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1.	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.
2.	Aquila, A., et al. (författare) The linac coherent light source single particle imaging road map 2015 Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4 Tidskriftsartikel (refereegranskat)abstract Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.
3.	Duane Loh, N., et al. (författare) Profiling structured beams using injected aerosols 2012 Ingår i: Proceedings of SPIE. - : SPIE. - 9780819492210 ; , s. 850403- Konferensbidrag (refereegranskat)abstract Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the beams in-situ profile is not directly accessible with imprint studies because the damage profile could be different from the actual beam profile. On the other hand, although a Shack-Hartmann sensor is capable of in-situ profiling, its lenses may be quickly damaged at the intense focus of hard X-ray FEL beams. We describe a new approach that probes the in-situ morphology of the intense FEL focus. By studying the translations in diffraction patterns from an ensemble of randomly injected sub-micron latex spheres, we were able to determine the non-Gaussian nature of the intense FEL beam at the Linac Coherent Light Source (SLAC National Laboratory) near the FEL focus. We discuss an experimental application of such a beam-profiling technique, and the limitations we need to overcome before it can be widely applied.
4.	Gomez, L. F., et al. (författare) Shapes and vorticities of superfluid helium nanodroplets 2014 Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 345:6199, s. 906-909 Tidskriftsartikel (refereegranskat)abstract Helium nanodroplets are considered ideal model systems to explore quantum hydrodynamics in self-contained, isolated superfluids. However, exploring the dynamic properties of individual droplets is experimentally challenging. In this work, we used single-shot femtosecond x-ray coherent diffractive imaging to investigate the rotation of single, isolated superfluid helium-4 droplets containing ~108 to 1011 atoms. The formation of quantum vortex lattices inside the droplets is confirmed by observing characteristic Bragg patterns from xenon clusters trapped in the vortex cores. The vortex densities are up to five orders of magnitude larger than those observed in bulk liquid helium. The droplets exhibit large centrifugal deformations but retain axially symmetric shapes at angular velocities well beyond the stability range of viscous classical droplets.
5.	Loh, N. D., et al. (författare) Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight 2012 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 486:7404, s. 513-517 Tidskriftsartikel (refereegranskat)abstract The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology(1) to climate science(2), yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate(3); visible light scattering provides insufficient resolution(4); and X-ray synchrotron studies have been limited to ensembles of particles(5). Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source(6) free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins(7), vibrational energy transfer by the hydrodynamic interaction of amino acids(8), and large-scale production of nanoscale structures by flame synthesis(9).
6.	Martin, A. V., et al. (författare) Femtosecond dark-field imaging with an X-ray free electron laser 2012 Ingår i: Optics Express. - 1094-4087. ; 20:12, s. 13501-13512 Tidskriftsartikel (refereegranskat)abstract The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.
7.	Martin, A. V., et al. (författare) Noise-robust coherent diffractive imaging with a single diffraction pattern 2012 Ingår i: Optics Express. - 1094-4087. ; 20:15, s. 16650-16661 Tidskriftsartikel (refereegranskat)abstract The resolution of single-shot coherent diffractive imaging at X-ray free-electron laser facilities is limited by the low signal-to-noise level of diffraction data at high scattering angles. The iterative reconstruction methods, which phase a continuous diffraction pattern to produce an image, must be able to extract information from these weak signals to obtain the best quality images. Here we show how to modify iterative reconstruction methods to improve tolerance to noise. The method is demonstrated with the hybrid input-output method on both simulated data and single-shot diffraction patterns taken at the Linac Coherent Light Source. (C) 2012 Optical Society of America
8.	Pedersoli, E., et al. (författare) Mesoscale morphology of airborne core-shell nanoparticle clusters : x-ray laser coherent diffraction imaging 2013 Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16 SI, s. 164033- Tidskriftsartikel (refereegranskat)abstract Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.
9.	Sanchez-Gonzalez, A., et al. (författare) Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning 2017 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8 Tidskriftsartikel (refereegranskat)abstract Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy, we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. This opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.
