[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: We report experimental results on x-ray diffraction of quantum-state-selected
and strongly aligned ensembles of the prototypical asymmetric rotor molecule
2,5-diiodobenzonitrile using the Linac Coherent Light Source. The experiments
demonstrate pioneering steps toward a new bottom-up approach to diffractive
imaging of distinct structures of individual, isolated gas-phase molecules. We
confirm several key ingredients of single molecule diffraction experiments: the
abilities to detect and count individual scattered x-ray photons in single shot
diffraction data, to deliver state-selected, e.g., structural-isomer-selected,
ensembles of molecules to the x-ray interaction volume, and to strongly align
the scattering molecules. Our approach, using ultrashort x-ray pulses, is
suitable to study ultrafast dynamics of isolated molecules.
[Show abstract][Hide abstract] 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<sup>21</sup> W/m<sup>2</sup> 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.
[Show abstract][Hide abstract] ABSTRACT: X-ray free-electron lasers provide unique opportunities for exploring ultrafast dynamics and for imaging the structures of complex systems. Understanding the response of individual atoms to intense X-rays is essential for most free-electron laser applications. First experiments have shown that, for light atoms, the dominant interaction mechanism is ionization by sequential electron ejection, where the highest charge state produced is defined by the last ionic state that can be ionized with one photon. Here, we report an unprecedentedly high degree of ionization of xenon atoms by 1.5 keV free-electron laser pulses to charge states with ionization energies far exceeding the photon energy. Comparing ion charge-state distributions and fluorescence spectra with state-of-the-art calculations, we find that these surprisingly high charge states are created via excitation of transient resonances in highly charged ions, and predict resonance enhanced absorption to be a general phenomenon in the interaction of intense X-rays with systems containing high-Z constituents.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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 analysis(1). 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 information(1-4). 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 technology(5) should enable structural determination from submicrometre protein crystals with atomic resolution.
[Show abstract][Hide abstract] ABSTRACT: Profiling structured beams produced by X-ray free-electron lasers (FELs) is crucial to both maximizing signal intensity for weakly scattering targets and interpreting their scattering patterns. Earlier ablative imprint studies describe how to infer the X-ray beam profile from the damage that an attenuated beam inflicts on a substrate. However, the beams in-situ profile is not directly accessible with imprint studies because the damage profile could be different from the actual beam profile. On the other hand, although a Shack-Hartmann sensor is capable of in-situ profiling, its lenses may be quickly damaged at the intense focus of hard X-ray FEL beams. We describe a new approach that probes the in-situ morphology of the intense FEL focus. By studying the translations in diffraction patterns from an ensemble of randomly injected sub-micron latex spheres, we were able to determine the non-Gaussian nature of the intense FEL beam at the Linac Coherent Light Source (SLAC National Laboratory) near the FEL focus. We discuss an experimental application of such a beam-profiling technique, and the limitations we need to overcome before it can be widely applied.
Proceedings of SPIE - The International Society for Optical Engineering 01/2012; 8504:850403-850403. DOI:10.1117/12.930075 · 0.20 Impact Factor
[Show abstract][Hide abstract] 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.
Physical Review B 12/2011; 84(21):214111. DOI:10.1103/PhysRevB.84.214111 · 3.74 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Results of coherent diffractive imaging experiments performed with soft X-rays (1-2 keV) at the Linac Coherent Light Source are presented. Both organic and inorganic nano-sized objects were injected into the XFEL beam as an aerosol focused with an aerodynamic lens. The high intensity and femtosecond duration of X-ray pulses produced by the Linac Coherent Light Source allow structural information to be recorded by X-ray diffraction before the particle is destroyed. Images were formed by using iterative methods to phase single shot diffraction patterns. Strategies for improving the reconstruction methods have been developed. This technique opens up exciting opportunities for biological imaging, allowing structure determination without freezing, staining or crystallization.
[Show abstract][Hide abstract] ABSTRACT: New generation synchrotron light sources, the X-ray free electron lasers, require a two dimensional focal plane instrumentation to perform X-ray imaging from below 100eV up to 25keV. The instruments have to face the accelerator bunch structure and energy bandwidth which is different for existing (FLASH, Hamburg and LCLS, Menlo Park) and future photon sources (SACLA, Harima and XFEL, Hamburg). Within the frame of the Center for Free Electron Laser Science (CFEL), a joint effort of the Max-Planck Society, DESY and the University of Hamburg, the MPI semiconductor laboratory developed, produced and operated large area X-ray CCD detectors with a format of nearly 60cm2 image area. They show outstanding characteristics: a high readout speed due to a complete parallel signal processing, high and homogeneous quantum efficiency, low signal noise, radiation hardness and a high pixel charge handling capacitance. We will present measurement results which demonstrate the X-ray spectroscopic and imaging capabilities of the fabricated devices. We will also report on the concept and the anticipated properties of the full, large scale system. The implementation of the detector into an experimental chamber to perform measurements e.g. of macromolecules in order to determine their structure at atomic resolutions will be shown.
