Amorphous HfO(2) and Hf(1-x)Si(x)O via a melt-and-quench scheme using ab initio molecular dynamics

We have performed ab initio molecular dynamics simulations to generate an atomic structure model of amorphous hafnium oxide (a-HfO(2)) via a melt-and-quench scheme. This structure is analyzed via bond-angle and partial pair distribution functions. These results give a Hf-O average nearest-neighbor distance of 2.2 angstrom, which should be compared to the bulk value, which ranges from 1.96 to 2.54 angstrom. We have also investigated the neutral O vacancy and a substitutional Si impurity for various sites, as well as the amorphous phase of Hf(1-x)Si(x)O(2) for x=0.25, 0375, and 0.5.

Spin dynamics of NiCl(2)-4SC(NH(2))(2) in the field-induced ordered phase

NiCl(2)-4SC(NH(2))(2) (known as DTN) is a spin-1 material with a strong single-ion anisotropy that is regarded as a new candidate for Bose-Einstein condensation (BEC) of spin degrees of freedom. We present a systematic study of the low-energy excitation spectrum of DTN in the field-induced magnetically ordered phase by means of high-field electron spin resonance measurements at temperatures down to 0.45 K. We argue that two gapped modes observed in the experiment can be consistently interpreted within a four-sublattice antiferromagnet model with a finite interaction between two tetragonal subsystems and unbroken axial symmetry. The latter is crucial for the interpretation of the field-induced ordering in DTN in terms of BEC.

Gauge invariance and classical dynamics of noncommutative particle theory

We consider a model of classical noncommutative particle in an external electromagnetic field. For this model, we prove the existence of generalized gauge transformations. Classical dynamics in Hamiltonian and Lagrangian form is discussed; in particular, the motion in the constant magnetic field is studied in detail. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3299296]

Soliton dynamics at an interface between a uniform medium and a nonlinear optical lattice

We study trapping and propagation of a matter-wave soliton through the interface between uniform medium and a nonlinear optical lattice. Different regimes for transmission of a broad and a narrow solitons are investigated. Reflections and transmissions of solitons are predicted as a function of the lattice phase. The existence of a threshold in the amplitude of the nonlinear optical lattice, separating the transmission and reflection regimes, is verified. The localized nonlinear surface state, corresponding to the soliton trapped by the interface, is found. Variational approach predictions are confirmed by numerical simulations for the original Gross-Pitaevskii equation with nonlinear periodic potentials.

Continuous structural transitions in quasi-one-dimensional classical Wigner crystals

We study the structural phase transitions in confined systems of strongly interacting particles. We consider infinite quasi-one-dimensional systems with different pairwise repulsive interactions in the presence of an external confinement following a power law. Within the framework of Landau's theory, we find the necessary conditions to observe continuous transitions and demonstrate that the only allowed continuous transition is between the single-and the double-chain configurations and that it only takes place when the confinement is parabolic. We determine analytically the behavior of the system at the transition point and calculate the critical exponents. Furthermore, we perform Monte Carlo simulations and find a perfect agreement between theory and numerics.

Structural and optical analysis of GaAsP/GaP core-shell nanowires

The structural and optical properties of GaAsP/GaP core-shell nanowires grown by gas source molecular beam epitaxy were investigated by transmission electron microscopy, Raman spectroscopy, photoluminescence (PL), and magneto-PL. The effects of surface depletion and compositional variations in the ternary alloy manifested as a redshift in GaAsP PL upon surface passivation, and a decrease in redshift in PL in the presence of a magnetic field due to spatial confinement of carriers.

Connectivity and dynamics of neuronal networks as defined by the shape of individual neurons

Biological neuronal networks constitute a special class of dynamical systems, as they are formed by individual geometrical components, namely the neurons. In the existing literature, relatively little attention has been given to the influence of neuron shape on the overall connectivity and dynamics of the emerging networks. The current work addresses this issue by considering simplified neuronal shapes consisting of circular regions (soma/axons) with spokes (dendrites). Networks are grown by placing these patterns randomly in the two-dimensional (2D) plane and establishing connections whenever a piece of dendrite falls inside an axon. Several topological and dynamical properties of the resulting graph are measured, including the degree distribution, clustering coefficients, symmetry of connections, size of the largest connected component, as well as three hierarchical measurements of the local topology. By varying the number of processes of the individual basic patterns, we can quantify relationships between the individual neuronal shape and the topological and dynamical features of the networks. Integrate-and-fire dynamics on these networks is also investigated with respect to transient activation from a source node, indicating that long-range connections play an important role in the propagation of avalanches.

