All Publications


  • Observation of shock-induced protein crystal damage during megahertz serial femtosecond crystallography PHYSICAL REVIEW RESEARCH Gruenbein, M. L., Foucar, L., Gorel, A., Hilpert, M., Kloos, M., Nass, K., Kovacs, G., Roome, C. M., Shoeman, R. L., Stricker, M., Carbajo, S., Colocho, W., Gilevich, S., Hunter, M., Lewandowski, J., Lutman, A., Koglin, J. E., Lane, T. J., van Driel, T., Sheppard, J., Vetter, S. L., Turner, J. L., Doak, R., Barends, T. M., Boutet, S., Aquila, A. L., Decker, F., Schlichting, I., Stan, C. A. 2021; 3 (1)
  • An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCrJ Assalauova, D., Kim, Y. Y., Bobkov, S., Khubbutdinov, R., Rose, M., Alvarez, R., Andreasson, J., Balaur, E., Contreras, A., DeMirci, H., Gelisio, L., Hajdu, J., Hunter, M. S., Kurta, R. P., Li, H., McFadden, M., Nazari, R., Schwander, P., Teslyuk, A., Walter, P., Xavier, P. L., Yoon, C. H., Zaare, S., Ilyin, V. A., Kirian, R. A., Hogue, B. G., Aquila, A., Vartanyants, I. A. 2020; 7 (Pt 6): 1102–13

    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.

    View details for DOI 10.1107/S2052252520012798

    View details for PubMedID 33209321

  • Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCrJ Lee, M., Geiger, J., Ishchenko, A., Han, G. W., Barty, A., White, T. A., Gati, C., Batyuk, A., Hunter, M. S., Aquila, A., Boutet, S., Weierstall, U., Cherezov, V., Liu, W. 2020; 7 (Pt 6): 976–84

    Abstract

    Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 A resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.

    View details for DOI 10.1107/S2052252520012701

    View details for PubMedID 33209312

  • Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses. Nature communications Nass, K., Gorel, A., Abdullah, M. M., V Martin, A., Kloos, M., Marinelli, A., Aquila, A., Barends, T. R., Decker, F., Bruce Doak, R., Foucar, L., Hartmann, E., Hilpert, M., Hunter, M. S., Jurek, Z., Koglin, J. E., Kozlov, A., Lutman, A. A., Kovacs, G. N., Roome, C. M., Shoeman, R. L., Santra, R., Quiney, H. M., Ziaja, B., Boutet, S., Schlichting, I. 2020; 11 (1): 1814

    Abstract

    X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter's correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

    View details for DOI 10.1038/s41467-020-15610-4

    View details for PubMedID 32286284

  • Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source. Scientific data Li, H. n., Nazari, R. n., Abbey, B. n., Alvarez, R. n., Aquila, A. n., Ayyer, K. n., Barty, A. n., Berntsen, P. n., Bielecki, J. n., Pietrini, A. n., Bucher, M. n., Carini, G. n., Chapman, H. N., Contreras, A. n., Daurer, B. J., DeMirci, H. n., Flűckiger, L. n., Frank, M. n., Hajdu, J. n., Hantke, M. F., Hogue, B. G., Hosseinizadeh, A. n., Hunter, M. S., Jönsson, H. O., Kirian, R. A., Kurta, R. P., Loh, D. n., Maia, F. R., Mancuso, A. P., Morgan, A. J., McFadden, M. n., Muehlig, K. n., Munke, A. n., Reddy, H. K., Nettelblad, C. n., Ourmazd, A. n., Rose, M. n., Schwander, P. n., Marvin Seibert, M. n., Sellberg, J. A., Sierra, R. G., Sun, Z. n., Svenda, M. n., Vartanyants, I. A., Walter, P. n., Westphal, D. n., Williams, G. n., Xavier, P. L., Yoon, C. H., Zaare, S. n. 2020; 7 (1): 404

    Abstract

    Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

    View details for DOI 10.1038/s41597-020-00745-2

    View details for PubMedID 33214568

  • Low-signal limit of X-ray single particle diffractive imaging OPTICS EXPRESS Ayyer, K., Morgan, A. J., Aquila, A., DeMirci, H., Hogue, B. G., Kirian, R. A., Xavier, P., Yoon, C., Chapman, H. N., Barty, A. 2019; 27 (26): 37816–33

    Abstract

    An outstanding question in X-ray single particle imaging experiments has been the feasibility of imaging sub 10-nm-sized biomolecules under realistic experimental conditions where very few photons are expected to be measured in a single snapshot and instrument background may be significant relative to particle scattering. While analyses of simulated data have shown that the determination of an average image should be feasible using Bayesian methods such as the EMC algorithm, this has yet to be demonstrated using experimental data containing realistic non-isotropic instrument background, sample variability and other experimental factors. In this work, we show that the orientation and phase retrieval steps work at photon counts diluted to the signal levels one expects from smaller molecules or with weaker pulses, using data from experimental measurements of 60-nm PR772 viruses. Even when the signal is reduced to a fraction as little as 1/256, the virus electron density determined using ab initio phasing is of almost the same quality as the high-signal data. However, we are still limited by the total number of patterns collected, which may soon be mitigated by the advent of high repetition-rate sources like the European XFEL and LCLS-II.

    View details for DOI 10.1364/OE.27.037816

    View details for Web of Science ID 000507254300061

    View details for PubMedID 31878556

  • Wavefront sensing at X-ray free-electron lasers. Journal of synchrotron radiation Seaberg, M., Cojocaru, R., Berujon, S., Ziegler, E., Jaggi, A., Krempasky, J., Seiboth, F., Aquila, A., Liu, Y., Sakdinawat, A., Lee, H. J., Flechsig, U., Patthey, L., Koch, F., Seniutinas, G., David, C., Zhu, D., Mikes, L., Makita, M., Koyama, T., Mancuso, A. P., Chapman, H. N., Vagovic, P. 2019; 26 (Pt 4): 1115–26

    Abstract

    Here a direct comparison is made between various X-ray wavefront sensing methods with application to optics alignment and focus characterization at X-ray free-electron lasers (XFELs). Focus optimization at XFEL beamlines presents unique challenges due to high peak powers as well as beam pointing instability, meaning that techniques capable of single-shot measurement and that probe the wavefront at an out-of-focus location are desirable. The techniques chosen for the comparison include single-phase-grating Talbot interferometry (shearing interferometry), dual-grating Talbot interferometry (moire deflectometry) and speckle tracking. All three methods were implemented during a single beam time at the Linac Coherent Light Source, at the X-ray Pump Probe beamline, in order to make a direct comparison. Each method was used to characterize the wavefront resulting from a stack of beryllium compound refractive lenses followed by a corrective phase plate. In addition, difference wavefront measurements with and without the phase plate agreed with its design to within lambda/20, which enabled a direct quantitative comparison between methods. Finally, a path toward automated alignment at XFEL beamlines using a wavefront sensor to close the loop is presented.

    View details for DOI 10.1107/S1600577519005721

    View details for PubMedID 31274435

  • Generation of high-intensity ultrasound through shock propagation in liquid jets PHYSICAL REVIEW FLUIDS Blaj, G., Liang, M., Aquila, A. L., Willmott, P. R., Koglin, J. E., Sierra, R. G., Robinson, J. S., Boutet, S., Stan, C. A. 2019; 4 (4)
  • The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Sierra, R. G., Batyuk, A., Sun, Z., Aquila, A., Hunter, M. S., Lane, T. J., Liang, M., Yoon, C., Alonso-Mori, R., Armenta, R., Castagna, J., Hollenbeck, M., Osier, T. O., Hayes, M., Aldrich, J., Curtis, R., Koglin, J. E., Rendahl, T., Rodriguez, E., Carbajo, S., Guillet, S., Paul, R., Hart, P., Nakahara, K., Carini, G., DeMirci, H., Dao, E., Hayes, B. M., Rao, Y. P., Chollet, M., Feng, Y., Fuller, F. D., Kupitz, C., Sato, T., Seaberg, M. H., Song, S., van Driel, T. B., Yavas, H., Zhu, D., Cohen, A. E., Wakatsuki, S., Boutet, S. 2019; 26: 346–57
  • Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. IUCrJ Shi, Y., Yin, K., Tai, X., DeMirci, H., Hosseinizadeh, A., Hogue, B. G., Li, H., Ourmazd, A., Schwander, P., Vartanyants, I. A., Yoon, C. H., Aquila, A., Liu, H. 2019; 6 (Pt 2): 331–40

    Abstract

    Using X-ray free-electron lasers (XFELs), it is possible to determine three-dimensional structures of nanoscale particles using single-particle imaging methods. Classification algorithms are needed to sort out the single-particle diffraction patterns from the large amount of XFEL experimental data. However, different methods often yield inconsistent results. This study compared the performance of three classification algorithms: convolutional neural network, graph cut and diffusion map manifold embedding methods. The identified single-particle diffraction data of the PR772 virus particles were assembled in the three-dimensional Fourier space for real-space model reconstruction. The comparison showed that these three classification methods lead to different datasets and subsequently result in different electron density maps of the reconstructed models. Interestingly, the common dataset selected by these three methods improved the quality of the merged diffraction volume, as well as the resolutions of the reconstructed maps.

    View details for PubMedID 30867930

  • The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source. Journal of synchrotron radiation Sierra, R. G., Batyuk, A. n., Sun, Z. n., Aquila, A. n., Hunter, M. S., Lane, T. J., Liang, M. n., Yoon, C. H., Alonso-Mori, R. n., Armenta, R. n., Castagna, J. C., Hollenbeck, M. n., Osier, T. O., Hayes, M. n., Aldrich, J. n., Curtis, R. n., Koglin, J. E., Rendahl, T. n., Rodriguez, E. n., Carbajo, S. n., Guillet, S. n., Paul, R. n., Hart, P. n., Nakahara, K. n., Carini, G. n., DeMirci, H. n., Dao, E. H., Hayes, B. M., Rao, Y. P., Chollet, M. n., Feng, Y. n., Fuller, F. D., Kupitz, C. n., Sato, T. n., Seaberg, M. H., Song, S. n., van Driel, T. B., Yavas, H. n., Zhu, D. n., Cohen, A. E., Wakatsuki, S. n., Boutet, S. n. 2019; 26 (Pt 2): 346–57

    Abstract

    The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.

    View details for PubMedID 30855242

  • Single-particle imaging without symmetry constraints at an X-ray free-electron laser IUCRJ Rose, M., Bobkov, S., Ayyer, K., Kurta, R. P., Dzhigaev, D., Kim, Y., Morgan, A. J., Yoon, C., Westphal, D., Bielecki, J., Sellberg, J. A., Williams, G., Maia, F. C., Yefanov, O. M., Ilyin, V., Mancuso, A. P., Chapman, H. N., Hogue, B. G., Aquila, A., Barty, A., Vartanyants, I. A. 2018; 5: 727–36

    Abstract

    The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.

    View details for PubMedID 30443357

  • High-accuracy wavefront sensing for x-ray free electron lasers OPTICA Liu, Y., Seaberg, M., Zhu, D., Krzywinski, J., Seiboth, F., Hardin, C., Cocco, D., Aquila, A., Nagler, B., Lee, H., Boutet, S., Feng, Y., Ding, Y., Marcus, G., Sakdinawat, A. 2018; 5 (8): 967–75
  • Deconvoluting the isotropic and anisotropic ultrafast x-ray scattering of gas-phase N-methylmorpholine following Rydberg excitation Stankus, B., Ruddock, J., Yong, H., Zotev, N., Bellshaw, D., Lane, T., Boutet, S., Liang, M., Carbajo, S., Robinson, J., Koglin, J., Aquila, A., Zhang, Y., Du, W., Goff, N., Chang, Y., Minitti, M., Kirrander, A., Weber, P. AMER CHEMICAL SOC. 2018
  • Ultrafast nonthermal heating of water initiated by an X-ray Free-Electron Laser PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Beyerlein, K. R., Jonsson, H., Alonso-Mori, R., Aquila, A., Barty, S., Barty, A., Bean, R., Koglin, J. E., Messerschmidt, M., Ragazzon, D., Sokaras, D., Williams, G. J., Hau-Riege, S., Boutet, S., Chapman, H. N., Imneanu, N. T., Caleman, C. 2018; 115 (22): 5652–57

    Abstract

    The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2 These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.

    View details for PubMedID 29760050

  • Stimulated X-Ray Emission Spectroscopy in Transition Metal Complexes PHYSICAL REVIEW LETTERS Kroll, T., Weninger, C., Alonso-Mori, R., Sokaras, D., Zhu, D., Mercadier, L., Majety, V. P., Marinelli, A., Lutman, A., Guetg, M. W., Decker, F., Boutet, S., Aquila, A., Koglin, J., Koralek, J., DePonte, D. P., Kern, J., Fuller, F. D., Pastor, E., Fransson, T., Zhang, Y., Yano, J., Yachandra, V. K., Rohringer, N., Bergmann, U. 2018; 120 (13): 133203

    Abstract

    We report the observation and analysis of the gain curve of amplified Kα x-ray emission from solutions of Mn(II) and Mn(VII) complexes using an x-ray free electron laser to create the 1s core-hole population inversion. We find spectra at amplification levels extending over 4 orders of magnitude until saturation. We observe bandwidths below the Mn 1s core-hole lifetime broadening in the onset of the stimulated emission. In the exponential amplification regime the resolution corrected spectral width of ∼1.7  eV FWHM is constant over 3 orders of magnitude, pointing to the buildup of transform limited pulses of ∼1  fs duration. Driving the amplification into saturation leads to broadening and a shift of the line. Importantly, the chemical sensitivity of the stimulated x-ray emission to the Mn oxidation state is preserved at power densities of ∼10^{20}  W/cm^{2} for the incoming x-ray pulses. Differences in signal sensitivity and spectral information compared to conventional (spontaneous) x-ray emission spectroscopy are discussed. Our findings build a baseline for nonlinear x-ray spectroscopy for a wide range of transition metal complexes in inorganic chemistry, catalysis, and materials science.

    View details for DOI 10.1103/PhysRevLett.120.133203

    View details for Web of Science ID 000428394800008

    View details for PubMedID 29694162

  • Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals JOURNAL OF APPLIED CRYSTALLOGRAPHY Awel, S., Kirian, R. A., Wiedorn, M. O., Beyerlein, K. R., Roth, N., Horke, D. A., Oberthuer, D., Knoska, J., Mariani, V., Morgan, A., Adriano, L., Tolstikova, A., Xavier, P., Yefanov, O., Aquila, A., Barty, A., Roy-Chowdhury, S., Hunter, M. S., James, D., Robinson, J. S., Weierstall, U., Rode, A. V., Bajt, S., Kuepper, J., Chapman, H. N. 2018; 51: 133–39

    Abstract

    High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.

