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In this paper we describe how to use the bifurcation structure of static localized solutions in one dimension to store information on a medium in such a way that no extrinsic grid is needed to locate the information. We demonstrate that these principles, deduced from the mathematics adapted to describe one-dimensional media, also allow one to store information on two-dimensional media.
We study the existence, the stability properties, and the bifurcation structure of static localized solutions in one dimension, near the robust existence of stable fronts between homogeneous solutions and periodic patterns.
Monolithic porous silica xerogels were synthesized by the sol-gel process, and their local structure was analysed by vibrational spectroscopy. The silica alcogels were prepared by a two-step hydrolytic polycondensation of tetraethoxysilane (TEOS) in isopropanol, with a water/TEOS molar ratio of 4. The hydrolysis step was catalysed by hydrochloric acid (HCl), with different HCl/TEOS molar ratios (ranging from 0.0005 to 0.009), and the condensation step was catalysed by ammonia (NH(3)), with different NH(3)/HCl molar ratios (ranging from 0.7 to 1.7). After appropriate ageing, the alcogels were washed with isopropanol and subcritically dried at atmospheric pressure. The diffuse reflectance infrared Fourier transform (DRIFT) spectra were analysed in terms of the main siloxane rings that form the silica particles, taking into account the splitting of the nu(as)Sibond;Obond;Si mode into pairs of longitudinal and transverse optic components, by long-range Coulomb interactions. It was proven that the proportion of residual silanol groups (which correlates with hydrophilicity), and the fraction of siloxane 6-rings (which correlates with porosity) may be tailored by adequate catalytic conditions, mostly by the hydrolysis pH. This was explained in terms of the reactions' mechanisms taking place in the two-step sol-gel process followed.
The Pb(Zr,Ti)O3 (PZT) disordered solid solution is widely used in piezoelectric applications owing to its excellent electromechanical properties. Six different structural phases have been observed for PZT at ambient pressure, each with different lattice parameters and average electric polarization. It is of significant interest to understand the microscopic origin of the complicated phase diagram and local structure of PZT. Here, using density functional theory calculations, we show that the distortions of the material away from the parent perovskite structure can be predicted from the local arrangement of the Zr and Ti cations. We use the chemical rules obtained from density functional theory to create a phenomenological model to simulate PZT structures. We demonstrate how changes in the Zr/Ti composition give rise to phase transitions in PZT through changes in the populations of various local Pb atom environments.
Local and global structural properties of the HIV-1 principal neutralizing epitope were studied in terms of NMR spectroscopy data reported in literature for the HIV-Haiti and HIV-RF isolates. To this effect, the NMR-based method comprising a probabilistic model of protein conformation in conjunction with the molecular mechanics and quantum chemical computations was used for determining the ensembles of conformers matching the NMR requirements and energy criteria. As a matter of record, the high resolution 3D structure models were constructed for the HIV-Haiti and HIV-RF immunogenic crowns, and their geometric parameters were collated with the ones of conformers derived previously for describing the conformational features of immunogenic tip of gp120 from Thailand and MN HIV-1 strains. The HIV-1 neutralization site was demonstrated to constitute in water solution highly flexible system sensitive to its environment. This inference is completely valid for the geometric space of dihedral angles where statistically significant differences in local structures of simulated conformers have been found for all virus isolates of interest. In spite of this fact, the stretch analyzed was shown to manifest a certain conservatism in the space of atomic coordinates, building up in four HIV-1 isolates two spatial folds similar to those observed in crystal for the V3 loop peptides bound to different neutralizing Fabs. The results are discussed in the light of literature data on HIV-1 neutralizing epitope structure.
The coordination and local structure of Si and Al in silicate glasses and melts have been studied using Si and Al K-edge X-ray absorption spectroscopy for the first time. It has been verified that in SiO2-P2O5 and Na2O-SiO2-P2O5 join phosphate silicate glasses, Si atoms remains tetrahedrally coordinated with oxygen when the content of P2O5 is below 32 mol%, but partial Si atoms become octahedrally coordinated with oxygen when the content of P2O5 increases above 32 mol%, and the proportion of the octahedrally coordinated Si atoms increases with the increasing content of P2O5. It has also been demonstrated that Al remains four-fold coordinated with oxygen in ambient NaAlSi2O6-NaAlSi3O8 glasses, but in the same composition glasses quenched at 4.4 GPa and 1,575 degrees C, partial Al atoms becomes five- and six-fold coordinated with oxygen, and at the same pressure and temperature, the proportions of five- and six-fold coordinated Al atoms increases with the increasing content of NaAlSi2O6 in the glasses. Thus, the pressure-induced coordination change of Al in aluminosilicate glasses and melts has been observed for the first time by Al K-edge X-ray absorption spectroscopy.
