Effect of silane functionalized alumina on poly(vinyl butyral) nanocomposite films: Thermal, mechanical, and moisture barrier studies

In this work, a hybrid-polymer nanocomposite film, based on polyvinyl butyral/amino-silane functionalized nano alumina, was fabricated by melt processing. The calcium degradation measurements suggest the functionalized nanocomposite films exhibit higher resistance towards moisture penetration as compared to the neat alumina loaded films. Thermal stability, mechanical strength, and contact angle studies of the composites were also conducted to evaluate the performance of the functionalized alumina loaded films. These nanocomposite films were encapsulated over Al/P3HT/ITO Schottky structured device. The changes observed in the current density of the devices to the applied voltage before and after accelerated aging conditions are presented. The nanocomposite with functionalized alumina films exhibits 50% change in current density, which is superior to that attained with neat and non-functionalized films. POLYM. COMPOS., 35:1426-1435, 2014. (c) 2013 Society of Plastics Engineers

Edge states of a three-dimensional topological insulator

We use the bulk Hamiltonian for a three-dimensional topological insulator such as Bi-2 Se-3 to study the states which appear on its various surfaces and along the edge between two surfaces. We use both analytical methods based on the surface Hamiltonians (which are derived from the bulk Hamiltonian) and numerical methods based on a lattice discretization of the bulk Hamiltonian. We find that the application of a potential barrier along an edge can give rise to states localized at that edge. These states have an unusual energy-momentum dispersion which can be controlled by applying a potential along the edge; in particular, the velocity of these states can be tuned to zero. The scattering and conductance across the edge is studied as a function of the edge potential. We show that a magnetic field in a particular direction can also give rise to zero energy states on certain edges. We point out possible experimental ways of looking for the various edge states.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

Water Vapor Barrier Material by Covalent Self-Assembly for Organic Device Encapsulation

Development of barrier materials for organic device encapsulation is of key interest for the commercialization of organic electronics. In this work, we have fabricated barrier films with ultralow water vapor permeabilities by reactive layer-by-layer approach. Using this technique, alternative layers of polyethylene imine and stearic acid were covalently bonded on a Surlyn film. The roughness, transparency and thickness of the films were determined by atomic force microscopy, UV-visible spectroscopy and scanning electron microscopy, respectively. Water vapor transmission rates through these films and the ability of these films to protect the organic photovoltaic devices was investigated. The films with covalently assembled bilayers exhibited lower water vapor transmission rates and maintained higher organic photovoltaic device efficiencies compared to the neat Surlyn film.

Beadex Function in the Motor Neurons Is Essential for Female Reproduction in Drosophila melanogaster

Drosophila melanogaster has served as an excellent model system for understanding the neuronal circuits and molecular mechanisms regulating complex behaviors. The Drosophila female reproductive circuits, in particular, are well studied and can be used as a tool to understand the role of novel genes in neuronal function in general and female reproduction in particular. In the present study, the role of Beadex, a transcription co-activator, in Drosophila female reproduction was assessed by generation of mutant and knock down studies. Null allele of Beadex was generated by transposase induced excision of P-element present within an intron of Beadex gene. The mutant showed highly compromised reproductive abilities as evaluated by reduced fecundity and fertility, abnormal oviposition and more importantly, the failure of sperm release from storage organs. However, no defect was found in the overall ovariole development. Tissue specific, targeted knock down of Beadex indicated that its function in neurons is important for efficient female reproduction, since its neuronal knock down led to compromised female reproductive abilities, similar to Beadex null females. Further, different neuronal class specific knock down studies revealed that Beadex function is required in motor neurons for normal fecundity and fertility of females. Thus, the present study attributes a novel and essential role for Beadex in female reproduction through neurons.

Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation

Cis-peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level-specific Gene Ontology molecular-function terms (also known as annotations) can be used in a statistically significant manner to identify cis-embedded segments in a protein linked to its molecular function. The present study identifies novel cis-peptide fragments, which are subsequently used for fragment-based function annotation. Annotation recall benchmarks interpreted using the receiver-operator characteristic plot returned an area-under-curve >0.9, corroborating the utility of the annotation method. In addition, we identified cis-peptide fragments occurring in conjunction with functionally important trans-peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology-based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis-peptide neighborhood of proteins.

Double Gaussian distribution of barrier height observed in densely packed GaN nanorods over Si (111) heterostructures

GaN nanorods were grown by plasma assisted molecular beam epitaxy on intrinsic Si (111) substrates which were characterized by powder X-ray diffraction, field emission scanning electron microscopy, and photoluminescence. The current-voltage characteristics of the GaN nanorods on Si (111) heterojunction were obtained from 138 to 493K which showed the inverted rectification behavior. The I-V characteristics were analyzed in terms of thermionic emission model. The temperature variation of the apparent barrier height and ideality factor along with the non-linearity of the activation energy plot indicated the presence of lateral inhomogeneities in the barrier height. The observed two temperature regimes in Richardson's plot could be well explained by assuming two separate Gaussian distribution of the barrier heights. (C) 2014 AIP Publishing LLC.

