SwePub - search: WFRF:(Marchesini J.)

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1.	Schael, S, et al. (author) Precision electroweak measurements on the Z resonance 2006 In: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454 Research review (peer-reviewed)abstract We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
2.	Abdollahi, S., et al. (author) Fermi Large Area Telescope Fourth Source Catalog 2020 In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 247:1 Journal article (peer-reviewed)abstract We present the fourth Fermi Large Area Telescope catalog (4FGL) of gamma-ray sources. Based on the first eight years of science data from the Fermi Gamma-ray Space Telescope mission in the energy range from 50 MeV to 1 TeV, it is the deepest yet in this energy range. Relative to the 3FGL catalog, the 4FGL catalog has twice as much exposure as well as a number of analysis improvements, including an updated model for the Galactic diffuse gamma-ray emission, and two sets of light curves (one-year and two-month intervals). The 4FGL catalog includes 5064 sources above 4 sigma significance, for which we provide localization and spectral properties. Seventy-five sources are modeled explicitly as spatially extended, and overall, 358 sources are considered as identified based on angular extent, periodicity, or correlated variability observed at other wavelengths. For 1336 sources, we have not found plausible counterparts at other wavelengths. More than 3130 of the identified or associated sources are active galaxies of the blazar class, and 239 are pulsars.
3.	Pedersoli, E., et al. (author) Mesoscale morphology of airborne core-shell nanoparticle clusters : x-ray laser coherent diffraction imaging 2013 In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 46:16 SI, s. 164033- Journal article (peer-reviewed)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.
4.	Duane Loh, N., et al. (author) Profiling structured beams using injected aerosols 2012 In: Proceedings of SPIE. - : SPIE. - 9780819492210 ; , s. 850403- Conference paper (peer-reviewed)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.
5.	Gomez, L. F., et al. (author) Shapes and vorticities of superfluid helium nanodroplets 2014 In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 345:6199, s. 906-909 Journal article (peer-reviewed)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.
6.	Loh, N. D., et al. (author) Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight 2012 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 486:7404, s. 513-517 Journal article (peer-reviewed)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).
7.	Martin, A. V., et al. (author) Femtosecond dark-field imaging with an X-ray free electron laser 2012 In: Optics Express. - 1094-4087. ; 20:12, s. 13501-13512 Journal article (peer-reviewed)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.
8.	Martin, A. V., et al. (author) Noise-robust coherent diffractive imaging with a single diffraction pattern 2012 In: Optics Express. - 1094-4087. ; 20:15, s. 16650-16661 Journal article (peer-reviewed)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
9.	Abdalla, M., et al. (author) Simulation of CO2 and Attribution Analysis at Six European Peatland Sites Using the ECOSSE Model 2014 In: Water, Air and Soil Pollution. - : Springer Science and Business Media LLC. - 1573-2932 .- 0049-6979. ; 225:11, s. 2182-2182 Journal article (peer-reviewed)abstract In this study, we simulated heterotrophic CO2 (Rh) fluxes at six European peatland sites using the ECOSSE model and compared them to estimates of Rh made from eddy covariance (EC) measurements. The sites are spread over four countries with different climates, vegetation and management. Annual Rh from the different sites ranged from 110 to 540 g C m(-2). The maximum annual Rh occurred when the water table (WT) level was between -10 and -25 cm and the air temperature was above 6.2 degrees C. The model successfully simulated seasonal trends for the majority of the sites. Regression relationships (r(2)) between the EC-derived and simulated Rh ranged from 0.28 to 0.76, and the root mean square error and relative error were small, revealing an acceptable fit. The overall relative deviation value between annual EC-derived and simulated Rh was small (-1 %) and model efficiency ranges across sites from -0.25 to +0.41. Sensitivity analysis highlighted that increasing temperature, decreasing precipitation and lowering WT depth could significantly increase Rh from soils. Thus, management which lowers the WT could significantly increase anthropogenic CO2, so from a carbon emissions perspective, it should be avoided. The results presented here demonstrate a robust basis for further application of the ECOSSE model to assess the impacts of future land management interventions on peatland carbon emissions and to help guide best practice land management decisions.
