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At least 55 records · Page 3Linked to original sources
PubMed2006

Small angle x-ray scattering study of local structure and collapse transition of (1,3)-beta-D-glucan-chitosan gels.

Scleroglucan is a (1,3)-beta-D-glucan polysaccharide produced by the fungus Sclerotium. Dissolved in water at room temperature it adopts a linear, rigid, triple helical structure. Gelation of scleroglucan can be obtained by Schiff-base formation between partly periodate oxidized scleroglucan and the primary amine groups of chitosan. The scleraldehyde-chitosan gels exhibit a collapse transition when exposed to volume fractions of isopropanol, Wp, larger than 65%. The aim of the present study is to provide structural information concerning the local polymer distribution and the collapse transition in (1,3)-beta-D-glucan-chitosan gels. Small angle x-ray scattering was used to investigate solutions and gels of scleroglucan in water, as well as in an aqueous mixture containing 65% isopropanol. The results reveal that in aqueous solution, the polysaccharide scleroglucan chains have an approximately cylindrical cross section of external diameter close to 17 A. The gels display the same local structure, but form clusters on a longer distance scale. For the collapsed gels in the water-isopropanol mixture, partial phase separation occurs in which ordered domains of approximate size of 110 A develop. This study indicates that local ordering in liquid-crystalline-type domains is a possible molecular mechanism contributing to the collapse of gels composed of semiflexible polymers. The triple helical structure of the molecule appears not to be conserved in the majority phase in this solvent, but it is conserved in the liquid crystalline domains.

2-Propanol↗
PubMed1999

Total neutron diffraction: a route to the correct local structure of disordered LaMo2O5 and its application to the model compound Zn2Mo3O8.

Analysis of Bragg diffraction is the normal route to the structure of crystalline materials. Here we demonstrate the use of total neutron diffraction in determining the local structure in the disordered lanthanum molybdate LaMo(2)O(5). An average structure with space-group symmetry P6(3)/mmc accounts for the Bragg scattering and shows that the compound contains the rare Mo(6)O(18) cluster and a unique type of Mo-Mo bonded sheet. However, this gives an incomplete picture of the structure, since it does not reveal how the sites with fractional occupancy are occupied at a local level. Two models describing possible local structures are constructed by removing symmetry elements present in the average structure. Total correlation functions, T(r), calculated from these structures, with space-group symmetry P6(3)mc and P3;m1, are compared with the experimental T(r) to show the validity of these local structures. The close relationship between the T(r)'s of the component structures gives an insight into why disorder occurs in LaMo(2)O(5). The calculated and experimental T(r)'s for a model compound, Zn(2)Mo(3)O(8), are compared to show the agreement expected from an ordered crystalline material. Remaining discrepancies between our model and the experimental T(r) give an insight into the origin of additional disorder in LaMo(2)O(5).

Journal Article↗
PubMed1993

Phase equilibria and local structure in binary lipid bilayers.

A molecular interaction model is used to describe the phase diagram of two-component phospholipid bilayer membranes of saturated phospholipids, DCnPC, with different acyl-chain lengths, n = 12,14,18,20. The interaction between acyl chains of different length is formulated in terms of a hydrophobic mismatch which permits the series of binary phase diagrams to be calculated in terms of a single 'universal' interaction parameter. The properties of the model are calculated by computer-simulation techniques which not only permit determination of the specific-heat function and the phase diagram but also reveal the local structure of the mixture in the different parts of the phase diagram. The local structure is described pictorially and characterized quantitatively in terms of a correlation function. It is shown that the non-ideal mixing of lipid species due to mismatch in the hydrophobic lengths leads to a progressively increasing local ordering as the chain-length difference is increased. A pronounced local structure is found to persist deep inside the fluid phase of the mixture. The local structure is discussed in relation to the features observed in the specific-heat function, for which theoretical data, as well as experimental data obtained from differential-scanning calorimetry are presented.

Computer Simulation↗
PubMed1999

Stability of localized structures in the Swift-Hohenberg equation.

We show that nonmonotonic (oscillatory) decay of the boundaries of phase domains is crucial for the stability of localized structures in systems described by Swift-Hohenberg equation. The less damped (more oscillatory) are the boundaries, the larger are the existence ranges of the localized structures. For very weakly damped spatial oscillations, higher-order localized structures are possible.

Journal Article↗
PubMed1997

Global topology & stability and local structure & dynamics in a synthetic spin-labeled four-helix bundle protein.