Structural, dielectric, and optical properties of yttrium calcium borate glasses

Structural and optical properties of stable glasses in the Y(2)O(3)-CaO-B(2)O(3) system, containing the same Y/Ca ratio as the YCa(4)O(BO(3))(3) (YCOB) crystal, were determined from Raman and reflectance infrared spectroscopy. Changes in optical functions with composition are associated with an increase in the number of non-bridging oxygen and to calcium/yttrium oxides content. Refractive indexes values (from 1.597 to 1.627 at lambda=2 mu m) are in good agreement with those of the YCOB crystal, an indication that these glasses are potential candidates for optical applications due to their ease of shaping as large bulk samples or fibers.

Isotropic and anisotropic spin-spin interactions and a quantum phase transition in a dinuclear Cu(II) compound

We report electron-paramagnetic resonance (EPR) studies at similar to 9.5 GHz (X band) and similar to 34 GHz (Q band) of powder and single-crystal samples of the compound Cu(2)[TzTs](4) [N-thiazol-2-yl-toluenesulfonamidatecopper(II)], C(40)H(36)Cu(2)N(8)O(8)S(8), having copper(II) ions in dinuclear units. Our data allow determining an antiferromagnetic interaction J(0)=(-113 +/- 1) cm(-1) (H(ex)=-J(0)S(1)center dot S(2)) between Cu(II) ions in the dinuclear unit and the anisotropic contributions to the spin-spin coupling matrix D (H(ani)=S(1)center dot D center dot S(2)), a traceless symmetric matrix with principal values D/4=(0.198 +/- 0.003) cm(-1) and E/4=(0.001 +/- 0.003) cm(-1) arising from magnetic dipole-dipole and anisotropic exchange couplings within the units. In addition, the single-crystal EPR measurements allow detecting and estimating very weak exchange couplings between neighbor dinuclear units, with an estimated magnitude parallel to J(')parallel to=(0.060 +/- 0.015) cm(-1). The interactions between a dinuclear unit and the ""environment"" of similar units in the structure of the compound produce a spin dynamics that averages out the intradinuclear dipolar interactions. This coupling with the environment leads to decoherence, a quantum phase transition that collapses the dipolar interaction when the isotropic exchange coupling with neighbor dinuclear units equals the magnitude of the intradinuclear dipolar coupling. Our EPR experiments provide a new procedure to follow the classical exchange-narrowing process as a shift and collapse of the line structure (not only as a change of the resonance width), which is described with general (but otherwise simple) theories of magnetic resonance. Using complementary procedures, our EPR measurements in powder and single-crystal samples allow measuring simultaneously three types of interactions differing by more than three orders of magnitude (between 113 cm(-1) and 0.060 cm(-1)).

Weak measurement: Effect of the detector dynamics

The contribution of the detector dynamics to the weak measurement is analyzed. According to the usual theory [Y. Aharonov, D. Z. Albert, and L. Vaidman, Phys. Rev. Lett. 60, 1351 (1988)] the outcome of a weak measurement with preselection and postselection can be expressed as the real part of a complex number: the weak value. By accounting for the Hamiltonian evolution of the detector, here we find that there is a contribution proportional to the imaginary part of the weak value to the outcome of the weak measurement. This is due to the coherence of the probe being essential for the concept of complex weak value to be meaningful. As a particular example, we consider the measurement of a spin component and find that the contribution of the imaginary part of the weak value is sizable.