The C epsilon H proton resonance of His-12 of reduced cysteine S-sulfonated bovine pancreatic ribonuclease A exhibits a nonlinear temperature dependence of the chemical shift in its 1H-NMR spectrum at an apparent pH of 3.0. At temperatures below ca. 35 degrees C, the temperature dependence of the chemical shift of the His-12 C epsilon H resonance is opposite in sign to those of His-48, His-105, and His-119. At temperatures above ca. 35 degrees C, the temperature dependence of the chemical shift of the His-12 C epsilon H resonance is similar to those of the other three His C epsilon H resonances. These data indicate the existence of an equilibrium between locally ordered and locally disordered environments of His-12 in the sulfonated protein at temperatures below ca. 35 degrees C. The ordered and disordered conformations interconvert at a rate that is fast relative to the 1H-NMR chemical shift time scale--i.e., the locally ordered structure has a lifetime of much less than 7 msec. These results demonstrate that short- and medium-range interactions can define short-lived local structures under conditions of temperature and solution composition at which the native protein structure is stable. Furthermore, they demonstrate the utility of reduced derivatives of disulfide-containing proteins as model systems for the identification of local structures that may play a role as early-forming chain-folding initiation structures.
Synaptosomes from rat cerebral cortex were impregnated in the zinc iodide--osmium (ZIO) solution. The fine structural localization of the ZIO impregnation product was studied and, in addition, the function-dependent features of the reaction were examined after electrical stimulation or potassium chloride treatment. It was revealed that: (i) Aldehyde prefixation resulted in an increase in the number of reactive synaptic vesicles in all types of synaptosomes; (ii) Electrical stimulation decreased the number of reactive vesicles in a voltage dependent manner; (iii) Potassium chloride treatment also reduced the reactivity of vesicles; the reduction was dependent on the concentration of potassium and duration of treatment; (iv) Experimental interventions leading to the release of neurotransmitters from the synaptic vesicles and to fatigue of the nerve terminals also resulted in a decrease of the ZIO-reaction product of synaptic vesicles in a manner proportional to the strength of stimuli.
In order to understand how the phosphorylation of histones affects the chromatin structure, we used electron microscopy, sedimentation velocity, circular dichroism and electric birefringence to monitor the salt-induced filament reversible solenoid transition of phosphorylated and native chromatin. Phosphorylation in vitro of chicken erythrocyte chromatin by cyclic-AMP-dependent protein kinase from porcine heart led to the modification of the histones H3 and H5 only, which were modified at a level of one phosphate and about three phosphate groups per molecule, respectively. In contrast to circular dichroism and sedimentation studies, which tend to suggest that phosphorylation of H3 and H5 does not affect chromatin structure, electron microscopy reveals that phosphorylation causes a relaxation of structure at low ionic strength. Electric birefringence and relaxation time measurements clearly prove that local structural changes are induced in chromatin: we observe a decrease of the steady-state birefringence with the appearance of a negative contribution in the signal and a marked increase of the flexibility of fibres. The component with the negative birefringence presents very short relaxation times, like those exhibited by small DNA fragments or individual nucleosomes. Two possibilities are then suggested. First, the conformational change is consistent with what would be expected from the presence of DNA segments loosely associated with the core histone H3. That the length of such segments could correspond to about one to two base-pairs per nucleosome strongly suggests that phosphorylation induces changes affecting some specific H3-DNA interactions only. This result could corroborate previous observations indicating that the N-terminal region of H3, where the site of phosphorylation is located, plays a decisive role in maintaining the superstructure of chromatin. Second, phosphorylation could introduce hinge points between each nucleosome. In this case, the negative birefringence results from partial orientation of the swinging nucleosomes. A possible mode of action of phosphorylation might be to weaken structural restraints imposed by histone H3, thus facilitating further condensation of chromatin.
To detect the local structural change in an interface between proteins induced by the substrate binding and dissociation, a solvatochromic fluorescent N(beta)-L-alanyl-5-(N,N-dimethylamino)-naphthalene-1-sulfonamide (DanAla) was introduced into 132 position of the dimer interface in BamHI. Before addition of the substrate, the fluorescence from the normal planer excited state of DanAla moiety was observed as a main emission, and thereby the DanAla in the dimer interface is located in the hydrophobic microenvironment. The incubation with the substrate for 20 min induced the gradual increase in fluorescence intensity around 430 nm. The fact reflects that the polarity is reduced by the slight structural change initiated by the formation of the complex with the substrate. Furthermore, the incubation for more than 20 min caused the slight decrease in fluorescence around 430 nm and an appearance of fluorescence (560 nm) due to twisted intramolecular charge transfer (TICT) excited state. Therefore, the DanAla is exposed to comparative polar environment after the dissociation of the substrate. The fluorescence lifetime as a minor component, which is attributed to the TICT excited state, was reduced by addition of the substrate. The results provide that the hydrophobicity in the dimer interface is increased by the substrate binding. Interestingly, we found that the structure of an initial form is different from that of a refolded form after the dissociation of the substrate using a spectral subtraction technique. We have achieved detection of the changing structure induced by the substrate binding and dissociation using a steady-state and time-resolved fluorescence.