A maleimide nitroxide spin-label (MAL-6) linked to a cysteine in the hydrophobic core and a coproporphyrin I (CP) appended on the N-terminus of a synthetic helix-loop-helix peptide ([alpha2]) have been used to examine the designed self-association of a four-helix bundle ([alpha2]2), focusing on the bundle topology and stability and the rotational dynamics of the spin-label. Gel-permeation chromatography demonstrated that the [alpha2] peptide and the peptide modified with a spin-label ([MAL-6-alpha2]), a coproporphyrin ([CP-alpha2]) and a coproporphyrin plus a spin-label ([CP-MAL-6-alpha2]) self-associate into four helix bundles in solution as designed. Circular dichroism (CD) spectra prove that all these peptides are highly alpha-helical, confirmed for [alpha2]2 by Fourier transform infrared (FTIR) spectroscopic analysis. Electron spin resonance (ESR) spectra of the two attached maleimide spin-labels in [MAL-6-alpha2]2 shows their effective rotational correlation time (tau(c)) is 7.3 +/- 0.5 ns, consistent with that expected for the tumbling of the four helix bundle itself, indicating the labels are immobilized. The ESR spectra were also unaltered by aqueous-phase paramagnetic ions, Ni(II), demonstrating all of the spin-labels are buried within the hydrophobic core. The lack of spin-spin interaction between the buried, immobilized spin-labels indicates they are remote (> 15 A) from each other, indicating an antiparallel topology of the monomers in [MAL-6-alpha2]2. The parent [alpha2]2 and the modified [MAL-6-alpha2]2 and [CP-alpha2]2 peptides are highly stable (deltaG(H2O) approximately 25 kcal/mol) as investigated by guanidine hydrochloride denaturation curves monitored by ESR and CD spectroscopies. Guanidine hydrochloride denaturation leads to a shorter correlation time of the spin-label, tau(c) < 1 ns, approaching that of an unrestricted spin-label in solution. In contrast, trifluoroethanol caused dissociation of [MAL-6-alpha2]2 to yield two [MAL-6-alpha2] monomers with retention of secondary structure and changed the tau(c) to 2.5 +/- 0.5 ns, indicating that a significant degree of motional restriction is imposed on the spin-label by the secondary structure. The coproporphyrin probes covalently attached to the N-termini of [CP-alpha2]2 and [CP-MAL-6-alpha2]2 provided evidence that the helical monomers of both were in a parallel orientation, in contrast to the antiparallel orientation determined for [MAL-6-alpha2]2. Consequently, the ESR spectra of [MAL-6-alpha2]2 and [CP-MAL-6-alpha2]2 reveal major structural differences in the local vicinity of the spin-labels due to the topological difference between these two bundles. The ESR spectra of [CP-MAL-6-alpha2]2 contains two distinct nitroxide populations, indicating that one spin-label remains buried in the hydrophobic core and the other is excluded to solvent in this parallel topology. Alleviation of the steric interactions causing one spin-label in [CP-MAL-6-alpha2]2 to be solvent-exposed by addition of [CP-alpha2]2 results in formation of the heterodimeric [CP-alpha2]/[CP-MAL-6-alpha2], as evidenced by insertion of all the spin-labels into hydrophobic cores. The changes in global topology and local structure as evidenced by this pair of spectral probes have relatively minor effects on the course of guanidine denaturation of these bundles.

Amino Acid Sequence↗
PubMed2005

Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.

MOTIVATION: In recent years, advances have been made in the ability of computational methods to discriminate between homologous and non-homologous proteins in the 'twilight zone' of sequence similarity, where the percent sequence identity is a poor indicator of homology. To make these predictions more valuable to the protein modeler, they must be accompanied by accurate alignments. Pairwise sequence alignments are inferences of orthologous relationships between sequence positions. Evolutionary distance is traditionally modeled using global amino acid substitution matrices. But real differences in the likelihood of substitutions may exist for different structural contexts within proteins, since structural context contributes to the selective pressure. RESULTS: HMMSUM (HMMSTR-based substitution matrices) is a new model for structural context-based amino acid substitution probabilities consisting of a set of 281 matrices, each for a different sequence-structure context. HMMSUM does not require the structure of the protein to be known. Instead, predictions of local structure are made using HMMSTR, a hidden Markov model for local structure. Alignments using the HMMSUM matrices compare favorably to alignments carried out using the BLOSUM matrices or structure-based substitution matrices SDM and HSDM when validated against remote homolog alignments from BAliBASE. HMMSUM has been implemented using local Dynamic Programming and with the Bayesian Adaptive alignment method.

