scholarly journals Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

2015 ◽  
Vol 30 ◽  
pp. 147-160 ◽  
Author(s):  
Xianyang Fang ◽  
Jason R Stagno ◽  
Yuba R Bhandari ◽  
Xiaobing Zuo ◽  
Yun-Xing Wang
2004 ◽  
Vol 37 (5) ◽  
pp. 757-765 ◽  
Author(s):  
L. E. Levine ◽  
G. G. Long

A new transmission X-ray imaging technique using ultra-small-angle X-ray scattering (USAXS) as a contrast mechanism is described. USAXS imaging can sometimes provide contrast in cases where radiography and phase-contrast imaging are unsuccessful. Images produced at different scattering vectors highlight different microstructural features within the same sample volume. When used in conjunction with USAXS scans, USAXS imaging provides substantial quantitative and qualitative three-dimensional information on the sizes, shapes and spatial arrangements of the scattering objects. The imaging technique is demonstrated on metal and biological samples.


2009 ◽  
Vol 42 (4) ◽  
pp. 649-659 ◽  
Author(s):  
J. J. K. Kirkensgaard ◽  
J. K. Holm ◽  
J. K. Larsen ◽  
D. Posselt

Small-angle X-ray scattering (SAXS) patterns are calculated from a three-dimensional model of photosynthetic thylakoid membranes. The intricate structure of the thylakoids is represented by sampling random `electron density points' on geometric surfaces. The simulation setup works as a virtual instrument, allowing direct comparison with experimental data. The simulations qualitatively reproduce experimental data and thus clarify the structural origin of the scattering features. This is used to explain recent SAXS measurements and as a guideline for new experiments and future quantitative modeling. The setup has general applicability for model testing purposes when modeling scattering from membrane systems of complex geometries.


2014 ◽  
Vol 47 (2) ◽  
pp. 810-815 ◽  
Author(s):  
Andreas Hofmann ◽  
Andrew E. Whitten

Small-angle X-ray scattering has established itself as a common technique in structural biology research. Here, two novel Java applications to aid modelling of three-dimensional macromolecular structures based on small-angle scattering data are described.MolScatis an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data.SAFIRis a program for interactive rigid-body modelling into low-resolution shapes restored from small-angle scattering data. The program has been designed with an emphasis on ease of use and intuitive handling. An embedded version ofMolScatis used to enable quick evaluation of the fit between the model and experimental scattering data.SAFIRalso provides options to refine macromolecular complexes with optional user-specified restraints against scattering data by means of a Monte Carlo approach.


2021 ◽  
Author(s):  
Tianjuan Yang ◽  
Jiahao Zhang ◽  
Jianyuan Ma ◽  
Shiyuan Liu ◽  
Xiuguo Chen

2015 ◽  
Vol 48 (5) ◽  
pp. 1355-1363 ◽  
Author(s):  
Daniel F. Sunday ◽  
Scott List ◽  
Jasmeet S. Chawla ◽  
R. Joseph Kline

The semiconductor industry is exploring new metrology techniques capable of meeting the future requirement to characterize three-dimensional structure where the critical dimensions are less than 10 nm. X-ray scattering techniques are one candidate owing to the sub-Å wavelengths which are sensitive to internal changes in electron density. Critical-dimension small-angle X-ray scattering (CDSAXS) has been shown to be capable of determining the average shape of a line grating. Here it is used to study a set of line gratings patternedviaa self-aligned multiple patterning process, which resulted in a set of mirrored lines, where the individual line shapes were asymmetric. The spacing between lines was systematically varied by sub-nm shifts. The model used to simulate the scattering was developed in stages of increasing complexity in order to justify the large number of parameters included. Comparisons between the models at different stages of development demonstrate that the measurement can determine differences in line shapes within the superlattice. The shape and spacing between lines within a given set were determined to sub-nm accuracy. This demonstrates the potential for CDSAXS as a high-resolution nanostructure metrology tool.


Methods ◽  
2016 ◽  
Vol 103 ◽  
pp. 18-24 ◽  
Author(s):  
Yuba R. Bhandari ◽  
Wei Jiang ◽  
Eric A. Stahlberg ◽  
Jason R. Stagno ◽  
Yun-Xing Wang

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