Signal to noise considerations for single crystal femtosecond time resolved crystallography of the Photoactive Yellow Protein

2014 ◽  
Vol 171 ◽  
pp. 439-455 ◽  
Author(s):  
Jasper J. van Thor ◽  
Mark M. Warren ◽  
Craig N. Lincoln ◽  
Matthieu Chollet ◽  
Henrik Till Lemke ◽  
...  
Keyword(s):  
Single Crystal ◽  
Structure Factor ◽  
Bragg Reflection ◽  
Threshold Concentration ◽  
Photoactive Yellow Protein ◽  
Signal To Noise ◽  
Time Resolved ◽  
X Ray ◽  
Mosaic Spread ◽  
Rotation Method

Femtosecond time resolved pump–probe protein X-ray crystallography requires highly accurate measurements of the photoinduced structure factor amplitude differences. In the case of femtosecond photolysis of single P63crystals of the Photoactive Yellow Protein, it is shown that photochemical dynamics place a considerable restraint on the achievable time resolution due to the requirement to stretch and add second order dispersion in order to generate threshold concentration levels in the interaction region. Here, we report on using a ‘quasi-cw’ approach to use the rotation method with monochromatic radiation and 2 eV bandwidth at 9.465 keV at the Linac Coherent Light Source operated in SASE mode. A source of significant Bragg reflection intensity noise is identified from the combination of mode structure and jitter with very small mosaic spread of the crystals and very low convergence of the XFEL source. The accuracy with which the three dimensional reflection is approximated by the ‘quasi-cw’ rotation method with the pulsed source is modelled from the experimentally collected X-ray pulse intensities together with the measured rocking curves. This model is extended to predict merging statistics for recently demonstrated self seeded mode generated pulse train with improved stability, in addition to extrapolating to single crystal experiments with increased mosaic spread. The results show that the noise level can be adequately modelled in this manner, indicating that the large intensity fluctuations dominate the merged signal-to-noise (I/σI) value. Furthermore, these results predict that using the self seeded mode together with more mosaic crystals, sufficient accuracy may be obtained in order to resolve typical photoinduced structure factor amplitude differences, as taken from representative synchrotron results.

Cancellation method to improve signal to noise ratio of an electrodeless microwave-biased ZnO single crystal x-ray detector

2022 ◽  
Vol 93 (1) ◽  
pp. 015006
Author(s):  
Xiaolong Zhao ◽  
Ming Ye ◽  
Zhi Cao ◽  
Danyang Huang ◽  
Tingting Fan ◽  
...  
Keyword(s):  
Single Crystal ◽  
Signal To Noise Ratio ◽  
Signal To Noise ◽  
X Ray ◽  
Noise Ratio ◽  
Zno Single Crystal

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

2003 ◽  
Vol 36 (2) ◽  
pp. 147-227 ◽  
Author(s):  
Michel H. J. Koch ◽  
Patrice Vachette ◽  
Dmitri I. Svergun
Keyword(s):  
High Resolution ◽  
Neutron Scattering ◽  
Small Angle ◽  
Structure Factor ◽  
Structural Changes ◽  
Biological Macromolecules ◽  
Time Resolved ◽  
Scattering Intensity ◽  
X Ray ◽  
Angle Scattering