    View details for PubMedID 29507547

  • Single Molecule Imaging Using X-ray Free Electron Lasers X-ray Free Electron Lasers Aquila, A., Barty, A. Springer International Publishing. 2018: 401–426
  • Developments Towards Imaging Nanoscale Biology with XFELs: Some Recent Examples and a Glance to the Future Microscopy and Microanalysis Mancuso, A. P., Aquila, A., Bean, R., Bielecki, J., Fortmann-Grote, C., Giewekemeyer, K., Kim, Y., Kurta, R., Letrun, R., Mehrjoo, M., Messerschmidt, M., Mills, G., Round, A., Sato, T., Schulz, J., Sikorski, M., Stern, S., Vagovic, P., Tschentscher, T. 2018; 24: 76-77
  • X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis. The journal of physical chemistry letters Jensen, S. n., Sullivan, B. T., Hartzler, D. A., Meza Aguilar, J. n., Awel, S. n., Bajt, S. n., Basu, S. n., Bean, R. n., Chapman, H. n., Conrad, C. n., Frank, M. n., Fromme, R. n., Martin-Garcia, J. M., Grant, T. D., Heymann, M. n., Hunter, M. S., Ketawala, G. n., Kirian, R. A., Knoska, J. n., Kupitz, C. n., Li, X. n., Liang, M. n., Lisova, S. n., Mariani, V. n., Mazalova, V. L., Messerschmidt, M. n., Moran, M. n., Nelson, G. n., Oberthuer, D. n., Schaffer, A. n., Sierra, R. G., Vaughn, N. n., Weierstall, U. n., Wiedorn, M. O., Xavier, P. L., Yang, J. H., Yefanov, O. n., Zatsepin, N. n., Aquila, A. L., Fromme, P. n., Boutet, S. n., Seidler, G. T., Pushkar, Y. N. 2018

    Abstract

    X-ray free electron lasers (XFELs) provide ultrashort intense X-ray pulses suitable to probe electron dynamics, but can also induce a multitude of nonlinear excitation processes. These affect spectroscopic measurements and interpretation, particularly for upcoming brighter XFELs. Here we identify and discuss the limits to observing classical spectroscopy, where only one photon is absorbed per atom for a Mn2+ in a light element (O, C, H) environment. X-ray emission spectroscopy (XES) with different incident photon energies, pulse intensities, and pulse durations is presented. A rate equation model based on sequential ionization and relaxation events is used to calculate populations of multiply ionized states during a single pulse and to explain the observed X-ray induced spectral lines shifts. This model provides easy estimation of spectral shifts, which is essential for experimental designs at XFELs, and illustrates that shorter X-ray pulses will not overcome sequential ionization but can reduce electron cascade effects.

    View details for PubMedID 30566358

  • Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography NATURE CHEMISTRY Coquelle, N., Sliwa, M., Woodhouse, J., Schiro, G., Adam, V., Aquila, A., Barends, T. M., Boutet, S., Byrdin, M., Carbajo, S., De la Mora, E., Doak, R., Feliks, M., Fieschi, F., Foucar, L., Guillon, V., Hilpert, M., Hunter, M. S., Jakobs, S., Koglin, J. E., Kovacsova, G., Lane, T. J., Levy, B., Liang, M., Nass, K., Ridard, J., Robinson, J. S., Roome, C. M., Ruckebusch, C., Seaberg, M., Thepaut, M., Cammarata, M., Demachy, I., Field, M., Shoeman, R. L., Bourgeois, D., Colletier, J., Schlichting, I., Weik, M. 2018; 10 (1): 31–37

    Abstract

    Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

    View details for DOI 10.1038/NCHEM.2853

    View details for Web of Science ID 000423143500009

    View details for PubMedID 29256511

  • Analysis of XFEL serial diffraction data from individual crystalline fibrils IUCRJ Wojtas, D. H., Ayyer, K., Liang, M., Mossou, E., Romoli, F., Seuring, C., Beyerlein, K. R., Bean, R. J., Morgan, A. J., Oberthuer, D., Fleckenstein, H., Heymann, M., Gati, C., Yefanov, O., Barthelmess, M., Ornithopoulou, E., Galli, L., Xavier, P., Ling, W., Frank, M., Yoon, C., White, T. A., Bajt, S., Mitraki, A., Boutet, S., Aquila, A., Barty, A., Forsyth, V., Chapman, H. N., Millane, R. P. 2017; 4: 795–811

    Abstract

    Serial diffraction data collected at the Linac Coherent Light Source from crystalline amyloid fibrils delivered in a liquid jet show that the fibrils are well oriented in the jet. At low fibril concentrations, diffraction patterns are recorded from single fibrils; these patterns are weak and contain only a few reflections. Methods are developed for determining the orientation of patterns in reciprocal space and merging them in three dimensions. This allows the individual structure amplitudes to be calculated, thus overcoming the limitations of orientation and cylindrical averaging in conventional fibre diffraction analysis. The advantages of this technique should allow structural studies of fibrous systems in biology that are inaccessible using existing techniques.

    View details for DOI 10.1107/S2052252517014324

    View details for Web of Science ID 000414266200013

    View details for PubMedID 29123682

    View details for PubMedCentralID PMC5668865

  • Focal Spot and Wavefront Sensing of an X-Ray Free Electron laser using Ronchi shearing interferometry SCIENTIFIC REPORTS Nagler, B., Aquila, A., Boutet, S., Galtier, E. C., Hashim, A., Hunter, M. S., Liang, M., Sakdinawat, A. E., Schroer, C. G., Schropp, A., Seaberg, M. H., Seiboth, F., van Driel, T., Xing, Z., Liu, Y., Lee, H. 2017; 7: 13698

    Abstract

    The Linac Coherent Light Source (LCLS) is an X-ray source of unmatched brilliance, that is advancing many scientific fields at a rapid pace. The highest peak intensities that are routinely produced at LCLS take place at the Coherent X-ray Imaging (CXI) instrument, which can produce spotsize at the order of 100 nm, and such spotsizes and intensities are crucial for experiments ranging from coherent diffractive imaging, non-linear x-ray optics and high field physics, and single molecule imaging. Nevertheless, a full characterisation of this beam has up to now not been performed. In this paper we for the first time characterise this nanofocused beam in both phase and intensity using a Ronchi Shearing Interferometric technique. The method is fast, in-situ, uses a straightforward optimization algoritm, and is insensitive to spatial jitter.

    View details for DOI 10.1038/s41598-017-13710-8

    View details for Web of Science ID 000413357500064

    View details for PubMedID 29057938

    View details for PubMedCentralID PMC5651859

  • Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses PHYSICAL REVIEW LETTERS Kurta, R. P., Donatelli, J. J., Yoon, C., Berntsen, P., Bielecki, J., Daurer, B. J., DeMirci, H., Fromme, P., Hantke, M., Maia, F. C., Munke, A., Nettelblad, C., Pande, K., Reddy, H. N., Sellberg, J. A., Sierra, R. G., Svenda, M., van der Schot, G., Vartanyants, I. A., Williams, G. J., Xavier, P., Aquila, A., Zwart, P. H., Mancuso, A. P. 2017; 119 (15): 158102

    Abstract

    We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

    View details for PubMedID 29077445

    View details for PubMedCentralID PMC5757528

  • Conformational landscape of a virus by single-particle X-ray scattering NATURE METHODS Hosseinizadeh, A., Mashayekhi, G., Copperman, J., Schwander, P., Dashti, A., Sepehr, R., Fung, R., Schmidt, M., Yoon, C., Hogue, B. G., Williams, G. J., Aquila, A., Ourmazd, A. 2017; 14 (9): 877-+

    Abstract

    Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

    View details for DOI 10.1038/NMETH.4395

    View details for Web of Science ID 000408776400016

    View details for PubMedID 28805793

  • Impact of B4C co-sputtering on structure and optical performance of Cr/Sc multilayer X-ray mirrors OPTICS EXPRESS Ghafoor, N., Eriksson, F., Aquila, A., Gullikson, E., Schaefers, F., Greczynski, G., Birch, J. 2017; 25 (15): 18274–87

    Abstract

    The influence of B4C incorporation during magnetron sputter deposition of Cr/Sc multilayers intended for soft X-ray reflective optics is investigated. Chemical analysis suggests formation of metal: boride and carbide bonds which stabilize an amorphous layer structure, resulting in smoother interfaces and an increased reflectivity. A near-normal incidence reflectivity of 11.7%, corresponding to a 67% increase, is achieved at λ = 3.11 nm upon adding 23 at.% (B + C). The advantage is significant for the multilayer periods larger than 1.8 nm, where amorphization results in smaller interface widths, for example, giving 36% reflectance and 99.89% degree of polarization near Brewster angle for a multilayer polarizer. The modulated ion-energy-assistance during the growth is considered vital to avoid intermixing during the interface formation even when B + C are added.

    View details for DOI 10.1364/OE.25.018274

    View details for Web of Science ID 000408584400128

    View details for PubMedID 28789315

  • Structural enzymology using X-ray free electron lasers. Structural dynamics Kupitz, C., Olmos, J. L., Holl, M., Tremblay, L., Pande, K., Pandey, S., Oberthür, D., Hunter, M., Liang, M., Aquila, A., Tenboer, J., Calvey, G., Katz, A., Chen, Y., Wiedorn, M. O., Knoska, J., Meents, A., Majriani, V., Norwood, T., Poudyal, I., Grant, T., Miller, M. D., Xu, W., Tolstikova, A., Morgan, A., Metz, M., Martin-Garcia, J. M., Zook, J. D., Roy-Chowdhury, S., Coe, J., Nagaratnam, N., Meza, D., Fromme, R., Basu, S., Frank, M., White, T., Barty, A., Bajt, S., Yefanov, O., Chapman, H. N., Zatsepin, N., Nelson, G., Weierstall, U., Spence, J., Schwander, P., Pollack, L., Fromme, P., Ourmazd, A., Phillips, G. N., Schmidt, M. 2017; 4 (4): 044003-?

    Abstract

    Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.

    View details for DOI 10.1063/1.4972069

    View details for PubMedID 28083542

  • Numerical simulations of the hard X-ray pulse intensity distribution at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Pardini, T., Aquila, A., Boutet, S., Cocco, D., Hau-Riege, S. P. 2017; 24: 738–43

    Abstract

    Numerical simulations of the current and future pulse intensity distributions at selected locations along the Far Experimental Hall, the hard X-ray section of the Linac Coherent Light Source (LCLS), are provided. Estimates are given for the pulse fluence, energy and size in and out of focus, taking into account effects due to the experimentally measured divergence of the X-ray beam, and measured figure errors of all X-ray optics in the beam path. Out-of-focus results are validated by comparison with experimental data. Previous work is expanded on, providing quantitatively correct predictions of the pulse intensity distribution. Numerical estimates in focus are particularly important given that the latter cannot be measured with direct imaging techniques due to detector damage. Finally, novel numerical estimates of improvements to the pulse intensity distribution expected as part of the on-going upgrade of the LCLS X-ray transport system are provided. We suggest how the new generation of X-ray optics to be installed would outperform the old one, satisfying the tight requirements imposed by X-ray free-electron laser facilities.

    View details for DOI 10.1107/S1600577517007032

    View details for Web of Science ID 000404629100002

    View details for PubMedID 28664879

    View details for PubMedCentralID PMC5493023

  • Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source SCIENTIFIC DATA Reddy, H. N., Yoon, C., Aquila, A., Awel, S., Ayyer, K., Barty, A., Berntsen, P., Bielecki, J., Bobkov, S., Bucher, M., Carini, G. A., Carron, S., Chapman, H., Daurer, B., DeMirci, H., Ekeberg, T., Fromme, P., Hajdu, J., Hanke, M., Hart, P., Hogue, B. G., Hosseinizadeh, A., Kim, Y., Kirian, R. A., Kurta, R. P., Larsson, D. D., Loh, N., Maia, F. C., Mancuso, A. P., Muhlig, K., Munke, A., Nam, D., Nettelblad, C., Ourmazd, A., Rose, M., Schwander, P., Seibert, M., Sellberg, J. A., Song, C., Spence, J. H., Svenda, M., Van der Schot, G., Vartanyants, I. A., Williams, G. J., Xavier, P. 2017; 4: 170079

    Abstract

    Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

    View details for PubMedID 28654088

  • Double-flow focused liquid injector for efficient serial femtosecond crystallography (vol 7, 44628, 2017) SCIENTIFIC REPORTS Oberthuer, D., Knoska, J., Wiedorn, M. O., Beyerlein, K. R., Bushnell, D. A., Kovaleva, E. G., Heymann, M., Gumprecht, L., Kirian, R. A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Doerner, K., Xavier, P., Yefanov, O., James, D. R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P. J., Sarler, B., Belsak, G., Macek, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M. S., Scheerer, P., Lipscomb, J. D., Weierstall, U., Kornberg, R. D., Spence, J. H., Pollack, L., Chapman, H. N., Bajt, S. 2017; 7: 46846

    Abstract

    This corrects the article DOI: 10.1038/srep44628.

    View details for DOI 10.1038/srep46846

    View details for Web of Science ID 000403843300001

    View details for PubMedID 28635955

    View details for PubMedCentralID PMC5478973

  • Se-SAD serial femtosecond crystallography datasets from selenobiotinyl-streptavidin SCIENTIFIC DATA Yoon, C. H., Demirci, H., Sierra, R. G., Dao, E. H., Ahmadi, R., Aksit, F., Aquila, A. L., Batyuk, A., Ciftci, H., Guillet, S., Hayes, M. J., Hayes, B., Lane, T. J., Liang, M., Lundstrom, U., Koglin, J. E., Mgbam, P., Rao, Y., Rendahl, T., Rodriguez, E., Zhang, L., Wakatsuki, S., Boutet, S., Holton, J. M., Hunter, M. S. 2017; 4

    Abstract

    We provide a detailed description of selenobiotinyl-streptavidin (Se-B SA) co-crystal datasets recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS) for selenium single-wavelength anomalous diffraction (Se-SAD) structure determination. Se-B SA was chosen as the model system for its high affinity between biotin and streptavidin where the sulfur atom in the biotin molecule (C10H16N2O3S) is substituted with selenium. The dataset was collected at three different transmissions (100, 50, and 10%) using a serial sample chamber setup which allows for two sample chambers, a front chamber and a back chamber, to operate simultaneously. Diffraction patterns from Se-B SA were recorded to a resolution of 1.9 Å. The dataset is publicly available through the Coherent X-ray Imaging Data Bank (CXIDB) and also on LCLS compute nodes as a resource for research and algorithm development.

    View details for DOI 10.1038/sdata.2017.55

    View details for Web of Science ID 000400151700004

    View details for PubMedID 28440794

  • Double-flow focused liquid injector for efficient serial femtosecond crystallography SCIENTIFIC REPORTS Oberthuer, D., Knoska, J., Wiedorn, M. O., Beyerlein, K. R., Bushnell, D. A., Kovaleva, E. G., Heymann, M., Gumprecht, L., Kirian, R. A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Doerner, K., Xavier, P., Yefanov, O., James, D. R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P. J., Sarler, B., Belsak, G., Macek, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M. S., Scheerer, P., Lipscomb, J. D., Weierstall, U., Kornberg, R. D., Spence, J. H., Pollack, L., Chapman, H. N., Bajt, S. 2017; 7: 44628

    Abstract

    Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double-flow focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices [corrected].

