Surface electron-energy-loss fine-structure investigation on the local structure of copper clusters on graphite.
Explore the source record for details and available documents.
Journal Article↗
SEARCH · Search PubMed
Results for “local structure”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Extended-range order, diverging static length scales, and local structure formation in cold Lennard-Jones fluids.
We report molecular-dynamics simulations on a three-dimensional, two-component Lennard-Jones fluid. We used 125 000 particles (equal numbers of A and B) at density N/V=1.29 and 34 temperatures T covering 5 x 10(4) > or =T > or =0.56. The pair potential was 4epsilon[(sigma(ij)/r)(12)-(sigma(ij)/r)(6)] with sigma(AA)=1, sigma(AB)=11/12, and sigma(BB)=5/6. We computed specific and generic radial distribution functions g(ij)(r), and several density-momentum dynamic correlation functions whose static (t=0) parts vanish by symmetry. Evidence is presented that our systems were adequately annealed to eliminate remnant initial order and were adequately equilibrated at each temperature. Static spatial correlations in cold Lennard-Jones liquids have longer ranges than are often reported: g(r)-1 unequal to 0 is found out to r > or =7 at T=2 and out to r > or =10 at T=0.56. |g(r)-1| has an envelope function that simultaneously fits both crests and troughs of g(r). The envelope function implies a temperature-dependent static length scale l(1); over (0.56 < or =T< or =100), l(1) approximately T(-0.3), contrary to suggestions that g(r) is temperature independent as the glass is approached. The highest-melting-point crystal that we identified melts at T(m) approximately 1.08. In the fluid phase, we observe short-range noncrystalline local structure formation in g(r) as the glass is approached. Local structure is only found below a local structure melting temperature T(mc)=2.0. Local structure vanishes above T=2. Local structure becomes more pronounced as temperature is reduced. However, at all temperatures at which there is local structure in g(r), the local structure is confined to r < or =4. Within the region r < or =4, the amplitude of the local structure diminishes with distance r from the central atom approximately as exp(-r/l(2)), thereby defining a second distance scale in the fluid. l(2), while more difficult to measure, appears to scale with temperature as l(2) approximately T(-0.6); l(2) is not the same as l(1). The static and dynamic properties of the local structure match properties assigned by Kivelson's glass model [S. A. Kivelson et al., J. Chem. Phys. 101, 2391 (1994)] to that model's frustration-limited local clusters.
Journal Article↗
Effects of Anions on Local Structure of Al and Si in Aluminosilicates.
Three kinds of amorphous aluminosilicates were synthesized by coprecipitation of silicic acid with aluminum hydroxide in the presence of different inorganic ions: sulfate, chloride, and nitrate. Although the bulk composition of the aluminosilicates obtained was not affected by anion species, their DTA spectra were significantly different, suggesting that their structures also differ. The local structure of Al and Si in the aluminosilicates was studied in detail by 27Al and 29Si MAS NMR. From the 27Al MAS NMR spectra and comparison between 29Si HD- and CP-MAS NMR spectra, it was concluded that the aluminosilicate obtained in the presence of sulfate ions has only a montmorillonite-like structure, whereas in the cases of chloride and nitrate, the solids are composed of three phases: aluminum hydroxide, silica, and the montmorillonite-like aluminosilicate. The difference in the local structure of Al and Si in the aluminosilicates was explained by the difference in interaction between the anions and aluminum ions. Copyright 1999 Academic Press.
Journal Article↗
Instantaneous normal mode analysis of orientational motions in liquid water: local structural effects.
We have investigated the effects of local structures on the orientational motions in liquid water in terms of the instantaneous normal mode (INM) analysis. The local structures of a molecule in liquid water are characterized by two different kinds of index: the asphericity parameter of its Voronoi polyhedron and the numbers of the H bonds donated and accepted by the molecule. According to the two kinds of index, the molecules in the simulated water are classified into subensembles, for which the rotational contributions to the INM spectrum are calculated. Our results indicate that by increasing the asphericity, the rotational contribution has a shift toward the high-frequency end in the real spectrum and a decrease in the fraction of the imaginary modes. Furthermore, we find that this shift essentially relies on the number of the donated H bonds of a molecule, but has almost nothing to do with that of the accepted H bonds. The local structural effects resulting from the geometry of water molecule are also discussed.
