The development of ultrashort X-ray pulse sources requires optics that keep the pulse length as short as possible. One source of pulse stretching is the penetration of the pulse into a crystal during diffraction. Another source is the inclination of the intensity front when the diffraction is asymmetric. The theory of short X-ray pulse diffraction has been well developed by many authors. As it is rather complicated, it is sometimes difficult to foresee the pulse behavior (mainly stretching) during diffraction in various crystal arrangements. In this article, a simple model is suggested that gives a qualitatively similar shape to the diffracted pulse which follows from exact theory. It allows proposal of what experimental arrangement is optimal to minimize the pulse stretching during diffraction. First, the effect of pulse stretching due to penetration into a crystal surface is studied. On the basis of this, the pulse profile change during diffraction by two crystals, either symmetric or asymmetric, is predicted.
- Keywords
- X-ray pulse diffraction, X-ray pulse stretching, short X-ray pulses,
- Publication type
- Journal Article MeSH
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.
- MeSH
- Cells MeSH
- Time Factors MeSH
- X-Ray Diffraction * MeSH
- Electrons MeSH
- Crystallography, X-Ray MeSH
- Lasers * MeSH
- Models, Molecular MeSH
- Nanoparticles MeSH
- Proteins MeSH
- Pulse MeSH
- X-Rays MeSH
- Cyanobacteria MeSH
- Models, Theoretical MeSH
- Publication type
- Journal Article MeSH
- Comment MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Names of Substances
- Proteins MeSH
This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012 photons per µm2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
- Keywords
- OmRV, Omono River virus, X-ray diffraction, diffraction before destruction, flash X-ray imaging, free-electron laser, virus,
- Publication type
- Journal Article MeSH
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
- Publication type
- Journal Article MeSH
We present a computational case study of X-ray single-particle imaging of hydrated proteins on an example of 2-Nitrogenase-Iron protein covered with water layers of various thickness, using a start-to-end simulation platform and experimental parameters of the SPB/SFX instrument at the European X-ray Free-Electron Laser facility. The simulations identify an optimal thickness of the water layer at which the effective resolution for imaging the hydrated sample becomes significantly higher than for the non-hydrated sample. This effect is lost when the water layer becomes too thick. Even though the detailed results presented pertain to the specific sample studied, the trends which we identify should also hold in a general case. We expect these findings will guide future single-particle imaging experiments using hydrated proteins.
- MeSH
- X-Ray Diffraction instrumentation methods MeSH
- Electrons MeSH
- Photons MeSH
- Lasers * MeSH
- Molecular Imaging methods MeSH
- Oxidoreductases chemistry radiation effects MeSH
- X-Rays adverse effects MeSH
- Molecular Dynamics Simulation * MeSH
- Water chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- nitrogenase reductase MeSH Browser
- Oxidoreductases MeSH
- Water MeSH
In this work, experimentally measured characteristics of a kilohertz laser-driven Cu plasma X-ray source that was recently commissioned at the ELI Beamlines facility are reported. The source can be driven either by an in-house developed high-contrast sub-20 fs near-infrared terawatt laser based on optical parametric chirped-pulse amplification technology or by a more conventional Ti:sapphire laser delivering 12 mJ and 45 fs pulses. The X-ray source parameters obtained with the two driving lasers are compared. A measured photon flux of the order up to 1012 Kα photons s-1 (4π)-1 is reported. Furthermore, experimental platforms for ultrafast X-ray diffraction and X-ray absorption and emission spectroscopy based on the reported source are described.
- Keywords
- Cu Kα lines, ELI Beamlines, laser-driven sources, plasma X-ray sources, sub-picosecond sources, time-resolved experiments, ultrafast,
- Publication type
- Journal Article MeSH
Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.
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.
[This corrects the article DOI: 10.1107/S2052252517003591.].
- Keywords
- OmRV, Omono River virus, X-ray diffraction, diffraction before destruction, flash X-ray imaging, free-electron laser, virus,
- Publication type
- Journal Article MeSH
- Published Erratum MeSH
Diamond bulk irradiated with a free-electron laser pulse of 6100 eV photon energy, 5 fs duration, at the ~19-25 eV/atom absorbed doses, is studied theoretically on its way to warm dense matter state. Simulations with our hybrid code XTANT show disordering on sub-100 fs timescale, with the diffraction peak (220) vanishing faster than the peak (111). The warm dense matter formation proceeds as a nonthermal damage of diamond with the band gap collapse triggering atomic disordering. Short-living graphite-like state is identified during a few femtoseconds between the disappearance of (220) peak and the disappearance of (111) peak. The results obtained are compared with the data from the recent experiment at SACLA, showing qualitative agreement. Challenges remaining for the accurate modeling of the transition of solids to warm dense matter state and proposals for supplementary measurements are discussed in detail.
- Publication type
- Journal Article MeSH