Proceedings of SPIE - The International Society for Optical Engineering 05/2011; DOI:10.1117/12.887034 · 0.20 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] ABSTRACT: Fourth generation accelerator-based light sources, such as VUV and X-ray Free Electron Lasers (FEL), deliver ultra-brilliant (∼1012–1013 photons per bunch) coherent radiation in femtosecond (∼10–100 fs) pulses and, thus, require novel focal plane instrumentation in order to fully exploit their unique capabilities. As an additional challenge for detection devices, existing (FLASH, Hamburg) and future FELs (LCLS, Menlo Park; SCSS, Hyogo and the European XFEL, Hamburg) cover a broad range of photon energies from the EUV to the X-ray regime with significantly different bandwidths and pulse structures reaching up to MHz micro-bunch repetition rates. Moreover, hundreds up to trillions of fragment particles, ions, electrons or scattered photons can emerge when a single light flash impinges on matter with intensities up to 1022 W/cm2.In order to meet these challenges, the Max Planck Advanced Study Group (ASG) within the Center for Free Electron Laser Science (CFEL) has designed the CFEL-ASG MultiPurpose (CAMP) chamber. It is equipped with specially developed photon and charged particle detection devices dedicated to cover large solid-angles. A variety of different targets are supported, such as atomic, (aligned) molecular and cluster jets, particle injectors for bio-samples or fixed target arrangements. CAMP houses 4π solid-angle ion and electron momentum imaging spectrometers (“reaction microscope”, REMI, or “velocity map imaging”, VMI) in a unique combination with novel, large-area, broadband (50 eV–25 keV), high-dynamic-range, single-photon-counting and imaging X-ray detectors based on the pnCCDs.This instrumentation allows a new class of coherent diffraction experiments in which both electron and ion emission from the target may be simultaneously monitored. This permits the investigation of dynamic processes in this new regime of ultra-intense, high-energy radiation—matter interaction. After an introduction into the salient features of the CAMP chamber and the properties of the redesigned REMI/VMI spectrometers, the new 1024×1024 pixel format pnCCD imaging detector system will be described in detail. Results of tests of four smaller format (256×512) devices of identical performance, conducted at FLASH and BESSY, will be presented and the concept as well as the anticipated properties of the full, large-scale system will be elucidated. The data obtained at both radiation sources illustrate the unprecedented performance of the X-ray detectors, which have a voxel size of 75×75×450 μm3 and a typical read-out noise of 2.5 electrons (rms) at an operating temperature of −50 °C.
Nuclear Instruments and Methods in Physics Research Section A Accelerators Spectrometers Detectors and Associated Equipment 03/2010; 614(3-614):483-496. DOI:10.1016/j.nima.2009.12.053 · 1.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: New generation synchrotron light sources, the X-ray free electron lasers, require a two dimensional focal plane instrumentation to perform X-ray imaging from below 100eV up to 25keV. The instruments have to face the accelerator bunch structure and energy bandwidth which is different for existing (FLASH, Hamburg) and future photon sources (LCLS, SCSS and XFEL). Within the frame of the Center for Free Electron Laser Science (CFEL), a joint effort of the Max-Planck Society, DESY and the University of Hamburg, the MPI semiconductor laboratory is developing and producing large area X-ray CCD detectors with a format of nearly 60cm<sup>2</sup> image area. They show outstanding characteristics: a high readout speed due to a complete parallel signal processing, high and homogeneous quantum efficiency, low signal noise, radiation hardness and a high pixel charge handling capacitance. We will present measurement results which demonstrate the X-ray spectroscopic and imaging capabilities of the devices. We will also report on the concept and the anticipated properties of the full, large scale system. The implementation of the detector into an experimental chamber to perform measurements, e.g. of macromolecules in order to determine their structure at atomic resolutions, will be shown.
[Show abstract][Hide abstract] ABSTRACT: We present the design and realization of a fast pn-charge coupled device (pnCCD) detector system with excellent sensitivity and energy resolution over a wide wavelength range from the VUV to hard X-rays along with two different types of application. In a spectroscopic measurement at the FLASH Free Electron Laser at DESY the signal peak of the monoenergetic 90 eV photons was clearly seperated from noise and higher harmonics of the laser. It had a FWHM of 35 eV. In a further experiment using white synchrotron radiation at BESSY the Bragg reflections from a multilayer sample were recorded while simultaneously resolving energy (5 keV ≪ E ≪ 35 keV) and space (75 μm) in one measurement.