Journal Article↗
Relationship between local structure and stability in hen egg white lysozyme mutant with alanine substituted for glycine.
We prepared five mutant lysozymes in which glycines whose dihedral angles are located in the region of the left-handed helix, Gly49, Gly67, Gly71, Gly102 and Gly117, were mutated to an alanine residue. From analyses of their thermal stabilities using differential scanning calorimetry, most of them were more destabilized than the native lysozyme, except for the G102A mutant, which has a stability similar to that of the native lysozyme at pH 2.7. As for the destabilized mutant lysozymes, their X-ray crystallographic analyses showed that their global structures did not change but that the local structures changed slightly. By examining the dihedral angles at the mutation sites based on X-ray crystallographic results, it was found that the dihedral angles at these mutation sites tended to adopt favorable values in a Ramachandran plot and that the extent and direction of their shifts from the original value had similar tendencies. Therefore, the change in dihedral angles may be the cause of the slight local structural changes around the mutation site. On the other hand, regarding the mutation of G102A, the global structure was almost identical with that of the native structure but the local structure was drastically changed. Therefore, it was suggested that the drastic local conformational change might be effective in releasing the unfavorable interaction of the native state at the mutation site.
Alanine↗
Exploring local structural organization of metabolic networks using subgraph patterns.
Metabolic networks of many cellular organisms share global statistical features. Their connectivity distributions follow the long-tailed power law and show the small-world property. In addition, their modular structures are organized in a hierarchical manner. Although the global topological organization of metabolic networks is well understood, their local structural organization is still not clear. Investigating local properties of metabolic networks is necessary to understand the nature of metabolism in living organisms. To identify the local structural organization of metabolic networks, we analysed the subgraphs of metabolic networks of 43 organisms from three domains of life. We first identified the network motifs of metabolic networks and identified the statistically significant subgraph patterns. We then compared metabolic networks from different domains and found that they have similar local structures and that the local structure of each metabolic network has its own taxonomical meaning. Organisms closer in taxonomy showed similar local structures. In addition, the common substrates of 43 metabolic networks were not randomly distributed, but were more likely to be constituents of cohesive subgraph patterns.
Algorithms↗
ENVIRON: a software package to compare protein three-dimensional structures with homologous sequences using local structural motifs.
This work presents a method to compare local clusters of interacting residues as observed in a known three-dimensional protein structure with corresponding clusters inferred from homologous protein sequences, assuming conserved protein folding. For this purpose the local environment of a selected residue in a known protein structure is defined as the ensemble of amino acids in contact with it in the folded state. Using a multiple sequence alignment to identify corresponding residues in homologous proteins, a detailed comparison can be performed between the local environment of a selected amino acid in the template protein structure and the expected local environments at the sets of equivalent residues, derived from the aligned protein sequences. The comparison makes it possible to detect conserved local features such as hydrogen bonding or complementarity in residue substitution. A global measure of environmental similarity is also defined, to search for conserved amino acid clusters subject to functional or structural constraints. The proposed approach is useful for investigating protein function as well as for site-directed mutagenesis experiments, where appropriate amino acid substitutions can be suggested by observing naturally occurring protein variants.
Algorithms↗
Local structure of channel ions in carbonate apatite.
Refinement of the single-crystal X-ray diffraction structure of a type A carbonate apatite [CAp; Ca10(PO4)6-y(CO3)x+(3/2)y(OH)2-2x, x=0.75, y=0.0; space group P3 ] has been continued with independent positional and isotropic displacement parameters for the carbonate oxygen atoms, reducing the residual indices significantly (R=0.024, Rw=0.020) and confirming the earlier structure assignment. The carbonate ion is located in the apatite channel at z approximately 0.5, and oriented with two oxygen atoms close to the c-axis. Rigid body refinement, giving a preferred structure, used a novel procedure for defining the ideal equilateral triangular geometry of the channel carbonate ion. Resolution of the channel carbonate ions in type A-B CAp (x=0.69, y=0.57; P63/m) is also improved. Channel carbonate ions in CAp are canted, rotated and displaced to optimize Ca2-O bond distances. The rotation of the A1 carbonate in type A-B CAp is opposite to that of the channel carbonate in type A CAp, due mainly to the accommodation of a second channel carbonate ion (A2). These structures simulate the local structure of type A carbonate in hydroxyapatite of bone and dental enamel.