10.	Andersen, J. R., et al. (author) Small-x phenomenology - Summary of the 3rd Lund small-x workshop in 2004 2006 In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 48:1, s. 53-105 Research review (peer-reviewed)abstract A third workshop on small-x physics, within the Small-x Collaboration, was held in Hamburg in May 2004 with the aim of overviewing recent theoretical progress in this area and summarizing the experimental status.
11.	Karlsen, T. H., et al. (author) The EASL–Lancet Liver Commission: protecting the next generation of Europeans against liver disease complications and premature mortality 2022 In: The Lancet. - 0140-6736. ; 399:10319, s. 61-116 Journal article (peer-reviewed)
12.	Lembrechts, Jonas J., et al. (author) Global maps of soil temperature 2022 In: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 28:9, s. 3110-3144 Journal article (peer-reviewed)abstract Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean=3.0±2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6±2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7±2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications.
13.	Aquila, A., et al. (author) The linac coherent light source single particle imaging road map 2015 In: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4 Journal article (peer-reviewed)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.
14.	Kupitz, Christopher, et al. (author) Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser 2014 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 513:7517, s. 261-265 Journal article (peer-reviewed)abstract Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.
15.	Lazarus, J.V., et al. (author) A cross-sectional study of the public health response to non-alcoholic fatty liver disease in Europe 2020 In: Journal of Hepatology. - : Elsevier. - 0168-8278 .- 1600-0641. ; 72:1, s. 14-24 Journal article (peer-reviewed)abstract Background & AimsNon-alcoholic fatty liver disease (NAFLD) is a growing public health problem worldwide and has become an important field of biomedical inquiry. We aimed to determine whether European countries have mounted an adequate public health response to NAFLD and non-alcoholic steatohepatitis (NASH).MethodsIn 2018 and 2019, NAFLD experts in 29 European countries completed an English-language survey on policies, guidelines, awareness, monitoring, diagnosis and clinical assessment in their country. The data were compiled, quality checked against existing official documents and reported descriptively.ResultsNone of the 29 participating countries had written strategies or action plans for NAFLD. Two countries (7%) had mentions of NAFLD or NASH in related existing strategies (obesity and alcohol). Ten (34%) reported having national clinical guidelines specifically addressing NAFLD and, upon diagnosis, all included recommendations for the assessment of diabetes and liver cirrhosis. Eleven countries (38%) recommended screening for NAFLD in all patients with either diabetes, obesity and/or metabolic syndrome. Five countries (17%) had referral algorithms for follow-up and specialist referral in primary care, and 7 (24%) reported structured lifestyle programmes aimed at NAFLD. Seven (24%) had funded awareness campaigns that specifically included prevention of liver disease. Four countries (14%) reported having civil society groups which address NAFLD and 3 countries (10%) had national registries that include NAFLD.ConclusionsWe found that a comprehensive public health response to NAFLD is lacking in the surveyed European countries. This includes policy in the form of a strategy, clinical guidelines, awareness campaigns, civil society involvement, and health systems organisation, including registries.Lay summaryWe conducted a survey on non-alcoholic fatty liver disease with experts in European countries, coupled with data extracted from official documents on policies, clinical guidelines, awareness, and monitoring. We found a general lack of national policies, awareness campaigns and civil society involvement, and few epidemiological registries.
