| 1. |
- Reddy, Hemanth K. N., et al.
(författare)
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Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source
- 2017
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Ingår i: Scientia Danica. Series H. Humanistica 4. - : Nature Publishing Group. - 1904-5506 .- 2052-4463. ; 4
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Tidskriftsartikel (refereegranskat)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 similar to 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.
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| 2. |
- Sobolev, Egor, et al.
(författare)
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Megahertz single-particle imaging at the European XFEL
- 2020
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Ingår i: Communications Physics. - : Springer Science and Business Media LLC. - 2399-3650. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of high repetition-rate X-ray free-electron lasers (XFELs) powered by superconducting accelerator technology enables the measurement of significantly more experimental data per day than was previously possible. The European XFEL is expected to provide 27,000 pulses per second, over two orders of magnitude more than any other XFEL. The increased pulse rate is a key enabling factor for single-particle X-ray diffractive imaging, which relies on averaging the weak diffraction signal from single biological particles. Taking full advantage of this new capability requires that all experimental steps, from sample preparation and delivery to the acquisition of diffraction patterns, are compatible with the increased pulse repetition rate. Here, we show that single-particle imaging can be performed using X-ray pulses at megahertz repetition rates. The results obtained pave the way towards exploiting high repetition-rate X-ray free-electron lasers for single-particle imaging at their full repetition rate.
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| 3. |
- Assalauova, Dameli, et al.
(författare)
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An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser
- 2020
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Ingår i: IUCrJ. - 2052-2525. ; 7, s. 1102-1113
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Tidskriftsartikel (refereegranskat)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.
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| 4. |
- Ekeberg, Tomas, 1983-, et al.
(författare)
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Observation of a single protein by ultrafast X-ray diffraction
- 2024
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Ingår i: Light. - : Springer Nature. - 2095-5545 .- 2047-7538. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Lazarev, Sergey, et al.
(författare)
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Influence of contacts and applied voltage on a structure of a single GaN nanowire
- 2021
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Ingår i: Applied Sciences (Switzerland). - : MDPI AG. - 2076-3417. ; 11:20
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Tidskriftsartikel (refereegranskat)abstract
- Semiconductor nanowires (NWs) have a broad range of applications for nano-and optoelectronics. The strain field of gallium nitride (GaN) NWs could be significantly changed when contacts are applied to them to form a final device, especially considering the piezoelectric properties of GaN. Investigation of influence of the metallic contacts on the structure of the NWs is of high importance for their applications in real devices. We have studied a series of different type of contacts and influence of the applied voltage bias on the contacted GaN NWs with the length of about 3 to 4 micrometers and with two different diameters of 200 nm and 350 nm. It was demonstrated that the NWs with the diameter of 200 nm are bend already by the interaction with the substrate. For all GaN NWs, significant structural changes were revealed after the contacts deposition. The results of our research may contribute to the future optoelectronic applications of the GaN nanowires.
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| 6. |
- Lazarev, Sergey, et al.
(författare)
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Structural Changes in a Single GaN Nanowire under Applied Voltage Bias
- 2018
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 18:9, s. 5446-5452
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Tidskriftsartikel (refereegranskat)abstract
- GaN nanowires (NWs) are promising building blocks for future optoelectronic devices and nanoelectronics. They exhibit stronger piezoelectric properties than bulk GaN. This phenomena may be crucial for applications of NWs and makes their study highly important. We report on an investigation of the structure evolution of a single GaN NW under an applied voltage bias along polar [0001] crystallographic direction until its mechanical break. The structural changes were investigated using coherent X-ray Bragg diffraction. The three-dimensional (3D) intensity distributions of the NWs without metal contacts, with contacts, and under applied voltage bias in opposite polar directions were analyzed. Coherent X-ray Bragg diffraction revealed the presence of significant bending of the NWs already after metal contacts deposition, which was increased at applied voltage bias. Employing analytical simulations based on elasticity theory and a finite element method (FEM) approach, we developed a 3D model of the NW bending under applied voltage. From this model and our experimental data, we determined the piezoelectric constant of the GaN NW to be about 7.7 pm/V in [0001] crystallographic direction. The ultimate tensile strength of the GaN NW was obtained to be about 1.22 GPa. Our work demonstrates the power of in operando X-ray structural studies of single NWs for their effective design and implementation with desired functional properties.
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| 7. |
- Li, Haoyuan, et al.
(författare)
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Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source
- 2020
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Ingår i: Scientific Data. - : NATURE RESEARCH. - 2052-4463. ; 7:1
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Tidskriftsartikel (refereegranskat)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 1.7keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 mu m x 1.7 mu m 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.
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| 8. |
- Munke, Anna, et al.
(författare)
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Data Descriptor : Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
- 2016
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 3
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Tidskriftsartikel (refereegranskat)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 wellcharacterized 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 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom 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.
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| 9. |
- Kurta, Ruslan P., et al.
(författare)
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Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses
- 2017
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 119:15
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Tidskriftsartikel (refereegranskat)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.
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| 10. |
- Makarov, Sergey, et al.
(författare)
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Soft X-ray diffraction patterns measured by a LiF detector with sub-micrometre resolution and an ultimate dynamic range
- 2020
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Ingår i: Journal of Synchrotron Radiation. - 0909-0495. ; 27, s. 625-632
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Tidskriftsartikel (refereegranskat)abstract
- The unique diagnostic possibilities of X-ray diffraction, small X-ray scattering and phase-contrast imaging techniques applied with high-intensity coherent X-ray synchrotron and X-ray free-electron laser radiation can only be fully realized if a sufficient dynamic range and/or spatial resolution of the detector is available. In this work, it is demonstrated that the use of lithium fluoride (LiF) as a photoluminescence (PL) imaging detector allows measuring of an X-ray diffraction image with a dynamic range of ∼107 within the sub-micrometre spatial resolution. At the PETRA III facility, the diffraction pattern created behind a circular aperture with a diameter of 5μm irradiated by a beam with a photon energy of 500eV was recorded on a LiF crystal. In the diffraction pattern, the accumulated dose was varied from 1.7 × 105Jcm-3 in the central maximum to 2 × 10-2Jcm-3 in the 16th maximum of diffraction fringes. The period of the last fringe was measured with 0.8μm width. The PL response of the LiF crystal being used as a detector on the irradiation dose of 500eV photons was evaluated. For the particular model of laser-scanning confocal microscope Carl Zeiss LSM700, used for the readout of the PL signal, the calibration dependencies on the intensity of photopumping (excitation) radiation (λ = 488nm) and the gain have been obtained.
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