scholarly journals Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

2017 ◽  
Vol 73 (5) ◽  
pp. 449-464 ◽  
Author(s):  
Sergei Grudinin ◽  
Maria Garkavenko ◽  
Andrei Kazennov
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Multipole Expansion ◽  
Adaptive Method ◽  
Sampling Theorem ◽  
Large Set ◽  
X Ray ◽  
X Ray Scattering ◽  
Comparable Accuracy ◽  
Ray Scattering

A new method calledPepsi-SAXSis presented that calculates small-angle X-ray scattering profiles from atomistic models. The method is based on the multipole expansion scheme and is significantly faster compared with other tested methods. In particular, using the Nyquist–Shannon–Kotelnikov sampling theorem, the multipole expansion order is adapted to the size of the model and the resolution of the experimental data. It is argued that by using the adaptive expansion order, this method has the same quadratic dependence on the number of atoms in the model as the Debye-based approach, but with a much smaller prefactor in the computational complexity. The method has been systematically validated on a large set of over 50 models collected from the BioIsis and SASBDB databases. Using a laptop, it was demonstrated thatPepsi-SAXSis about seven, 29 and 36 times faster compared withCRYSOL,FoXSand the three-dimensional Zernike method inSAStbx, respectively, when tested on data from the BioIsis database, and is about five, 21 and 25 times faster compared withCRYSOL,FoXSandSAStbx, respectively, when tested on data from SASBDB. On average,Pepsi-SAXSdemonstrates comparable accuracy in terms of χ2toCRYSOLandFoXSwhen tested on BioIsis and SASBDB profiles. Together with a small allowed variation of adjustable parameters, this demonstrates the effectiveness of the method.Pepsi-SAXSis available at http://team.inria.fr/nano-d/software/pepsi-saxs.

X-ray imaging with ultra-small-angle X-ray scattering as a contrast mechanism

2004 ◽  
Vol 37 (5) ◽  
pp. 757-765 ◽  
Author(s):  
L. E. Levine ◽  
G. G. Long
Keyword(s):  
Small Angle ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Sample Volume ◽  
Contrast Imaging ◽  
X Ray ◽  
X Ray Scattering ◽  
X Ray Imaging ◽  
Contrast Mechanism ◽  
Ray Scattering

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.

Simulation of small-angle X-ray scattering from thylakoid membranes

2009 ◽  
Vol 42 (4) ◽  
pp. 649-659 ◽  
Author(s):  
J. J. K. Kirkensgaard ◽  
J. K. Holm ◽  
J. K. Larsen ◽  
D. Posselt
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
Virtual Instrument ◽  
Three Dimensional ◽  
Thylakoid Membranes ◽  
Three Dimensional Model ◽  
General Applicability ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

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.

scholarly journals Two practical Java software tools for small-angle X-ray scattering analysis of biomolecules

2014 ◽  
Vol 47 (2) ◽  
pp. 810-815 ◽  
Author(s):  
Andreas Hofmann ◽  
Andrew E. Whitten
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Ease Of Use ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Three Dimensional Models ◽  
Ray Scattering

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.

Simulations of the transmission small angle x-ray scattering for three-dimensional architectures

2021 ◽  
Author(s):  
Tianjuan Yang ◽  
Jiahao Zhang ◽  
Jianyuan Ma ◽  
Shiyuan Liu ◽  
Xiuguo Chen
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Determining the shape and periodicity of nanostructures using small-angle X-ray scattering

2015 ◽  
Vol 48 (5) ◽  
pp. 1355-1363 ◽  
Author(s):  
Daniel F. Sunday ◽  
Scott List ◽  
Jasmeet S. Chawla ◽  
R. Joseph Kline
Keyword(s):  
Small Angle ◽  
Semiconductor Industry ◽  
Three Dimensional ◽  
Critical Dimension ◽  
Dimensional Structure ◽  
Critical Dimensions ◽  
X Ray ◽  
Line Shapes ◽  
X Ray Scattering ◽  
Ray Scattering

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.

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