An average structure model of the intermediate phase between sodalite and cancrinite

2019 ◽  
Vol 234 (5) ◽  
pp. 351-361
Author(s):  
Hilke Petersen ◽  
Haishuang Zhao ◽  
Lars Robben ◽  
Ute Kolb ◽  
Thorsten M. Gesing
Keyword(s):  
Intermediate Phase ◽  
Hexagonal Lattice ◽  
Stoichiometric Composition ◽  
Three Dimensional ◽  
Unit Cell ◽  
Structure Model ◽  
Average Structure ◽  
Powder Samples ◽  
Average Lattice ◽  
Stacking Disorder

Abstract Powder samples of the intermediate phase between sodalite and cancrinite (INT) have been synthesized hydrothermally. The formation of the INT phase was proved by both PXRD and TGA analysis and its stoichiometric composition was found to be |Na6.95(1)(CO3)0.48(2) (H2O)6.18(6)|[AlSiO4]6. The comparison of the intensity ratios of PXRD data with a SCXRD measurement indicates the formation of a comparable phase with the typical strong stacking disorder. The hexagonal lattice parameters with a=1266.3(2) pm and c=1586(1) pm and the unit cell setting were determined by Pawley fits. The average lattice and the stacking disorder along c axis could be confirmed by the reconstruction of three-dimensional ADT data. The average structure of INT was modeled considering only the combination of naturally existing (zeolitic) cages, restricted by the actual number of layers per unit cell. The possible combinations were further reduced by considering the amount of incorporated species. Through the comparison of simulated electron diffraction pattern to measured data the modeled framework could be confirmed. Using relative positions of the incorporated species in the natural cages as well as electron densities calculated by using only the framework of INT the positions of these species could be described.

A new model for packing of type-I collagen molecules in the native fibril

1981 ◽  
Vol 1 (10) ◽  
pp. 801-810 ◽  
Author(s):  
Karl A. Piez ◽  
Benes L. Trus
Keyword(s):  
Type I Collagen ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Equatorial Region ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Left Handed ◽  
Crystal Model ◽  
Collagen Molecules

A specific fibril model is presented consisting of bundles of five-stranded microfibrils, which are usually disordered (except axially) but under lateral compression become ordered. The features are as follows (where D = 234 residues or 67 nm): (1) D-staggered collagen molecules 4.5 D long in the helical microfibril have a left-handed supercoil with a pitch of 400–700 residues, but microfibrils need not have helical symmetry. (2) Straight-tilted 0.5-D overlap regions on a near-hexagonal lattice contribute the discrete x-ray diffraction reflections arising from lateral order, while the gap regions remain disordered. (3) The overlap regions are equivalent, but are crystallographically distinguished by systematic displacements from the near-hexagonal lattice. (4) The unit cell is the same as in a recently proposed three-dimensional crystal model, and calculated intensities in the equatorial region of the x-ray diffraction pattern agree with observed values.

Intergrowth polytypoids as modulated structures: a superspace description of the Sr n (Nb,Ti) n O3n + 2 compound series

2001 ◽  
Vol 57 (4) ◽  
pp. 471-484 ◽  
Author(s):  
L. Elcoro ◽  
J. M. Perez-Mato ◽  
R. L. Withers
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Separation Distance ◽  
Space Group ◽  
Space Groups ◽  
Cell Parameters ◽  
Average Structure ◽  
Layer Stacking ◽  
Compound Series ◽  
Three Dimensional Space

