scholarly journals Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs

2020 ◽  
Vol 27 (3) ◽  
pp. 633-645
Author(s):  
Jungmin Kim ◽  
Jong Goo Kim ◽  
Hosung Ki ◽  
Chi Woo Ahn ◽  
Hyotcherl Ihee
Keyword(s):  
Quantum Noise ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Liquid Solution ◽  
Solution Phase ◽  
Scattering Data ◽  
Time Resolved ◽  
X Ray ◽  
The Future ◽  
The Difference

Elucidating the structural dynamics of small molecules and proteins in the liquid solution phase is essential to ensure a fundamental understanding of their reaction mechanisms. In this regard, time-resolved X-ray solution scattering (TRXSS), also known as time-resolved X-ray liquidography (TRXL), has been established as a powerful technique for obtaining the structural information of reaction intermediates and products in the liquid solution phase and is expected to be applied to a wider range of molecules in the future. A TRXL experiment is generally performed at the beamline of a synchrotron or an X-ray free-electron laser (XFEL) to provide intense and short X-ray pulses. Considering the limited opportunities to use these facilities, it is necessary to verify the plausibility of a target experiment prior to the actual experiment. For this purpose, a program has been developed, referred to as S-cube, which is short for a Solution Scattering Simulator. This code allows the routine estimation of the shape and signal-to-noise ratio (SNR) of TRXL data from known experimental parameters. Specifically, S-cube calculates the difference scattering curve and the associated quantum noise on the basis of the molecular structure of the target reactant and product, the target solvent, the energy of the pump laser pulse and the specifications of the beamline to be used. Employing a simplified form for the pair-distribution function required to calculate the solute–solvent cross term greatly increases the calculation speed as compared with a typical TRXL data analysis. Demonstrative applications of S-cube are presented, including the estimation of the expected TRXL data and SNR level for the future LCLS-II HE beamlines.

scholarly journals Robust X-ray angular correlations for the study of meso-structures

2017 ◽  
Vol 50 (3) ◽  
pp. 805-819 ◽  
Author(s):  
Julien R. Lhermitte ◽  
Cheng Tian ◽  
Aaron Stein ◽  
Atikur Rahman ◽  
Yugang Zhang ◽  
...  
Keyword(s):  
Structural Information ◽  
Signal To Noise Ratio ◽  
Scattering Data ◽  
Native Solution ◽  
X Ray ◽  
Angular Correlations ◽  
Structural Order ◽  
Self Assembling ◽  
Cross Correlation Analysis ◽  
Data Masking

As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly to recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.

Periodically poled KTA crystal investigated using coherent X-ray beams

2000 ◽  
Vol 33 (4) ◽  
pp. 1149-1153 ◽  
Author(s):  
P. Pernot-Rejmánková ◽  
P. A. Thomas ◽  
P. Cloetens ◽  
F. Lorut ◽  
J. Baruchel ◽  
...  
Keyword(s):  
Phase Difference ◽  
Domain Walls ◽  
Structural Information ◽  
Periodically Poled ◽  
Synchrotron Source ◽  
X Ray ◽  
Diffracted Waves ◽  
Coherent Beams ◽  
Diffraction Imaging ◽  
The Difference

The distribution of inverted ferroelectric domains on the surface and within the bulk of a periodically poled KTA (KTiOAsO4) single crystal has been observed using a simple X-ray diffraction imaging setup which takes advantage of the highly coherent beams available at a third-generation synchrotron source, such as the ESRF. This technique allows one to reveal the phase difference between the waves that are Bragg diffracted from adjacent domainsviafree-space propagation (Fresnel diffraction). The phase difference of the diffracted waves is mainly produced by the difference in phases of the structure factors involved, and contains precise structural information about the nature of the domain walls.

scholarly journals REGALS: a general method to deconvolve X-ray scattering data from evolving mixtures

2020 ◽  
Author(s):  
Steve P. Meisburger ◽  
Da Xu ◽  
Nozomi Ando
Keyword(s):  
A Priori ◽  
Scattering Data ◽  
Biological Macromolecules ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Open Source Software Package ◽  
Saxs Analysis ◽  
Structural Methods ◽  
Ray Scattering

AbstractMixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput, or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori. To address this issue, we introduce the REGALS method (REGularized Alternating Least Squares), which incorporates simple expectations about the data as prior knowledge and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, which makes it well-suited for exploring datasets with unknown species. Here we apply REGALS to analyze experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing, and time-resolved temperature jump. Based on its performance with these challenging datasets, we anticipate that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and python and is available freely as an open-source software package.

scholarly journals Understanding the properties of energy materials from their local structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C860-C860
Author(s):  
Hyunjeong Kim
Keyword(s):  
Structural Information ◽  
Lithium Ion ◽  
Structural Features ◽  
Scattering Data ◽  
Energy Materials ◽  
X Ray ◽  
Atomic Pair Distribution Function ◽  
Structure Probing ◽  
Atomic Pair ◽  
Pdf Analysis

Numerous energy materials with improved properties often show nano- or heavily disordered structural features which are hardly characterized by the conventional crystallographic technique alone. By using the atomic pair distribution function (PDF) analysis [1]on X-ray and neutron total scattering data, we have investigated various energy materials to elucidate structural features closely linked to their properties. Some of the examples are heavily disordered V1-xTixH2 for hydrogen storage [2] and layered Li1.2Mn0.567Ni0.166Co0.067O2 cathode material for lithium ion batteries. These materials possess an intricate structure and could easily lead to misleading results if one relies on only one structure probing technique. In this talk, I will show how their structural information was extracted from the x-ray and neutron PDFs obtained at BL22XU at SPring-8 and NOVA at J-PARC, respectively and how it was used with information available from other techniques to understand the properties of these energy materials.

