origin and possibly related to interband transitions between the Cu-I-Cu-II sublattices.
  •  
40.
  • Hort, O., et al. (författare)
  • ELI beamlines user oriented high-harmonic beamline
  • 2020
  • Ingår i: Optics InfoBase Conference Papers. - 2162-2701.
  • Konferensbidrag (refereegranskat)abstract
    • We present latest progress and experimental capabilities of user-oriented XUV beamline based on high harmonic generation (HHG). The focal length of the HHG was recently extended to 5 meters, upscaling the overall XUV photon flux.
  •  
41.
  • Hort, O., et al. (författare)
  • High-flux source of coherent XUV pulses for user applications
  • 2019
  • Ingår i: Optics Express. - 1094-4087 .- 1094-4087. ; 27:6, s. 8871-8883
  • Tidskriftsartikel (refereegranskat)abstract
    • We present experimental results obtained at a user-oriented XUV beamline implemented at the ELI Beamlines facility. The coherent XUV radiation is produced via high harmonic generation in gases in a loose focusing geometry. The heamline is designed to be driven by 1 kHz, 100 mJ, 20 Is pulses centered at a wavelength of 830 nm. Results such as XUV spectra, beam wavefront and pulse energy obtained during the heamline commissioning with a commercial 1 kHz, 5 mJ, 40 fs laser system are presented. A unique XUV spectrometer for source characterization designed to reach a very high sensitivity is described in detail, and we demonstrate a novel technique for single shot and every shot. XUV pulse energy measurement. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement.
  •  
42.
  • Iwan, Bianca, et al. (författare)
  • Explosion, ion acceleration and molecular fragmentation of methane clusters in the pulsed beam of a free-electron laser
  • 2012
  • Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 86:3, s. 033201-
  • Tidskriftsartikel (refereegranskat)abstract
    • X-ray lasers offer new possibilities for creating and probing extreme states of matter. We used intense and short x-ray pulses from the FLASH soft x-ray laser to trigger the explosions of CH4 and CD4 molecules and their clusters. The results show that the explosion dynamics depends on cluster size and indicate a transition from Coulomb explosion to hydrodynamic expansion in larger clusters. The explosion of CH4 and CD4 clusters shows a strong isotope effect: The heavier deuterons acquire higher kinetic energies than the lighter protons. This may be due to an extended inertial confinement of deuterons vs. protons near a rapidly charging cluster core during exposure.
  •  
43.
  • Iwan, Bianca S, et al. (författare)
  • TOF-OFF : A method for determining focal positions in tightly focused free-electron laser experiments by measurement of ejected ions
  • 2011
  • Ingår i: High Energy Density Physics. - : Elsevier BV. - 1574-1818. ; 7:4, s. 336-342
  • Tidskriftsartikel (refereegranskat)abstract
    • Pulse intensities greater than 1017 Watt/cm2 were reached at the FLASH soft X-ray laser in Hamburg, Germany, using an off-axis parabolic mirror to focus 15 fs pulses of 5–70 μJ energy at 13.5 nm wavelength to a micron-sized spot. We describe the interaction of such pulses with niobium and vanadium targets and their deuterides. The beam produced craters in the solid targets, and we measured the kinetic energy of ions ejected from these craters. Ions with several keV kinetic energy were observed from craters approaching 5 μm in depth when the sample was at best focus. We also observed the onset of saturation in both ion acceleration and ablation with pulse intensities exceeding 1016 W/cm2, when the highest detected ion energies and the crater depths tend to saturate with increasing intensity. A general difficulty in working with micron and sub-micron focusing optics is finding the exact focus of the beam inside a vacuum chamber. Here we propose a direct method to measure the focal position to a resolution better than the Rayleigh length. The method is based on the correlation between the energies of ejected ions and the physical dimensions of the craters. We find that the focus position can be quickly determined from the ion time-of-flight (TOF) data as the target is scanned through the expected focal region. The method does not require external access to the sample or venting the vacuum chamber. Profile fitting employed to analyze the TOF data can extend resolution beyond the actual scanning step size.
  •  
44.
  • Johansson, Linda C, 1983, et al. (författare)
  • Lipidic phase membrane protein serial femtosecond crystallography.
  • 2012
  • Ingår i: Nature methods. - : Springer Science and Business Media LLC. - 1548-7105 .- 1548-7091. ; 9:3, s. 263-265
  • Tidskriftsartikel (refereegranskat)abstract
    • X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.
  •  
45.
  • Jonsson, H. O., et al. (författare)
  • Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
  • 2017
  • Ingår i: IUCrJ. - : International Union of Crystallography (IUCr). - 2052-2525. ; 4, s. 778-784
  • Tidskriftsartikel (refereegranskat)abstract
    • Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.