Algorithms↗
PubMed1977

Giant cell tumor of bone: fine structural localization of acid phosphatase.

The fine structural localization of acid phosphatase in the different cells in a benign giant cell tumor of bone has been studied. Stromal cells type 1 and 2 (fibroblast-like and macrophage-like, respectively) showed the presence of lead phosphate precipitate following incubation in a Gomori-type lead salt medium only in conventional lysosomes. In the multinucleated giant cells, the final product was deposited over lysosome-like organelles, and also over Golgi cisternae, vesicles, and vacuoles. Furthermore, evidence for presence of acid phosphatase was obtained in smooth-surfaced tubular, sausage-, horse-shoe-, and ring-shaped structures and over digestive vacuoles of autophagic or heterophagic origin. Finally, in these cells, many of the tubular and vacuolar elements located subjacent to areas of the plasma membrane with microvillous specializations (abortive brush borders?) were shown to carry acid phosphatase.

Acid Phosphatase↗
PubMed1978

Giant cell tumor of bone. Fine structural localization of alkaline phosphatase.

The fine structural localization of nonspecific alkaline phosphatase was elucidated in two giant cell tumors of bone using lead as capturing ion and beta-glycerophosphate as substrate in the incubation solution. Lead phosphate precipitate--indicating presence of alkaline phosphatase--was demonstrated on the plasma membranes, and the membranes bordering vesicles and vacuoles of presumed endocytotic nature, in giant cells and type 1 stromal cells (fibroblast-like cells). The findings support the view that stromal cells type I and giant cells are histogenetically related.

Adult↗
PubMed2006

Local structure formation in simulations of two small proteins.

Massively parallel all-atom, explicit solvent molecular dynamics simulations were used to explore the formation and existence of local structure in two small alpha-helical proteins, the villin headpiece and the helical fragment B of protein A. We report on the existence of transient helices and combinations of helices in the unfolded ensemble, and on the order of formation of helices, which appears to largely agree with previous experimental results. Transient local structure is observed even in the absence of overall native structure. We also calculate sets of residue-residue pairs that are statistically predictive of the formation of given local structures in our simulations.

Computer Simulation↗
PubMed2005

A phenomenological theory of spatially structured local synaptic connectivity.

The structure of local synaptic circuits is the key to understanding cortical function and how neuronal functional modules such as cortical columns are formed. The central problem in deciphering cortical microcircuits is the quantification of synaptic connectivity between neuron pairs. I present a theoretical model that accounts for the axon and dendrite morphologies of pre- and postsynaptic cells and provides the average number of synaptic contacts formed between them as a function of their relative locations in three-dimensional space. An important aspect of the current approach is the representation of a complex structure of an axonal/dendritic arbor as a superposition of basic structures-synaptic clouds. Each cloud has three structural parameters that can be directly estimated from two-dimensional drawings of the underlying arbor. Using empirical data available in literature, I applied this theory to three morphologically different types of cell pairs. I found that, within a wide range of cell separations, the theory is in very good agreement with empirical data on (i) axonal-dendritic contacts of pyramidal cells and (ii) somatic synapses formed by the axons of inhibitory interneurons. Since for many types of neurons plane arborization drawings are available from literature, this theory can provide a practical means for quantitatively deriving local synaptic circuits based on the actual observed densities of specific types of neurons and their morphologies. It can also have significant implications for computational models of cortical networks by making it possible to wire up simulated neural networks in a realistic fashion.

Journal Article↗
PubMed2005

Bouncing localized structures in a liquid-crystal light-valve experiment.

Experimental evidence of bouncing localized structures in a nonlinear optical system is reported. Oscillations in the position of the localized states are described by a consistent amplitude equation, which we call the Lifshitz normal form equation, in analogy with phase transitions. Localized structures are shown to arise close to the Lifshtiz point, where nonvariational terms drive the dynamics into complex and oscillatory behaviors.

Journal Article↗
PubMed2006

Storage of localized structure matrices in nematic liquid crystals.

We show experimentally that large matrices of localized structures can be stored as elementary pixels in a nematic liquid crystal cell. Based on optical feedback with phase modulated input beam, our system allows us to store, erase, and actualize the localized structures in the matrix.

Crystallography↗
PubMed2005

Role of local structure on motions on the potential energy landscape for a model supercooled polymer.

