scholarly journals Inferring the particle-wise dynamics of amorphous solids from the local structure at the jamming point

Soft Matter ◽  
2021 ◽  
Author(s):  
Rafael Díaz Hernández Rojas ◽  
Giorgio Parisi ◽  
Federico Ricci-Tersenghi
Keyword(s):  
Local Structure ◽  
Structural Information ◽  
Amorphous Solids ◽  
Contact Network ◽  
Particles Dynamics

Structural information from the contact network at jamming can be used to infer the statistics of the particles' dynamics near such point. Histograms show that particles with similar local structure (i.e. similar colours) move statistically alike.

COVARIATION ANALYSIS OF LOCAL AMINO ACID SEQUENCES IN RECURRENT PROTEIN LOCAL STRUCTURES

2005 ◽  
Vol 03 (06) ◽  
pp. 1391-1409 ◽  
Author(s):  
LU-YONG WANG
Keyword(s):  
Protein Folding ◽  
Amino Acid ◽  
Local Structure ◽  
Structural Information ◽  
Statistical Significance ◽  
Amino Acid Sequences ◽  
Structural Motifs ◽  
Systematic Analysis ◽  
Local Structures ◽  
Covariation Analysis

Local structural information is supposed to be frequently encoded in local amino acid sequences. Previous research only indicated that some local structure positions have specific residue preferences in some particular local structures. However, correlated pairwise replacements for interacting residues in recurrent local structural motifs from unrelated proteins have not been studied systematically. We introduced a new method fusing statistical covariation analysis and local structure-based alignment. Systematic analysis of structure-based multiple alignments of recurrent local structures from unrelated proteins in representative subset of Protein Databank indicates that covarying residue pairs with statistical significance exist in local structural motifs, in particular β-turns and helix caps. These residue pairs are mostly linked through polar functional groups with direct or indirect hydrogen bonding. Hydrophobic interaction is also a major factor in constraining pairwise amino acid residue replacement in recurrent local structures. We also found correlated residue pairs that are not clearly linked with through-space interactions. The physical constrains underlying these covariations are less clear. Overall, covarying residue pairs with statistical significance exist in local structures from unrelated proteins. The existence of sequence covariations in local structural motifs from unrelated proteins indicates that many relics of local relations are still retained in the tertiary structures after protein folding. It supports the notion that some local structural information is encoded in local sequences and the local structural codes could play important roles in determining native state protein folding topology.

A combined LX-NMR and molecular dynamics investigation of the bulk and local structure of ionic liquid crystals

Soft Matter ◽  
2019 ◽  
Vol 15 (22) ◽  
pp. 4486-4497 ◽  
Author(s):  
Maria Enrica Di Pietro ◽  
Tommaso Margola ◽  
Giorgio Celebre ◽  
Giuseppina De Luca ◽  
Giacomo Saielli
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Liquid Crystals ◽  
Nmr Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Structural Information ◽  
Ionic Liquid Crystals ◽  
Dynamics Simulations ◽  
Unique Power

The unique power of NMR spectroscopy in anisotropic media (LX-NMR) as a tool to obtain local and bulk structural information, combined with the effectiveness of molecular dynamics simulations at the atomistic level, shows very attractive potentialities for the study of Ionic Liquid Crystals.

scholarly journals From local structure to a global framework: recognition of protein folds

2014 ◽  
Vol 11 (95) ◽  
pp. 20131147 ◽  
Author(s):  
Agnel Praveen Joseph ◽  
Alexandre G. de Brevern
Keyword(s):  
Local Structure ◽  
Structure Prediction ◽  
Structural Information ◽  
Protein Structures ◽  
Fold Recognition ◽  
Protein Fold ◽  
Major Area ◽  
Huge Amount ◽  
Protein Fold Recognition ◽  
Structural Environment

Protein folding has been a major area of research for many years. Nonetheless, the mechanisms leading to the formation of an active biological fold are still not fully apprehended. The huge amount of available sequence and structural information provides hints to identify the putative fold for a given sequence. Indeed, protein structures prefer a limited number of local backbone conformations, some being characterized by preferences for certain amino acids. These preferences largely depend on the local structural environment. The prediction of local backbone conformations has become an important factor to correctly identifying the global protein fold. Here, we review the developments in the field of local structure prediction and especially their implication in protein fold recognition.

scholarly journals Packing concave molecules in crystals and amorphous solids: on the connection between shape and local structure

2015 ◽  
Vol 113 (17-18) ◽  
pp. 2755-2769 ◽  
Author(s):  
Cerridwen Jennings ◽  
Malcolm Ramsay ◽  
Toby Hudson ◽  
Peter Harrowell
Keyword(s):  
Local Structure ◽  
Amorphous Solids

scholarly journals Adaptation of Symmetric Positive Semi-Definite Matrices for the Analysis of Textured Images

2018 ◽  
Vol 18 (1) ◽  
pp. 51-68
Author(s):  
Adib Akl
Keyword(s):  
Adaptive Algorithm ◽  
Local Structure ◽  
Structural Information ◽  
Local Variation ◽  
Local Orientation ◽  
Accurate Analysis ◽  
Structure Estimation ◽  
Gradient Fields ◽  
Degree Of Anisotropy ◽  
The Way

Abstract This paper addresses the analysis of textured images using the symmetric positive semi-definite matrix. In particular, a field of symmetric positive semi-definite matrices is used to estimate the structural information represented by the local orientation and the degree of anisotropy in structured and sinusoid-like textured images. In order to ensure faithful local structure estimation, an adaptive algorithm for the regularization of the extent of gradient fields smoothing is proposed. Results obtained on different texture samples show the strength of the proposed method in accurately representing the local variation of orientations in the underlying textured images, which paves the way towards an accurate analysis of the texture structures.