    View details for PubMedID 28300169

  • Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Gati, C., Oberthuer, D., Yefanov, O., Bunker, R. D., Stellato, F., Chiu, E., Yeh, S., Aquila, A., Basu, S., Bean, R., Beyerlein, K. R., Botha, S., Boutet, S., DePonte, D. P., Doak, R., Fromme, R., Galli, L., Grotjohann, I., James, D. R., Kupitz, C., Lomb, L., Messerschmidt, M., Nass, K., Rendek, K., Shoeman, R. L., Wang, D., Weierstall, U., White, T. A., Williams, G. J., Zatsepin, N. A., Fromme, P., Spence, J. H., Goldie, K. N., Jehle, J. A., Metcalf, P., Barty, A., Chapman, H. N. 2017; 114 (9): 2247–52

    Abstract

    To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.

    View details for PubMedID 28202732

  • Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser. Nature communications Hunter, M. S., Yoon, C. H., Demirci, H., Sierra, R. G., Dao, E. H., Ahmadi, R., Aksit, F., Aquila, A. L., Ciftci, H., Guillet, S., Hayes, M. J., Lane, T. J., Liang, M., Lundström, U., Koglin, J. E., Mgbam, P., Rao, Y., Zhang, L., Wakatsuki, S., Holton, J. M., Boutet, S. 2016; 7: 13388-?

    Abstract

    Structural information about biological macromolecules near the atomic scale provides important insight into the functions of these molecules. To date, X-ray crystallography has been the predominant method used for macromolecular structure determination. However, challenges exist when solving structures with X-rays, including the phase problem and radiation damage. X-ray-free electron lasers (X-ray FELs) have enabled collection of diffraction information before the onset of radiation damage, yet the majority of structures solved at X-ray FELs have been phased using external information via molecular replacement. De novo phasing at X-ray FELs has proven challenging due in part to per-pulse variations in intensity and wavelength. Here we report the solution of a selenobiotinyl-streptavidin structure using phases obtained by the anomalous diffraction of selenium measured at a single wavelength (Se-SAD) at the Linac Coherent Light Source. Our results demonstrate Se-SAD, routinely employed at synchrotrons for novel structure determination, is now possible at X-ray FELs.

    View details for DOI 10.1038/ncomms13388

    View details for PubMedID 27811937

    View details for PubMedCentralID PMC5097167

  • Liquid explosions induced by X-ray laser pulses NATURE PHYSICS Stan, C. A., Milathianaki, D., Laksmono, H., Sierra, R. G., McQueen, T. A., Messerschmidt, M., Williams, G. J., Koglin, J. E., Lane, T. J., Hayes, M. J., Guillet, S. A., Liang, M., Aquila, A. L., Willmott, P. R., Robinson, J. S., Gumerlock, K. L., Botha, S., Nass, K., Schlichting, I., Shoeman, R. L., Stone, H. A., Boutet, S. 2016; 12 (10): 966-971

    View details for DOI 10.1038/NPHYS3779

    View details for Web of Science ID 000385337700021

  • Native phasing of x-ray free-electron laser data for a G protein-coupled receptor SCIENCE ADVANCES Batyuk, A., Galli, L., Ishchenko, A., Han, G., Gati, C., Popov, P. A., Lee, M., Stauch, B., White, T. A., Barty, A., Aquila, A., Hunter, M. S., Liang, M., Boutet, S., Pu, M., Liu, Z., Nelson, G., James, D., Li, C., Zhao, Y., Spence, J. H., Liu, W., Fromme, P., Katritch, V., Weierstall, U., Stevens, R. C., Cherezov, V. 2016; 2 (9): e1600292

    Abstract

    Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of "diffraction-before-destruction." However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.

    View details for PubMedID 27679816

  • Open data set of live cyanobacterial cells imaged using an X-ray laser SCIENTIFIC DATA van der Schot, G., Svenda, M., Maia, F. C., Hantke, M. F., DePonte, D. P., Seibert, M., Aquila, A., Schulz, J., Kirian, R. A., Liang, M., Stellato, F., Bari, S., Iwan, B., Andreasson, J., Timneanu, N., Bielecki, J., Westphal, D., de Almeida, F., Odic, D., Hasse, D., Carlsson, G. H., Larsson, D. D., Barty, A., Martin, A. V., Schorb, S., Bostedt, C., Bozek, J. D., Carron, S., Ferguson, K., Rolles, D., Rudenko, A., Epp, S. W., Foucar, L., Rudek, B., Erk, B., Hartmann, R., Kimmel, N., Holl, P., Englert, L., Loh, N., Chapman, H. N., Andersson, I., Hajdu, J., Ekeberg, T. 2016; 3: 160058

    Abstract

    Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

    View details for PubMedID 27479514

  • Design of the mirror optical systems for coherent diffractive imaging at the SPB/SFX instrument of the European XFEL JOURNAL OF OPTICS Bean, R. J., Aquila, A., Samoylova, L., Mancuso, A. P. 2016; 18 (7)
  • Negative Pressures and Spallation in Water Drops Subjected to Nanosecond Shock Waves JOURNAL OF PHYSICAL CHEMISTRY LETTERS Stan, C. A., Willmott, P. R., Stone, H. A., Koglin, J. E., Liang, M., Aquila, A. L., Robinson, J. S., Gumerlock, K. L., Blaj, G., Sierra, R. G., Boutet, S., Guillet, S. A., Curtis, R. H., Vetter, S. L., Loos, H., Turner, J. L., Decker, F. 2016; 7 (11): 2055-2062

    Abstract

    Most experimental studies of cavitation in liquid water at negative pressures reported cavitation at tensions significantly smaller than those expected for homogeneous nucleation, suggesting that achievable tensions are limited by heterogeneous cavitation. We generated tension pulses with nanosecond rise times in water by reflecting cylindrical shock waves, produced by X-ray laser pulses, at the internal surface of drops of water. Depending on the X-ray pulse energy, a range of cavitation phenomena occurred, including the rupture and detachment, or spallation, of thin liquid layers at the surface of the drop. When spallation occurred, we evaluated that negative pressures below -100 MPa were reached in the drops. We model the negative pressures from shock reflection experiments using a nucleation-and-growth model that explains how rapid decompression could outrun heterogeneous cavitation in water, and enable the study of stretched water close to homogeneous cavitation pressures.

    View details for DOI 10.1021/acs.jpclett.6b00687

    View details for Web of Science ID 000377239200020

    View details for PubMedID 27182751

  • Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data IUCRJ Nass, K., Meinhart, A., Barends, T. M., Foucar, L., Gorel, A., Aquila, A., Botha, S., Doak, R., Koglin, J., Liang, M., Shoeman, R. L., Williams, G., Boutet, S., Schlichting, I. 2016; 3: 180–91

    Abstract

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) offers unprecedented possibilities for macromolecular structure determination of systems that are prone to radiation damage. However, phasing XFEL data de novo is complicated by the inherent inaccuracy of SFX data, and only a few successful examples, mostly based on exceedingly strong anomalous or isomorphous difference signals, have been reported. Here, it is shown that SFX data from thaumatin microcrystals can be successfully phased using only the weak anomalous scattering from the endogenous S atoms. Moreover, a step-by-step investigation is presented of the particular problems of SAD phasing of SFX data, analysing data from a derivative with a strong anomalous signal as well as the weak signal from endogenous S atoms.

    View details for DOI 10.1107/S2052252516002980

    View details for Web of Science ID 000379597700004

    View details for PubMedID 27158504

    View details for PubMedCentralID PMC4856140

  • Macromolecular diffractive imaging using imperfect crystals NATURE Ayyer, K., Yefanov, O. M., Oberthuer, D., Roy-Chowdhury, S., Galli, L., Mariani, V., Basu, S., Coe, J., Conrad, C. E., Fromme, R., Schaffer, A., Droener, K., James, D., Kupitz, C., Metz, M., Nelson, G., Xavier, P., Beyerlein, K. R., Schmidt, M., Sarrou, I., Spence, J. H., Weierstall, U., White, T. A., Yang, J., Zhao, Y., Liang, M., Aquila, A., Hunter, M. S., Robinson, J. S., Koglin, J. E., Boutet, S., Fromme, P., Barty, A., Chapman, H. N. 2016; 530 (7589): 202-+

    Abstract

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.

    View details for PubMedID 26863980

    View details for PubMedCentralID PMC4839592

  • Femtosecond and nanometre visualization of structural dynamics in superheated nanoparticles NATURE PHOTONICS Gorkhover, T., Schorb, S., Coffee, R., Adolph, M., Foucar, L., Rupp, D., Aquila, A., Bozek, J. D., Epp, S. W., Erk, B., Gumprecht, L., Holmegaard, L., Hartmann, A., Hartmann, R., Hauser, G., Holl, P., Hoemke, A., Johnsson, P., Kimmel, N., Kuehnel, K., Messerschmidt, M., Reich, C., Rouzee, A., Rudek, B., Schmidt, C., Schulz, J., Soltau, H., Stern, S., Weidenspointner, G., White, B., Kuepper, J., Strueder, L., Schlichting, I., Ullrich, J., Rolles, D., Rudenko, A., Moeller, T., Bostedt, C. 2016; 10 (2): 93-+
  • Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific data Munke, A., Andreasson, J., Aquila, A., Awel, S., Ayyer, K., Barty, A., Bean, R. J., Berntsen, P., Bielecki, J., Boutet, S., Bucher, M., Chapman, H. N., Daurer, B. J., Demirci, H., Elser, V., Fromme, P., Hajdu, J., Hantke, M. F., Higashiura, A., Hogue, B. G., Hosseinizadeh, A., Kim, Y., Kirian, R. A., Reddy, H. K., Lan, T., Larsson, D. S., Liu, H., Loh, N. D., Maia, F. R., Mancuso, A. P., Mühlig, K., Nakagawa, A., Nam, D., Nelson, G., Nettelblad, C., Okamoto, K., Ourmazd, A., Rose, M., van der Schot, G., Schwander, P., Seibert, M. M., Sellberg, J. A., Sierra, R. G., Song, C., Svenda, M., Timneanu, N., Vartanyants, I. A., Westphal, D., Wiedorn, M. O., Williams, G. J., Xavier, P. L., Yoon, C. H., Zook, J. 2016; 3: 160064-?

    Abstract

    Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

    View details for DOI 10.1038/sdata.2016.64

    View details for PubMedID 27478984

    View details for PubMedCentralID PMC4968191

  • Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. Scientific data Ekeberg, T., Svenda, M., Seibert, M. M., Abergel, C., Maia, F. R., Seltzer, V., Deponte, D. P., Aquila, A., Andreasson, J., Iwan, B., Jönsson, O., Westphal, D., Odic, D., Andersson, I., Barty, A., Liang, M., Martin, A. V., Gumprecht, L., Fleckenstein, H., Bajt, S., Barthelmess, M., Coppola, N., Claverie, J., Loh, N. D., Bostedt, C., Bozek, J. D., Krzywinski, J., Messerschmidt, M., Bogan, M. J., Hampton, C. Y., Sierra, R. G., Frank, M., Shoeman, R. L., Lomb, L., Foucar, L., Epp, S. W., Rolles, D., Rudenko, A., Hartmann, R., Hartmann, A., Kimmel, N., Holl, P., Weidenspointner, G., Rudek, B., Erk, B., Kassemeyer, S., Schlichting, I., Strüder, L., Ullrich, J., Schmidt, C., Krasniqi, F., Hauser, G., Reich, C., Soltau, H., Schorb, S., Hirsemann, H., Wunderer, C., Graafsma, H., Chapman, H., Hajdu, J. 2016; 3: 160060-?

    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.

    View details for DOI 10.1038/sdata.2016.60

    View details for PubMedID 27479754

    View details for PubMedCentralID PMC4968188

  • Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II NATURE METHODS Sierra, R. G., Gati, C., Laksmono, H., Dao, E. H., Gul, S., Fuller, F., Kern, J., Chatterjee, R., Ibrahim, M., Brewster, A. S., Young, I. D., Michels-Clark, T., Aquila, A., Liang, M., Hunter, M. S., Koglin, J. E., Boutet, S., Junco, E. A., Hayes, B., Bogan, M. J., Hampton, C. Y., Puglisi, E. V., Sauter, N. K., Stan, C. A., Zouni, A., Yano, J., Yachandra, V. K., Soltis, S. M., Puglisi, J. D., DeMirci, H. 2016; 13 (1): 59-?

    Abstract

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

    View details for DOI 10.1038/NMETH.3667

    View details for Web of Science ID 000367463600028

    View details for PubMedCentralID PMC4890631

  • Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nature methods Sierra, R. G., Gati, C. n., Laksmono, H. n., Dao, E. H., Gul, S. n., Fuller, F. n., Kern, J. n., Chatterjee, R. n., Ibrahim, M. n., Brewster, A. S., Young, I. D., Michels-Clark, T. n., Aquila, A. n., Liang, M. n., Hunter, M. S., Koglin, J. E., Boutet, S. n., Junco, E. A., Hayes, B. n., Bogan, M. J., Hampton, C. Y., Puglisi, E. V., Sauter, N. K., Stan, C. A., Zouni, A. n., Yano, J. n., Yachandra, V. K., Soltis, S. M., Puglisi, J. D., DeMirci, H. n. 2016; 13 (1): 59–62

    Abstract

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

    View details for PubMedID 26619013

  • Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging BIOPHYSICAL JOURNAL Giewekemeyer, K., Hackenberg, C., Aquila, A., Wilke, R. N., Groves, M. R., Jordanova, R., Lamzin, V. S., Borchers, G., Saksl, K., Zozulya, A. V., Sprung, M., Mancuso, A. P. 2015; 109 (9): 1986–95

    Abstract

    The structural investigation of noncrystalline, soft biological matter using x-rays is of rapidly increasing interest. Large-scale x-ray sources, such as synchrotrons and x-ray free electron lasers, are becoming ever brighter and make the study of such weakly scattering materials more feasible. Variants of coherent diffractive imaging (CDI) are particularly attractive, as the absence of an objective lens between sample and detector ensures that no x-ray photons scattered by a sample are lost in a limited-efficiency imaging system. Furthermore, the reconstructed complex image contains quantitative density information, most directly accessible through its phase, which is proportional to the projected electron density of the sample. If applied in three dimensions, CDI can thus recover the sample's electron density distribution. As the extension to three dimensions is accompanied by a considerable dose applied to the sample, cryogenic cooling is necessary to optimize the structural preservation of a unique sample in the beam. This, however, imposes considerable technical challenges on the experimental realization. Here, we show a route toward the solution of these challenges using ptychographic CDI (PCDI), a scanning variant of coherent imaging. We present an experimental demonstration of the combination of three-dimensional structure determination through PCDI with a cryogenically cooled biological sample--a budding yeast cell (Saccharomyces cerevisiae)--using hard (7.9 keV) synchrotron x-rays. This proof-of-principle demonstration in particular illustrates the potential of PCDI for highly sensitive, quantitative three-dimensional density determination of cryogenically cooled, hydrated, and unstained biological matter and paves the way to future studies of unique, nonreproducible biological cells at higher resolution.