We have conducted detailed Monte Carlo and molecular dynamics simulations of a model glass forming polymeric system near its apparent glass transition temperature. We have characterized the local structure of the glass using a Voronoi-Delaunay analysis of local particle arrangements. After a perturbative face elimination, we find that a significant fraction of Voronoi polyhedra consist of 12 pentagonal faces, a sign of icosahedral ordering. Further, we have identified metabasins of particle vibrations on the potential energy landscape on the basis of persistence of particle positions and neighbors over a simulated trajectory. We find that the residence times for vibrations are correlated with a particular Voronoi volume and number of neighbors of a particle; the largest metabasins correspond to particles whose average Voronoi volume is close to the value expected on the basis of the density, and whose approximate number of neighbors is close to 12. The local distortion around a particle, measured in terms of the tetrahedricity of the Delaunay simplices, reveals that the particles with a higher degree of local distortion are likely to transition faster to a neighboring metabasin. In addition to the transition between metabasins, we have also examined the influence of vibrations at inherent structures (IS) on the local structure, and find that the the low frequency modes at the IS exhibit the greatest curvature with respect to the local structure. We believe that these results establish an important connection between the local structure of glass formers and the activated dynamics, thereby providing insights into the origins of dynamic heterogeneities.

Cold Temperature↗
PubMed2003

Control of localized structures in an optical feedback interferometer.

We report a detailed experimental investigation of the dependence of localized structures, observed in a nonlinear optical device, on several control parameters. A first step of the study consists in the determination of the region of existence of localized states as a function of the system variables. Subsequently, we show how different control parameters can be used to the aim of tuning several localized structures properties; among these, of particular relevance are the contrast and the amplitude and frequency of the oscillations appearing on the tails of the structures. A discussion of the relation between the localized states here studied and the one predicted by general model for pattern forming systems is also given.

Biophysical Phenomena↗
PubMed2000

Interaction of localized structures in an optical pattern-forming system

We report on the observation and interaction of dissipative localized structures in an optical pattern-forming system. Single localized structures are found to have oscillatory decaying tails originating from diffraction. We observe bound states of two or more constituents. These clusters contain several preferred mutual distances. Numerical simulations show that the corresponding interactions are mediated by the oscillatory tails.

Journal Article↗
PubMed2001

Structure localization in brain images: application to relevant image selection.

Recent advances in imaging have lead to increases in the number of images/study. Automated methods to select relevant images are critical to effectively convey study results. The proposed method combines natural language processing (NLP) and automatic structure localization to identify relevant images of a MR brain study. NLP extracts relevant locations of findings. Two algorithms were implemented and evaluated for structure localization. The first method involves registration of patient dataset to a labeled atlas. The second method involves an eigenimage search using a training set of images. A prototype was developed and tested on MR brain studies of nine patients. With the registration method, slices containing the relevant structure agreed with expert selection in 98% of cases. Structure localization by eigenimage search was able to locate the lateral ventricles correctly in all the test cases. The proposed method provides an accurate method for identifying relevant slices of an imaging study.

Algorithms↗
PubMed1987

Local structure analyzers as determinants of preattentive pattern discrimination.

Contemporary literature suggests that preattentive texture or pattern discrimination is induced by differences between local structure features or "textons." This paper presents a model for the description of such local structure features based on the computation of local autocorrelations within the image. By means of this structure model a measure of structure dissimilarity is introduced. Experiments have been carried out to test a hypothesized relation between the detectability of a target pattern in a field of background patterns and the value of the structure dissimilarity measure. The experimental results show that it seems justified to relate, in a quantitative way, the detectability of the target pattern to the value of the structure dissimilarity measure.

Form Perception↗
PubMed2005

Electronic and local structural changes in Li(2+x)Ti3O7 ramsdellite compounds upon electrochemical Li-ion insertion reactions by X-ray absorption spectroscopy.

Electronic and local structural changes in ramsdellite-type Li(2+x)Ti3O7 compound were investigated by X-ray absorption spectroscopy (XAS) measurements. Upon electrochemical Li-ion insertions, the host lattice with ramsdellite structure is retained, indicated by X-ray powder diffraction. Ti K-edge extended X-ray absorption fine structure (EXAFS) analysis shows, however, slight local structural distortions around Ti ions. The energy shifts and the changes in the peak intensity of Ti K-edge and Ti L-edge XAS reveal the reducing oxidation states of Ti ions as the amount of electrochemically-inserted Li-ion increases. Equally important, oxide ions have a significant effect on the electronic transfer process, suggested by O K-edge XAS. These results on electronic structural changes were interpreted using the Zaanen-Sawatzky-Allen scheme.

Journal Article↗