Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules

X-ray free electron lasers (XFEL) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges both in terms of experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classification tasks using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering (FXS) algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. We envision skopi as a resource to aid the development of on-the-fly feedback during non-crystalline experiments at XFEL facilities, which will provide critical insights into biomolecular structure and function.

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A high-pressure cryocooling method for protein crystals and biological samples with reduced background X-ray scatter

Journal of Applied Crystallography ◽

10.1107/s0021889812045013 ◽

2012 ◽

Vol 46 (1) ◽

pp. 234-241 ◽

Cited By ~ 11

Author(s):

Chae Un Kim ◽

Jennifer L. Wierman ◽

Richard Gillilan ◽

Enju Lima ◽

Sol M. Gruner

Keyword(s):

High Pressure ◽

Biological Samples ◽

Protein Crystal ◽

High Background ◽

X Ray ◽

Coherent Diffraction Imaging ◽

X Ray Scattering ◽

Alternative Method ◽

Helium Gas ◽

Diffraction Imaging

High-pressure cryocooling has been developed as an alternative method for cryopreservation of macromolecular crystals and successfully applied for various technical and scientific studies. The method requires the preservation of crystal hydration as the crystal is pressurized with dry helium gas. Previously, crystal hydration was maintained either by coating crystals with a mineral oil or by enclosing crystals in a capillary which was filled with crystallization mother liquor. These methods are not well suited to weakly diffracting crystals because of the relatively high background scattering from the hydrating materials. Here, an alternative method of crystal hydration, called capillary shielding, is described. The specimen is kept hydratedviavapor diffusion in a shielding capillary while it is being pressure cryocooled. After cryocooling, the shielding capillary is removed to reduce background X-ray scattering. It is shown that, compared to previous crystal-hydration methods, the new hydration method produces superior crystal diffraction with little sign of crystal damage. Using the new method, a weakly diffracting protein crystal may be properly pressure cryocooled with little or no addition of external cryoprotectants, and significantly reduced background scattering can be observed from the resulting sample. Beyond the applications for macromolecular crystallography, it is shown that the method has great potential for the preparation of noncrystalline hydrated biological samples for coherent diffraction imaging with future X-ray sources.

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Coherent X-ray scattering beamline at port 9C of Pohang Light Source II

Journal of Synchrotron Radiation ◽

10.1107/s1600577513025629 ◽

2013 ◽

Vol 21 (1) ◽

pp. 264-267 ◽

Cited By ~ 5

Author(s):

Chung-Jong Yu ◽

Hae Cheol Lee ◽

Chan Kim ◽

Wonsuk Cha ◽

Jerome Carnis ◽

...

Keyword(s):

Light Source ◽

Correlation Spectroscopy ◽

X Rays ◽

Photon Correlation ◽

X Ray ◽

Coherent Diffraction Imaging ◽

X Ray Scattering ◽

Pohang Light Source ◽

Diffraction Imaging ◽

Ray Scattering

The coherent X-ray scattering beamline at the 9C port of the upgraded Pohang Light Source (PLS-II) at Pohang Accelerator Laboratory in Korea is introduced. This beamline provides X-rays of 5–20 keV, and targets coherent X-ray experiments such as coherent diffraction imaging and X-ray photon correlation spectroscopy. The main parameters of the beamline are summarized, and some preliminary experimental results are described.

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The Potential of EuPRAXIA@SPARC_LAB for Radiation Based Techniques

Condensed Matter ◽

10.3390/condmat4010030 ◽

2019 ◽

Vol 4 (1) ◽

pp. 30 ◽

Cited By ~ 2

Author(s):

Antonella Balerna ◽

Samanta Bartocci ◽

Giovanni Batignani ◽

Alessandro Cianchi ◽

Enrica Chiadroni ◽

...

Keyword(s):