16.	Metzger, Christine, et al. (author) CO2 fluxes and ecosystem dynamics at five European treeless peatlands - merging data and process oriented modeling 2015 In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 12:1, s. 125-146 Journal article (peer-reviewed)abstract The carbon dioxide (CO2) exchange of five different peatland systems across Europe with a wide gradient in land use intensity, water table depth, soil fertility and climate was simulated with the process oriented CoupModel. The aim of the study was to find out whether CO2 fluxes, measured at different sites, can be explained by common processes and parameters or to what extend a site specific configuration is needed. The model was calibrated to fit measured CO2 fluxes, soil temperature, snow depth and leaf area index (LAI) and resulting differences in model parameters were analyzed. Finding site independent model parameters would mean that differences in the measured fluxes could be explained solely by model input data: water table, meteorological data, management and soil inventory data. Seasonal variability in the major fluxes was well captured, when a site independent configuration was utilized for most of the parameters. Parameters that differed between sites included the rate of soil organic decomposition, photosynthetic efficiency, and regulation of the mobile carbon (C) pool from senescence to shooting in the next year. The largest difference between sites was the rate coefficient for heterotrophic respiration. Setting it to a common value would lead to underestimation of mean total respiration by a factor of 2.8 up to an overestimation by a factor of 4. Despite testing a wide range of different responses to soil water and temperature, rate coefficients for heterotrophic respiration were consistently the lowest on formerly drained sites and the highest on the managed sites. Substrate decomposability, pH and vegetation characteristics are possible explanations for the differences in decomposition rates. Specific parameter values for the timing of plant shooting and senescence, the photosynthesis response to temperature, litter fall and plant respiration rates, leaf morphology and allocation fractions of new assimilates, were not needed, even though the gradient in site latitude ranged from 48 degrees N (southern Germany) to 68 degrees N (northern Finland) differed largely in their vegetation. This was also true for common parameters defining the moisture and temperature response for decomposition, leading to the conclusion that a site specific interpretation of these processes is not necessary. In contrast, the rate of soil organic decomposition, photosynthetic efficiency, and the regulation of the mobile carbon pool need to be estimated from available information on specific soil conditions, vegetation and management of the ecosystems, to be able to describe CO2 fluxes under different conditions.
17.	Aquila, Andrew, et al. (author) Time-resolved protein nanocrystallography using an X-ray free-electron laser 2012 In: Optics Express. - 1094-4087. ; 20:3, s. 2706-2716 Journal article (peer-reviewed)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.
18.	Bogan, M. J., et al. (author) Single-shot femtosecond x-ray diffraction from randomly oriented ellipsoidal nanoparticles 2010 In: Physical Review Special Topics - Accelerators and Beams. - 1098-4402. ; 13:9, s. 094701- Journal article (peer-reviewed)abstract Coherent diffractive imaging of single particles using the single-shot "diffract and destroy" approach with an x-ray free electron laser (FEL) was recently demonstrated. A high-resolution low-noise coherent diffraction pattern, representative of the object before it turns into a plasma and explodes, results from the interaction of the FEL with the particle. Iterative phase retrieval algorithms are used to reconstruct two-dimensional projection images of the object from the recorded intensities alone. Here we describe the first single-shot diffraction data set that mimics the data proposed for obtaining 3D structure from identical particles. Ellipsoidal iron oxide nanoparticles (250 nm x 50 nm) were aerosolized and injected through an aerodynamic lens stack into a soft x-ray FEL. Particle orientation was not controlled with this injection method. We observed that, at the instant the x-ray pulse interacts with the particle, a snapshot of the particle's orientation is encoded in the diffraction pattern. The results give credence to one of the technical concepts of imaging individual nanometer and subnanometer-sized objects such as single molecules or larger clusters of molecules using hard x-ray FELs and will be used to help develop robust algorithms for determining particle orientations and 3D structure.