A new, unified superspace approach to the structural characterization of the perovskite-related Sr n (Nb,Ti) n O3n + 2 compound series, strontium niobium/titanium oxide, is presented. To a first approximation, the structure of any member of this compound series can be described in terms of the stacking of (110)-bounded perovskite slabs, the number of atomic layers in a single perovskite slab varying systematically with composition. The various composition-dependent layer-stacking sequences can be interpreted in terms of the structural modulation of a common underlying average structure. The average interlayer separation distance is directly related to the average structure periodicity along the layer stacking direction, while an inherent modulation thereof is produced by the presence of different types of layers (particularly vacant layers) along this stacking direction. The fundamental atomic modulation is therefore occupational and can be described by means of crenel (step-like) functions which define occupational atomic domains in the superspace, similarly to what occurs for quasicrystals. While in a standard crystallographic approach, one must describe each structure (in particular the space group and cell parameters) separately for each composition, the proposed superspace model is essentially common to the whole compound series. The superspace symmetry group is unique, while the primary modulation wavevector and the width of some occupation domains vary linearly with composition. For each rational composition, the corresponding conventional three-dimensional space group can be derived from the common superspace group. The resultant possible three-dimensional space groups are in agreement with all the symmetries reported for members of the series. The symmetry-breaking phase transitions with temperature observed in many compounds can be explained in terms of a change in superspace group, again in common for the whole compound series. Inclusion of the incommensurate phases, present in many compounds of the series, lifts the analysis into a five-dimensional superspace. The various four-dimensional superspace groups reported for this incommensurate phase at different compositions are shown to be predictable from a proposed five-dimensional superspace group apparently common to the whole compound series. A comparison with the scarce number of refined structures in this system and the homologous (Nb,Ca)6Ti6O20 compound demonstrates the suitability of the proposed formalism.

A gravity model of the basement structure in the Santa Maria Basin, California

Geophysics ◽  
1986 ◽  
Vol 51 (5) ◽  
pp. 1127-1140 ◽  
Author(s):  
Paul M. Kieniewicz ◽  
Bruce P. Luyendyk
Keyword(s):  
Short Wavelength ◽  
Large Scale ◽  
Bouguer Anomaly ◽  
Three Dimensional ◽  
Average Density ◽  
Structure Model ◽  
Basement Structure ◽  
Santa Maria Basin ◽  
Clastic Rocks ◽  
Santa Maria

The Santa Maria Basin in southern California is a lowland bounded on the south by the Santa Ynez River fault and on the northeast by the Little Pine‐Foxen Canyon‐Santa Maria River faults. It contains Neogene sedimentary rocks which rest unconformably on a basement of Cretaceous and older clastic rocks. Analysis of over 4 000 gravity stations obtained from the Defense Mapping Agency suggests that the Bouguer anomaly contains a short‐wavelength component arising from a variable‐density contrast between the basin’s Neogene units and the Cretaceous basement. A three‐dimensional inversion of the short‐wavelength component (constrained by wells drilled to basement) yields a structure model of the basement and the average density of the overlying sediments, assuming that the basement does not contain large‐scale density variations. The density anomalies modeled in the Neogene sediments, showing higher densities in the basin troughs, can be related to diagenetic changes in the silica facies of the Monterey and Sisquoc formations. The basement structure model shows the basin as composed of parallel ridges and troughs, trending west‐northwest and bounded by steep slopes interpreted as fault scarps. The basin is bounded on the west by a north‐south trending slope which may also represent a fault scarp.

Pseudo-C11b Phase Formation of Titanium Disilicide During the C49 to C54 Transition

1997 ◽  
Vol 481 ◽  
Author(s):  
Patrick L. Smith ◽  
Richard Ortega ◽  
Bill Brennan
Keyword(s):  
Thin Films ◽  
Plane Wave ◽  
Intermediate Phase ◽  
Unit Cell ◽  
Silicon Substrates ◽  
Unit Cell Parameters ◽  
Titanium Disilicide ◽  
Cell Parameters ◽  
Chemical Signatures ◽  
Pseudo Potential

ABSTRACTThe formation of TiSi2 thin films using the SALICIDE process on doped and undoped silicon substrates was studied. XRD TEM, AES, RBS and four probe Rs were used to characterize the material. Unit cell parameters and energetics were determined. Results confirm electrical and chemical signatures consistent with the known C49 conversion to C54. However, XRD indicated a structurally different intermediate phase occurs during the C49 to C54 transformation. Modeling was performed based on C11b structure (14/mmm) type, with the Ti and Si atoms arranged similarly to those in MoSi2. The unit cell was determined to be a = 4.428 Å, b = 4.779 Å, c = 9.078 Å with a Fmmm space group and total pseudo-potential plane wave calculations based on crystallographic simulations of −103.96 ev/Atom.