    View details for DOI 10.1016/j.bpj.2015.08.047

    View details for Web of Science ID 000364009200024

    View details for PubMedID 26536275

    View details for PubMedCentralID PMC4643197

  • Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation SCIENCE Barends, T. M., Foucar, L., Ardevol, A., Nass, K., Aquila, A., Botha, S., Doak, R., Falahati, K., Hartmann, E., Hilpert, M., Heinz, M., Hoffmann, M. C., Koefinger, J., Koglin, J. E., Kovacsova, G., Liang, M., Milathianaki, D., Lemke, H. T., Reinstein, J., Roome, C. M., Shoeman, R. L., Williams, G. J., Burghardt, I., Hummer, G., Boutet, S., Schlichting, I. 2015; 350 (6259): 445–50

    Abstract

    The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.

    View details for PubMedID 26359336

  • The linac coherent light source single particle imaging road map STRUCTURAL DYNAMICS Aquila, A., Barty, A., Bostedt, C., Boutet, S., Carini, G., Deponte, D., DRELL, P., Doniach, S., Downing, K. H., Earnest, T., Elmlund, H., Elser, V., Guehr, M., Hajdu, J., Hastings, J., Hau-Riege, S. P., Huang, Z., Lattman, E. E., Maia, F. R., Marchesini, S., Ourmazd, A., Pellegrini, C., Santra, R., Schlichting, I., Schroer, C., Spence, J. C., Vartanyants, I. A., Wakatsuki, S., Weis, W. I., Williams, G. J. 2015; 2 (4)

    View details for DOI 10.1063/1.4918726

    View details for Web of Science ID 000360649200003

  • Serial femtosecond X-ray diffraction of enveloped virus microcrystals STRUCTURAL DYNAMICS Lawrence, R. M., Conrad, C. E., Zatsepin, N. A., Grant, T. D., Liu, H., James, D., Nelson, G., Subramanian, G., Aquila, A., Hunter, M. S., Liang, M., Boutet, S., Coe, J., Spence, J. H., Weierstall, U., Liu, W., Fromme, P., Cherezov, V., Hogue, B. G. 2015; 2 (4): 041720

    Abstract

    Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.

    View details for DOI 10.1063/1.4929410

    View details for Web of Science ID 000360649200022

    View details for PubMedID 26798819

    View details for PubMedCentralID PMC4711640

  • A novel inert crystal delivery medium for serial femtosecond crystallography IUCRJ Conrad, C. E., Basu, S., James, D., Wang, D., Schaffer, A., Roy-Chowdhury, S., Zatsepin, N. A., Aquila, A., Coe, J., Gati, C., Hunter, M. S., Koglin, J. E., Kupitz, C., Nelson, G., Subramanian, G., White, T. A., Zhao, Y., Zook, J., Boutet, S., Cherezov, V., Spence, J. H., Fromme, R., Weierstall, U., Fromme, P. 2015; 2: 421–30

    Abstract

    Serial femtosecond crystallography (SFX) has opened a new era in crystallo-graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

    View details for PubMedID 26177184

  • Fluence thresholds for grazing incidence hard x-ray mirrors APPLIED PHYSICS LETTERS Aquila, A., Sobierajski, R., Ozkan, C., Hajkova, V., Burian, T., Chalupsky, J., Juha, L., Stoermer, M., Bajt, S., Klepka, M. T., Dluzewski, P., Morawiec, K., Ohashi, H., Koyama, T., Tono, K., Inubushi, Y., Yabashi, M., Sinn, H., Tschentscher, T., Mancuso, A. P., Gaudin, J. 2015; 106 (24)

    View details for DOI 10.1063/1.4922380

    View details for Web of Science ID 000356618700016

  • High numerical aperture multilayer Laue lenses SCIENTIFIC REPORTS Morgan, A. J., Prasciolu, M., Andrejczuk, A., Krzywinski, J., Meents, A., Pennicard, D., Graafsma, H., Barty, A., Bean, R. J., Barthelmess, M., Oberthuer, D., Yefanov, O., Aquila, A., Chapman, H. N., Bajt, S. 2015; 5: 9892

    Abstract

    The ever-increasing brightness of synchrotron radiation sources demands improved X-ray optics to utilise their capability for imaging and probing biological cells, nanodevices, and functional matter on the nanometer scale with chemical sensitivity. Here we demonstrate focusing a hard X-ray beam to an 8 nm focus using a volume zone plate (also referred to as a wedged multilayer Laue lens). This lens was constructed using a new deposition technique that enabled the independent control of the angle and thickness of diffracting layers to microradian and nanometer precision, respectively. This ensured that the Bragg condition is satisfied at each point along the lens, leading to a high numerical aperture that is limited only by its extent. We developed a phase-shifting interferometric method based on ptychography to characterise the lens focus. The precision of the fabrication and characterisation demonstrated here provides the path to efficient X-ray optics for imaging at 1 nm resolution.

    View details for PubMedID 26030003

  • The Coherent X-ray Imaging instrument at the Linac Coherent Light Source JOURNAL OF SYNCHROTRON RADIATION Liang, M., Williams, G. J., Messerschmidt, M., Seibert, M., Montanez, P. A., Hayes, M., Milathianaki, D., Aquila, A., Hunter, M. S., Koglin, J. E., Schafer, D. W., Guillet, S., Busse, A., Bergan, R., Olson, W., Fox, K., Stewart, N., Curtis, R., Miahnahri, A., Boutet, S. 2015; 22: 514–19

    Abstract

    The Coherent X-ray Imaging (CXI) instrument specializes in hard X-ray, in-vacuum, high power density experiments in all areas of science. Two main sample chambers, one containing a 100 nm focus and one a 1 µm focus, are available, each with multiple diagnostics, sample injection, pump-probe and detector capabilities. The flexibility of CXI has enabled it to host a diverse range of experiments, from biological to extreme matter.

    View details for DOI 10.1107/S160057751500449X

    View details for Web of Science ID 000353920300009

    View details for PubMedID 25931062

    View details for PubMedCentralID PMC4416669

  • Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams JOURNAL OF SYNCHROTRON RADIATION Nass, K., Foucar, L., Barends, T. M., Hartmann, E., Botha, S., Shoeman, R. L., Doak, R., Alonso-Mori, R., Aquila, A., Bajt, S., Barty, A., Bean, R., Beyerlein, K. R., Bublitz, M., Drachmann, N., Gregersen, J., Joensson, H., Kabsch, W., Kassemeyer, S., Koglin, J. E., Krumrey, M., Mattle, D., Messerschmidt, M., Nissen, P., Reinhard, L., Sitsel, O., Sokaras, D., Williams, G. J., Hau-Riege, S., Timneanu, N., Caleman, C., Chapman, H. N., Boutet, S., Schlichting, I. 2015; 22: 225–38

    Abstract

    Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe-4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe-4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

    View details for PubMedID 25723924

  • Imaging single cells in a beam of live cyanobacteria with an X-ray laser NATURE COMMUNICATIONS van der Schot, G., Svenda, M., Maia, F. C., Hantke, M., DePonte, D. P., Seibert, M., Aquila, A., Schulz, J., Kirian, R., Liang, M., Stellato, F., Iwan, B., Andreasson, J., Timneanu, N., Westphal, D., Almeida, F., Odic, D., Hasse, D., Carlsson, G. H., Larsson, D. D., Barty, A., Martin, A. V., Schorb, S., Bostedt, C., Bozek, J. D., Rolles, D., Rudenko, A., Epp, S., Foucar, L., Rudek, B., Hartmann, R., Kimmel, N., Holl, P., Englert, L., Loh, N., Chapman, H. N., Andersson, I., Hajdu, J., Ekeberg, T. 2015; 6: 5704

    Abstract

    There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

    View details for PubMedID 25669616

  • Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser OPTICS EXPRESS Caleman, C., Timneanu, N., Martin, A. V., Jonsson, H., Aquila, A., Barty, A., Scott, H. A., White, T. A., Chapman, H. N. 2015; 23 (2): 1213–31

    Abstract

    In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

    View details for DOI 10.1364/OE.23.001213

    View details for Web of Science ID 000349166100061

    View details for PubMedID 25835880

  • Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser OPTICS EXPRESS Rath, A. D., Timneanu, N., Maia, F. C., Bielecki, J., Fleckenstein, H., Iwan, B., Svenda, M., Hasse, D., Carlsson, G., Westphal, D., Muhlig, K., Hantke, M., Ekeberg, T., Seibert, M., Zani, A., Liang, M., Stellato, F., Kirian, R., Bean, R., Barty, A., Galli, L., Nass, K., Barthelmess, M., Aquila, A., Toleikis, S., Treusch, R., Roling, S., Woestmann, M., Zacharias, H., Chapman, H. N., Bajt, S., DePonte, D., Hajdu, J., Andreasson, J. 2014; 22 (23): 28914–25

    Abstract

    We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 10¹⁶W/cm² with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

    View details for DOI 10.1364/OE.22.028914

    View details for Web of Science ID 000345268500111

    View details for PubMedID 25402130

  • Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser NATURE Kupitz, C., Basu, S., Grotjohann, I., Fromme, R., Zatsepin, N. A., Rendek, K. N., Hunter, M. S., Shoeman, R. L., White, T. A., Wang, D., James, D., Yang, J., Cobb, D. E., Reeder, B., Sierra, R. G., Liu, H., Barty, A., Aquila, A. L., Deponte, D., Kirian, R. A., Bari, S., Bergkamp, J. J., Beyerlein, K. R., Bogan, M. J., Caleman, C., Chao, T., Conrad, C. E., Davis, K. M., Fleckenstein, H., Galli, L., Hau-Riege, S. P., Kassemeyer, S., Laksmono, H., Liang, M., Lomb, L., Marchesini, S., Martin, A. V., Messerschmidt, M., Milathianaki, D., Nass, K., Ros, A., Roy-Chowdhury, S., Schmidt, K., Seibert, M., Steinbrener, J., Stellato, F., Yan, L., Yoon, C., Moore, T. A., Moore, A. L., Pushkar, Y., Williams, G. J., Boutet, S., Doak, R. B., Weierstall, U., Frank, M., Chapman, H. N., Spence, J. C., Fromme, P. 2014; 513 (7517): 261-?

    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.

    View details for DOI 10.1038/nature13453

    View details for Web of Science ID 000341362800056

    View details for PubMedCentralID PMC4821544

  • Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser NATURE METHODS Arnlund, D., Johansson, L. C., Wickstrand, C., Barty, A., Williams, G. J., Malmerberg, E., Davidsson, J., Milathianaki, D., DePonte, D. P., Shoeman, R. L., Wang, D., James, D., Katona, G., Westenhoff, S., White, T. A., Aquila, A., Bari, S., Berntsen, P., Bogan, M., van Driel, T., Doak, R., Kjaer, K., Frank, M., Fromme, R., Grotjohann, I., Henning, R., Hunter, M. S., Kirian, R. A., Kosheleva, I., Kupitz, C., Liang, M., Martin, A. V., Nielsen, M., Messerschmidt, M., Seibert, M., Sjohamn, J., Stellato, F., Weierstall, U., Zatsepin, N. A., Spence, J. H., Fromme, P., Schlichting, I., Boutet, S., Groenhof, G., Chapman, H. N., Neutze, R. 2014; 11 (9): 923–26

    Abstract

    We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.

    View details for PubMedID 25108686

    View details for PubMedCentralID PMC4149589

  • High-dynamic-range coherent diffractive imaging: ptychography using the mixed-mode pixel array detector JOURNAL OF SYNCHROTRON RADIATION Giewekemeyer, K., Philipp, H. T., Wilke, R. N., Aquila, A., Osterhoff, M., Tate, M. W., Shanks, K. S., Zozulya, A. V., Salditt, T., Gruner, S. M., Mancuso, A. P. 2014; 21: 1167–74

    Abstract

    Coherent (X-ray) diffractive imaging (CDI) is an increasingly popular form of X-ray microscopy, mainly due to its potential to produce high-resolution images and the lack of an objective lens between the sample and its corresponding imaging detector. One challenge, however, is that very high dynamic range diffraction data must be collected to produce both quantitative and high-resolution images. In this work, hard X-ray ptychographic coherent diffractive imaging has been performed at the P10 beamline of the PETRA III synchrotron to demonstrate the potential of a very wide dynamic range imaging X-ray detector (the Mixed-Mode Pixel Array Detector, or MM-PAD). The detector is capable of single photon detection, detecting fluxes exceeding 1 × 10(8) 8-keV photons pixel(-1) s(-1), and framing at 1 kHz. A ptychographic reconstruction was performed using a peak focal intensity on the order of 1 × 10(10) photons µm(-2) s(-1) within an area of approximately 325 nm × 603 nm. This was done without need of a beam stop and with a very modest attenuation, while `still' images of the empty beam far-field intensity were recorded without any attenuation. The treatment of the detector frames and CDI methodology for reconstruction of non-sensitive detector regions, partially also extending the active detector area, are described.

    View details for DOI 10.1107/S1600577514013411

    View details for Web of Science ID 000341687000034

    View details for PubMedID 25178008

    View details for PubMedCentralID PMC4151683

  • Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1 IUCRJ Lee, H., Cherni, I., Yu, H., Fromme, R., Doran, J. D., Grotjohan, I., Mittman, M., Basu, S., Deb, A., Doerner, K., Aquila, A., Barty, A., Boutet, S., Chapman, H. N., Doak, R., Hunter, M. S., James, D., Kirian, R. A., Kupitz, C., Lawrence, R. M., Liu, H., Nass, K., Schlichting, I., Schmidt, K. E., Seibert, M., Shoeman, R. L., Spence, J. H., Stellato, F., Weierstall, U., Williams, G. J., Yoon, C., Wang, D., Zatsepin, N. A., Hogue, B. G., Matoba, N., Fromme, P., Mor, T. S. 2014; 1: 305–17

    Abstract

    CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.