  •  
46.
  • Jönsson, H. Olof, et al. (författare)
  • Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
  • 2017
  • Ingår i: IUCrJ. - 2052-2525. ; 4:6, s. 778-784
  • Tidskriftsartikel (refereegranskat)abstract
    • Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.
  •  
47.
  • Khakurel, Krishna P., et al. (författare)
  • Kilohertz Macromolecular Crystallography Using an EIGER Detector at Low X-ray Fluxes
  • 2020
  • Ingår i: Crystals. - : MDPI. - 2073-4352. ; 10:12
  • Tidskriftsartikel (refereegranskat)abstract
    • Time-resolved in-house macromolecular crystallography is primarily limited by the capabilities of the in-house X-ray sources. These sources can only provide a time-averaged structure of the macromolecules. A significant effort has been made in the development of in-house laser-driven ultrafast X-ray sources, with one of the goals as realizing the visualization of the structural dynamics of macromolecules at a very short timescale within the laboratory-scale infrastructure. Most of such in-house ultrafast X-ray sources are operated at high repetition rates and usually deliver very low flux. Therefore, the necessity of a detector that can operate at the repetition rate of the laser and perform extremely well under low flux conditions is essential. Here, we present experimental results demonstrating the usability of the hybrid-pixel detectors, such as Eiger X 1M, and provide experimental proof that they can be successfully operated to collect macromolecular crystallographic data up to a detector frame rate of 3 kHz from synchrotron sources. Our results also show that the data reduction and structural analysis are successful at such high frame rates and fluxes as low as 10(8) photons/s, which is comparable to the values expected from a typical laser-driven X-ray source.
  •  
48.
  • Khakurel, Krishna P., et al. (författare)
  • Macromolecular nanocrystal structural analysis with electron and X-rays: A comparative review
  • 2019
  • Ingår i: Molecules. - : MDPI AG. - 1420-3049 .- 1420-3049. ; 24:19
  • Forskningsöversikt (refereegranskat)abstract
    • Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
  •  
49.
  • Klimesova, Eva, et al. (författare)
  • A multipurpose end-station for atomic, molecular and optical sciences and coherent diffractive imaging at ELI beamlines
  • 2021
  • Ingår i: The European Physical Journal Special Topics. - : Springer Nature. - 1951-6355 .- 1951-6401. ; 230:23, s. 4183-4194
  • Tidskriftsartikel (refereegranskat)abstract
    • We report on the status of a users' end-station, MAC: a Multipurpose station for Atomic, molecular and optical sciences and Coherent diffractive imaging, designed for studies of structure and dynamics of matter in the femtosecond time-domain. MAC is located in the E1 experimental hall on the high harmonic generation (HHG) beamline of the ELI Beamlines facility. The extreme ultraviolet beam from the HHG beamline can be used at the MAC end-station together with a synchronized pump beam (which will cover the NIR/Vis/UV or THz range) for time-resolved experiments on different samples. Sample delivery systems at the MAC end-station include a molecular beam, a source for pure or doped clusters, ultrathin cylindrical or flat liquid jets, and focused beams of substrate-free nanoparticles produced by an electrospray or a gas dynamic virtual nozzle combined with an aerodynamic lens stack. We further present the available detectors: electron/ion time-of-flight and velocity map imaging spectrometers and an X-ray camera, and discuss future upgrades: a magnetic bottle electron spectrometer, production of doped nanodroplets and the planned developments of beam capabilities at the MAC end-station.
  •  
50.
  • Klimešová, Eva, et al. (författare)
  • Plasma channel formation in NIR laser-irradiated carrier gas from an aerosol nanoparticle injector
  • 2019
  • Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
  • Tidskriftsartikel (refereegranskat)abstract
    • © 2019, The Author(s). Aerosol nanoparticle injectors are fundamentally important for experiments where container-free sample handling is needed to study isolated nanoparticles. The injector consists of a nebuliser, a differential pumping unit, and an aerodynamic lens to create and deliver a focused particle beam to the interaction point inside a vacuum chamber. The tightest focus of the particle beam is close to the injector tip. The density of the focusing carrier gas is high at this point. We show here how this gas interacts with a near infrared laser pulse (800 nm wavelength, 120 fs pulse duration) at intensities approaching 1016 Wcm−2. We observe acceleration of gas ions to kinetic energies of 100s eV and study their energies as a function of the carrier gas density. Our results indicate that field ionisation by the intense near-infrared laser pulse opens up a plasma channel behind the laser pulse. The observations can be understood in terms of a Coulomb explosion of the created underdense plasma channel. The results can be used to estimate gas background in experiments with the injector and they open up opportunities for a new class of studies on electron and ion dynamics in nanoparticles surrounded by a low-density gas.
  •  
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