scholarly journals Singular value decomposition as a tool for background corrections in time-resolved XFEL scattering data

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130336 ◽  
Author(s):  
Kristoffer Haldrup
Keyword(s):  
Singular Value Decomposition ◽  
Singular Value ◽  
Scattering Data ◽  
High Time Resolution ◽  
Light Sources ◽  
Time Resolved ◽  
X Ray ◽  
Very Large Datasets ◽  
Chaotic Nature ◽  
Value Decomposition

The development of new X-ray light sources, XFELs, with unprecedented time and brilliance characteristics has led to the availability of very large datasets with high time resolution and superior signal strength. The chaotic nature of the emission processes in such sources as well as entirely novel detector demands has also led to significant challenges in terms of data analysis. This paper describes a heuristic approach to datasets where spurious background contributions of a magnitude similar to (or larger) than the signal of interest prevents conventional analysis approaches. The method relies on singular-value decomposition of no-signal subsets of acquired datasets in combination with model inputs and appears generally applicable to time-resolved X-ray diffuse scattering experiments.

Time-resolved XAFS measurement using quick-scanning techniques at BSRF

2017 ◽  
Vol 24 (3) ◽  
pp. 674-678 ◽  
Author(s):  
Shengqi Chu ◽  
Lirong Zheng ◽  
Pengfei An ◽  
Hui Gong ◽  
Tiandou Hu ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
High Energy ◽  
High Energy Resolution ◽  
Double Crystal ◽  
Time Resolved ◽  
Edge Structure ◽  
X Ray ◽  
Double Crystal Monochromator ◽  
Good Signal ◽  
X Ray Absorption

A new quick-scanning X-ray absorption fine-structure (QXAFS) system has been established on beamline 1W1B at the Beijing Synchrotron Radiation Facility. As an independent device, the QXAFS system can be employed by other beamlines equipped with a double-crystal monochromator to carry out quick energy scans and data acquisition. Both continuous-scan and trapezoidal-scan modes are available in this system to satisfy the time scale from subsecond (in the X-ray absorption near-edge structure region) to 1 min. Here, the trapezoidal-scan method is presented as being complementary to the continuous-scan method, in order to maintain high energy resolution and good signal-to-noise ratio. The system is demonstrated to be very reliable and has been combined with in situ cells to carry out time-resolved XAFS studies.

Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospects

2010 ◽  
Vol 66 (2) ◽  
pp. 270-280 ◽  
Author(s):  
Jeongho Kim ◽  
Kyung Hwan Kim ◽  
Jae Hyuk Lee ◽  
Hyotcherl Ihee
Keyword(s):  
Single Molecule ◽  
Reaction Dynamics ◽  
Liquid Solution ◽  
Substantial Improvement ◽  
Photon Flux ◽  
Solvation Dynamics ◽  
Structural Transitions ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray

In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100 ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of the X-ray free-electron laser (XFEL) will bring a substantial improvement in pulse duration, photon flux and coherence of X-ray pulses, making time-resolved X-ray diffraction even more powerful. This technical breakthrough is envisioned to revolutionize the field of reaction dynamics associated with time-resolved diffraction methods. Examples of candidates for the first femtosecond X-ray diffraction experiments using highly coherent sub-100 fs pulses generated from XFELs are presented in this paper. They include the chemical reactions of small molecules in the gas and solution phases, solvation dynamics and protein structural transitions. In these potential experiments, ultrafast reaction dynamics and motions of coherent rovibrational wave packets will be monitored in real time. In addition, high photon flux and coherence of XFEL-generated X-ray pulses give the prospect of single-molecule diffraction experiments.

scholarly journals Structural Dynamics of C2F4I2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography

2021 ◽  
Vol 22 (18) ◽  
pp. 9793
Author(s):  
Jain Gu ◽  
Seonggon Lee ◽  
Seunghwan Eom ◽  
Hosung Ki ◽  
Eun Hyuk Choi ◽  
...  
Keyword(s):  
Reaction Dynamics ◽  
Molecular Structures ◽  
Solution Phase ◽  
Reaction Pathways ◽  
Time Resolved ◽  
Solvent Interactions ◽  
X Ray ◽  
Exchange Correlation ◽  
Solvent Dependence ◽  
Halogen Elimination

The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute–solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase.

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.

Introduction

2018 ◽  
Author(s):  
Eaton E. Lattman ◽  
Thomas D. Grant ◽  
Edward H. Snell
Keyword(s):  
Structural Biology ◽  
Single Molecule ◽  
Small Angle ◽  
Structural Information ◽  
Complementary Technique ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Future ◽  
The Relationship ◽  
Basic Level

This chapter provides an introduction to small angle solution scattering with particular reference to the complementary technique of X-ray crystallography and the relationship between the two. It describes at its most basic level the theoretical underpinnings of solution scattering starting from a single molecule and how this information is sampled in crystals versus in solution. A brief introduction is given to some of the primary types of structural information that can be obtained from experiments. The chapter concludes discussing some of the most common applications of the technique in structural biology, and where the future is likely headed.

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