10.	Barillot, T., et al. (författare) Correlation-Driven Transient Hole Dynamics Resolved in Space and Time in the Isopropanol Molecule 2021 Ingår i: Physical Review X. - : American Physical Society. - 2160-3308. ; 11:3 Tidskriftsartikel (refereegranskat)abstract The possibility of suddenly ionized molecules undergoing extremely fast electron hole (or hole) dynamics prior to significant structural change was first recognized more than 20 years ago and termed charge migration. The accurate probing of ultrafast electron hole dynamics requires measurements that have both sufficient temporal resolution and can detect the localization of a specific hole within the molecule. We report an investigation of the dynamics of inner valence hole states in isopropanol where we use an x-ray pump-x-ray probe experiment, with site and state-specific probing of a transient hole state localized near the oxygen atom in the molecule, together with an ab initio theoretical treatment. We record the signature of transient hole dynamics and make the first tentative observation of dynamics driven by frustrated Auger-Meitner transitions. We verify that the effective hole lifetime is consistent with our theoretical prediction. This state-specific measurement paves the way to widespread application for observations of transient hole dynamics localized in space and time in molecules and thus to charge transfer phenomena that are fundamental in chemical and material physics.
11.	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.
12.	Bolognesi, P., et al. (författare) A study of the dynamical energy flow in uracil 2015 Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 635 Tidskriftsartikel (refereegranskat)abstract The time resolved photoionization of C 1s in uracil following excitation of the neutral molecule by 260 nm pulses has been studied at LCLS.
13.	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.
14.	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.
15.	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.
16.	Rohringer, N., et al. (författare) Stimulated X-Ray Raman Scattering with Free-Electron Laser Sources 2016 Ingår i: X-Ray Lasers 2014. - Cham : Springer. - 0930-8989. - 9783319195216 - 9783319195209 ; , s. 201-207 Bokkapitel (refereegranskat)abstract Stimulated electronic x-ray Raman scattering is the building block for several proposed x-ray pump probe techniques, that would allow the study of electron dynamics at unprecedented timescales.We present high spectral resolution data on stimulated electronic x-ray Raman scattering in a gas sample of neon using a self-amplified spontaneous emission x-ray free-electron laser. Despite the limited spectral coherence and broad bandwidth of these sources, high-resolution spectra can be obtained by statistical methods, opening the path to coherent stimulated x-ray Raman spectroscopy. An extension of these ideas to molecules and the results of a recent experiment in CO are discussed.
17.	Rolles, D., et al. (författare) Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules 2014 Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 47:12 Tidskriftsartikel (refereegranskat)abstract We present time-resolved femtosecond photoelectron momentum images and angular distributions of dissociating, laser-aligned 1,4-dibromobenzene (C6H4Br2) molecules measured in a near-infrared pump, soft-x-ray probe experiment performed at an x-ray free-electron laser. The observed alignment dependence of the bromine 2p photoelectron angular distributions is compared to density functional theory calculations and interpreted in terms of photoelectron diffraction. While no clear time-dependent effects are observed in the angular distribution of the Br(2p) photoelectrons, other, low-energy electrons show a pronounced dependence on the time delay between the near-infrared laser and the x-ray pulse.
18.	Sanchez-Gonzalez, A., et al. (författare) Auger electron and photoabsorption spectra of glycine in the vicinity of the oxygen K-edge measured with an X-FEL 2015 Ingår i: Journal of Physics B-Atomic Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 48:23 Tidskriftsartikel (refereegranskat)abstract We report the first measurement of the near oxygen K-edge auger spectrum of the glycine molecule. Our work employed an x-ray free electron laser as the photon source operated with input photon energies tunable between 527 and 547 eV. Complete electron spectra were recorded at each photon energy in the tuning range, revealing resonant and non-resonant auger structures. Finally ab initio theoretical predictions are compared with the measured above the edge auger spectrum and an assignment of auger decay channels is performed.
19.	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.
20.	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.
21.	Fang, L., et al. (författare) Multiple Ionization and Double Core-hole Production in Molecules using the LCLS X-ray FEL 2012 Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 388:3, s. 032028- Tidskriftsartikel (refereegranskat)abstract We used the world's first hard x-ray FEL to investigate the response of molecular systems to the ultra-intense, femtosecond x-ray radiation. We report sequential multiphoton ionization, frustrated absorption and double core hole production mechanisms.
22.	Frasinski, L. J., et al. (författare) Dynamics of Hollow Atom Formation in Intense X-Ray Pulses Probed by Partial Covariance Mapping 2013 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 111:7, s. 073002- Tidskriftsartikel (refereegranskat)abstract When exposed to ultraintense x-radiation sources such as free electron lasers (FELs) the innermost electronic shell can efficiently be emptied, creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of noncrystallized complex biological samples. We demonstrate the capacity of a correlation method called partial covariance mapping'' to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualized with unprecedented ease and the map reveals hitherto unobserved nonlinear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.