Structural models for yttrium aluminium borate laser glasses: NMR and EPR studies of the system (Y(2)O(3))(0.2)-(Al(2)O(3))(x)-(B(2)O(3))(0.8-x)

The structure of laser glasses in the system (Y(2)O(3))(0.2){(Al(2)O(3))(x))(B(2)O(3))(0.8-x)} (0.15 <= x <= 0.40) has been investigated by means of (11)B, (27)Al, and (89)Y solid state NMR as well as electron spin echo envelope modulation (ESEEM) of Yb-doped samples. The latter technique has been applied for the first time to an aluminoborate glass system. (11)B magic-angle spinning (MAS)-NMR spectra reveal that, while the majority of the boron atoms are three-coordinated over the entire composition region, the fraction of three-coordinated boron atoms increases significantly with increasing x. Charge balance considerations as well as (11)B NMR lineshape analyses suggest that the dominant borate species are predominantly singly charged metaborate (BO(2/2)O(-)), doubly charged pyroborate (BO(1/2)(O(-))(2)), and (at x = 0.40) triply charged orthoborate groups. As x increases along this series, the average anionic charge per trigonal borate group increases from 1.38 to 2.91. (27)Al MAS-NMR spectra show that the alumina species are present in the coordination states four, five and six, and the fraction of four-coordinated Al increases markedly with increasing x. All of the Al coordination states are in intimate contact with both the three-and the four-coordinate boron species and vice versa, as indicated by (11)B/(27)Al rotational echo double resonance (REDOR) data. These results are consistent with the formation of a homogeneous, non-segregated glass structure. (89)Y solid state NMR spectra show a significant chemical shift trend, reflecting that the second coordination sphere becomes increasingly ""aluminate-like'' with increasing x. This conclusion is supported by electron spin echo envelope modulation (ESEEM) data of Yb-doped glasses, which indicate that both borate and aluminate species participate in the medium range structure of the rare-earth ions, consistent with a random spatial distribution of the glass components.

Crystallization and preliminary structural analysis of the giant haemoglobin from Glossoscolex paulistus at 3.2 angstrom

Glossoscolex paulistus is a free-living earthworm encountered in south-east Brazil. Its oxygen transport requirements are undertaken by a giant extracellular haemoglobin, or erythrocruorin (HbGp), which has an approximate molecular mass of 3.6 MDa and, by analogy with its homologue from Lumbricus terrestris (HbLt), is believed to be composed of a total of 180 polypeptide chains. In the present work the full 3.6 MDa particle in its cyanomet state was purified and crystallized using sodium citrate or PEG8000 as precipitant. The crystals contain one-quarter of the full particle in the asymmetric unit of the I222 cell and have parameters of a = 270.8 angstrom, b = 320.3 angstrom and c = 332.4 angstrom. Diffraction data were collected to 3.15 angstrom using synchrotron radiation on beamline X29A at the Brookhaven National Laboratory and represent the highest resolution data described to date for similar erythrocruorins. The structure was solved by molecular replacement using a search model corresponding to one-twelfth of its homologue from HbLt. This revealed that HbGp belongs to the type I class of erythrocruorins and provided an interpretable initial electron density map in which many features including the haem groups and disulfide bonds could be identified.

Structural and magnetic properties of the oxyborate Co(5)Ti(O(2)BO(3))(2)

We present an extensive study of the oxyborate material Co(5)Ti(O(2)BO(3))(2) using x-ray, magnetic, and thermodynamic measurements. This material belongs to a family of oxyborates known as ludwigites which presents low-dimensional subunits in the form of three leg ladders in its structure. Differently from previously investigated ludwigites the present material does not show long-range magnetic order although it goes into a spin-glass state at low temperatures. The different techniques employed in this paper allow for a characterization of the structure, the nature of the low-energy excitations and the magnetic anisotropy of this system. Its unique magnetic behavior is discussed and compared with those of other magnetic ludwigites.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni

Schistosomes are unable to synthesize purines de novo and depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds to Schistosoma mansoni PNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

Evolutionary dynamics on rugged fitness landscapes: Exact dynamics and information theoretical aspects

The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the random energy model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three distinct regimes: pure diffusion or stasis for short times, depending on the fitness of the initial configuration, and a spin-glass regime for large times. The dynamic transition between these dynamical regimes is marked by discontinuities in the mean-fitness as well as in the overlap with the initial reference sequence. The relaxation to equilibrium is described by an inverse time decay. In the ferromagnetic REM, we find in addition to these three regimes, a ferromagnetic regime where the overlap and the mean-fitness are frozen. In this case, the system relaxes to equilibrium in a finite time. The relevance of our results to information processing aspects of evolution is discussed.