    View details for PubMedID 25295172

  • Femtosecond x-ray photoelectron diffraction on gas-phase dibromobenzene molecules JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS Rolles, D., Boll, R., Adolph, M., Aquila, A., Bostedt, C., Bozek, J. D., Chapman, H. N., Coffee, R., Coppola, N., Decleva, P., Delmas, T., Epp, S. W., Erk, B., Filsinger, F., Foucar, L., Gumprecht, L., Hoemke, A., Gorkhover, T., Holmegaard, L., Johnsson, P., Kaiser, C., Krasniqi, F., Kuehnel, K., Maurer, J., Messerschmidt, M., Moshammer, R., Quevedo, W., Rajkovic, I., Rouzee, A., Rudek, B., Schlichting, I., Schmidt, C., Schorb, S., Schroeter, C. D., Schulz, J., Stapelfeldt, H., Stener, M., Stern, S., Techert, S., Thogersen, J., Vrakking, M. J., Rudenko, A., Kuepper, J., Ullrich, J. 2014; 47 (12)
  • Investigation of surface topology of printed nanoparticle layers using wide-angle low-Q scattering JOURNAL OF SYNCHROTRON RADIATION Jonah, E. O., Haerting, M., Gullikson, E., Aquila, A., Britton, D. T. 2014; 21: 547–53

    Abstract

    A new small-angle scattering technique in reflection geometry is described which enables a topological study of rough surfaces. This is achieved by using long-wavelength soft X-rays which are scattered at wide angles but in the low-Q range normally associated with small-angle scattering. The use of nanometre-wavelength radiation restricts the penetration to a thin surface layer which follows the topology of the surface, while moving the scattered beam to wider angles preventing shadowing by the surface features. The technique is, however, only applicable to rough surfaces for which there is no specular reflection, so that only the scattered beam was detected by the detector. As an example, a study of the surfaces of rough layers of silicon produced by the deposition of nanoparticles by blade-coating is presented. The surfaces of the blade-coated layers have rough features of the order of several micrometers. Using 2 nm and 13 nm X-rays scattered at angular ranges of 5° ≤ θ ≤ 51° and 5° ≤ θ ≤ 45°, respectively, a combined range of scattering vector of 0.00842 Å(-1) ≤ Q ≤ 0.4883 Å(-1) was obtained. Comparison with previous transmission SAXS and USAXS studies of the same materials indicates that the new method does probe the surface topology rather than the internal microstructure.

    View details for DOI 10.1107/S160057751400410X

    View details for Web of Science ID 000335142900012

    View details for PubMedID 24763644

  • X-Ray Diffraction from Isolated and Strongly Aligned Gas-Phase Molecules with a Free-Electron Laser PHYSICAL REVIEW LETTERS Kuepper, J., Stern, S., Holmegaard, L., Filsinger, F., Rouzee, A., Rudenko, A., Johnsson, P., Martin, A. V., Adolph, M., Aquila, A., Bajt, S., Barty, A., Bostedt, C., Bozek, J., Caleman, C., Coffee, R., Coppola, N., Delmas, T., Epp, S., Erk, B., Foucar, L., Gorkhover, T., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Holl, P., Hoemke, A., Kimmel, N., Krasniqi, F., Kuehnel, K., Maurer, J., Messerschmidt, M., Moshammer, R., Reich, C., Rudek, B., Santra, R., Schlichting, I., Schmidt, C., Schorb, S., Schulz, J., Soltau, H., Spence, J. H., Starodub, D., Strueder, L., Thogersen, J., Vrakking, M. J., Weidenspointner, G., White, T. A., Wunderer, C., Meijer, G., Ullrich, J., Stapelfeldt, H., Rolles, D., Chapman, H. N. 2014; 112 (8)
  • Automated identification and classification of single particle serial femtosecond X-ray diffraction data OPTICS EXPRESS Andreasson, J., Martin, A. V., Liang, M., Timneanu, N., Aquila, A., Wang, F., Iwan, B., Svenda, M., Ekeberg, T., Hantke, M., Bielecki, J., Rolles, D., Rudenko, A., Foucar, L., Hartmann, R., Erk, B., Rudek, B., Chapman, H. N., Hajdu, J., Barty, A. 2014; 22 (3): 2497–2510

    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.

    View details for DOI 10.1364/OE.22.002497

    View details for Web of Science ID 000332518100035

    View details for PubMedID 24663542

  • Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature Kupitz, C. n., Basu, S. n., Grotjohann, I. n., Fromme, R. n., Zatsepin, N. A., Rendek, K. N., Hunter, M. S., Shoeman, R. L., White, T. A., Wang, D. n., James, D. n., Yang, J. H., Cobb, D. E., Reeder, B. n., Sierra, R. G., Liu, H. n., Barty, A. n., Aquila, A. L., Deponte, D. n., Kirian, R. A., Bari, S. n., Bergkamp, J. J., Beyerlein, K. R., Bogan, M. J., Caleman, C. n., Chao, T. C., Conrad, C. E., Davis, K. M., Fleckenstein, H. n., Galli, L. n., Hau-Riege, S. P., Kassemeyer, S. n., Laksmono, H. n., Liang, M. n., Lomb, L. n., Marchesini, S. n., Martin, A. V., Messerschmidt, M. n., Milathianaki, D. n., Nass, K. n., Ros, A. n., Roy-Chowdhury, S. n., Schmidt, K. n., Seibert, M. n., Steinbrener, J. n., Stellato, F. n., Yan, L. n., Yoon, C. n., Moore, T. A., Moore, A. L., Pushkar, Y. n., Williams, G. J., Boutet, S. n., Doak, R. B., Weierstall, U. n., Frank, M. n., Chapman, H. N., Spence, J. C., Fromme, P. n. 2014; 513 (7517): 261–65

    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.

    View details for PubMedID 25043005

    View details for PubMedCentralID PMC4821544

  • Imaging molecular structure through femtosecond photoelectron diffraction on aligned and oriented gas-phase molecules FARADAY DISCUSSIONS Boll, R., Rouzee, A., Adolph, M., Anielski, D., Aquila, A., Bari, S., Bomme, C., Bostedt, C., Bozek, J. D., Chapman, H. N., Christensen, L., Coffee, R., Coppola, N., De, S., Decleva, P., Epp, S. W., Erk, B., Filsinger, F., Foucar, L., Gorkhover, T., Gumprecht, L., Hoemke, A., Holmegaard, L., Johnsson, P., Kienitz, J. S., Kierspel, T., Krasniqi, F., Kuehnel, K., Maurer, J., Messerschmidt, M., Moshammer, R., Mueller, N. M., Rudek, B., Savelyev, E., Schlichting, I., Schmidt, C., Scholz, F., Schorb, S., Schulz, J., Seltmann, J., Stener, M., Stern, S., Techert, S., Thogersen, J., Trippel, S., Viefhaus, J., Vrakking, M., Stapelfeldt, H., Kuepper, J., Ullrich, J., Rudenko, A., Rolles, D. 2014; 171: 57–80

    Abstract

    This paper gives an account of our progress towards performing femtosecond time-resolved photoelectron diffraction on gas-phase molecules in a pump-probe setup combining optical lasers and an X-ray free-electron laser. We present results of two experiments aimed at measuring photoelectron angular distributions of laser-aligned 1-ethynyl-4-fluorobenzene (C(8)H(5)F) and dissociating, laser-aligned 1,4-dibromobenzene (C(6)H(4)Br(2)) molecules and discuss them in the larger context of photoelectron diffraction on gas-phase molecules. We also show how the strong nanosecond laser pulse used for adiabatically laser-aligning the molecules influences the measured electron and ion spectra and angular distributions, and discuss how this may affect the outcome of future time-resolved photoelectron diffraction experiments.

    View details for DOI 10.1039/c4fd00037d

    View details for Web of Science ID 000345529900003

    View details for PubMedID 25290160

  • Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography NATURE COMMUNICATIONS Johansson, L. C., Arnlund, D., Katona, G., White, T. A., Barty, A., DePonte, D. P., Shoeman, R. L., Wickstrand, C., Sharma, A., Williams, G. J., Aquila, A., Bogan, M. J., Caleman, C., Davidsson, J., Doak, R., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M. S., Kassemeyer, S., Kirian, R. A., Kupitz, C., Liang, M., Lomb, L., Malmerberg, E., Martin, A. V., Messerschmidt, M., Nass, K., Redecke, L., Seibert, M., Sjoehamn, J., Steinbrener, J., Stellato, F., Wang, D., Wahlgren, W. Y., Weierstall, U., Westenhoff, S., Zatsepin, N. A., Boutet, S., Spence, J. H., Schlichting, I., Chapman, H. N., Fromme, P., Neutze, R. 2013; 4: 2911

    Abstract

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.

    View details for PubMedID 24352554

  • Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers OPTICS EXPRESS Park, H. J., Loh, N. D., Sierra, R. G., Hampton, C. Y., Starodub, D., Martin, A. V., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Lomb, L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J., Elser, V. 2013; 21 (23): 28729-28742

    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.

    View details for DOI 10.1364/OE.21.028729

    View details for Web of Science ID 000327494000115

    View details for PubMedID 24514385

  • Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS Pedersoli, E., Loh, N. D., Capotondi, F., Hampton, C. Y., Sierra, R. G., Starodub, D., Bostedt, C., Bozek, J., Nelson, A. J., Aslam, M., Li, S., Dravid, V. P., Martin, A. V., Aquila, A., Barty, A., Fleckenstein, H., GUMPRECHT, L., Liang, M., Nass, K., Schulz, J., White, T. A., Coppola, N., Bajt, S., Barthelmess, M., Graafsma, H., Hirsemann, H., Wunderer, C., Epp, S. W., Erk, B., Rudek, B., Rudenko, A., Foucar, L., Kassemeyer, S., Lomb, L., Rolles, D., Shoeman, R. L., Steinbrener, J., Hartmann, R., Hartmann, A., Hauser, G., Holl, P., Kimmel, N., Reich, C., Soltau, H., Weidenspointner, G., Benner, W. H., Farquar, G. R., Hau-Riege, S. P., Hunter, M. S., Ekeberg, T., Hantke, M., Maia, F. R., Tobias, H. J., Marchesini, S., Frank, M., Strueder, L., Schlichting, I., Ullrich, J., Chapman, H. N., Bucksbaum, P. H., Kiskinova, M., Bogan, M. J. 2013; 46 (16)
  • Sensing the wavefront of x-ray free-electron lasers using aerosol spheres OPTICS EXPRESS Loh, N. D., Starodub, D., Lomb, L., Hampton, C. Y., Martin, A. V., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J. 2013; 21 (10): 12385-12394

    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 10(21) 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.

    View details for DOI 10.1364/OE.21.012385

    View details for Web of Science ID 000319339600072

    View details for PubMedID 23736456

  • Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser SCIENCE Redecke, L., Nass, K., DePonte, D. P., White, T. A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T. M., Boutet, S., Williams, G. J., Messerschmidt, M., Seibert, M., Aquila, A., Arnlund, D., Bajt, S., Barth, T., Bogan, M. J., Caleman, C., Chao, T., Doak, R., Fleckenstein, H., Frank, M., Fromme, R., Galli, L., Grotjohann, I., Hunter, M. S., Johansson, L. C., Kassemeyer, S., Katona, G., Kirian, R. A., Koopmann, R., Kupitz, C., Lomb, L., Martin, A. V., Mogk, S., Neutze, R., Shoeman, R. L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N. A., Spence, J. H., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H. N. 2013; 339 (6116): 227–30

    Abstract

    The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.

    View details for PubMedID 23196907

  • Results from single shot grazing incidence hard x-ray damage measurements conducted at the SACLA FEL Aquila, A., Ozkan, C., Sobierajski, R., Hajkova, V., Burian, T., Chalupsky, J., Juha, L., Stoermer, M., Ohashi, H., Koyama, T., Tono, K., Inubushi, Y., Yabashi, M., Sinn, H., Tschentscher, T., Mancuso, A. P., Gaudin, J., Juha, L., Bajt, S., London, R., Hudec, R., Pina, L. SPIE-INT SOC OPTICAL ENGINEERING. 2013

    View details for DOI 10.1117/12.2017725

    View details for Web of Science ID 000329577700013

  • Characterizing the focus of a multilayer coated off-axis parabola for FLASH beam at lambda=4.3 nm Leontowich, A. G., Aquila, A., Stellato, F., Bean, R., Fleckenstein, H., Prasciolu, M., Liang, M., DePonte, D. P., Barty, A., Wang, F., Andreasson, J., Hajdu, J., Chapman, H. N., Bajt, S., Juha, L., Bajt, S., London, R., Hudec, R., Pina, L. SPIE-INT SOC OPTICAL ENGINEERING. 2013

    View details for DOI 10.1117/12.2022403

    View details for Web of Science ID 000329577700022

  • Single-particle structure determination by correlations of snapshot X-ray diffraction patterns NATURE COMMUNICATIONS Starodub, D., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bostedt, C., Bozek, J. D., Coppola, N., Doak, R. B., Epp, S. W., Erk, B., Foucar, L., GUMPRECHT, L., Hampton, C. Y., Hartmann, A., Hartmann, R., Holl, P., Kassemeyer, S., Kimmel, N., Laksmono, H., Liang, M., Loh, N. D., Lomb, L., Martin, A. V., Nass, K., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Sierra, R. G., Soltau, H., Steinbrener, J., Stellato, F., Stern, S., Weidenspointner, G., Frank, M., Ullrich, J., Strueder, L., Schlichting, I., Chapman, H. N., Spence, J. C., Bogan, M. J. 2012; 3

    Abstract

    Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.

    View details for DOI 10.1038/ncomms2288

    View details for Web of Science ID 000316356700043

    View details for PubMedID 23232406

  • Ultra-efficient ionization of heavy atoms by intense X-ray free-electron laser pulses NATURE PHOTONICS Rudek, B., Son, S., Foucar, L., Epp, S. W., Erk, B., Hartmann, R., Adolph, M., Andritschke, R., Aquila, A., Berrah, N., Bostedt, C., Bozek, J., Coppola, N., Filsinger, F., Gorke, H., Gorkhover, T., Graafsma, H., Gumprecht, L., Hartmann, A., Hauser, G., Herrmann, S., Hirsemann, H., Holl, P., Hoemke, A., Journel, L., Kaiser, C., Kimmel, N., Krasniqi, F., Kuehnel, K., Matysek, M., Messerschmidt, M., Miesner, D., Moeller, T., Moshammer, R., Nagaya, K., Nilsson, B., Potdevin, G., Pietschner, D., Reich, C., Rupp, D., Schaller, G., Schlichting, I., Schmidt, C., Schopper, F., Schorb, S., Schroeter, C., Schulz, J., Simon, M., Soltau, H., Strueder, L., Ueda, K., Weidenspointner, G., Santra, R., Ullrich, J., Rudenko, A., Rolles, D. 2012; 6 (12): 858-865
  • High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography SCIENCE Boutet, S., Lomb, L., Williams, G. J., Barends, T. R., Aquila, A., Doak, R. B., Weierstall, U., Deponte, D. P., Steinbrener, J., Shoeman, R. L., Messerschmidt, M., Barty, A., White, T. A., Kassemeyer, S., Kirian, R. A., Seibert, M. M., Montanez, P. A., Kenney, C., Herbst, R., Hart, P., Pines, J., Haller, G., Gruner, S. M., Philipp, H. T., Tate, M. W., Hromalik, M., Koerner, L. J., van Bakel, N., Morse, J., Ghonsalves, W., Arnlund, D., Bogan, M. J., Caleman, C., Fromme, R., Hampton, C. Y., Hunter, M. S., Johansson, L. C., Katona, G., Kupitz, C., Liang, M., Martin, A. V., Nass, K., Redecke, L., Stellato, F., Timneanu, N., Wang, D., Zatsepin, N. A., Schafer, D., Defever, J., Neutze, R., Fromme, P., Spence, J. C., Chapman, H. N., Schlichting, I. 2012; 337 (6092): 362-364