23.	Kassemeyer, Stephan, et al. (författare) Femtosecond free-electron laser x-ray diffraction data sets for algorithm development 2012 Ingår i: Optics Express. - 1094-4087. ; 20:4, s. 4149-4158 Tidskriftsartikel (refereegranskat)abstract We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
24.	Koopmann, Rudolf, et al. (författare) In vivo protein crystallization opens new routes in structural biology 2012 Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 9:3, s. 259-262 Tidskriftsartikel (refereegranskat)abstract Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo–grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
25.	Larsson, Mats, et al. (författare) Double core-hole formation in small molecules at the LCLS free electron laser 2013 Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164030- Tidskriftsartikel (refereegranskat)abstract We have investigated nonlinear processes in small molecules by x-ray photoelectron spectroscopy using the Linac Coherent Light Source free electron laser, and by simulations. The main focus of the experiments was the formation of the two-site double core-hole (tsDCH) states in the molecules CO2, N2O and N-2. These experiments are described in detail and the results are compared with simulations of the photoelectron spectra. The double core-hole states, and in particular the tsDCH states, have been predicted to be highly sensitive to the chemical environment. The theory behind this chemical sensitivity is validated by the experiments. Furthermore, our simulations of the relative integrated intensities of the peaks associated with the nonlinear processes show that this type of simulation, in combination with experimental data, provides a useful tool for estimating the duration of ultra-short x-ray pulses.
26.	Li, S., et al. (författare) Two-dimensional correlation analysis for x-ray photoelectron spectroscopy 2021 Ingår i: Journal of Physics B. - : Institute of Physics Publishing (IOPP). - 0953-4075 .- 1361-6455. ; 54:14 Tidskriftsartikel (refereegranskat)abstract X-ray photoelectron spectroscopy (XPS) measures the binding energy of core-level electrons, which are well-localised to specific atomic sites in a molecular system, providing valuable information on the local chemical environment. The technique relies on measuring the photoelectron spectrum upon x-ray photoionisation, and the resolution is often limited by the bandwidth of the ionising x-ray pulse. This is particularly problematic for time-resolved XPS, where the desired time resolution enforces a fundamental lower limit on the bandwidth of the x-ray source. In this work, we report a novel correlation analysis which exploits the correlation between the x-ray and photoelectron spectra to improve the resolution of XPS measurements. We show that with this correlation-based spectral-domain ghost imaging method we can achieve sub-bandwidth resolution in XPS measurements. This analysis method enables XPS for sources with large bandwidth or spectral jitter, previously considered unfeasible for XPS measurements.
27.	Lomb, Lukas, et al. (författare) Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser 2011 Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 84:21, s. 214111-1-214111-6 Tidskriftsartikel (refereegranskat)abstract X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
28.	McFarland, B.K., et al. (författare) Experimental strategies for optical pump - soft x-ray probe experiments at the LCLS 2014 Ingår i: Journal of Physics: Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 488, s. 012015- Tidskriftsartikel (refereegranskat)
29.	McFarland, B. K., et al. (författare) Ultrafast X-ray Auger probing of photoexcited molecular dynamics 2014 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4235- Tidskriftsartikel (refereegranskat)abstract Molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation-X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C-O bond stretch in the pi pi* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the n pi* state.
30.	Mucke, Melanie, et al. (författare) Covariance mapping of two-photon double core hole states in C2H2 and C2H6 produced by an x-ray free electron laser 2015 Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 17 Tidskriftsartikel (refereegranskat)abstract Few-photon ionization and relaxation processes in acetylene (C2H2) and ethane (C2H6) were investigated at the linac coherent light source x-ray free electron laser (FEL) at SLAC, Stanford using a highly efficient multi-particle correlation spectroscopy technique based on a magnetic bottle. The analysis method of covariance mapping has been applied and enhanced, allowing us to identify electron pairs associated with double core hole (DCH) production and competing multiple ionization processes including Auger decay sequences. The experimental technique and the analysis procedure are discussed in the light of earlier investigations of DCH studies carried out at the same FEL and at third generation synchrotron radiation sources. In particular, we demonstrate the capability of the covariance mapping technique to disentangle the formation of molecular DCH states which is barely feasible with conventional electron spectroscopy methods.
