scholarly journals Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions

Biomolecules ◽  
2014 ◽  
Vol 4 (3) ◽  
pp. 725-773 ◽  
Author(s):  
Siobhan Toal ◽  
Reinhard Schweitzer-Stenner
Keyword(s):  
Nearest Neighbor ◽  
Local Order ◽  
Unfolded State

scholarly journals Favored local structures in amorphous colloidal packings measured by microbeam X-ray diffraction

2017 ◽  
Vol 114 (39) ◽  
pp. 10344-10349 ◽  
Author(s):  
Amelia C. Y. Liu ◽  
Rico F. Tabor ◽  
Martin D. de Jonge ◽  
Stephen T. Mudie ◽  
Timothy C. Petersen
Keyword(s):  
Disordered Systems ◽  
Amorphous Materials ◽  
Nearest Neighbor ◽  
Orientational Order ◽  
Amorphous Structure ◽  
Local Order ◽  
X Ray ◽  
Angular Correlations ◽  
Scanning Transmission ◽  
Bond Orientational Order

Local structure and symmetry are keys to understanding how a material is formed and the properties it subsequently exhibits. This applies to both crystals and amorphous and glassy materials. In the case of amorphous materials, strong links between processing and history, structure and properties have yet to be made because measuring amorphous structure remains a significant challenge. Here, we demonstrate a method to quantify proportions of the bond-orientational order of nearest neighbor clusters [Steinhardt, et al. (1983) Phys Rev B 28:784–805] in colloidal packings by statistically analyzing the angular correlations in an ensemble of scanning transmission microbeam small-angle X-ray scattering (μSAXS) patterns. We show that local order can be modulated by tuning the potential between monodisperse, spherical colloidal silica particles using salt and surfactant additives and that more pronounced order is obtained by centrifugation than sedimentation. The order in the centrifuged glasses reflects the ground state order in the dispersion at lower packing fractions. This diffraction-based method can be applied to amorphous systems across decades in length scale to connect structure to behavior in disordered systems with a range of particle interactions.

scholarly journals Haldane insulator in the 1D nearest-neighbor extended Bose-Hubbard model with cavity-mediated long-range interactions

2020 ◽  
Vol 93 (6) ◽  
Author(s):  
Johannes Sicks ◽  
Heiko Rieger
Keyword(s):  
Hubbard Model ◽  
Quantum Monte Carlo ◽  
Nearest Neighbor ◽  
Mean Field ◽  
Local Order ◽  
One Dimensional ◽  
Hubbard Models ◽  
Long Range Interactions ◽  
Non Local ◽  
The One

Abstract In the one-dimensional Bose-Hubbard model with on-site and nearest-neighbor interactions, a gapped phase characterized by an exotic non-local order parameter emerges, the Haldane insulator. Bose-Hubbard models with cavity-mediated global range interactions display phase diagrams, which are very similar to those with nearest-neighbor repulsive interactions, but the Haldane phase remains elusive there. Here we study the one-dimensional Bose-Hubbard model with nearest-neighbor and cavity-mediated global-range interactions and scrutinize the existence of a Haldane Insulator phase. With the help of extensive quantum Monte-Carlo simulations we find that in the Bose-Hubbard model with only cavity-mediated global-range interactions no Haldane phase exists. For a combination of both interactions, the Haldane Insulator phase shrinks rapidly with increasing strength of the cavity-mediated global-range interactions. Thus, in spite of the otherwise very similar behavior the mean-field like cavity-mediated interactions strongly suppress the non-local order favored by nearest-neighbor repulsion in some regions of the phase diagram. Graphical abstract

Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

2015 ◽  
Vol 21 (13) ◽  
pp. 5173-5192 ◽  
Author(s):  
Siobhan E. Toal ◽  
Nina Kubatova ◽  
Christian Richter ◽  
Verena Linhard ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Unfolded State

scholarly journals Corrigendum: Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues

2017 ◽  
Vol 23 (71) ◽  
pp. 18084-18087
Author(s):  
Siobhan E. Toal ◽  
Nina Kubatova ◽  
Christian Richter ◽  
Verena Linhard ◽  
Harald Schwalbe ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Unfolded State

scholarly journals Isomorph Invariance of Higher-Order Structural Measures in Four Lennard–Jones Systems

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1746
Author(s):  
Mahajabin Rahman ◽  
Benjamin M. G. D. Carter ◽  
Shibu Saw ◽  
Ian M. Douglass ◽  
Lorenzo Costigliola ◽  
...  
Keyword(s):  
Phase Diagram ◽  
Nearest Neighbor ◽  
Excess Entropy ◽  
Orientational Order ◽  
Higher Order ◽  
Local Order ◽  
Lennard Jones ◽  
Bond Orientational Order ◽  
Thermodynamic Phase ◽  
Condensed Liquid

In the condensed liquid phase, both single- and multicomponent Lennard–Jones (LJ) systems obey the “hidden-scale-invariance” symmetry to a good approximation. Defining an isomorph as a line of constant excess entropy in the thermodynamic phase diagram, the consequent approximate isomorph invariance of structure and dynamics in appropriate units is well documented. However, although all measures of the structure are predicted to be isomorph invariant, with few exceptions only the radial distribution function (RDF) has been investigated. This paper studies the variation along isomorphs of the nearest-neighbor geometry quantified by the occurrence of Voronoi structures, Frank–Kasper bonds, icosahedral local order, and bond-orientational order. Data are presented for the standard LJ system and for three binary LJ mixtures (Kob–Andersen, Wahnström, NiY2). We find that, while the nearest-neighbor geometry generally varies significantly throughout the phase diagram, good invariance is observed along the isomorphs. We conclude that higher-order structural correlations are no less isomorph invariant than is the RDF.

Observation of Superlattice Dislocations on Cube Planes in Ni3Al

1973 ◽  
Vol 31 ◽  
pp. 174-175 ◽  
Author(s):  
J. M. Oblak ◽  
W. H. Rand
Keyword(s):  
Nearest Neighbor ◽  
Antiphase Boundary ◽  
Nearest Neighbors ◽  
High Energy ◽  
Cross Slip ◽  
Octahedral Plane ◽  
Trapping Mechanism ◽  
Slip Traces

The energy of an a/2 <110> shear antiphase. boundary in the Ll2 expected to be at a minimum on {100} cube planes because here strue ture is there is no violation of nearest-neighbor order. The latter however does involve the disruption of second nearest neighbors. It has been suggested that cross slip of paired a/2 <110> dislocations from octahedral onto cube planes is an important dislocation trapping mechanism in Ni3Al; furthermore, slip traces consistent with cube slip are observed above 920°K.Due to the high energy of the {111} antiphase boundary (> 200 mJ/m2), paired a/2 <110> dislocations are tightly constricted on the octahedral plane and cannot be individually resolved.

Application of Lattice Imaging Techniques to Amorphous Films

1975 ◽  
Vol 33 ◽  
pp. 8-9
Author(s):  
S. R. Herd ◽  
P. Chaudhari
Keyword(s):  
Nearest Neighbor ◽  
Random Network ◽  
Imaging Techniques ◽  
Network Models ◽  
Accurate Method ◽  
Direct Transmission ◽  
Lattice Imaging ◽  
Transmission Electron ◽  
Lattice Planes ◽  
Nearest Neighbor Distances

Electron diffraction and direct transmission have been used extensively to study the local atomic arrangement in amorphous solids and in particular Ge. Nearest neighbor distances had been calculated from E.D. profiles and the results have been interpreted in terms of the microcrystalline or the random network models. Direct transmission electron microscopy appears the most direct and accurate method to resolve this issue since the spacial resolution of the better instruments are of the order of 3Å. In particular the tilted beam interference method is used regularly to show fringes corresponding to 1.5 to 3Å lattice planes in crystals as resolution tests.

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