    Abstract

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

    View details for DOI 10.1126/science.1217737

    View details for Web of Science ID 000306542600057

    View details for PubMedID 22653729

  • Noise-robust coherent diffractive imaging with a single diffraction pattern OPTICS EXPRESS Martin, A. V., Wang, F., Loh, N. D., Ekeberg, T., Maia, F. C., Hantke, M., van der Schot, G., Hampton, C. Y., Sierra, R. G., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strueder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., Chapman, H. N. 2012; 20 (15): 16650–61
  • Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight NATURE Loh, N. D., Hampton, C. Y., Martin, A. V., Starodub, D., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Lomb, L., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. M., GUMPRECHT, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S. P., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Bucksbaum, P., Hodgson, K. O., Strueder, L., Ullrich, J., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J. 2012; 486 (7404): 513-517

    Abstract

    The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. 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 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, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

    View details for DOI 10.1038/nature11222

    View details for Web of Science ID 000305760600039

    View details for PubMedID 22739316

  • Nanoplasma Dynamics of Single Large Xenon Clusters Irradiated with Superintense X-Ray Pulses from the Linac Coherent Light Source Free-Electron Laser PHYSICAL REVIEW LETTERS Gorkhover, T., Adolph, M., Rupp, D., Schorb, S., Epp, S. W., Erk, B., Foucar, L., Hartmann, R., Kimmel, N., Kuehnel, K., Rolles, D., Rudek, B., Rudenko, A., Andritschke, R., Aquila, A., Bozek, J. D., Coppola, N., Erke, T., Filsinger, F., Gorke, H., Graafsma, H., GUMPRECHT, L., Hauser, G., Herrmann, S., Hirsemann, H., Hoemke, A., Holl, P., Kaiser, C., Krasniqi, F., Meyer, J., Matysek, M., Messerschmidt, M., Miessner, D., Nilsson, B., Pietschner, D., Potdevin, G., Reich, C., Schaller, G., Schmidt, C., Schopper, F., Schroeter, C. D., Schulz, J., Soltau, H., Weidenspointner, G., Schlichting, I., Strueder, L., Ullrich, J., Moeller, T., Bostedt, C. 2012; 108 (24)

    Abstract

    The plasma dynamics of single mesoscopic Xe particles irradiated with intense femtosecond x-ray pulses exceeding 10(16)  W/cm2 from the Linac Coherent Light Source free-electron laser are investigated. Simultaneous recording of diffraction patterns and ion spectra allows eliminating the influence of the laser focal volume intensity and particle size distribution. The data show that for clusters illuminated with intense x-ray pulses, highly charged ionization fragments in a narrow distribution are created and that the nanoplasma recombination is efficiently suppressed.

    View details for DOI 10.1103/PhysRevLett.108.245005

    View details for Web of Science ID 000306342000018

    View details for PubMedID 23004284

  • Femtosecond dark-field imaging with an X-ray free electron laser OPTICS EXPRESS Martin, A. V., Loh, N. D., Hampton, C. Y., Sierra, R. G., Wang, F., Aquila, A., Bajt, S., Barthelmess, M., Bostedt, C., Bozek, J. D., Coppola, N., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Liang, M., Lomb, L., Maia, F. C., Marchesini, S., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schulz, J., Shoeman, R. L., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strueder, L., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C. B., Barty, A., Schlichting, I., Bogan, M. J., Chapman, H. N. 2012; 20 (12): 13501–12

    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.

    View details for DOI 10.1364/OE.20.013501

    View details for Web of Science ID 000305463600086

    View details for PubMedID 22714377

  • CrystFEL: a software suite for snapshot serial crystallography JOURNAL OF APPLIED CRYSTALLOGRAPHY White, T. A., Kirian, R. A., Martin, A. V., Aquila, A., Nass, K., Barty, A., Chapman, H. N. 2012; 45: 335–41
  • In vivo protein crystallization opens new routes in structural biology NATURE METHODS Koopmann, R., Cupelli, K., Redecke, L., Nass, K., Deponte, D. P., White, T. A., Stellato, F., Rehders, D., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M. J., Bostedt, C., Boutet, S., Bozek, J. D., Caleman, C., Coppola, N., Davidsson, J., Doak, R. B., Ekeberg, T., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C. Y., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Hunter, M. S., Kassemeyer, S., Kirian, R. A., Lomb, L., Maia, F. R., Kimmel, N., Martin, A. V., Messerschmidt, M., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M. M., Shoeman, R. L., Sierra, R. G., Soltau, H., Stern, S., Strueder, L., Timneanu, N., Ullrich, J., Wang, X., Weidenspointner, G., Weierstall, U., Williams, G. J., Wunderer, C. B., Fromme, P., Spence, J. C., Stehle, T., Chapman, H. N., Betzel, C., Duszenko, M. 2012; 9 (3): 259-U54

    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.

    View details for DOI 10.1038/NMETH.1859

    View details for Web of Science ID 000300890400020

    View details for PubMedID 22286384

    View details for PubMedCentralID PMC3429599

  • High-efficiency x-ray gratings with asymmetric-cut multilayers JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION Bajt, S., Chapman, H. N., Aquila, A., Gullikson, E. 2012; 29 (3): 216–30

    Abstract

    We present the fabrication and analysis of efficient and highly dispersive gratings for the x-ray and extreme ultraviolet (EUV) regime. We show that an asymmetric-cut multilayer structure can act as a near-perfect blazed grating. The precision and high line density are achieved by layer deposition of materials, which can be controlled to the angstrom level. We demonstrate this in the EUV regime with two structures made by cutting and polishing magnetron-sputtered multilayer mirrors of over 2000 bilayers thick, each with a period of 6.88 nm. These were cut at angles of 2.9° and 7.8° to the surface. Within the 3% bandwidth rocking curve of the multilayer, the angular dispersion of the diffracted wave was in agreement with the grating equation for elements with 7250 and 19,700 line pairs/mm, respectively. The dependence of the measured efficiency was in excellent agreement with a formulation of dynamical diffraction theory for multilayered structures. At a wavelength of 13.2 nm, the efficiency of the first-order diffraction was over 95% of the reflectivity of the uncut multilayer. We predict that such structures should also be effective at shorter x-ray wavelengths. Both the Laue (transmitting) and Bragg (reflecting) geometries are incorporated in our formalism, which is applied to the analysis of multilayer Laue lenses and focusing and dispersing Bragg optics.

    View details for DOI 10.1364/JOSAA.29.000216

    View details for Web of Science ID 000301064100005

    View details for PubMedID 22472750

  • Lipidic phase membrane protein serial femtosecond crystallography NATURE METHODS Johansson, L. C., Arnlund, D., White, T. A., Katona, G., Deponte, D. P., Weierstall, U., Doak, R. B., Shoeman, R. L., Lomb, L., Malmerberg, E., Davidsson, J., Nass, K., Liang, M., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M. J., Bostedt, C., Bozek, J. D., Caleman, C., Coffee, R., Coppola, N., Ekeberg, T., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C. Y., Hartmann, R., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Hunter, M. S., Kassemeyer, S., Kimmel, N., Kirian, R. A., Maia, F. R., Marchesini, S., Martin, A. V., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M. M., Sierra, R. G., Soltau, H., Starodub, D., Stellato, F., Stern, S., Strueder, L., Timneanu, N., Ullrich, J., Wahlgren, W. Y., Wang, X., Weidenspointner, G., Wunderer, C., Fromme, P., Chapman, H. N., Spence, J. C., Neutze, R. 2012; 9 (3): 263-U59

    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.

    View details for DOI 10.1038/NMETH.1867

    View details for Web of Science ID 000300890400021

    View details for PubMedID 22286383

    View details for PubMedCentralID PMC3438231

  • Femtosecond free-electron laser x-ray diffraction data sets for algorithm development OPTICS EXPRESS Kassemeyer, S., Steinbrener, J., Lomb, L., Hartmann, E., Aquila, A., Barty, A., Martin, A. V., Hampton, C. Y., Bajt, S., Barthelmess, M., Barends, T. R., Bostedt, C., Bott, M., Bozek, J. D., Coppola, N., Cryle, M., Deponte, D. P., Doak, R. B., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hartmann, A., Hartmann, R., Hauser, G., Hirsemann, H., Hoemke, A., Holl, P., Jonsson, O., Kimmel, N., Krasniqi, F., Liang, M., Maia, F. R., Marchesini, S., Nass, K., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schmidt, C., Schulz, J., Shoeman, R. L., Sierra, R. G., Soltau, H., Spence, J. C., Starodub, D., Stellato, F., Stern, S., Stier, G., Svenda, M., Weidenspointner, G., Weierstall, U., White, T. A., Wunderer, C., Frank, M., Chapman, H. N., Ullrich, J., Strueder, L., Bogan, M. J., Schlichting, I. 2012; 20 (4): 4149-4158

    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.

    View details for Web of Science ID 000301041900078

    View details for PubMedID 22418172

  • Time-resolved protein nanocrystallography using an X-ray free-electron laser OPTICS EXPRESS Aquila, A., Hunter, M. S., Doak, R., Kirian, R. A., Fromme, P., White, T. A., Andreasson, J., Arnlund, D., Bajt, S., Barends, T. M., Barthelmess, M., Bogan, M. J., Bostedt, C., Bottin, H., Bozek, J. D., Caleman, C., Coppola, N., Davidsson, J., DePonte, D. P., Elser, V., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Frank, M., Fromme, R., Graafsma, H., Grotjohann, I., Gumprecht, L., Hajdu, J., Hampton, C. Y., Hartmann, A., Hartmann, R., Hauriege, S., Hauser, G., Hirsemann, H., Holl, P., Holton, J. M., Hoemke, A., Johansson, L., Kimmel, N., Kassemeyer, S., Krasniqi, F., Kuehnel, K., Liang, M., Lomb, L., Malmerberg, E., Marchesini, S., Martin, A. V., Maia, F. C., Messerschmidt, M., Nass, K., Reich, C., Neutze, R., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schmidt, C., Schmidt, K. E., Schulz, J., Seibert, M., Shoeman, R. L., Sierra, R., Soltau, H., Starodub, D., Stellato, F., Stern, S., Strueder, L., Timneanu, N., Ullrich, J., Wang, X., Williams, G. J., Weidenspointner, G., Weierstall, U., Wunderer, C., Barty, A., Spence, J. H., Chapman, H. N. 2012; 20 (3): 2706–16

    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.

    View details for PubMedID 22330507

  • Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements. Nature photonics Barty, A. n., Caleman, C. n., Aquila, A. n., Timneanu, N. n., Lomb, L. n., White, T. A., Andreasson, J. n., Arnlund, D. n., Bajt, S. n., Barends, T. R., Barthelmess, M. n., Bogan, M. J., Bostedt, C. n., Bozek, J. D., Coffee, R. n., Coppola, N. n., Davidsson, J. n., Deponte, D. P., Doak, R. B., Ekeberg, T. n., Elser, V. n., Epp, S. W., Erk, B. n., Fleckenstein, H. n., Foucar, L. n., Fromme, P. n., Graafsma, H. n., Gumprecht, L. n., Hajdu, J. n., Hampton, C. Y., Hartmann, R. n., Hartmann, A. n., Hauser, G. n., Hirsemann, H. n., Holl, P. n., Hunter, M. S., Johansson, L. n., Kassemeyer, S. n., Kimmel, N. n., Kirian, R. A., Liang, M. n., Maia, F. R., Malmerberg, E. n., Marchesini, S. n., Martin, A. V., Nass, K. n., Neutze, R. n., Reich, C. n., Rolles, D. n., Rudek, B. n., Rudenko, A. n., Scott, H. n., Schlichting, I. n., Schulz, J. n., Seibert, M. M., Shoeman, R. L., Sierra, R. G., Soltau, H. n., Spence, J. C., Stellato, F. n., Stern, S. n., Strüder, L. n., Ullrich, J. n., Wang, X. n., Weidenspointner, G. n., Weierstall, U. n., Wunderer, C. B., Chapman, H. N. 2012; 6: 35–40

    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 information1-4. 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.

    View details for PubMedID 24078834

    View details for PubMedCentralID PMC3783007

  • In-band and out-of-band reflectance calibrations of the EUV multilayer mirrors of the Atmospheric Imaging Assembly instrument aboard the Solar Dynamics Observatory Soufli, R., Spiller, E., Windt, D. L., Robinson, J. C., Gullikson, E. M., Rodriguez-de Marcos, L., Fernandez-Perea, M., Baker, S. L., Aquila, A. L., Dollar, F. J., Antonio Mendez, J., Larruquert, J. I., Golub, L., Boerner, P., Takahashi, T., Murray, S. S., DenHerder, J. W. SPIE-INT SOC OPTICAL ENGINEERING. 2012

    View details for DOI 10.1117/12.927274

    View details for Web of Science ID 000312391600095

  • Modeling of XFEL induced ionization and atomic displacement in protein nanocrystals Caleman, C., Timneanu, N., Martin, A. V., White, T. A., Scott, H. A., Barty, A., Aquila, A., Chapman, H. N., Moeller, S. P., Yabashi, M., HauRiege, S. P. SPIE-INT SOC OPTICAL ENGINEERING. 2012

    View details for DOI 10.1117/12.929294

    View details for Web of Science ID 000311837900011

  • Profiling structured beams using injected aerosols Conference on X-Ray Free-Electron Lasers - Beam Diagnostics, Beamline Instrumentation, and Applications Loh, N. D., Starodub, D., Lomb, L., Hampton, C. Y., Martin, A. V., Sierra, R. G., Barty, A., Aquila, A., Schulz, J., Steinbrener, J., Shoeman, R. L., Kassemeyer, S., Bostedt, C., Bozek, J., Epp, S. W., Erk, B., Hartmann, R., Rolles, D., Rudenko, A., Rudek, B., Foucar, L., Kimmel, N., Weidenspointner, G., Hauser, G., Holl, P., Pedersoli, E., Liang, M., Hunter, M. S., Gumprecht, L., Coppola, N., Wunderer, C., Graafsma, H., Maia, F. R., Ekeberg, T., Hantke, M., Fleckenstein, H., Hirsemann, H., Nass, K., White, T. A., Tobias, H. J., Farquar, G. R., Benner, W. H., Hau-Riege, S., Reich, C., Hartmann, A., Soltau, H., Marchesini, S., Bajt, S., Barthelmess, M., Strueder, L., Ullrich, J., Bucksbaum, P., Hodgson, K. O., Frank, M., Schlichting, I., Chapman, H. N., Bogan, M. J. SPIE-INT SOC OPTICAL ENGINEERING. 2012

    View details for DOI 10.1117/12.930075

    View details for Web of Science ID 000311837900002

  • Self-terminating diffraction gates femtosecond X-ray nanocrystallography measurements NATURE PHOTONICS Barty, A., Caleman, C., Aquila, A., Timneanu, N., Lomb, L., White, T. A., Andreasson, J., Arnlund, D., Bajt, S., Barends, T. R., Barthelmess, M., Bogan, M. J., Bostedt, C., Bozek, J. D., Coffee, R., Coppola, N., Davidsson, J., Deponte, D. P., Doak, R. B., Ekeberg, T., Elser, V., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Fromme, P., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C. Y., Hartmann, R., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Hunter, M. S., Johansson, L., Kassemeyer, S., Kimmel, N., Kirian, R. A., Liang, M., Maia, F. R., Malmerberg, E., Marchesini, S., Martin, A. V., Nass, K., Neutze, R., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Scott, H., Schlichting, I., Schulz, J., Seibert, M. M., Shoeman, R. L., Sierra, R. G., Soltau, H., Spence, J. C., Stellato, F., Stern, S., Strueder, L., Ullrich, J., Wang, X., Weidenspointner, G., Weierstall, U., Wunderer, C. B., Chapman, H. N. 2012; 6 (1): 35-40

    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 information1-4. 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.