Apatites↗
Bistability between different localized structures in nonlinear optics.
We report the observation of different localized structures coexisting for the same parameter values in an extended system. The experimental findings are carried out in a nonlinear optical interferometer and are fully confirmed by numerical simulations. The existence of each kind of localized structure is put in relation to a corresponding delocalized pattern observed. A quantitative evaluation of the range of pump parameter allowing bistability between localized structures is given. The phenomenon reported results to be robust in parameter space.
Journal Article↗
Evolution of the local structure around Ti atoms in NaAlH4 doped with TiCl3 or Ti13.6THF by ball milling using X-ray absorption and X-ray photoelectron spectroscopy.
X-ray absorption and X-ray photoelectron spectroscopy are used to investigate NaAlH4 doped with 5 mol % of Ti on the basis of either TiCl3 or Ti13.6THF by ball milling. X-ray photoelectron spectroscopy (XPS) analysis of TiCl3 or Ti colloid doped samples indicates that Ti species do not remain on the sample surface but are driven into the material with increasing milling time. The surface concentration of Ti continues to decrease during subsequent cycles under hydrogen. After several cycles, it reaches a constant value of 0.5 at. % independently of the nature of the precursor. Moreover, metallic aluminum is already present at the surface after 2 min of ball milling in the case of TiCl3 doped Na-alanate, whereas it is totally absent in the case of Ti colloid doped samples at any milling time. Upon cycling, the atomic concentration of metallic Al at the surface evolves with the reaction under hydrogen, in contrast to the Ti concentration. Analysis of the binding energies of samples doped with TiCl3 or Ti colloid, after eight desorption/absorption cycles, reveals that the Na, O, and Ti environment remains the same, while the Al environment undergoes changes. According to the extended X-ray absorption fine structure (EXAFS) analysis of TiCl3 doped Na-alanate, the local structure around Ti during the first cycle is close to that of metallic Ti but in a more distorted state. In the case of the Ti colloid doped sample, a stripping of the oxygen shell occurs. After eight cycles, a similar intermetallic phase between Ti and Al is present in the hydrogenated state of TiCl3 or Ti colloid doped samples. The local structure around Ti atoms after eight cycles consists of Al and Ti backscatterers with a Ti-Al distance of 2.79 angstroms and a Ti-Ti distance of 3.88 angstroms. This local structure is not exactly the TiAl3 phase because it differs significantly from the alloy phase in its fine structure and lacks long-range order. Volumetric measurements performed on these samples indicate that the formation of this local structure is responsible for the reduction of the reversible hydrogen capacity with the increasing number of cycles. Moreover, the formation of the alloy-like phase is correlated with a decrease of the desorption/absorption reaction rate.
Journal Article↗
Patterns and localized structures in population dynamics.
Patterns, fronts, and localized structures of a prototypical model for population dynamics interaction are studied. The physical content of the model is the coexistence of a simple random walk for the motion of the individuals with a nonlinearity in the competitive struggle for resources which simultaneously stresses the Allee effect and interaction at a distance. Mathematically, the model is variational and exhibits coexistence between different stable extended states. Solutions are obtained, the phase diagram is constructed, and the emergence of localized structures is investigated.
Biophysics↗
Sequence-specific local structural variations in solution structures of d(CGXX'CG)2 and d(CAXX'TG)2 self-complementary deoxyribonucleic acids.