31.	Murphy, B. F., et al. (författare) Femtosecond X-ray-induced explosion of C-60 at extreme intensity 2014 Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5 Tidskriftsartikel (refereegranskat)abstract Understanding molecular femtosecond dynamics under intense X-ray exposure is critical to progress in biomolecular imaging and matter under extreme conditions. Imaging viruses and proteins at an atomic spatial scale and on the time scale of atomic motion requires rigorous, quantitative understanding of dynamical effects of intense X-ray exposure. Here we present an experimental and theoretical study of C-60 molecules interacting with intense X-ray pulses from a free-electron laser, revealing the influence of processes not previously reported. Our work illustrates the successful use of classical mechanics to describe all moving particles in C-60, an approach that scales well to larger systems, for example, biomolecules. Comparisons of the model with experimental data on C-60 ion fragmentation show excellent agreement under a variety of laser conditions. The results indicate that this modelling is applicable for X-ray interactions with any extended system, even at higher X-ray dose rates expected with future light sources.
32.	Sahlén, Martin, et al. (författare) Experimental Verification of the Chemical Sensitivity of Two-Site Double Core-Hole States Formed by an X-Ray Free-Electron Laser 2012 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 108:15, s. 153003- Tidskriftsartikel (refereegranskat)abstract We have performed x-ray two-photon photoelectron spectroscopy using the Linac Coherent Light Source x-ray free-electron laser in order to study double core-hole (DCH) states of CO2, N2O, and N-2. The experiment verifies the theory behind the chemical sensitivity of two-site DCH states by comparing a set of small molecules with respect to the energy shift of the two-site DCH state and by extracting the relevant parameters from this shift.
33.	Saleacuten, P., et al. (författare) X-ray FEL-induced Double Core-Hole Formation in Polyatomic Molecules 2012 Ingår i: Journal of Physics, Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 388:2, s. 022083- Tidskriftsartikel (refereegranskat)abstract We use extremely intense, ultrashort soft X-Ray pulses generated by the LCLS X-Ray Free Electron Laser to investigate the production of molecular double core-hole states by sequential two-photon X-Ray absorption. The effect of critical LCLS parameters such as the number of photons per pulse, the pulse duration, and the focal spot size on the photoelectron and Auger spectra is modeled in detail and the results of these simulations are used as an aid in the interpretation of the experimental spectra obtained. The emphasis is on double core-hole formation in small polyatomic molecules such as CO2.
34.	Seibert, M. Marvin, et al. (författare) Single mimivirus particles intercepted and imaged with an X-ray laser 2011 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81 Tidskriftsartikel (refereegranskat)abstract X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
35.	Zhaunerchyk, Vitali, et al. (författare) Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation 2015 Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 48:24 Tidskriftsartikel (refereegranskat)abstract Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. The results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).
36.	Zhaunerchyk, Vitali, et al. (författare) Using covariance mapping to investigate the dynamics of multi-photon ionization processes of Ne atoms exposed to X-FEL pulses 2013 Ingår i: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16, s. 164034- Tidskriftsartikel (refereegranskat)abstract We report on a detailed investigation into the electron emission processes of Ne atoms exposed to intense femtosecond x-ray pulses, provided by the Linac Coherent Light Source Free Electron Laser (FEL) at Stanford. The covariance mapping technique is applied to analyse the data, and the capability of this approach to disentangle both linear and nonlinear correlation features which may be hidden on coincidence maps of the same data set is demonstrated. Different correction techniques which enable improvements on the quality of the spectral features extracted from the covariance maps are explored. Finally, a method for deriving characteristics of the x-ray FEL pulses based on covariance mapping in combination with model simulations is presented.
37.	Berrah, Nora, et al. (författare) Double-core-hole spectroscopy for chemical analysis with an intense X-ray femtosecond laser 2011 Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 108:41, s. 16912-16915 Tidskriftsartikel (refereegranskat)abstract Theory predicts that double-core-hole (DCH) spectroscopy can provide a new powerful means of differentiating between similar chemical systems with a sensitivity not hitherto possible. Although DCH ionization on a single site in molecules was recently measured with double-and single-photon absorption, double-core holes with single vacancies on two different sites, allowing unambiguous chemical analysis, have remained elusive. Here we report that direct observation of double-core holes with single vacancies on two different sites produced via sequential two-photon absorption, using short, intense X-ray pulses from the Linac Coherent Light Source free-electron laser and compare it with theoretical modeling. The observation of DCH states, which exhibit a unique signature, and agreement with theory proves the feasibility of the method. Our findings exploit the ultrashort pulse duration of the free-electron laser to eject two core electrons on a time scale comparable to that of Auger decay and demonstrate possible future X-ray control of physical inner-shell processes.
38.	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.
39.	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.