    View details for DOI 10.1038/NPHOTON.2011.297

    View details for Web of Science ID 000298416200013

    View details for PubMedCentralID PMC3783007

  • Multiphoton Ionization of Xenon at the LCLS Free-Electron Laser Rudek, B., Rolles, D., Rudenko, A., Epp, S., Foucar, L., Erk, B., Hartmann, R., Kimmel, N., Holl, P., Reich, C., Strueder, L., Hirsemann, H., Ueda, K., Simon, M., Berrah, N., Bostedt, C., Bozek, J., Schorb, S., Messerschmidt, M., Adolph, M., Gorkhover, T., Rupp, D., Moeller, T., Schulz, J., Gumprecht, L., Aquila, A., Filsinger, F., Kuehnel, K., Ullrich, J., Williams, I. D., VanDerHart, H. W., McCann, J. F., Crothers, D. S. IOP PUBLISHING LTD. 2012
  • Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser PHYSICAL REVIEW B Lomb, L., Barends, T. R., Kassemeyer, S., Aquila, A., Epp, S. W., Erk, B., Foucar, L., Hartmann, R., Rudek, B., Rolles, D., Rudenko, A., Shoeman, R. L., Andreasson, J., Bajt, S., Barthelmess, M., Barty, A., Bogan, M. J., Bostedt, C., Bozek, J. D., Caleman, C., Coffee, R., Coppola, N., Deponte, D. P., Doak, R. B., Ekeberg, T., Fleckenstein, H., Fromme, P., Gebhardt, M., Graafsma, H., Gumprecht, L., Hampton, C. Y., Hartmann, A., Hauser, G., Hirsemann, H., Holl, P., Holton, J. M., Hunter, M. S., Kabsch, W., Kimmel, N., Kirian, R. A., Liang, M., Maia, F. R., Meinhart, A., Marchesini, S., Martin, A. V., Nass, K., Reich, C., Schulz, J., Seibert, M. M., Sierra, R., Soltau, H., Spence, J. C., Steinbrener, J., Stellato, F., Stern, S., Timneanu, N., Wang, X., Weidenspointner, G., Weierstall, U., White, T. A., Wunderer, C., Chapman, H. N., Ullrich, J., Strueder, L., Schlichting, I. 2011; 84 (21)

    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.

    View details for DOI 10.1103/PhysRevB.84.214111

    View details for Web of Science ID 000298487500004

    View details for PubMedCentralID PMC3786679

  • Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering OPTICS EXPRESS Yoon, C., Schwander, P., Abergel, C., Andersson, I., Andreasson, J., Aquila, A., Bajt, S., Barthelmess, M., Barty, A., Bogan, M. J., Bostedt, C., Bozek, J., Chapman, H. N., Claverie, J., Coppola, N., DePonte, D. P., Ekeberg, T., Epp, S. W., Erk, B., Fleckenstein, H., Foucar, L., Graafsma, H., Gumprecht, L., Hajdu, J., Hampton, C. Y., Hartmann, A., Hartmann, E., Hartmann, R., Hauser, G., Hirsemann, H., Holl, P., Kassemeyer, S., Kimmel, N., Kiskinova, M., Liang, M., Loh, N., Lomb, L., Maia, F. C., Martin, A. V., Nass, K., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schlichting, I., Schulz, J., Seibert, M., Seltzer, V., Shoeman, R. L., Sierra, R. G., Soltau, H., Starodub, D., Steinbrener, J., Stier, G., Strueder, L., Svenda, M., Ullrich, J., Weidenspointner, G., White, T. A., Wunderer, C., Ourmazd, A. 2011; 19 (17): 16542–49

    Abstract

    Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

    View details for DOI 10.1364/OE.19.016542

    View details for Web of Science ID 000293894900092

    View details for PubMedID 21935018

  • Structure-factor analysis of femtosecond micro-diffraction patterns from protein nanocrystals ACTA CRYSTALLOGRAPHICA SECTION A Kirian, R. A., White, T. A., Holton, J. M., Chapman, H. N., Fromme, P., Barty, A., Lomb, L., Aquila, A., Maia, F. C., Martin, A. V., Fromme, R., Wang, X., Hunter, M. S., Schmidt, K. E., Spence, J. H. 2011; 67: 131–40

    Abstract

    A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution. The data were collected at the Linac Coherent Light Source (the first hard-X-ray laser user facility), to which was fitted a hydrated protein nanocrystal injector jet, according to the method of serial crystallography. The data are single 'still' diffraction snapshots, each from a different nanocrystal with sizes ranging between 100 nm and 2 µm, so the angular width of Bragg peaks was dominated by crystal-size effects. These results were compared with single-crystal data recorded from large crystals of Photosystem I at the Advanced Light Source and the quality of the data was found to be similar. The implications for improving the efficiency of data collection by allowing the use of very small crystals, for radiation-damage reduction and for time-resolved diffraction studies at room temperature are discussed.

    View details for DOI 10.1107/S0108767310050981

    View details for Web of Science ID 000287450300001

    View details for PubMedID 21325716

    View details for PubMedCentralID PMC3066792

  • Femtosecond X-ray protein nanocrystallography NATURE Chapman, H. N., Fromme, P., Barty, A., White, T. A., Kirian, R. A., Aquila, A., Hunter, M. S., Schulz, J., DePonte, D. P., Weierstall, U., Doak, R., Maia, F. C., Martin, A. V., Schlichting, I., Lomb, L., Coppola, N., Shoeman, R. L., Epp, S. W., Hartmann, R., Rolles, D., Rudenko, A., Foucar, L., Kimmel, N., Weidenspointner, G., Holl, P., Liang, M., Barthelmess, M., Caleman, C., Boutet, S., Bogan, M. J., Krzywinski, J., Bostedt, C., Bajt, S., Gumprecht, L., Rudek, B., Erk, B., Schmidt, C., Hoemke, A., Reich, C., Pietschner, D., Strueder, L., Hauser, G., Gorke, H., Ullrich, J., Herrmann, S., Schaller, G., Schopper, F., Soltau, H., Kuehnel, K., Messerschmidt, M., Bozek, J. D., Hau-Riege, S. P., Frank, M., Hampton, C. Y., Sierra, R. G., Starodub, D., Williams, G. J., Hajdu, J., Timneanu, N., Seibert, M., Andreasson, J., Rocker, A., Joensson, O., Svenda, M., Stern, S., Nass, K., Andritschke, R., Schroeter, C., Krasniqi, F., Bott, M., Schmidt, K. E., Wang, X., Grotjohann, I., Holton, J. M., Barends, T. M., Neutze, R., Marchesini, S., Fromme, R., Schorb, S., Rupp, D., Adolph, M., Gorkhover, T., Andersson, I., Hirsemann, H., Potdevin, G., Graafsma, H., Nilsson, B., Spence, J. H. 2011; 470 (7332): 73–U81

    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 (∼200 nm to 2 μm 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.

    View details for PubMedID 21293373

  • Single mimivirus particles intercepted and imaged with an X-ray laser NATURE Seibert, M. M., Ekeberg, T., Maia, F. R., Svenda, M., Andreasson, J., Joensson, O., Odic, D., Iwan, B., Rocker, A., Westphal, D., Hantke, M., Deponte, D. P., Barty, A., Schulz, J., Gumprecht, L., Coppola, N., Aquila, A., Liang, M., White, T. A., Martin, A., Caleman, C., Stern, S., Abergel, C., Seltzer, V., Claverie, J., Bostedt, C., Bozek, J. D., Boutet, S., Miahnahri, A. A., Messerschmidt, M., Krzywinski, J., Williams, G., Hodgson, K. O., Bogan, M. J., Hampton, C. Y., Sierra, R. G., Starodub, D., Andersson, I., Bajt, S., Barthelmess, M., Spence, J. C., Fromme, P., Weierstall, U., Kirian, R., Hunter, M., Doak, R. B., Marchesini, S., Hau-Riege, S. P., Frank, M., Shoeman, R. L., Lomb, L., Epp, S. W., Hartmann, R., Rolles, D., Rudenko, A., Schmidt, C., Foucar, L., Kimmel, N., Holl, P., Rudek, B., Erk, B., Hoemke, A., Reich, C., Pietschner, D., Weidenspointner, G., Strueder, L., Hauser, G., Gorke, H., Ullrich, J., Schlichting, I., Herrmann, S., Schaller, G., Schopper, F., Soltau, H., Kuehnel, K., Andritschke, R., Schroeter, C., Krasniqi, F., Bott, M., Schorb, S., Rupp, D., Adolph, M., Gorkhover, T., Hirsemann, H., Potdevin, G., Graafsma, H., Nilsson, B., Chapman, H. N., Hajdu, J. 2011; 470 (7332): 78-U86

    Abstract

    X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. 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. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline 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. 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.

    View details for DOI 10.1038/nature09748

    View details for Web of Science ID 000286886400037

    View details for PubMedID 21293374

    View details for PubMedCentralID PMC4038304

  • Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser. Physical review. B, Condensed matter and materials physics Lomb, L. n., Barends, T. R., Kassemeyer, S. n., Aquila, A. n., Epp, S. W., Erk, B. n., Foucar, L. n., Hartmann, R. n., Rudek, B. n., Rolles, D. n., Rudenko, A. n., Shoeman, R. L., Andreasson, J. n., Bajt, S. n., Barthelmess, M. n., Barty, A. n., Bogan, M. J., Bostedt, C. n., Bozek, J. D., Caleman, C. n., Coffee, R. n., Coppola, N. n., Deponte, D. P., Doak, R. B., Ekeberg, T. n., Fleckenstein, H. n., Fromme, P. n., Gebhardt, M. n., Graafsma, H. n., Gumprecht, L. n., Hampton, C. Y., Hartmann, A. n., Hauser, G. n., Hirsemann, H. n., Holl, P. n., Holton, J. M., Hunter, M. S., Kabsch, W. n., Kimmel, N. n., Kirian, R. A., Liang, M. n., Maia, F. R., Meinhart, A. n., Marchesini, S. n., Martin, A. V., Nass, K. n., Reich, C. n., Schulz, J. n., Seibert, M. M., Sierra, R. n., Soltau, H. n., Spence, J. C., Steinbrener, J. n., Stellato, F. n., Stern, S. n., Timneanu, N. n., Wang, X. n., Weidenspointner, G. n., Weierstall, U. n., White, T. A., Wunderer, C. n., Chapman, H. N., Ullrich, J. n., Strüder, L. n., Schlichting, I. n. 2011; 84 (21): 214111

    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.

    View details for PubMedID 24089594

    View details for PubMedCentralID PMC3786679

  • Single particle imaging with soft X-rays at the Linac Coherent Light Source Conference on Advances in X-ray Free-Electron Lasers - Radiation Schemes, X-ray Optics, and Instrumentation Martin, A. V., Andreasson, J., Aquila, A., Bajt, S., Barends, T. R., Barthelmess, M., Barty, A., Benner, W. H., Bostedt, C., Bozek, J. D., Bucksbaum, P., Caleman, C., Coppola, N., Deponte, D. P., Ekeberg, T., Epp, S. W., Erk, B., Farquar, G. R., Fleckenstein, H., Foucar, L., Frank, M., Gumprecht, L., Hampton, C. Y., Hantke, M., Hartmann, A., Hartmann, E., Hartmann, R., Hau-Riege, S. P., Hauser, G., Holl, P., Hoemke, A., Jonssonn, O., Kassemeyer, S., Kimmel, N., Kiskinova, M., Krasniqi, F., Krzywinski, J., Liang, M., Loh, N. D., Lomb, L., Maia, F. R., Marchesini, S., Messerschmidt, M., Nass, K., Odic, D., Pedersoli, E., Reich, C., Rolles, D., Rudek, B., Rudenko, A., Schmidt, C., Schulz, J., Seibert, M. M., Shoeman, R. L., Sierra, R. G., Soltau, H., Starodub, D., Steinbrener, J., Stellato, F., Strueder, L., Svenda, M., Tobias, H., Ullrich, J., Weidenspointner, G., Westphal, D., White, T. A., Williams, G., Hajdu, J., Schlichting, I., Bogan, M. J., Chapman, H. N. SPIE-INT SOC OPTICAL ENGINEERING. 2011

    View details for DOI 10.1117/12.886754

    View details for Web of Science ID 000293180500004

  • Polarization measurements of plasma excited X-ray lasers Aquila, A., Bleiner, D., Balmer, J., Bajt, S., Dunn, J., Klisnick, A. SPIE-INT SOC OPTICAL ENGINEERING. 2011

    View details for DOI 10.1117/12.893317

    View details for Web of Science ID 000297632800026

  • Moving the Frontier of Quantum Control into the Soft X-Ray Spectrum INTERNATIONAL JOURNAL OF OPTICS Aquila, A., Drescher, M., Laarmann, T., Barthelmess, M., Chapman, H. N., Bajt, S. 2011
  • Optical constants of magnetron-sputtered magnesium films in the 25-1300 eV energy range JOURNAL OF APPLIED PHYSICS Vidal-Dasilva, M., Aquila, A. L., Gullikson, E. M., Salmassi, F., Larruquert, J. I. 2010; 108 (6)

    View details for DOI 10.1063/1.3481457

    View details for Web of Science ID 000282646400035

  • Measuring the Structure of Epitaxially Assembled Block Copolymer Domains with Soft X-ray Diffraction MACROMOLECULES Stein, G. E., Liddle, J., Aquila, A. L., Gullikson, E. M. 2010; 43 (1): 433–41

    View details for DOI 10.1021/ma901914b

    View details for Web of Science ID 000273268700057

  • Tri-material multilayer coatings with high reflectivity and wide bandwidth for 25 to 50 nm extreme ultraviolet light OPTICS EXPRESS Aquila, A., Salmassi, F., Liu, Y., Gullikson, E. M. 2009; 17 (24): 22102–7

    Abstract

    Magnesium/silicon carbide (Mg/SiC) multilayers have been fabricated with normal incidence reflectivity in the vicinity of 40% to 50% for wavelengths in the 25 to 50 nm wavelength range. However many applications, for example solar telescopes and ultrafast studies using high harmonic generation sources, desire larger bandwidths than provided by high reflectivity Mg/SiC multilayers. We investigate introducing a third material, Scandium, to create a tri-material Mg/Sc/SiC multilayer allowing an increase the bandwidth while maintaining high reflectivity.

