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 Real-space modeling for complex structures based on small-angle X-ray scattering

2021 ◽  
Vol 54 (5) ◽  
pp. 1290-1297
Author(s):  
Kazuhiko Omote ◽  
Tomoyuki Iwata
Keyword(s):  
Small Angle ◽  
Three Dimensional ◽  
Finite Size ◽  
Real Space ◽  
Three Dimensional Model ◽  
X Ray ◽  
X Ray Scattering ◽  
Space Modeling ◽  
Primary Particles ◽  
Ray Scattering

A three-dimensional real-space model has been created for hierarchical materials by matching observed and simulated small-angle X-ray scattering patterns. The simulation is performed by arranging the positions of small primary particles and constructing an aggregate structure in a finite-sized cell. In order to avoid the effect of the finite size of the cell, the cell size is extended to infinity by introducing an asymptotic form of the long-range correlations among the primary particles. As a result, simulations for small-angle X-ray scattering patterns can be performed correctly in the low-wavenumber regime (<0.1 nm−1), allowing the model to handle hundred-nanometre-scale structures composed of primary particles of a few nanometres in size. An aerogel structure was determined using this model, resulting in an excellent match with the experimental scattering pattern. The resultant three-dimensional model can generate cross-sectional images similar to those obtained by transmission electron microscopy, and the calculated pore-size distribution is in accord with that derived from the gas adsorption method.

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.

scholarly journals Determination of nanostructure of liposomes containing two model drugs by X-ray scattering from a synchrotron source

2013 ◽  
Vol 20 (5) ◽  
pp. 721-728 ◽  
Author(s):  
Alexandr Nasedkin ◽  
Jan Davidsson ◽  
Mont Kumpugdee-Vollrath
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
Structural Parameters ◽  
Water Layer ◽  
Synchrotron Source ◽  
X Ray ◽  
X Ray Scattering ◽  
Extract Information ◽  
Ray Scattering

Small-angle X-ray scattering has been employed to study how the introduction of paracetamol and acetylsalicylic acid into a liposome bilayer system affects the system's nanostructure. An X-ray scattering model, developed for multilamellar liposome systems [Pabstet al.(2000),Phys. Rev. E,62, 4000–4009], has been used to fit the experimental data and to extract information on how structural parameters, such as the number and thickness of the bilayers of the liposomes, thickness of the water layer in between the bilayers, size and volume of the head and tail groups, are affected by the drugs and their concentration. Even though the experimental data reveal a complicated picture of the drug–bilayer interaction, they clearly show a correlation between nanostructure, drug and concentration in some aspects. The localization of the drugs in the bilayers is discussed.

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

scholarly journals Measuring the specific surface area of mesoporous silica using x-ray scattering

2014 ◽  
Vol 70 (a1) ◽  
pp. C599-C599
Author(s):  
Julien Cambedouzou ◽  
Olivier Diat
Keyword(s):  
Experimental Data ◽  
Specific Surface ◽  
Surface Area ◽  
Mesoporous Materials ◽  
Specific Surface Area ◽  
Small Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Mcm 41 ◽  
Ray Scattering

The development of porous silica or carbon material with high specific surface area raises a high interest in the field of materials science given their potential interest in a wide range of applications including catalysis, water treatment or drug delivery. Among these mesoporous structures, those consisting of one-dimensional pores aligned along a compact hexagonal packing are of prime importance and can be referred to as "hexagonal mesoporous materials" (HMPM). The most famous silica structures of this kind are MCM-41 and SBA-15. The same symmetry can be found in carbon mesoporous materials, for example in FDU-15 structures. The precise characterization of HMPM is necessary for most of the applications envisioned for these materials (pore size, pore density, specific surface and sometimes thickness of the functionalization layer). Small angle X-ray scattering techniques offer the opportunity to determine the mean structural parameters of HMPM. Although different approaches can be found in the literature in order to numerically reproduce the experimental data obtained on HMPM or hexagonal liquid crystals, when the sample is a powder, fitting the experimental data in absolute scale with numerical models becomes necessary. However, with a large scattering contribution of grain at low q vector as well as short range correlation contribution at large q, the analysis is not so simple. In this paper, we propose a comprehensive study [1] devoted to the quantitative interpretation of small-angle scattering patterns of HMPM in terms of structure and specific surface estimation based on the formalism proposed by Spalla et al. [2]. In the case of two real samples, namely a SBA-15 and a MCM-41 powder, the specific surface area of the mesopores is estimated and is discussed in the light of gas adsorption measurements.

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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