40.	Ekeberg, Tomas, et al. (författare) Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser 2015 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 114:9, s. 098102:1-6 Tidskriftsartikel (refereegranskat)
41.	Farrell, J. P., et al. (författare) Ultrafast X-ray probe of nucleobase photoprotection 2012 Ingår i: Quantum Electronics and Laser Science Conference. - 9781467318396 ; , s. 6327153- Konferensbidrag (refereegranskat)abstract We will present first results of a UV-pump X-ray-probe study of the photoprotection mechanism of thymine. The experiment used element specific Auger spectroscopy and was carried out at the LCLS.
42.	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.
43.	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.
44.	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.
45.	Kuepper, Jochen, et al. (författare) X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser 2014 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:8, s. 083002- Tidskriftsartikel (refereegranskat)abstract We report experimental results on x-ray diffraction of quantum-state-selected and strongly aligned ensembles of the prototypical asymmetric rotor molecule 2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments demonstrate first steps toward a new approach to diffractive imaging of distinct structures of individual, isolated gas-phase molecules. We confirm several key ingredients of single molecule diffraction experiments: the abilities to detect and count individual scattered x-ray photons in single shot diffraction data, to deliver state-selected, e.g., structural-isomer-selected, ensembles of molecules to the x-ray interaction volume, and to strongly align the scattering molecules. Our approach, using ultrashort x-ray pulses, is suitable to study ultrafast dynamics of isolated molecules.
46.	Loh, N. Duane, et al. (författare) Sensing the wavefront of x-ray free-electron lasers using aerosol spheres 2013 Ingår i: Optics Express. - 1094-4087. ; 21:10, s. 12385-12394 Tidskriftsartikel (refereegranskat)abstract Characterizing intense, focused x-ray free electron laser (FEL) pulses is crucial for their use in diffractive imaging. We describe how the distribution of average phase tilts and intensities on hard x-ray pulses with peak intensities of 1021 W/m(2) can be retrieved from an ensemble of diffraction patterns produced by 70 nm-radius polystyrene spheres, in a manner that mimics wavefront sensors. Besides showing that an adaptive geometric correction may be necessary for diffraction data from randomly injected sample sources, our paper demonstrates the possibility of collecting statistics on structured pulses using only the diffraction patterns they generate and highlights the imperative to study its impact on single-particle diffractive imaging.
47.	Lundholm, Ida V., et al. (författare) Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging 2018 Ingår i: IUCrJ. - : International Union of Crystallography. - 2052-2525. ; 5, s. 531-541 Tidskriftsartikel (refereegranskat)abstract Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
48.	McFarland, B. K., et al. (författare) Probing nucleobase photoprotection with soft x-rays 2013 Ingår i: XVIIITH INTERNATIONAL CONFERENCE ON ULTRAFAST PHENOMENA. - : EDP Sciences. - 9782759809561 ; , s. 07004- Konferensbidrag (refereegranskat)abstract Nucleobases absorb strongly in the ultraviolet region, leading to molecular excitation into reactive states. The molecules avoid the photoreactions by funnelling the electronic energy into less reactive states on an ultrafast timescale via non-Born-Oppenheimer dynamics. Current theory on the nucleobase thymine discusses two conflicting pathways for the photoprotective dynamics. We present our first results of our free electron laser based UV-pump soft x-ray-probe study of the photoprotection mechanism of thymine. We use the high spatial sensitivity of the Auger electrons emitted after the soft x-ray pulse induced core ionization. Our transient spetra show two timescales on the order of 200 fs and 5 ps, in agreement with previous (all UV) ultrafast experiments. The timescales appear at different Auger kinetic energies which will help us to decipher the molecular dynamics.
49.	Park, Hyung Joo, et al. (författare) Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers 2013 Ingår i: Optics Express. - 1094-4087. ; 21:23, s. 28729-28742 Tidskriftsartikel (refereegranskat)abstract Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.
50.	Sorensen, S. L., et al. (författare) From synchrotrons for XFELs : The soft x-ray near-edge spectrum of the ESCA molecule 2020 Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 53:24 Tidskriftsartikel (refereegranskat)abstract A predictive understanding of soft x-ray near-edge absorption spectra of small molecules is an enduring theoretical challenge and of current interest for x-ray probes of molecular dynamics. We report the experimental absorption spectrum for the electron spectroscopy for chemical analysis (ESCA) molecule (ethyl trifluoroacetate) near the carbon 1s absorption edge between 285-300 eV. The ESCA molecule with four chemically distinct carbon sites has previously served as a theoretical benchmark for photoelectron spectra and now for photoabsorption spectra. We report a simple edge-specific approach for systematically expanding standard basis sets to properly describe diffuse Rydberg orbitals and the importance of triple excitations in equation-of-motion coupled-cluster calculations of the energy interval between valence and Rydberg excitations.

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