scholarly journals Particle orientation from distribution of explosion fragments in XFEL experiment

2014 ◽  
Vol 70 (a1) ◽  
pp. C295-C295
Author(s):  
Faigel Gyula ◽  
Zoltan Jurek
Keyword(s):  
Single Molecule ◽  
Outer Boundary ◽  
Heavy Atom ◽  
Particle Orientation ◽  
Single Molecule Imaging ◽  
X Ray ◽  
Heavy Atoms ◽  
Diffraction Patterns ◽  
Counting Statistics ◽  
Dynamics Simulations

In many XFEL experiments small objects with unknown orientations are introduced into the x-ray beam. However, understanding the measured quantities it would be desirable to know their orientations. This is the situation in the case of single-molecule imaging one of the main target areas of X-ray free-electron lasers. Here, the solution to the orientation problem is based on the possibility of orienting the large number of low-counting-statistics 2D diffraction patterns taken at random orientations of identical replicas of the sample. This is a difficult process and the low statistics limits the usability of these methods and ultimately it could prevent single-molecule imaging. We suggest a new approach, which avoids the use of the diffraction patterns. We propose to determine the sample orientation through identifying the direction of ejection fragments. The orientation of the sample is measured together with the diffraction pattern by detecting some fragments of the Coulomb explosion. We show by molecular-dynamics simulations that from the angular distribution of the fragments one can obtain the orientation of the samples [1].The figure shows the distribution of heavy atoms coming from different depth of the sample ( upper panel homogeneous, lower panel inhomogeneous model samples, and left to right is heavy atom at the outer boundary, halfway to center and at the center).

Further studies of low-angle X-ray diffraction patterns of collagen

1959 ◽  
Vol 252 (1269) ◽  
pp. 197-216 ◽  
Keyword(s):  
Electron Microscopy ◽  
Density Distribution ◽  
Heavy Atom ◽  
Diffraction Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Heavy Atoms ◽  
Density Distributions ◽  
Wide Range ◽  
Diffraction Patterns

Experiments were carried out on the drying of collagen fibres in vacuo at temperatures up to 200°C. Low-angle X-ray diffraction patterns of material so treated differed markedly from those of collagen dried in vacuo at room temperature, which invalidates the comparison of the latter with density distributions observed by electron microscopy. One-dimensional Patterson functions plotted for a wide range of protein hydration, together with some evidence from electron microscopy, provided helpful pointers to the density distribution in dry collagen, and strong evidence in support of a model for wet collagen consisting of a rectangular density distribution function, such that each period along the fibril has a band of higher density and an interband of lower density. The width of the band was found to be 0·46 of the period by making use of results obtained by ‘staining’ the fibres with heavy atoms. This model of the wet fibres, and the use of difference Patterson functions, made possible the elucidation of the effects of staining with silver nitrate, iodine, phosphotungstic acid, and osmium tetroxide. The major features of the distributions of these stains could be deter­mined with results consistent with the observations of electron microscopy, for those stains detectable by this means. The diffraction method was successful in detecting heavy-atom staining not visible in the electron microscope. Each of the stains considered gave somewhat similar staining patterns, a prominent feature of which was a pair of dense bands 0·8 d ( d being half the collagen period) apart, at the ends of the wet collagen band. Most of the iodine which entered these particular sites was very easily removed, but some of it was more firmly bound in these and other positions.

scholarly journals Single-molecule imaging with longer X-ray laser pulses

IUCrJ ◽  
2015 ◽  
Vol 2 (6) ◽  
pp. 661-674 ◽  
Author(s):  
Andrew V. Martin ◽  
Justine K. Corso ◽  
Carl Caleman ◽  
Nicusor Timneanu ◽  
Harry M. Quiney
Keyword(s):  
Single Molecule ◽  
Laser Pulses ◽  
Bragg Diffraction ◽  
Single Molecule Imaging ◽  
X Ray ◽  
Damage Models ◽  
Statistical Fluctuations ◽  
Damage Processes ◽  
The Impact ◽  
Serial Femtosecond Crystallography

During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the `self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5–10 fs, but can succeed for pulses 50–100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage (`damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30–50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

