Generation of Ligand Specificity and Modes of Oligomerization in beta-Prism I Fold Lectins

beta-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.

Floquet generation of Majorana end modes and topological invariants

We show how Majorana end modes can be generated in a one-dimensional system by varying some of the parameters in the Hamiltonian periodically in time. The specific model we consider is a chain containing spinless electrons with a nearest-neighbor hopping amplitude, a p-wave superconducting term, and a chemical potential; this is equivalent to a spin-1/2 chain with anisotropic XY couplings between nearest neighbors and a magnetic field applied in the (z) over cap direction. We show that varying the chemical potential (or magnetic field) periodically in time can produce Majorana modes at the ends of a long chain. We discuss two kinds of periodic driving, periodic delta-function kicks, and a simple harmonic variation with time. We discuss some distinctive features of the end modes such as the inverse participation ratio of their wave functions and their Floquet eigenvalues which are always equal to +/- 1 for time-reversal-symmetric systems. For the case of periodic delta-function kicks, we use the effective Hamiltonian of a system with periodic boundary conditions to define two topological invariants. The first invariant is a well-known winding number, while the second invariant has not appeared in the literature before. The second invariant is more powerful in that it always correctly predicts the numbers of end modes with Floquet eigenvalues equal to + 1 and -1, while the first invariant does not. We find that the number of end modes can become very large as the driving frequency decreases. We show that periodic delta-function kicks in the hopping and superconducting terms can also produce end modes. Finally, we study the effect of electron-phonon interactions (which are relevant at finite temperatures) and a random noise in the chemical potential on the Majorana modes.

Failure modes and fatigue behavior of conventional and refilled friction stir spot welds in AA 6061-T6 sheets

The fatigue behavior of conventional friction stir spot welding (FSSW) and friction stir spot welding refilled by the friction forming process (FSSW-FFP) in aluminum 6061-T6 lap shear specimens, are investigated based on the experimental observations. Optical micrographs of the welds after fatigue failure in both the cases are examined to study the fatigue crack propagation and failure modes. Experimental results indicate that the fatigue strength of the FSSW-FFP weld samples is higher than that of the conventional FSSW samples at all loads. Fracture surfaces are analyzed in detail using the scanning electron microscope. (C) 2013 Elsevier Ltd. All rights reserved.

Goldstone modes and bifurcations in phase-separated binary condensates at finite temperature

We show that the third Goldstone mode, which emerges in binary condensates at phase separation, persists to higher interspecies interaction for density profiles where one component is surrounded on both sides by the other component. This is not the case with symmetry-broken density profiles where one species is entirely to the left and the other is entirely to the right. We, then, use Hartree-Fock-Bogoliubov theory with Popov approximation to examine the mode evolution at T not equal 0 and demonstrate the existence of mode bifurcation near the critical temperature. The Kohn mode, however, exhibits deviation from the natural frequency at finite temperatures after the phase separation. This is due to the exclusion of the noncondensate atoms in the dynamics.

Transition in vortex breakdown modes in a coaxial isothermal unconfined swirling jet

This paper reports first observations of transition in recirculation pattern from an open-bubble type axisymmetric vortex breakdown to partially open bubble mode through an intermediate, critical regime of conical sheet formation in an unconfined, co-axial isothermal swirling flow. This time-mean transition is studied for two distinct flow modes which are characterized based on the modified Rossby number (Ro(m)), i.e., Ro(m) <= 1 and Ro(m) > 1. Flow modes with Ro(m) <= 1 are observed to first undergo cone-type breakdown and then to partially open bubble state as the geometric swirl number (S-G) is increased by similar to 20% and similar to 40%, respectively, from the baseline open-bubble state. However, the flow modes with Ro(m) > 1 fail to undergo such sequential transition. This distinct behavior is explained based on the physical significance associated with Ro(m) and the swirl momentum factor (xi). In essence, xi represents the ratio of angular momentum distributed across the flow structure to that distributed from central axis to the edge of the vortex core. It is observed that xi increases by similar to 100% in the critical swirl number band where conical breakdown occurs as compared to its magnitude in the S-G regime where open bubble state is seen. This results from the fact that flow modes with Ro(m) <= 1 are dominated by radial pressure gradient due to swirl/rotational effect when compared to radial pressure deficit arising from entrainment (due to the presence of co-stream). Consequently, the imparted swirl tends to penetrate easily towards the central axis causing it to spread laterally and finally undergo conical sheet breakdown. However, the flow modes with Ro(m) > 1 are dominated by pressure deficit due to entrainment effect. This blocks the radial inward penetration of imparted angular momentum thus preventing the lateral spread of these flow modes. As such these structures fail to undergo cone mode of vortex breakdown which is substantiated by a mere 30%-40% rise in xi in the critical swirl number range. (C) 2014 AIP Publishing LLC.