Xafs as a Direct Local Structural Probe in Revealing the Effects of C Presence in B Diffusion in Sige Layers

2004 ◽  
Vol 810 ◽  
Author(s):  
M. Alper Sahiner ◽  
Parviz Ansari ◽  
Malcolm S. Carroll ◽  
Charles W. Magee ◽  
Steven W. Novak ◽  
...  
Keyword(s):  
Local Structure ◽  
Direct Evidence ◽  
Structural Information ◽  
Chemical Vapor ◽  
Si Substrates ◽  
Boron Doped ◽  
Structural Probe ◽  
Diffusion Mechanisms ◽  
X Ray Absorption ◽  
Secondary Ion

ABSTRACTThe local structural information around the germanium atom in boron doped SiGe alloys is important in understanding the dopant diffusion mechanisms. Epitaxial SiGe test structures with B and C markers were grown on Si substrates by using rapid thermal chemical vapor deposition (RTCVD). The local structure around the Ge atom was probed using Ge K-edge x-ray absorption fine structure spectroscopy (XAFS) to determine the effects of the B and C on the Ge sites. The concentration profiles obtained from secondary ion mass spectroscopy are correlated with the Ge XAFS results. The modifications on the local structure around the Ge atoms are revealed from the multiple scattering analyses on the Ge near-neighbors. First and second shell XAFS fits to the B doped SiGe samples indicate a direct evidence of the Ge trapping of the B atoms whereas the C is randomly distributed to the Si lattice sites.

Measurement and Reduction of Radiation Damage in Frozen Hydrated Crystalline Specimens

1978 ◽  
Vol 36 (3) ◽  
pp. 70-77 ◽  
Author(s):  
R.M. Glaeser ◽  
S.B. Hayward
Keyword(s):  
Diffraction Pattern ◽  
Structural Information ◽  
Structural Disorder ◽  
Structural Features ◽  
Biological Macromolecules ◽  
Diffraction Intensity ◽  
Object Structure ◽  
Specimen Material ◽  
Unit Cells ◽  
Identical Unit

Highly ordered or crystalline biological macromolecules become severely damaged and structurally disordered after a brief electron exposure. Evidence that damage and structural disorder are occurring is clearly given by the fading and eventual disappearance of the specimen's electron diffraction pattern. The fading and disappearance of sharp diffraction spots implies a corresponding disappearance of periodic structural features in the specimen. By the same token, there is a oneto- one correspondence between the disappearance of the crystalline diffraction pattern and the disappearance of reproducible structural information that can be observed in the images of identical unit cells of the object structure. The electron exposures that result in a significant decrease in the diffraction intensity will depend somewhat upon the resolution (Bragg spacing) involved, and can vary considerably with the chemical makeup and composition of the specimen material.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

High-Resolution Scanning Electron Microscopy of Biological Specimens

1988 ◽  
Vol 46 ◽  
pp. 186-187
Author(s):  
M. Müller ◽  
R. Hermann
Keyword(s):  
High Resolution ◽  
Freeze Drying ◽  
Room Temperature ◽  
Structural Information ◽  
Freeze Substitution ◽  
Critical Point Drying ◽  
Sem Study ◽  
Major Factors ◽  
Structural Preservation ◽  
Preparation Techniques

Three major factors must be concomitantly assessed in order to extract relevant structural information from the surface of biological material at high resolution (2-3nm).Procedures based on chemical fixation and dehydration in graded solvent series seem inappropriate when aiming for TEM-like resolution. Cells inevitably shrink up to 30-70% of their initial volume during gehydration; important surface components e.g. glycoproteins may be lost. These problems may be circumvented by preparation techniques based on cryofixation. Freezedrying and freeze-substitution followed by critical point drying yields improved structural preservation in TEM. An appropriate preservation of dimensional integrity may be achieved by freeze-drying at - 85° C. The sample shrinks and may partially collapse as it is warmed to room temperature for subsequent SEM study. Observations at low temperatures are therefore a necessary prerequisite for high fidelity SEM. Compromises however have been unavoidable up until now. Aldehyde prefixation is frequently needed prior to freeze drying, rendering the sample resistant to treatment with distilled water.

Ultimate resolution and information in electron microscopy

1991 ◽  
Vol 49 ◽  
pp. 496-497
Author(s):  
D. Van Dyck
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Transfer Function ◽  
Information Transfer ◽  
Communication Channel ◽  
Structural Information ◽  
Information Rate ◽  
Noise Power ◽  
Signal Power ◽  
Imaging Device

An (electron) microscope can be considered as a communication channel that transfers structural information between an object and an observer. In electron microscopy this information is carried by electrons. According to the theory of Shannon the maximal information rate (or capacity) of a communication channel is given by C = B log2 (1 + S/N) bits/sec., where B is the band width, and S and N the average signal power, respectively noise power at the output. We will now apply to study the information transfer in an electron microscope. For simplicity we will assume the object and the image to be onedimensional (the results can straightforwardly be generalized). An imaging device can be characterized by its transfer function, which describes the magnitude with which a spatial frequency g is transferred through the device, n is the noise. Usually, the resolution of the instrument ᑭ is defined from the cut-off 1/ᑭ beyond which no spadal information is transferred.

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