1. Introduction 1482. Basics of X-ray and neutron scattering 1492.1 Elastic scattering of electromagnetic radiation by a single electron 1492.2 Scattering by assemblies of electrons 1512.3 Anomalous scattering and long wavelengths 1532.4 Neutron scattering 1532.5 Transmission and attenuation 1553. Small-angle scattering from solutions 1563.1 Instrumentation 1563.2 The experimental scattering pattern 1573.3 Basic scattering functions 1593.4 Global structural parameters 1613.4.1 Monodisperse systems 1613.4.2 Polydisperse systems and mixtures 1633.5 Characteristic functions 1644. Modelling 1664.1 Spherical harmonics 1664.2 Shannon sampling 1694.3 Shape determination 1704.3.1 Modelling with few parameters: molecular envelopes 1714.3.2 Modelling with many parameters: bead models 1734.4 Modelling domain structure and missing parts of high-resolution models 1784.5 Computing scattering patterns from atomic models 1844.6 Rigid-body refinement 1875. Applications 1905.1 Contrast variation studies of ribosomes 1905.2 Structural changes and catalytic activity of the allosteric enzyme ATCase 1916. Interactions between molecules in solution 2036.1 Linearizing the problem for moderate interactions: the second virial coefficient 2046.2 Determination of the structure factor 2057. Time-resolved measurements 2118. Conclusions 2159. Acknowledgements 21610. References 216A self-contained presentation of the main concepts and methods for interpretation of X-ray and neutron-scattering patterns of biological macromolecules in solution, including a reminder of the basics of X-ray and neutron scattering and a brief overview of relevant aspects of modern instrumentation, is given. For monodisperse solutions the experimental data yield the scattering intensity of the macromolecules, which depends on the contrast between the solvent and the particles as well as on their shape and internal scattering density fluctuations, and the structure factor, which is related to the interactions between macromolecules. After a brief analysis of the information content of the scattering intensity, the two main approaches for modelling the shape and/or structure of macromolecules and the global minimization schemes used in the calculations are presented. The first approach is based, in its more advanced version, on the spherical harmonics approximation and relies on few parameters, whereas the second one uses bead models with thousands of parameters. Extensions of bead modelling can be used to model domain structure and missing parts in high-resolution structures. Methods for computing the scattering patterns from atomic models including the contribution of the hydration shell are discussed and examples are given, which also illustrate that significant differences sometimes exist between crystal and solution structures. These differences are in some cases explainable in terms of rigid-body motions of parts of the structures. Results of two extensive studies – on ribosomes and on the allosteric protein aspartate transcarbamoylase – illustrate the application of the various methods. The unique bridge between equilibrium structures and thermodynamic or kinetic aspects provided by scattering techniques is illustrated by modelling of intermolecular interactions, including crystallization, based on an analysis of the structure factor and recent time-resolved work on assembly and protein folding.

scholarly journals Thermal behavior of single-crystal scintillators for high-speed X-ray imaging

2019 ◽  
Vol 26 (1) ◽  
pp. 205-214 ◽  
Author(s):  
Alan Kastengren
Keyword(s):  
Single Crystal ◽  
High Speed ◽  
Thermal Loading ◽  
Indirect Detection ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
Damage And Failure ◽  
Light Levels ◽  
X Ray Imaging

Indirect detection of X-rays using single-crystal scintillators is a common approach for high-resolution X-ray imaging. With the high X-ray flux available from synchrotron sources and recent advances in high-speed visible-light cameras, these measurements are increasingly used to obtain time-resolved images of dynamic phenomena. The X-ray flux on the scintillator must, in many cases, be limited to avoid thermal damage and failure of the scintillator, which in turn limits the obtainable light levels from the scintillator. In this study, a transient one-dimensional numerical simulation of the temperature and stresses within three common scintillator crystals (YAG, LuAG and LSO) used for high-speed X-ray imaging is presented. Various conditions of thermal loading and convective cooling are also presented.

scholarly journals Impact of lossy compression of X-ray projections onto reconstructed tomographic slices

2020 ◽  
Vol 27 (5) ◽  
pp. 1326-1338
Author(s):  
Federica Marone ◽  
Jakob Vogel ◽  
Marco Stampanoni
Keyword(s):  
Signal To Noise Ratio ◽  
Lossy Compression ◽  
High Signal ◽  
Signal To Noise ◽  
Time Resolved ◽  
Data Archiving ◽  
X Ray ◽  
Compression Factor ◽  
Significant Burden ◽  
Noise Ratio