Majorana edge modes in the Kitaev model

We study the Majorana modes, both equilibrium and Floquet, which can appear at the edges of the Kitaev model on the honeycomb lattice. We first present the analytical solutions known for the equilibrium Majorana edge modes for both zigzag and armchair edges of a semi-infinite Kitaev model and chart the parameter regimes in which they appear. We then examine how edge modes can be generated if the Kitaev coupling on the bonds perpendicular to the edge is varied periodically in time as periodic delta-function kicks. We derive a general condition for the appearance and disappearance of the Floquet edge modes as a function of the drive frequency for a generic d-dimensional integrable system. We confirm this general condition for the Kitaev model with a finite width by mapping it to a one-dimensional model. Our numerical and analytical study of this problem shows that Floquet Majorana modes can appear on some edges in the kicked system even when the corresponding equilibrium Hamiltonian has no Majorana mode solutions on those edges. We support our analytical studies by numerics for a finite sized system which show that periodic kicks can generate modes at the edges and the corners of the lattice.

Low-frequency modes in an equatorial shallow-water model with moisture gradients

Motivated by observations of the mean state of tropical precipitable water (PW), a moist, first baroclinic mode, shallow-water system on an equatorial beta-plane with a background saturation profile that depends on latitude and longitude is studied. In the presence of a latitudinal moisture gradient, linear analysis of the non-rotating problem reveals large-scale, symmetric, eastward and westward propagating unstable modes. The introduction of a zonal moisture gradient breaks the east-west symmetry of the unstable modes. The effects of rotation are then included by numerically solving the resulting eigenvalue problem on an equatorial beta-plane. With a purely meridional moisture gradient, the system supports large-scale, low-frequency, eastward and westward moving neutral modes. Some of the similarities, and some of the discrepancies of these modes with intraseasonal tropical waves are pointed out. Finally, a zonal moisture gradient in the presence of rotation renders some of the aforementioned neutral modes unstable. In particular, according to observations of large-scale, low-frequency tropical variability, it is seen that regions where the background saturation profile increases (decreases) to the east favour eastward (westward) moving moist modes.

Diffusion of components via different modes during growth of the A15-V(3)Gaphase

Based on an interdiffusion study using an incremental diffusion couple in the V-Ga binary system, we have shown that V diffuses via the lattice, whereas Ga does so via grain boundaries, for the growth of the V3Ga phase. We estimate the contributions from the two different mechanisms, which are usually difficult to delineate in an interdiffusion study. Available tracer diffusion studies and the atomic arrangement in the crystal structure have been considered for a discussion on the diffusion mechanisms.

Wave propagation of phonon and phason displacement modes in quasicrystals: Determination of wave parameters

The paper presents the study of wave propagation in quasicrystals. Our interest is in the computation of the wavenumber (k(n)) and group speed (c(g)) of the phonon and phason displacement modes of one, two, and three dimensional quasicrystals. These wave parameter expressions are derived and computed using the elasto-hydrodynamic equations for quasicrystals. For the computation of the wavenumber and group speeds, we use Fourier transform approximation of the phonon and the phason displacement modes. The characteristic equations obtained are a polynomial equation of the wavenumber (k(n)), with frequency as a parameter. The corresponding group speeds (c(g)) for different frequencies are then computed from the wavenumber k(n). The variation of wavenumber and group speeds with frequency is plotted for the 1-D quasicrystal, 2-D decagonal Al-Ni-Co quasicrystals, and 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. From the wavenumber and group speeds plots, we obtain the cut-off frequencies for different spatial wavenumber eta(m). The results show that for 1-D, 2-D, and 3-D quasicrystals, the phonon displacement modes are non-dispersive for low values of eta(m) and becomes dispersive for increasing values of eta(m). The cut-off frequencies are not observed for very low values of eta(m), whereas the cut-off frequency starts to appear with increasing eta(m). The group speeds of the phason displacement modes are orders of magnitude lower than that of the phonon displacement modes, showing that the phason modes do not propagate, and they are essentially the diffusive modes. The group speeds of the phason modes are also not influenced by eta(m). The group speeds for the 2-D quasicrystal at 35 kHz is also simulated numerically using Galerkin spectral finite element methods in frequency domain and is compared with the results obtained using wave propagation analysis. The effect of the phonon and phason elastic constants on the group speeds is studied using 3-D icosahedral Al-Pd-Mn and Zn-Mg-Sc quasicrystals. It is also shown that the phason elastic constants and the coupling coefficient do not affect the group speeds of the phonon displacement modes. (C) 2015 AIP Publishing LLC.