    View details for DOI 10.1364/OE.17.022102

    View details for Web of Science ID 000272229400083

    View details for PubMedID 19997456

  • Optical constants of evaporation-deposited silicon monoxide films in the 7.1-800 eV photon energy range JOURNAL OF APPLIED PHYSICS Fernandez-Perea, M., Vidal-Dasilva, M., Larruquert, J. I., Aznarez, J. A., Mendez, J. A., Gullikson, E., Aquila, A., Soufli, R. 2009; 105 (11)

    View details for DOI 10.1063/1.3123768

    View details for Web of Science ID 000267053200038

  • Sub-micron focusing of a soft X-ray Free Electron Laser beam Bajt, S., Chapman, H. N., Nelson, A. J., Lee, R. W., Toleikis, S., Mirkarimi, P., Alameda, J. B., Baker, S. L., Vollmer, H., Graff, R. T., Aquila, A., Gullikson, E. M., Ilse, J., Spiller, E. A., Krzywinski, J., Juha, L., Chalupsky, J., Hajkova, V., Hajdu, J., Tschentscher, T., Juha, L., Bajt, S., Sobierajski, R. SPIE-INT SOC OPTICAL ENGINEERING. 2009

    View details for DOI 10.1117/12.822498

    View details for Web of Science ID 000299776200014

  • Optical constants of magnetron-sputtered boron carbide thin films from photoabsorption data in the range 30 to 770 eV APPLIED OPTICS Soufli, R., Aquila, A. L., Salmassi, F., Fernandez-Perea, M., Gullikson, E. M. 2008; 47 (25): 4633–39

    Abstract

    This work discusses the experimental determination of the optical constants (refractive index) of DC-magnetron-sputtered boron carbide films in the 30-770 eV photon energy range. Transmittance measurements of three boron carbide films with thicknesses of 54.2, 79.0, and 112.5 nm were performed for this purpose. These are believed to be the first published experimental data for the refractive index of boron carbide films in the photon energy range above 160 eV and for the near-edge x-ray absorption fine structure regions around the boron K (188 eV), carbon K (284.2 eV), and oxygen K (543.1 eV) absorption edges. The density, composition, surface chemistry, and morphology of the films were also investigated using Rutherford backscattering, x-ray photoelectron spectroscopy, atomic force microscopy, scanning electron microscopy, and extreme ultraviolet reflectance measurements.

    View details for DOI 10.1364/AO.47.004633

    View details for Web of Science ID 000259413000021

    View details for PubMedID 18758535

  • Absolute sensitivity calibration of extreme ultraviolet photoresists OPTICS EXPRESS Naulleau, P. P., Gullikson, E. M., Aquila, A., George, S., Niakoula, D. 2008; 16 (15): 11519–24

    Abstract

    One of the major challenges facing the commercialization of extreme ultraviolet (EUV) lithography remains simultaneously achieving resist sensitivity, line-edge roughness, and resolution requirement. Sensitivity is of particular concern owing to its direct impact on source power requirements. Most current EUV exposure tools have been calibrated against a resist standard with the actual calibration of the standard resist dating back to EUV exposures at Sandia National Laboratories in the mid 1990s. Here we report on an independent sensitivity calibration of two baseline resists from the SEMATECH Berkeley MET tool performed at the Advanced Light Source Calibrations and Standards beamline. The results show the baseline resists to be approximately 1.9 times faster than previously thought based on calibration against the long standing resist standard.

    View details for DOI 10.1364/OE.16.011519

    View details for Web of Science ID 000258069100075

    View details for PubMedID 18648473

  • Single-cycle nonlinear optics SCIENCE Goulielmakis, E., Schultze, M., Hofstetter, M., Yakovlev, V. S., Gagnon, J., Uiberacker, M., Aquila, A. L., Gullikson, E. M., Attwood, D. T., Kienberger, R., Krausz, F., Kleineberg, U. 2008; 320 (5883): 1614–17

    Abstract

    Nonlinear optics plays a central role in the advancement of optical science and laser-based technologies. We report on the confinement of the nonlinear interaction of light with matter to a single wave cycle and demonstrate its utility for time-resolved and strong-field science. The electric field of 3.3-femtosecond, 0.72-micron laser pulses with a controlled and measured waveform ionizes atoms near the crests of the central wave cycle, with ionization being virtually switched off outside this interval. Isolated sub-100-attosecond pulses of extreme ultraviolet light (photon energy approximately 80 electron volts), containing approximately 0.5 nanojoule of energy, emerge from the interaction with a conversion efficiency of approximately 10(-6). These tools enable the study of the precision control of electron motion with light fields and electron-electron interactions with a resolution approaching the atomic unit of time ( approximately 24 attoseconds).

    View details for DOI 10.1126/science.1157846

    View details for Web of Science ID 000256886700041

    View details for PubMedID 18566281

  • Metrologies for the phase characterization of attosecond extreme ultraviolet optics OPTICS LETTERS Aquila, A., Salmassi, F., Gullikson, E. 2008; 33 (5): 455–57

    Abstract

    Extreme ultraviolet (EUV) optics play a key role in attosecond science since only with higher photon energies is it possible to achieve the wide spectral bandwidth required for ultrashort pulses. Multilayer EUV mirrors have been proposed and are being developed to temporally shape (compress) attosecond pulses. To fully characterize a multilayer optic for pulse applications requires not only knowledge of the reflectivity, as a function of photon energy, but also the reflected phase of the mirror. We develop the metrologies to determine the reflected phase of an EUV multilayer mirror using the photoelectric effect. The proposed method allows one to determine the optic's impulse response and hence its pulse characteristics.

    View details for DOI 10.1364/OL.33.000455

    View details for Web of Science ID 000254565700015

    View details for PubMedID 18311290

  • Development, characterization and experimental performance of x-ray optics for the LCLS free-electron laser Soufli, R., Pivovaroff, M. J., Baker, S. L., Robinson, J. C., Gullikson, E. M., McCarville, T. J., Stefan, P. M., Aquila, A. L., Ayers, J., McKernan, M. A., Bionta, R. M., Goto, S., Khounsary, A. M., Morawe, C. SPIE-INT SOC OPTICAL ENGINEERING. 2008

    View details for DOI 10.1117/12.796876

    View details for Web of Science ID 000263954400033

  • Extreme ultraviolet resist outgassing and its effect on nearby optics Denbeaux, G., Garg, R., Mbanaso, C., Waterman, J., Yankulin, L., Antohe, A., Fan, Y., Montgomery, W., Dean, K., Orvek, K., Wuest, A., Wei, Y., Goodwin, F., Wood, O., Koay, C., Gullikson, E., Aquila, A., Tarrio, C., Grantham, S., Bajt, S., Schellenberg, F. M. SPIE-INT SOC OPTICAL ENGINEERING. 2008

    View details for DOI 10.1117/12.772670

    View details for Web of Science ID 000256898400043

  • Optical constants of electron-beam evaporated boron films in the 6.8-900 eV photon energy range JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION Fernandez-Perea, M., Larruquert, J. I., Aznarez, J. A., Mendez, J. A., Vidal-Dasilva, M., Gullikson, E., Aquila, A., Soufli, R., Fierro, J. G. 2007; 24 (12): 3800–3807

    Abstract

    The optical constants of electron-beam evaporated boron from 6.8 to 900 eV were calculated through transmittance measurements of boron thin films deposited onto carbon-coated microgrids or LiF substrates in ultrahigh-vacuum conditions. In the low-energy part of the spectrum the measurements were performed in situ on freshly deposited samples, whereas in the high-energy range the samples were exposed to the atmosphere before the measurements. The extinction coefficient was calculated directly from the transmittance data, and a Kramers-Kronig analysis that combined the current data with data from the literature was performed to determine the dispersive part of the index of refraction. Finally, two different sum-rule tests were performed that indicated the good consistency of the data.

    View details for DOI 10.1364/JOSAA.24.003800

    View details for Web of Science ID 000252126600032

    View details for PubMedID 18059933

  • Multilayers for next generation x-ray sources Bajt, S., Chapman, H. N., Spiller, E., Hau-Riege, S., Alameda, J., Nelson, A. J., Walton, C. C., Kjornrattanawanich, B., Aquila, A., Dollar, F., Gullikson, E., Tarrio, C., Grantham, S., Juha, L., Sobierajski, R. H., Wabnitz, H. SPIE-INT SOC OPTICAL ENGINEERING. 2007

    View details for DOI 10.1117/12.724786

    View details for Web of Science ID 000249095600014

  • Developments in realistic design for aperiodic Mo/Si multilayer mirrors OPTICS EXPRESS Aquila, A. L., Salmassi, F., Dollar, F., Liu, Y., Gullikson, M. 2006; 14 (21): 10073–78

    Abstract

    Aperiodic multilayers have been designed for various applications, using numeric algorithms and analytical solutions, for many years with varying levels of success. This work developed a more realistic model for simulating aperiodic Mo/Si multilayers to be used in these algorithms by including the formation of MoSi(2). Using a genetic computer code we were able to optimize a 45 masculine multilayer for a large bandpass reflection multilayer that gave good agreement with the model.

    View details for DOI 10.1364/OE.14.010073

    View details for Web of Science ID 000241517400059

    View details for PubMedID 19529401

  • Oxidation resistance and microstructure of ruthenium-capped extreme ultraviolet lithography multilayers Bajt, S., Dai, Z., Nelson, E. J., Wall, M. A., Alameda, J. B., Nguyen, N. Q., Baker, S. L., Robinson, J. C., Taylor, J. S., Aquila, A., Edwards, N. SPIE-INT SOCIETY OPTICAL ENGINEERING. 2006

    View details for DOI 10.1117/1.22010271

    View details for Web of Science ID 000239497100011

  • Oxidation resistance of Ru-capped EUV multilayers Bajt, S., Dai, Z. R., Nelson, E. J., Wall, M. A., Alameda, J., Nguyen, N., Baker, S., Robinson, J. C., Taylor, J. S., Clift, M., Aquila, A., Gullikson, E. M., Edwards, N. V., Mackay, R. S. SPIE-INT SOC OPTICAL ENGINEERING. 2005: 118–27

    View details for DOI 10.1117/12.597443

    View details for Web of Science ID 000229586500012

  • Substrate smoothing for high-temperature condenser operation in EUVL source environments Soufli, R., Baker, S. L., Ratti, S., Robinson, J. C., Bajt, S. A., Alameda, J. B., Spiller, E., Taylor, J. S., Gullikson, E. M., Dollar, F. J., Aquila, A. L., Bristol, R. L., Mackay, R. S. SPIE-INT SOC OPTICAL ENGINEERING. 2005: 140–45

    View details for DOI 10.1117/12.606466

    View details for Web of Science ID 000229586500014

  • Grating arrays for high-throughput soft X-ray spectrometers Rasmussen, A., Aquila, A., Bookbinder, J., Chang, C., Gullikson, E., Heilmann, R. K., Kahn, S. M., Paerels, F., Schattenburg, M., Citterio, O., ODell, S. L. SPIE-INT SOC OPTICAL ENGINEERING. 2004: 248–59

    View details for DOI 10.1117/12.510045

    View details for Web of Science ID 000189421500026

  • Iridium optical constants for the Chandra X-ray Observatory from reflectance measurements of 0.05-12 keV Graessle, D. E., Soufli, R., Aquila, A. L., Gullikson, E. M., Blake, R. L., Burek, A. J., Flanagan, K. A., Siegmund, O. H. SPIE-INT SOC OPTICAL ENGINEERING. 2004: 469–81

    View details for DOI 10.1117/12.506132

    View details for Web of Science ID 000189441700045

  • Measurements of the optical constants of scandium in the 50-1300eV range Aquila, A. L., Salmassi, F., Gullikson, E. M., Eriksson, F., Birch, J., Soufli, R., Seely, J. F. SPIE-INT SOC OPTICAL ENGINEERING. 2004: 64–71

    View details for DOI 10.1117/12.563615

    View details for Web of Science ID 000225039500007

  • Iridium optical constants from synchroton reflectance measurements over 0.05-to 12-KeV x-ray energies Graessle, D. E., Soufli, R., Nelson, A. J., Evans, C. L., Aquila, A. L., Gullikson, E. M., Blake, R. L., Burek, A. J., Soufli, R., Seely, J. F. SPIE-INT SOC OPTICAL ENGINEERING. 2004: 72–83

    View details for DOI 10.1117/12.563160

    View details for Web of Science ID 000225039500008

  • Coherent soft x-ray generation in the water window with quasi-phase matching SCIENCE Gibson, E. A., Paul, A., Wagner, N., Tobey, R., Gaudiosi, D., Backus, S., Christov, I. P., Aquila, A., Gullikson, E. M., Attwood, D. T., Murnane, M. M., Kapteyn, H. C. 2003; 302 (5642): 95–98

    Abstract

    We demonstrate enhanced generation of coherent light in the "water window" region of the soft x-ray spectrum at 4.4 nanometers, using quasi-phase-matched frequency conversion of ultrafast laser pulses. By periodically modulating the diameter of a gas-filled hollow waveguide, the phase mismatch normally present between the laser light and the generated soft x-ray light can be partially compensated. This makes it possible to use neon gas as the nonlinear medium to coherently convert light up to the water window, illustrating that techniques of nonlinear optics can be applied effectively in the soft x-ray region of the spectrum. These results advance the prospects for compact coherent soft x-ray sources for applications in biomicroscopy and in chemical spectroscopy.

    View details for DOI 10.1126/science.1088654

    View details for Web of Science ID 000185678500042

    View details for PubMedID 14526077

  • Design and performance of capping layers for extreme-ultraviolet multilayer mirrors APPLIED OPTICS Bajt, S. A., Chapman, H. N., Nguyen, N., Alameda, J., Robinson, J. C., Malinowski, M., Gullikson, E., Aquila, A., Tarrio, C., Grantham, S. 2003; 42 (28): 5750–58

    Abstract

    Multilayer lifetime has emerged as one of the major issues for the commercialization of extreme-ultraviolet lithography (EUVL). We describe the performance of an oxidation-resistant capping layer of Ru atop multilayers that results in a reflectivity above 69% at 13.2 nm, which is suitable for EUVL projection optics and has been tested with accelerated electron-beam and extreme-ultraviolet (EUV) light in a water-vapor environment. Based on accelerated exposure results, we calculated multilayer lifetimes for all reflective mirrors in a typical commercial EUVL tool and concluded that Ru-capped multilayers have approximately 40x longer lifetimes than Si-capped multilayers, which translates to 3 months to many years, depending on the mirror dose.

    View details for DOI 10.1364/AO.42.005750

    View details for Web of Science ID 000185584600019

    View details for PubMedID 14528939

  • Comparison of extreme ultraviolet reflectance measurements JOURNAL OF MICROLITHOGRAPHY MICROFABRICATION AND MICROSYSTEMS Scholze, F., Tummler, J., Gullikson, E., Aquila, A. 2003; 2 (3): 233–35

    View details for DOI 10.1171/1.1583735

    View details for Web of Science ID 000221817800011