scholarly journals PyQCstrc.ico: a computing package for structural modelling of icosahedral quasicrystals

2021 ◽  
Vol 54 (4) ◽  
Author(s):  
Tsunetomo Yamada
Keyword(s):  
Dimensional Structure ◽  
Initial Structure ◽  
Building Structure ◽  
Structure Model ◽  
Structural Modelling ◽  
Complicated Shape ◽  
Higher Dimensional ◽  
Icosahedral Quasicrystals ◽  
Periodic Arrangement

The atomic structure of quasicrystals (QCs) is described as a section of a higher-dimensional structure that consists of a periodic arrangement of occupation domains (ODs). Determination of the shape of ODs and their partitioning is crucial in the structural analysis of QCs. However, owing to the complicated shape of ODs, building the initial structure model requires a great deal of time and effort. Thus, a computer program for building structure models of QCs is needed. Presented here is a Python3 package for structure modelling of icosahedral QCs.

Ab Initio Structure Determination of Quasicrystals via Single Crystal X-Ray Diffraction

2003 ◽  
Vol 805 ◽  
Author(s):  
Hiroyuki Takakura ◽  
Akiji Yamamoto ◽  
Marc de Boissieu ◽  
Taku J Sato ◽  
An Pang Tsai
Keyword(s):  
Single Crystal ◽  
Ab Initio ◽  
Structure Determination ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Higher Dimensional ◽  
Icosahedral Quasicrystals ◽  
Ab Initio Structure

ABSTRACTA standard approach for structure solution of ordinary crystals begins with solving the phase problem. We show that a similar procedure can be taken even in the case of quasicrystals using single crystal X-ray diffraction by applying an ab initio structure determination method called the low density elimination method. The first picture of the occupation domains, which must be specified in a higher-dimensional structure determination of quasicrystals, is obtained from a phase-reconstructed density. We present six-dimensional densities determined by this method and give their interpretation for several different types of icosahedral quasicrystals.

scholarly journals Computational prediction of an icosahedral quasicrystal

2014 ◽  
Vol 70 (a1) ◽  
pp. C890-C890
Author(s):  
Michael Engel ◽  
Pablo Damasceno ◽  
Carolyn Phillips ◽  
Sharon Glotzer
Keyword(s):  
Self Assembly ◽  
Computational Prediction ◽  
Real Space ◽  
Icosahedral Quasicrystal ◽  
Icosahedral Symmetry ◽  
Structure Model ◽  
Colloidal Systems ◽  
Naturally Occurring ◽  
Higher Dimensional ◽  
Icosahedral Quasicrystals

From the first quasicrystal discovered in the laboratory 30 years ago to the only known specimen of naturally occurring quasicrystals, quasicrystals with icosahedral symmetry have received great attention. There are more than one hundred stable icosahedral quasicrystals in metallic alloys; all are identified by their diffraction spectra. Despite this abundance, resolving the positions of the atoms within the solid has been possible only indirectly. Moreover, unlike dodecagonal and other axial quasicrystals, icosahedral quasicrystals have been observed neither in simulations nor in non-atomic (e.g. micellar or colloidal) systems, where real-space information would be available. Here we present an icosahedral quasicrystal discovered in computer simulation via self-assembly from the liquid phase. We provide a structure model by analyzing atomic surfaces and report the presence of phason flips. Our results constitute a direct microscopic confirmation of the higher-dimensional crystallographic description of icosahedral quasicrystals.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Fast calibration of CBED patterns for quantitative analysis

1993 ◽  
Vol 51 ◽  
pp. 674-675
Author(s):  
M.A. Gribelyuk ◽  
M. Rühle
Keyword(s):  
Reciprocal Lattice ◽  
Accurate Determination ◽  
Incident Beam ◽  
Crystal Thickness ◽  
Structure Model ◽  
Beam Direction ◽  
Transmitted Beam ◽  
Reciprocal Vector ◽  
On Line

A new method is suggested for the accurate determination of the incident beam direction K, crystal thickness t and the coordinates of the basic reciprocal lattice vectors V1 and V2 (Fig. 1) of the ZOLZ plans in pixels of the digitized 2-D CBED pattern. For a given structure model and some estimated values Vest and Kest of some point O in the CBED pattern a set of line scans AkBk is chosen so that all the scans are located within CBED disks.The points on line scans AkBk are conjugate to those on A0B0 since they are shifted by the reciprocal vector gk with respect to each other. As many conjugate scans are considered as CBED disks fall into the energy filtered region of the experimental pattern. Electron intensities of the transmitted beam I0 and diffracted beams Igk for all points on conjugate scans are found as a function of crystal thickness t on the basis of the full dynamical calculation.

Indexing approximants of icosahedral quasicrystals

1999 ◽  
Vol 55 (6) ◽  
pp. 975-983 ◽  
Author(s):  
M. Quiquandon ◽  
A. Katz ◽  
F. Puyraimond ◽  
D. Gratias
Keyword(s):  
Unit Cell ◽  
Dimensional Lattice ◽  
Geometrical Properties ◽  
Actual Model ◽  
Icosahedral Quasicrystals ◽  
Low Dimensional

It is well known that the crystallography of approximants is directly related to that of the parent quasicrystal, once its unit-cell vectors are identified as parallel projections of certain N-dimensional lattice nodes {\bf A}^{i}. Derived here are explicit simple relations for calculating the shear matrices {\boldvarepsilon} and the related crystallographic properties of the corresponding approximants, including diffraction indexing and the determination of the lattice in perpendicular space. Applied to low-dimensional approximants, the derivation shows that the systematic `accidental' extinction rules observed in the pentagonal phases are generic extinctions that are due to the geometrical properties of the projected 1D lattice and are independent of the actual model of the quasicrystal.

scholarly journals Determination of the alpha-actinin-binding site on actin filaments by cryoelectron microscopy and image analysis.

1994 ◽  
Vol 126 (2) ◽  
pp. 433-443 ◽  
Author(s):  
A McGough ◽  
M Way ◽  
D DeRosier
Keyword(s):  
Image Analysis ◽  
Smooth Muscle ◽  
Binding Sites ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Actin Binding ◽  
Dimensional Structure ◽  
Outer Face ◽  
Actin Binding Domain

The three-dimensional structure of actin filaments decorated with the actin-binding domain of chick smooth muscle alpha-actinin (alpha A1-2) has been determined to 21-A resolution. The shape and location of alpha A1-2 was determined by subtracting maps of F-actin from the reconstruction of decorated filaments. alpha A1-2 resembles a bell that measures approximately 38 A at its base and extends 42 A from its base to its tip. In decorated filaments, the base of alpha A1-2 is centered about the outer face of subdomain 2 of actin and contacts subdomain 1 of two neighboring monomers along the long-pitch (two-start) helical strands. Using the atomic model of F-actin (Lorenz, M., D. Popp, and K. C. Holmes. 1993. J. Mol. Biol. 234:826-836.), we have been able to test directly the likelihood that specific actin residues, which have been previously identified by others, interact with alpha A1-2. Our results indicate that residues 86-117 and 350-375 comprise distinct binding sites for alpha-actinin on adjacent actin monomers.

Study on Multi-Dimensional Structure Model for Agricultural Products Logistics Organization in China

ICCTP 2009 ◽  
2009 ◽  
Author(s):  
Xinsheng Yao ◽  
Guangyin Xu ◽  
Jianhua Qu ◽  
Jianguang Wei ◽  
Shasha Fan
Keyword(s):  
Agricultural Products ◽  
Dimensional Structure ◽  
Structure Model
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