Acoustic response of vortex breakdown modes in a coaxial isothermal unconfined swirling jet

The present experimental work is concerned with the study of amplitude dependent acoustic response of an isothermal coaxial swirling jet. The excitation amplitude is increased in five distinct steps at the burner's Helmholtz resonator mode (i.e., 100 Hz). Two flow states are compared, namely, sub-critical and super-critical vortex breakdown (VB) that occur before and after the critical conical sheet breakdown, respectively. The geometric swirl number is varied in the range 2.14-4.03. Under the influence of external pulsing, global response characteristics are studied based on the topological changes observed in time-averaged 2D flow field. These are obtained from high resolution 2D PIV (particle image velocimetry) in the longitudinal-mid plane. PIV results also illustrate the changes in the normalized vortex core coordinates (r(vcc)/(r(vcc))(0) (Hz), y(vcc)/(y(vcc))(0) (Hz)) of internal recirculation zone (IRZ). A strong forced response is observed at 100 Hz (excitation frequency) in the convectively unstable region which get amplified based on the magnitude of external forcing. The radial extent of this forced response region at a given excitation amplitude is represented by the acoustic response region (b). The topological placement of the responsive convectively unstable region is a function of both the intensity of imparted swirl (characterized by swirl number) and forcing amplitude. It is observed that for sub-critical VB mode, an increase in the excitation amplitude till a critical value shifts the vortex core centre (particularly, the vortex core moves downstream and radially outwards) leading to drastic fanning-out/widening of the IRZ. This is accompanied by similar to 30% reduction in the recirculation velocity of the IRZ. It is also observed that b < R (R: radial distance from central axis to outer shear layer-OSL). At super-critical amplitudes, the sub-critical IRZ topology transits back (the vortex core retracts upstream and radially inwards) and finally undergoes a transverse shrinkage ((r(vcc))/(r(vcc))(0 Hz) decreases by similar to 20%) when b >= R. In contrast, the vortex core of super-critical breakdown mode consistently spreads radially outwards and is displaced further downstream. Finally, the IRZ fans-out at the threshold excitation amplitude. However, the acoustic response region b is still less than R. This is explained based on the characteristic geometric swirl number (S-G) of the flow regimes. The super-critical flow mode with higher S-G (hence, higher radial pressure drop due to rotational effect which scales as Delta P similar to rho u theta(2) and acts inwards towards the center line) compared to sub-critical state imposes a greater resistance to the radial outward spread of b. As a result, the acoustic energy supplied to the super-critical flow mode increases the degree of acoustic response at the pulsing frequency and energizes its harmonics (evident from power spectra). As a disturbance amplifier, the stronger convective instability mode within the flow structure of super-critical VB causes the topology to widen/fan-out severely at threshold excitation amplitude. (C) 2015 AIP Publishing LLC.

Electromechanical Analysis of Tapered Piezoelectric Bimorph at High Electric Field

Piezoelectric bimorph laminar actuator of tapered width exhibits better performance for out-of-plane deflection compared to the rectangular surface area, while consuming equal surface area. This paper contains electromechanical analysis and modeling of a tapered width piezoelectric bimorph laminar actuator at high electric field in static state. The analysis is based on the second order constitutive equations of piezoelectric material, assuming small strain and large electric field to capture its behavior at high electric field. Analytical expressions are developed for block force, output strain energy, output energy density, input electrical energy, capacitance and energy efficiency at high electric field. The analytical expressions show that for fixed length, thickness, and surface area of the actuator, how the block force and output strain energy gets improved in a tapered surface actuator compared to a rectangular surface. Constant thickness, constant length and constant surface area of the actuator ensure constant mass, and constant electrical capacitance. We consider high electric field in both series and parallel electrical connection for the analysis. Part of the analytical results is validated with the experimental results, which are reported in earlier literature.