19.	Budishchev, A., et al. (author) Evaluation of a plot-scale methane emission model using eddy covariance observations and footprint modelling 2014 In: Biogeosciences. - : Copernicus GmbH. - 1726-4189. ; 11:17, s. 4651-4664 Journal article (peer-reviewed)abstract Most plot-scale methane emission models - of which many have been developed in the recent past - are validated using data collected with the closed-chamber technique. This method, however, suffers from a low spatial representativeness and a poor temporal resolution. Also, during a chamber-flux measurement the air within a chamber is separated from the ambient atmosphere, which negates the influence of wind on emissions. Additionally, some methane models are validated by upscaling fluxes based on the area-weighted averages of modelled fluxes, and by comparing those to the eddy covariance (EC) flux. This technique is rather inaccurate, as the area of upscaling might be different from the EC tower footprint, therefore introducing significant mismatch. In this study, we present an approach to validate plot-scale methane models with EC observations using the footprint-weighted average method. Our results show that the fluxes obtained by the footprint-weighted average method are of the same magnitude as the EC flux. More importantly, the temporal dynamics of the EC flux on a daily timescale are also captured (r(2) = 0.7). In contrast, using the area-weighted average method yielded a low (r(2) = 0.14) correlation with the EC measurements. This shows that the footprint-weighted average method is preferable when validating methane emission models with EC fluxes for areas with a heterogeneous and irregular vegetation pattern.
20.	Chapman, Henry N, et al. (author) Femtosecond X-ray protein nanocrystallography. 2011 In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7 Journal article (peer-reviewed)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.	Loh, N. D., et al. (author) Cryptotomography : Reconstructing 3D Fourier Intensities from Randomly Oriented Single-Shot Diffraction Patterns 2010 In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 104:22, s. 225501-1-225501-5 Journal article (peer-reviewed)abstract We reconstructed the 3D Fourier intensity distribution of monodisperse prolate nanoparticles using single-shot 2D coherent diffraction patterns collected at DESY's FLASH facility when a bright, coherent, ultrafast x-ray pulse intercepted individual particles of random, unmeasured orientations. This first experimental demonstration of cryptotomography extended the expansion-maximization-compression framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. This work is an important step towards realizing single-shot diffraction imaging of single biomolecules.
22.	Loh, N. Duane, et al. (author) Sensing the wavefront of x-ray free-electron lasers using aerosol spheres 2013 In: Optics Express. - 1094-4087. ; 21:10, s. 12385-12394 Journal article (peer-reviewed)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.
23.	Park, Hyung Joo, et al. (author) Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers 2013 In: Optics Express. - 1094-4087. ; 21:23, s. 28729-28742 Journal article (peer-reviewed)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.
24.	Parkinson, Dilworth Y., et al. (author) Real-Time Data-Intensive Computing 2016 In: Proceedings Of The 12Th International Conference On Synchrotron Radiation Instrumentation (SRI2015). - : Author(s). - 9780735413986 Conference paper (peer-reviewed)abstract Today users visit synchrotrons as sources of understanding and discovery-not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a "super-facility", giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data-despite its high rate and volume-is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.
25.	Bajt, Sasa, et al. (author) Camera for coherent diffractive imaging and holography with a soft-x-ray free-electron laser 2008 In: Applied Optics. - 1559-128X .- 2155-3165. ; 47:10, s. 1673-1683 Journal article (peer-reviewed)abstract We describe a camera to record coherent scattering patterns with a soft-x-ray free-electron laser (FEL). The camera consists of a laterally graded multilayer mirror, which reflects the diffraction pattern onto a CCD detector. The mirror acts as a bandpass filter for both the wavelength and the angle, which isolates the desired scattering pattern from nonsample scattering or incoherent emission from the sample. The mirror also solves the particular problem of the extreme intensity of the FEL pulses, which are focused to greater than 10(14) W/cm2. The strong undiffracted pulse passes through a hole in the mirror and propagates onto a beam dump at a distance behind the instrument rather than interacting with a beam stop placed near the CCD. The camera concept is extendable for the full range of the fundamental wavelength of the free electron laser in Hamburg (FLASH) FEL (i.e., between 6 and 60 nm) and into the water window. We have fabricated and tested various multilayer mirrors for wavelengths of 32, 16, 13.5, and 4.5 nm. At the shorter wavelengths mirror roughness must be minimized to reduce scattering from the mirror. We have recorded over 30,000 diffraction patterns at the FLASH FEL with no observable mirror damage or degradation of performance.

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