Laser System ◽

Dynamical Behavior ◽

Pump Probe ◽

X Ray ◽

Water Window ◽

Coherent Diffraction Imaging ◽

X Ray Scattering ◽

X Band ◽

Diffraction Imaging ◽

X Ray Absorption

A proposal for building a Free Electron Laser, EuPRAXIA@SPARC_LAB, at the Laboratori Nazionali di Frascati, is at present under consideration. This FEL facility will provide a unique combination of a high brightness GeV-range electron beam generated in a X-band RF linac, a 0.5 PW-class laser system and the first FEL source driven by a plasma accelerator. The FEL will produce ultra-bright pulses, with up to 10 12 photons/pulse, femtosecond timescale and wavelength down to 3 nm, which lies in the so called “water window”. The experimental activity will be focused on the realization of a plasma driven short wavelength FEL able to provide high-quality photons for a user beamline. In this paper, we describe the main classes of experiments that will be performed at the facility, including coherent diffraction imaging, soft X-ray absorption spectroscopy, Raman spectroscopy, Resonant Inelastic X-ray Scattering and photofragmentation measurements. These techniques will allow studying a variety of samples, both biological and inorganic, providing information about their structure and dynamical behavior. In this context, the possibility of inducing changes in samples via pump pulses leading to the stimulation of chemical reactions or the generation of coherent excitations would tremendously benefit from pulses in the soft X-ray region. High power synchronized optical lasers and a TeraHertz radiation source will indeed be made available for THz and pump–probe experiments and a split-and-delay station will allow performing XUV-XUV pump–probe experiments.

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Simulation of Coherent Diffraction Imaging Based on Scanning Transimission X-Ray Microscopy of Shanghai Synchrotron Radiation Facility

Acta Optica Sinica ◽

10.3788/aos201131.0418001 ◽

2011 ◽

Vol 31 (4) ◽

pp. 0418001

Author(s):

谭兴兴 Tan Xingxing ◽

刘海岗 Liu Haigang ◽

郭智 Guo Zhi ◽

吴衍青 Wu Yanqing ◽

许子健 Xu Zijian ◽

...

Keyword(s):

Synchrotron Radiation ◽

Shanghai Synchrotron Radiation Facility ◽

X Ray ◽

Coherent Diffraction Imaging ◽

Diffraction Imaging

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Multi-beam X-ray ptychography for high-throughput coherent diffraction imaging

Scientific Reports ◽

10.1038/s41598-020-76412-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yudong Yao ◽

Yi Jiang ◽

Jeffrey A. Klug ◽

Michael Wojcik ◽

Evan R. Maxey ◽

...

Keyword(s):

Fresnel Zone ◽

Field Of View ◽

X Ray ◽

Single Beam ◽

Coherent Diffraction Imaging ◽

Diffraction Imaging ◽

Extended Field ◽

Resolution Imaging ◽

Diffraction Patterns ◽

Scanning Mechanism

Abstract X-ray ptychography is a rapidly developing coherent diffraction imaging technique that provides nanoscale resolution on extended field-of-view. However, the requirement of coherence and the scanning mechanism limit the throughput of ptychographic imaging. In this paper, we propose X-ray ptychography using multiple illuminations instead of single illumination in conventional ptychography. Multiple locations of the sample are simultaneously imaged by spatially separated X-ray beams, therefore, the obtained field-of-view in one scan can be enlarged by a factor equal to the number of illuminations. We have demonstrated this technique experimentally using two X-ray beams focused by a house-made Fresnel zone plate array. Two areas of the object and corresponding double illuminations were successfully reconstructed from diffraction patterns acquired in one scan, with image quality similar with those obtained by conventional single-beam ptychography in sequence. Multi-beam ptychography approach increases the imaging speed, providing an efficient way for high-resolution imaging of large extended specimens.

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Continuous scanning for Bragg coherent X-ray imaging

Scientific Reports ◽

10.1038/s41598-020-69678-5 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Ni Li ◽

Maxime Dupraz ◽

Longfei Wu ◽

Steven J. Leake ◽

Andrea Resta ◽

...

Keyword(s):

Flow Reactor ◽

Light Sources ◽

Pt Nanoparticle ◽

Strain Fields ◽

X Ray ◽

Coherent Diffraction Imaging ◽

Scan Time ◽

X Ray Imaging ◽

Continuous Scanning ◽

Diffraction Imaging

Abstract We explore the use of continuous scanning during data acquisition for Bragg coherent diffraction imaging, i.e., where the sample is in continuous motion. The fidelity of continuous scanning Bragg coherent diffraction imaging is demonstrated on a single Pt nanoparticle in a flow reactor at $$400\,^\circ \hbox {C}$$ 400 ∘ C in an Ar-based gas flowed at 50 ml/min. We show a reduction of 30% in total scan time compared to conventional step-by-step scanning. The reconstructed Bragg electron density, phase, displacement and strain fields are in excellent agreement with the results obtained from conventional step-by-step scanning. Continuous scanning will allow to minimise sample instability under the beam and will become increasingly important at diffraction-limited storage ring light sources.

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