In this study, the solution structures of eight self-complementary deoxyribonucleic acid molecules, d(CGXX'CG)2 and d(CAXX'TG)2 (where X = C, G, T or A and X' is complementary to X), have been determined using NMR interproton distances, endocyclic sugar torsion angles, backbone torsion angles and hydrogen bond constraints. Based on the structural data obtained in solution, a novel sequence-specific local structure function, sigma LS, composed of the sum of the contributions from the helix twist omega, base roll rho, base-pair slide delta delta and propeller twist omega, is introduced to describe their sequence-specific local structures. Sigma LS is found to produce an acceptable correlation (r = 0.96) with the relative local stability (delta G0 10) of a base-pair-step. This result demonstrates that in addition to the inter-strand purine-purine clashes, the base morphology of nearest-neighbor base-pairs is also important in defining the local geometry of base-pairs. Thus, in analyzing the base-pair structural parameter blocks of trimers are used as the basic unit whereas for the base-pair-step structural parameters, the basic unit is composed of blocks of tetramers. The omega LS-delta G(zero) 10 correlation is the first experimental evidence demonstrating the relationship between the relative local stabilities and the sequence-specific local structures of DNA duplexes. It also forms the basis for using the trimer-tetramer model for the prediction of sequence-specific local structures of deoxyribonucleic acid molecules.
Algorithms↗
Excitability mediated by localized structures in a dissipative nonlinear optical cavity.
We find and characterize an excitability regime mediated by localized structures in a dissipative nonlinear optical cavity. The scenario is that stable localized structures exhibit a Hopf bifurcation to self-pulsating behavior, that is followed by the destruction of the oscillation in a saddle-loop bifurcation. Beyond this point there is a regime of excitable localized structures under the application of suitable perturbations. Excitability emerges from the spatial dependence since the system does not exhibit any excitable behavior locally. We show that the whole scenario is organized by a Takens-Bogdanov codimension-2 bifurcation point.
Journal Article↗
Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces.
In order to address the recognition mechanism of the fragments of antibody variable regions, termed Fv, toward their target antigen, an x-ray crystal structure of an anti-hen egg white lysozyme antibody (HyHEL-10) Fv fragment complexed with its cognate antigen, hen egg white lysozyme (HEL), was solved at 2.3 A. The overall structure of the complex is similar to that reported in a previous article dealing with the Fab fragment-HEL complex (PDB ID code,). However, the areas of Fv covered by HEL upon complex formation increased by about 100 A(2) in comparison with the Fab-HEL complex, and two local structural differences were observed in the heavy chain of the variable region (VH). In addition, small but significant local structural changes were observed in the antigen, HEL. The x-ray data permitted the identification of two water molecules between the VH and HEL and six water molecules retained in the interface between the antigen and the light chain complementarity determining regions (CDRs) 2 and 3 (CDR-L2 and CDR-L3). These water molecules bridge the antigen-antibody interface through hydrogen bond formation in the VL-HEL interface. Eleven water molecules were found to complete the imperfect VH-VL interface, suggesting that solvent molecules mediate the stabilization of interaction between variable regions. These results suggest that the unfavorable effect of deletion of constant regions on the antigen-antibody interaction is compensated by an increase in favorable interactions, including structural changes in the antigen-antibody interface and solvent-mediated hydrogen bond formation upon complex formation, which may lead to a minimum decreased affinity of the antibody Fv fragment toward its antigen.
Amino Acid Sequence↗
Combined solid state NMR and X-ray diffraction investigation of the local structure of the five-coordinate silicon in fluoride-containing as-synthesized STF zeolite.
The local structure of the [SiO(4/2)F]- unit in fluoride-containing as-synthesized STF zeolite has been experimentally determined by a combination of solid-state NMR and microcrystal X-ray diffraction to be very close to trigonal bipyramidal. Because the fluoride ions are disordered over two sites, the resulting local structure of the [SiO(4/2)F]- unit from a conventional XRD refinement is an average between tetrahedral SiO(4/2) and five-coordinate [[SiO(4/2)F]-, giving an apparent F-Si distance longer than expected. The correct F-Si distance was determined by slow spinning MAS and fast spinning (19)F/(29)Si CP and REDOR solid-state NMR experiments and found to be between 1.72 and 1.79 A. In light of this, the X-ray structure was re-refined, including the disorder at Si3. The resulting local structure of the [SiO(4/2)F]- unit was very close to trigonal bipyramidal with a F-Si distance of 1.744 (6) A, in agreement with the NMR results and the prediction of Density Functional Theory calculations. In addition, further evidence for the existence of a covalent F-Si bond is provided by a (19)F-->(29)Si refocused INEPT experiment. The resonance for the five-coordinate species at -147.5 ppm in the (29)Si spectrum is a doublet due to the (19)F/(29)Si J-coupling of 165 Hz. The peaks in this doublet have remarkably different effective chemical shift anisotropies due to the interplay of the CSA, dipolar coupling, and J-coupling tensors. The distortions from tetrahedral geometry of the neighboring silicon atoms to the five-coordinate Si3 atom are manifested in increased delta(aniso) values. This information, along with F-Si distances measured by (19)F-->(29)Si CP experiments, makes it possible to assign half of the (29)Si resonances to unique tetrahedral sites. As well as determining the local geometry of the [SiO(4/2)F]- unit, the work presented here demonstrates the complementarity of the solid-state NMR and X-ray diffraction techniques and the advantages of using them together.