Layer-by-Layer Assembly of Nafion on Surlyn with Ultrahigh Water Vapor Barrier

A layer-by-layer approach was used for the fabrication of multilayer films for ultra high gas barrier applications. The ultra high gas barrier material was designed by incorporating Nafion layer in between bilayers of poly(ethylene imine) and poly(acrylic acid) on a Surlyn substrate. When the barrier film with self-assembled Nafion is exposed to the moist environment, Nafion absorbs and desorbs water molecules simultaneously, thereby reducing the ingress of moisture in to the film. In order to study the effect of Nafion, the fabricated barrier materials with and without the presence of Nafion were tested for water vapor barrier properties. The barrier films were further used for encapsulating organic photovoltaic devices and were evaluated for their potential use in barrier applications. The devices encapsulated with the films containing Nafion exhibited better performance when subjected to accelerated aging conditions. Therefore, this study demonstrates the effectiveness of self-assembled Nafion in reducing the water vapor permeability by nearly five orders of magnitude and in increasing the lifetimes of organic devices by similar to 22 times under accelerated weathering conditions.

Two-point correlation function of an exclusion process with hole-dependent rates

We consider an exclusion process on a ring in which a particle hops to an empty neighboring site with a rate that depends on the number of vacancies n in front of it. In the steady state, using the well-known mapping of this model to the zero-range process, we write down an exact formula for the partition function and the particle-particle correlation function in the canonical ensemble. In the thermodynamic limit, we find a simple analytical expression for the generating function of the correlation function. This result is applied to the hop rate u(n) = 1 + (b/n) for which a phase transition between high-density laminar phase and low-density jammed phase occurs for b > 2. For these rates, we find that at the critical density, the correlation function decays algebraically with a continuously varying exponent b - 2. We also calculate the two-point correlation function above the critical density and find that the correlation length diverges with a critical exponent nu = 1/(b - 2) for b < 3 and 1 for b > 3. These results are compared with those obtained using an exact series expansion for finite systems.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. (C) 2014 Elsevier Ltd. All rights reserved.

Transverse single spin asymmetry in e plus p up arrow -> e plus J/psi plus X and Q(2) evolution of Sivers function-II

We present estimates of single spin asymmetry in the electroproduction of J/psi taking into account the transverse momentum-dependent (TMD) evolution of the gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS and eRHIC energies using the color evaporation model of J/psi. We have calculated the asymmetry using recent parameters extracted by Echevarria et al. using the Collins-Soper-Sterman approach to TMD evolution. These recent TMD evolution fits are based on the evolution kernel in which the perturbative part is resummed up to next-to-leading logarithmic accuracy. We have also estimated the asymmetry by using parameters which had been obtained by a fit by Anselmino et al., using both an exact numerical and an approximate analytical solution of the TMD evolution equations. We find that the variation among the different estimates obtained using TMD evolution is much smaller than between these on one hand and the estimates obtained using DGLAP evolution on the other. Even though the use of TMD evolution causes an overall reduction in asymmetries compared to the ones obtained without it, they remain sizable. Overall, upon use of TMD evolution, predictions for asymmetries stabilize.

Logarithmic corrections to twisted indices from the quantum entropy function

We compute logarithmic corrections to the twisted index B-6(g) in four-dimensional N = 4 and N = 8 string theories using the framework of the Quantum Entropy Function. We find that these vanish, matching perfectly with the large-charge expansion of the corresponding microscopic expressions.

Quick, Decentralized, Energy-Efficient One-Shot Max Function Computation Using Timer-Based Selection

In several wireless sensor networks, it is of interest to determine the maximum of the sensor readings and identify the sensor responsible for it. We propose a novel, decentralized, scalable, energy-efficient, timer-based, one-shot max function computation (TMC) algorithm. In it, the sensor nodes do not transmit their readings in a centrally pre-defined sequence. Instead, the nodes are grouped into clusters, and computation occurs over two contention stages. First, the nodes in each cluster contend with each other using the timer scheme to transmit their reading to their cluster-heads. Thereafter, the cluster-heads use the timer scheme to transmit the highest sensor reading in their cluster to the fusion node. One new challenge is that the use of the timer scheme leads to collisions, which can make the algorithm fail. We optimize the algorithm to minimize the average time required to determine the maximum subject to a constraint on the probability that it fails to find the maximum. TMC significantly lowers average function computation time, average number of transmissions, and average energy consumption compared to approaches proposed in the literature.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Gamma oscillations in the midbrain spatial attention network: linking circuits to function

Gamma-band (25-140 Hz) oscillations are ubiquitous in mammalian forebrain structures involved in sensory processing, attention, learning and memory. The optic tectum (01) is the central structure in a midbrain network that participates critically in controlling spatial attention. In this review, we summarize recent advances in characterizing a neural circuit in this midbrain network that generates large amplitude, space-specific, gamma oscillations in the avian OT, both in vivo and in vitro. We describe key physiological and pharmacological mechanisms that produce and regulate the structure of these oscillations. The extensive similarities between midbrain gamma oscillations in birds and those in the neocortex and hippocampus of mammals, offer important insights into the functional significance of a midbrain gamma oscillatory code.