Modern detectors used at synchrotron tomographic microscopy beamlines typically have sensors with more than 4–5 mega-pixels and are capable of acquiring 100–1000 frames per second at full frame. As a consequence, a data rate of a few TB per day can easily be exceeded, reaching peaks of a few tens of TB per day for time-resolved tomographic experiments. This data needs to be post-processed, analysed, stored and possibly transferred, imposing a significant burden onto the IT infrastructure. Compression of tomographic data, as routinely done for diffraction experiments, is therefore highly desirable. This study considers a set of representative datasets and investigates the effect of lossy compression of the original X-ray projections onto the final tomographic reconstructions. It demonstrates that a compression factor of at least three to four times does not generally impact the reconstruction quality. Potentially, compression with this factor could therefore be used in a transparent way to the user community, for instance, prior to data archiving. Higher factors (six to eight times) can be achieved for tomographic volumes with a high signal-to-noise ratio as it is the case for phase-retrieved datasets. Although a relationship between the dataset signal-to-noise ratio and a safe compression factor exists, this is not simple and, even considering additional dataset characteristics such as image entropy and high-frequency content variation, the automatic optimization of the compression factor for each single dataset, beyond the conservative factor of three to four, is not straightforward.

scholarly journals On the interpretation of X-ray, single crystal, rotation photographs

1926 ◽  
Vol 113 (763) ◽  
pp. 117-160 ◽  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
The Other ◽  
X Rays ◽  
X Ray ◽  
Powder Method ◽  
Convenient Form ◽  
Other Hand ◽  
Rotation Method ◽  
Laue Method

In the development of the study of crystals by X-rays the methods used divide themselves naturally into four types : the Bragg Ionisation Spectrometer method, the Laue method, the Powder method of Debye and Scherrer, and the Rotating Crystal method of Rinne, Schiebold and Polyani. The techniques of the first three of these methods are fully explained in such books as ‘ X-Rays and Crystal Structure,’ by W. H. and W. L. Bragg, ‘ The Structure of Crystals,’ by Wyckoff, and ‘ Krystalle und Rontgenstrahlen,’ by Ewald, as well as in original papers. On the other hand, the rotation method is only slightly touched on in these works, the literature is scattered in a great number of papers, and the technique has not so far been described at any length in a convenient form. Particularly in English, references to it are scanty. In this paper the author has tried to give a concise account of the method, together with various types of charts and tables as it is used in the Davy Faraday Laboratory. The methods described differ in certain respects from those used on the Continent,* but they have been found to be rapid and sufficiently accurate.

Time-resolved small-angle x-ray scattering measurements of a polymer bicontinuous microemulsion structure factor under shear

2002 ◽  
Vol 66 (4) ◽  
Author(s):  
Franklin E. Caputo ◽  
Wesley R. Burghardt ◽  
Kasiraman Krishnan ◽  
Frank S. Bates ◽  
Timothy P. Lodge
Keyword(s):  
Small Angle ◽  
Structure Factor ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Bicontinuous Microemulsion ◽  
Scattering Measurements ◽  
Ray Scattering

A method of material design for systematic absence of X-ray diffraction

2010 ◽  
Vol 25 (S1) ◽  
pp. S48-S51
Author(s):  
Huan-hua Wang
Keyword(s):  
Solid Solution ◽  
Structure Factor ◽  
Material Design ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
Xrd Pattern ◽  
X Ray ◽  
X Ray Scattering ◽  
Calculation Process

Materials with systematic absence of X-ray diffraction (XRD) peaks are desirable for conducting some special researches using X-ray diffraction or time-resolved X-ray scattering. This paper proposes a method for designing this kind of materials. It utilizes solid solution to reduce the structure factor of a selected reflection to zero by choosing proper components and their contents to let the reflection amplitudes from different atomic layers in a unit cell of the solid solution cancel each other completely. This method on how to select a solid solvent and how to calculate its content was illustrated using SrTiO3 as an example. A solid solution Sr1−xCaxTiO3 with a systematic absence of the (001) diffraction can be designed, and the value of x can be determined to be x=0.54 using an iteration calculation process. This result was verified by the experimental XRD pattern of a Sr0.46Ca0.54TiO3 sample.

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