Quantitative Imaging of Single, Unstained Viruses with Coherent X-rays

Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and myoglobin based on X-ray diffraction analysis in the 1950s, X-ray crystallography has become the primary methodology used to determine the 3D structure of macromolecules. However, biological specimens such as cells, organelles, viruses and many important macromolecules are difficult or impossible to crystallize, and hence their structures are not accessible by crystallography. Here we report, for the first time, the recording and reconstruction of X-ray diffraction patterns from single, unstained viruses. The structure of the viral capsid inside a virion was visualized. This work opens the door for quantitative X-ray imaging of a broad range of specimens from protein machineries, viruses and organelles to whole cells. Moreover, our experiment is directly transferable to the use of X-ray free electron lasers, and represents a major experimental milestone towards the X-ray imaging of single macromolecules.Comment: 16 pages, 5 figure

X-ray resonant exchange scattering investigations of rare earth intermetallic compounds: TbNi2B2C, TbCu2Ge2, and GdAgSb2

A coherent review on the x-ray resonant exchange scattering and basic recapitulation of phenomenological aspects of magnetic interactions were attempted in this thesis. Further, application of the XRES technique to understand the physical origin of various magnetic structures of TbNi2B2 C, TbCu2Ge2 and GdAgSb2 single crystals were tried as a main effort.;TbNi2B2C orders in a longitudinal spin wave structure below TN = 14.5 K. Concomitant with the magnetic ordering, structural phase transition from tetragonal phase (T \u3e TN) to orthorhombic phase occurred. The modulation direction was resolved to be along the longer axis in the basal plane. The wave vector also showed strong temperature dependence and smooth lock-in transition to tau = 611 with the onset of the ferromagnetism at TWFM ~ 8 K. Tb ion\u27s ferromagnetic component was directly observed by x-ray magnetic circular dichroism experiments. A microscopic model was also constructed to account for the ferromagnetism.;Resonant and nonresonant scatterings on TbCu2Ge2 revealed a spin reorientation. By combining the two techniques together, the direction of the magnetic moment in the basal plane was extracted which displayed moment reorientation from [010] (Tt \u3c T \u3c TN) to the ground state configuration of the [110] direction.;Ab initio magnetic structure determination was made on the GdAgSb2. Taking advantage of the polarization analysis and vector properties of the scattering cross sections, the magnetic moment direction as well as modulation wave vector was determined

Atomic level three-dimensional structure of individual particles with XFELs

11Ysciescopu

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity.

We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 ± 1.0 nm and 4.0 ± 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.

SACLAのX線自由電子レーザーを用いた新規タンパク質立体構造決定に世界で初めて成功. 京都大学プレスリリース. 2015-09-14.Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection

Single-scatter channel impulse response model of non-line-of-sight ultraviolet communications

Previous studies on the temporal characteristics of single-scatter transmission in non-line-of-sight (NLOS) ultraviolet communications (UVC) were based on the prolate-spheroidal coordinate system. In this work, a novel single-scatter channel impulse response (CIR) model is proposed in the spherical coordinate system, which is more natural and comprehensible than the prolate-spheroidal coordinate system in practical applications. Additionally, the results of the widely accepted Monte-Carlo (MC)-based channel model of NLOS UVC are provided to verify the proposed single-scatter CIR model. Results indicate that the computational time costed by the proposed single-scatter CIR model is decreased to less than 0.7% of the MC-based one with comparable accuracy in assessing the temporal characteristics of NLOS UVC channels.Comment: 10 pages, 4 figure

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity

We report 3D coherent diffractive imaging (CDI) of Au/Pd core-shell nanoparticles with 6.1 nm spatial resolution with elemental specificity. We measured single-shot diffraction patterns of the nanoparticles using intense x-ray free electron laser pulses. By exploiting the curvature of the Ewald sphere and the symmetry of the nanoparticle, we reconstructed the 3D electron density of 34 core-shell structures from these diffraction patterns. To extract 3D structural information beyond the diffraction signal, we implemented a super-resolution technique by taking advantage of CDI's quantitative reconstruction capabilities. We used high-resolution model fitting to determine the Au core size and the Pd shell thickness to be 65.0 +/- 1.0 nm and 4.0 +/- 0.5 nm, respectively. We also identified the 3D elemental distribution inside the nanoparticles with an accuracy of 3%. To further examine the model fitting procedure, we simulated noisy diffraction patterns from a Au/Pd core-shell model and a solid Au model and confirmed the validity of the method. We anticipate this super-resolution CDI method can be generally used for quantitative 3D imaging of symmetrical nanostructures with elemental specificity.111Ysciescopu

Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source

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.11Ysciescopu

Implication of Non-electrostatic Contribution to Deionization in Flow-Electrode CDI: Case Study of Nitrate Removal From Contaminated Source Waters

While flow-electrode capacitive deionization (FCDI) operated in short-circuited closed cycle (SCC) mode appears to hold promise for removal of salt from brackish source waters, there has been limited investigation on the removal of other water constituents such as nitrate, fluoride or bromide in combination with salt removal. Of particular concern is the effectiveness of FCDI when ions, such as nitrate, are recognized to non-electrostatically adsorb strongly to activated carbon particles thereby potentially rendering it difficult to regenerate these particles. In this study, SCC FCDI was used to desalt source waters containing nitrate at different concentrations. Results indicate that nitrate can be removed from source waters using FCDI to concentrations <1 mg NO3-N L−1 though a lower quality target such as 10 mg L−1 would be more cost-effective, particularly where the influent nitrate concentration is high (50 mg NO3-N L−1). Although studies of the fate of nitrate in the FCDI system show that physico-chemical adsorption of nitrate to the carbon initially plays a vital role in nitrate removal, the ongoing process of nitrate removal is not significantly affected by this phenomenon with this lack of effect most likely due to the continued formation of electrical double layers enabling capacitive nitrate removal. In contrast to conventional CDI systems, constant voltage mode is shown to be more favorable in maintaining stable effluent quality in SCC FCDI because the decrease in electrical potential that occurs in constant current operation leads to a reduction in the extent of salt removal from the brackish source waters. Through periodic replacement of the electrolyte at a water recovery of 91.4%, we show that the FCDI system can achieve a continuous desalting performance with the effluent NO3-N concentration below 1 mg NO3-N L−1 at low energy consumption (~0.5 kWh m−3) but high productivity