Majorana modes and transport across junctions of superconductors and normal metals

We study Majorana modes and transport in one-dimensional systems with a p-wave superconductor (SC) and normal metal leads. For a system with an SC lying between two leads, it is known that there is a Majorana mode at the junction between the SC and each lead. If the p-wave pairing Delta changes sign or if a strong impurity is present at some point inside the SC, two additional Majorana modes appear near that point. We study the effect of all these modes on the sub-gap conductance between the leads and the SC. We derive an analytical expression as a function of Delta and the length L of the SC for the energy shifts of the Majorana modes at the junctions due to hybridization between them; the shifts oscillate and decay exponentially as L is increased. The energy shifts exactly match the location of the peaks in the conductance. Using bosonization and the renormalization group method, we study the effect of interactions between the electrons on Delta and the strengths of an impurity inside the SC or the barriers between the SC and the leads; this in turn affects the Majorana modes and the conductance. Finally, we propose a novel experimental realization of these systems, in particular of a system where Delta changes sign at one point inside the SC.

Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C

Transactivator protein C is required for the expression of bacteriophage Mu late genes from lys, I, P and mom promoters during lytic life cycle of the phage. The mechanism of transcription activation of mom gene by C protein is well understood. C activates transcription at Pmom by initial unwinding of the promoter DNA, thereby facilitating RNA polymerase (RNAP) recruitment. Subsequently, C interacts with the (sic) subunit of RNAP to enhance promoter clearance. The mechanism by which C activates other late genes of the phage is not known. We carried out promoter-polymerase interaction studies with all the late gene promoters to determine the individual step of C mediated activation. Unlike at P-mom, at the other three promoters, RNAP recruitment and closed complex formation are not C dependent. Instead, the action of C at P-lys, P-I, and P-P is during the isomerization from closed complex to open complex with no apparent effect at other steps of initiation pathway. The mechanism of transcription activation of mom and other late promoters by their common activator is different. This distinction in the mode of activation (promoter recruitment and escape versus isomerization) by the same activator at different promoters appears to be important for optimized expression of each of the late genes.

Identification of dominant modes in random dynamical and aeroelastic systems

Identification of dominant modes is an important step in studying linearly vibrating systems, including flow-induced vibrations. In the presence of uncertainty, when some of the system parameters and the external excitation are modeled as random quantities, this step becomes more difficult. This work is aimed at giving a systematic treatment to this end. The ability to capture the time averaged kinetic energy is chosen as the primary criterion for selection of modes. Accordingly, a methodology is proposed based on the overlap of probability density functions (pdf) of the natural and excitation frequencies, proximity of the natural frequencies of the mean or baseline system, modal participation factor, and stochastic variation of mode shapes in terms of the modes of the baseline system - termed here as statistical modal overlapping. The probabilistic descriptors of the natural frequencies and mode shapes are found by solving a random eigenvalue problem. Three distinct vibration scenarios are considered: (i) undamped arid damped free vibrations of a bladed disk assembly, (ii) forced vibration of a building, and (iii) flutter of a bridge model. Through numerical studies, it is observed that the proposed methodology gives an accurate selection of modes. (C) 2015 Elsevier Ltd. All rights reserved.

Structural modification and enhanced magnetic properties with two phonon modes in Ca-Co codoped BiFeO3 nanoparticles

Bi1-xCaxFe1-xCoxO3 nanoparticles with x=0.0, 0.05, 0.10 and 0.15 were successfully synthesized by cost effective tartaric acid based sol gel route. The alkali earth metal Ca2+ ions and transition metal Co3+ ions codoping at A and B-sites of BiFeO3 results in structural distortion and phase transformation. Rietveld refinement of XRD patterns suggested the coexistence of rhombohedral and orthorhombic phases in codoped BiFeO3 samples. Both XRD and Raman scattering studies showed the compressive lattice distortion in the samples induced by codoping of Ca2+ and Co3+ ions. Two-phonon Raman spectra exhibited the improvement of magnetization in these samples. X-ray photoelectron spectroscopy (XPS) showed the dominancy of Fe3+ and Co3+ oxidation states along with the shifting of the binding energy of Bi 4f orbital which confirms the substitution Ca2+ at Bi-site. The magnetic study showed the enhancement in room temperature ferromagnetic behavior with co-substitution consistent with Rama analysis. The gradual change in line shape of electron spin resonance spectra indicated the local distortion induced by codoping. (C) 2015 Published by Elsevier Ltd and Techna Group S.r.l.