We determine the local structure of isolated positively charged muonium (Mu+) in heavily doped p-type GaAs based on muon level crossing resonance and zero applied field muon spin depolarization data. These measurements provide the first direct experimental confirmation that Mu+, and by analogy H+, is located within a stretched Ga-As bond. The distances between Mu+ and the nearest neighbor Ga and As atoms are estimated to be 1.83 +/- 0.10 A; and 1.76 +/- 0.10 A, respectively. These results are compared to existing theoretical calculations on the structure of hydrogen in GaAs and additionally provide data on the induced electric field gradients.
The local aluminum structure in zeolite mordenite was studied at temperatures up to 1000 K in a vacuum by Al K-edge X-ray absorption near-edge structure (XANES) spectroscopy. The interatomic aluminum-oxygen distances and the number of coordinating oxygen atoms were determined by Fourier transform analyses of experimental Al K-edge XANES spectra and the fits of the nearest oxygen atoms contributions, using a limited number of variables. The values of fixed parameters for Fourier transform and fit are established from the spectrum of Na-mordenite, considered the reference compound for the studied zeolites H-mordenites, which was also used to test the accuracy and the stability of the determined structural parameters. To reveal the aluminum coordination in H-mordenite at various temperatures, the Fourier transform peak of the coordinating oxygen polyhedron was fitted first with a single-shell model, and the obtained structural information was refined by the fits, on the basis of the most plausible models for the aluminum coordination environment. The choice of such models for each temperature was performed according to the qualitative predictions on the aluminum local atomic structure provided by the preedge data analysis and 27Al magic angle spinning (MAS) NMR experiments. By this method, the presence of sixfold aluminum atoms, aside from the fourfold ones, in H-mordenite at room temperature was revealed quantitatively, and the concentrations of these mixed coordinations were determined; the structural distortion of the oxygen tetrahedron around aluminum in dehydrated H-mordenite at T = 575 K was found to be strong, and the corresponding Al-O distances for this distortion were obtained; for H-mordenite at 985 K, the presence of threefold coordinated aluminum atoms, aside from the fourfold ones, was revealed, and an estimate of the amount of threefold aluminum was given.
The electron paramagnetic resonance (EPR) parameters g factors g(parallel) and g(perpendicular) as well as the local structure for Er3+ in scheelite-type BaWO4 are theoretically investigated by using the perturbation formulas of the EPR parameters for a 4f11 ion under tetragonal symmetry. In these formulas, the contributions to the EPR parameters arising from the second-order perturbation terms and the admixture of different states are included. It is found that the impurity-ligand bonding angles (or the polar angles) related to the fourfold axis in the tetragonal Er3+ center are about 1.5 degrees smaller than those in pure crystal. The calculated EPR parameters are in agreement with the observed values. The validity of the results is discussed.
The small viscosity asymptotics of the inertial range of local structure and of the wall region in wallbounded turbulent shear flow are compared. The comparison leads to a sharpening of the dichotomy between Reynolds number dependent scaling (power-type) laws and the universal Reynolds number independent logarithmic law in wall turbulence. It further leads to a quantitative prediction of an essential difference between them, which is confirmed by the results of a recent experimental investigation. These results lend support to recent work on the zero viscosity limit of the inertial range in turbulence.
The nonlinear propagation of ultrashort laser pulses launched into the air is investigated. The formation of optical light "bullets," or spatially localized structures, has been experimentally observed recently. Their stability is shown as due to the occurrence of a dynamical balance between two opposite nonlinear effects: an optical focusing Kerr effect balanced by a defocusing self-induced multiphoton partial ionization of the neutral gas. Characteristics of the "bullets" are predicted analytically and confirmed numerically. They are found to be in agreement with observations.
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The local structure and electronic properties of Mn in Na doped lanthanum manganites have been investigated by means of Mn-K edge XAFS, at various temperatures ranging from RT to 30 K. The hole content depends on the amount of doping, both with Na which injects two holes per doping atom and with oxygen nonstoichiometry. The holes are annihilated by oxygen under-stoichiometry via the formation of oxygen vacancies; the presence of a greater static disorder in the orthorhombic manganites is evidenced by both EXAFS and XANES analysis. In the rombohedral samples, a single Mn-O distance is found. In addition, the trend of the EXAFS Debye-Waller factors for the Mn-O distance can be fitted with a simple Einstein model, with no static disorder at low temperature. This evidence suggests small disorder of polaronic and of Jahn-Teller origin in the rombohedral samples at low temperatures, which is in contrast with what was found for the orthorhombic samples below T(c).
We study, analytically and numerically, the effect of frequency detunings and relaxation processes in laser media on stability and bifurcations of dissipative optical localized structures (DOLS's) in a transversely one-dimensional laser with a saturable absorber. The approximate envelope equation, with an intensity dependent effective coefficient of the diffusion, is derived. Andronov-Hopf bifurcations resulting from frequency detuning and leading to oscillatory DOLS's are analyzed numerically. A numerical and analytical study of bifurcations of transversely motionless DOLS's in a laser with finite relaxation rates of amplifying and absorbing media is performed. New types of DOLS's are found, including those moving with a large transverse velocity and those moving with a periodically oscillating transverse velocity. Hysteresis between different types of DOLS's is demonstrated.