Televisualization: An Aid To Collaborative Research In Molecular Structure Biology

1998 ◽  
Vol 4 (S2) ◽  
pp. 32-33
Author(s):  
M. F. Schmid ◽  
P. Matsudaira ◽  
M. T. Dougherty ◽  
M. B. Sherman ◽  
C. Henn ◽  
...  
Keyword(s):  
Image Processing ◽  
Actin Filaments ◽  
Collaborative Research ◽  
Horseshoe Crab ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Limulus Polyphemus ◽  
Dimensional Structure ◽  
Cross Linking ◽  
Tilt Series

Collaboration between local microscopists and image processing specialists, and their remote biological colleagues, has been hampered by the difficulty of i) transferring the three-dimensional reconstructions of macromolecules resulting from the cryomicroscopy and image processing, ii) viewing the results in a meaningful way, and iii) communicating the results and the interpretations derived therefrom to each other.The acrosomal process is an intracellular quasi-crystalline organelle in the head of the sperm of the horseshoe crab Limulus polyphemus. It consists of 100 - 130 actin-scruin filaments packed together in a pseudo-hexagonal lattice and is up to 60 μm long with a diameter of 0.1 μm. Scruin-scruin interactions are responsible for cross-linking the actin filaments together in the bundle. Our goal was to reveal interfilament interactions in the bundle. We have taken tilt series images in the electron microscope to reconstruct its three-dimensional structure at 45 Å resolution.

scholarly journals Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey

2020 ◽  
Vol 31 (3) ◽  
pp. 47-61
Author(s):  
Uus Saepuloh ◽  
Diah Iskandriati ◽  
Joko Pamungkas ◽  
Dedy Duryadi Solihin ◽  
Sela Septima Mariya ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Cynomolgus Monkey ◽  
Tertiary Structure ◽  
Vaccine Development ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Nucleotide Position ◽  
Structure Model ◽  
Three Dimensional Structure ◽  
Hiv 1

Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284–4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.

Consistent Asymptotic Expansion Multiscale Formulation for Heterogeneous Column Structure

2012 ◽  
Vol 134 (3) ◽  
Author(s):  
Dongdong Wang ◽  
Pinkang Xie ◽  
Lingming Fang
Keyword(s):  
Asymptotic Expansion ◽  
Displacement Field ◽  
Three Dimensional ◽  
Axial Direction ◽  
Unit Cell ◽  
Local Unit ◽  
Cell Problem ◽  
Element Discretization ◽  
Free Condition ◽  
Column Structure

A consistent asymptotic expansion multiscale formulation is presented for analysis of the heterogeneous column structure, which has three dimensional periodic reinforcements along the axial direction. The proposed formulation is based upon a new asymptotic expansion of the displacement field. This new multiscale displacement expansion has a three dimensional form, more specifically, it takes into account the axial periodic property but simultaneously keeps the cross section dimensions in the global scale. Thus, this formulation inherently reflects the characteristics of the column structure, i.e., the traction free condition on the circumferential surfaces. Subsequently, the global equilibrium problem and the local unit cell problem are consistently derived based upon the proposed asymptotic displacement field. It turns out that the global homogenized problem is the standard axial equilibrium equation, while the local unit cell problem is completely three dimensional which is subjected to the periodic boundary condition on axial surfaces as well as the traction free condition on circumferential surfaces of the unit cell. Thereafter, the variational formulation and finite element discretization of the unit cell problem are discussed. The effectiveness of the present formulation is illustrated by several numerical examples.

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