Journal Article↗
Small angle X-ray scattering studies on local structure of tobacco mosaic virus RNA in solution.
Effects of temperature and ionic strength (S) on the local structure of tobacco mosaic virus RNA in phosphate buffer solution are studied by analyzing the small-angle X-ray scattering (SAXS) curves. The root-mean-square radius of a cross-section of RNA chain was kept at 0.845+/-0.005 nm over a wide range of S from 0.2 to 0.003 at 20 degrees C, whereas it gradually diminished from 0.85 to 0.61 nm when the temperature is raised from 20 to 50 degrees C at S = 0.2. Nevertheless, all of SAXS curves reflecting the backbone structures were equally mimicked by theoretical ones of freely hinged rod (FHR) models, i.e. several straight rods joined with freely hinged joints in the form of a combination of the letter Y, if the constituent rod lengths in the models are adjusted. From these facts, it is suggested that the local structure of the RNA chain in aqueous solution is characterized by an essential feature that unpaired bases in the partially double-stranded helix are constantly far isolated from each other along the helix and the rod-like structure of the helix is preserved over a range of helical contents. Such a characteristic local structure of the chain is entirely collapsed in the formamide solution at 50 degrees C.
Buffers↗
Local structures of nanocrystalline GaN studied by XAFS.
X-ray absorption fine structure (XAFS) was used to investigate the local structures around Ga atoms in the hexagonal nanocrystalline and crystalline GaN under 78 and 300 K. For the first nearest neighbor coordination shell of Ga-N. the average bond length R (0.194 nm), coordination number N (4.0), thermal disorder sigma (0.0052 nm) and static disorder sigmaS (0.0007 nm) are neatly independent of the measured temperature and crystalline state. This indicates that the Ga-N covalent bond is much stronger, and the 4 nitrogen atoms in first nearest neighbor around Ga atoms keep the tetrahedral structure (Td). For the second nearest neighbor coordination shell of Ga-Ga, their bond lengths are about 0.318 nm. However, the sigmaS (0.0057 nm) of nanocrystalline GaN is 0.0047 nm larger than that of crystalline GaN (0.001 nm), and the sigmaT of nanocrystalline is 0.0053 nm and 0.0085 nm at the temperature of 78 and 300 K, respectively. The result indicates that the difference of local structure around Ga atoms between nanocrystalline and crystalline GaN occurs mainly at the Ga-Ga second nearest-neighbor coordination shell. The reason is explained as the local lattice distortion and unsaturated surface atoms existing in nanocrystalline GaN.
Journal Article↗
Prediction of local structure in proteins using a library of sequence-structure motifs.
We describe a new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements. The library was generated using an automated method for finding correlations between protein sequence and local structure, and contains most previously described local sequence-structure correlations as well as new relationships, including a diverging type-II beta-turn, a frayed helix, and a proline-terminated helix. The query sequence is scanned for segments 7 to 19 residues in length that strongly match one of the 82 patterns in the library. Matching segments are assigned the three-dimensional structure characteristic of the corresponding sequence pattern, and backbone torsion angles for the entire query sequence are then predicted by piecing together mutually compatible segment predictions. In predictions of local structure in a test set of 55 proteins, about 50% of all residues, and 76% of residues covered by high-confidence predictions, were found in eight-residue segments within 1.4 A of their true structures. The predictions are complementary to traditional secondary structure predictions because they are considerably more specific in turn regions, and may contribute to ab initio tertiary structure prediction and fold recognition.
Algorithms↗