Simulations of X-ray diffraction of shock-compressed single-crystal tantalum with synchrotron undulator sources

2018 ◽  
Vol 25 (3) ◽  
pp. 748-756 ◽  
Author(s):  
M. X. Tang ◽  
Y. Y. Zhang ◽  
J. C. E ◽  
S. N. Luo
Keyword(s):  
Single Crystal ◽  
Large Scale ◽  
Incident Beam ◽  
Wave Structure ◽  
X Ray Diffraction ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Case Transmission ◽  
Dynamics Simulations

Polychromatic synchrotron undulator X-ray sources are useful for ultrafast single-crystal diffraction under shock compression. Here, simulations of X-ray diffraction of shock-compressed single-crystal tantalum with realistic undulator sources are reported, based on large-scale molecular dynamics simulations. Purely elastic deformation, elastic–plastic two-wave structure, and severe plastic deformation under different impact velocities are explored, as well as an edge release case. Transmission-mode diffraction simulations consider crystallographic orientation, loading direction, incident beam direction, X-ray spectrum bandwidth and realistic detector size. Diffraction patterns and reciprocal space nodes are obtained from atomic configurations for different loading (elastic and plastic) and detection conditions, and interpretation of the diffraction patterns is discussed.

scholarly journals Toward the Generation of an Isolated TW-Attosecond X-ray Pulse in XFEL

2018 ◽  
Vol 8 (9) ◽  
pp. 1588 ◽  
Author(s):  
Yong Parc ◽  
Chi Shim ◽  
Dong Kim
Keyword(s):  
Single Molecule ◽  
Free Electron ◽  
Free Electron Laser ◽  
Single Molecule Imaging ◽  
X Ray ◽  
Ultrafast Science ◽  
Single Spike ◽  
Electron Clouds

The isolated terawatt (TW) attosecond (as) hard X-ray pulse will expand the scope of ultrafast science, including the examination of phenomena that have not been studied before, such as the dynamics of electron clouds in atoms, single-molecule imaging, and examining the dynamics of hollow atoms. Therefore, several schemes for the generation of an isolated TW-as X-ray pulse in X-ray free electron laser (XFEL) facilities have been proposed with the manipulation of electron properties such as emittance or current. In a multi-spike scheme, a series of current spikes were employed to amplify the X-ray pulse. A single-spike scheme in which a TW-as X-ray pulse can be generated by a single current spike was investigated for ideal parameters for the XFEL machine. This paper reviews the proposed schemes and assesses the feasibility of each scheme.

scholarly journals Incoherent x-ray scattering in single molecule imaging

2014 ◽  
Vol 16 (7) ◽  
pp. 073042 ◽  
Author(s):  
J M Slowik ◽  
S-K Son ◽  
G Dixit ◽  
Z Jurek ◽  
R Santra
Keyword(s):  
Single Molecule ◽  
Single Molecule Imaging ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Preliminary X-ray analysis of a new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis

1998 ◽  
Vol 54 (3) ◽  
pp. 454-457 ◽  
Author(s):  
Amanda A. Brindley ◽  
Andrew R. Dalby ◽  
Michail N. Isupov ◽  
Jennifer A. Littlechild
Keyword(s):  
Heavy Atom ◽  
Crystal Form ◽  
Dihydrogen Phosphate ◽  
Data Set ◽  
X Ray ◽  
Heavy Atoms ◽  
Corallina Officinalis ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Rotation Function

A new crystal form of the vanadium-dependent bromoperoxidase from Corallina officinalis has been obtained. The crystals exhibit a `teardrop' morphology and are grown from 2 M ammonium dihydrogen phosphate pH 5 and diffract to beyond 1.7 Å resolution. They are in tetragonal space group P4222 with unit-cell dimensions of a = b = 201.9, c = 178.19 Å, α = β = γ = 90°. A 2.3 Å resolution native data set has been collected at the Hamburg Synchrotron. A mercury derivative data set has also been collected, and the heavy-atom positions have been determined. The self-rotation function and the positions of the heavy atoms are consistent with the molecule being a dodecamer with local 23 symmetry.

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