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.

Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies. (c) 2015 AIP Publishing LLC.

The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function

Translation initiation in Hepatitis C Virus (HCV) is mediated by Internal Ribosome Entry Site (IRES), which is independent of cap-structure and uses a limited number of canonical initiation factors. During translation initiation IRES-40S complex formation depends on high affinity interaction of IRES with ribosomal proteins. Earlier, it has been shown that ribosomal protein S5 (RPS5) interacts with HCV IRES. Here, we have extensively characterized the HCV IRES-RPS5 interaction and demonstrated its role in IRES function. Computational modelling and RNA-protein interaction studies demonstrated that the beta hairpin structure within RPS5 is critically required for the binding with domains II and IV. Mutations disrupting IRES-RPS5 interaction drastically reduced the 80S complex formation and the corresponding IRES activity. Computational analysis and UV cross-linking experiments using various IRES-mutants revealed interplay between domains II and IV mediated by RPS5. In addition, present study demonstrated that RPS5 interaction is unique to HCV IRES and is not involved in 40S-3 ` UTR interaction. Further, partial silencing of RPS5 resulted in preferential inhibition of HCV RNA translation. However, global translation was marginally affected by partial silencing of RPS5. Taken together, results provide novel molecular insights into IRES-RPS5 interaction and unravel its functional significance in mediating internal initiation of translation.

Direct measurements of growing amorphous order and non-monotonic dynamic correlations in a colloidal glass-former

The transformation of flowing liquids into rigid glasses is thought to involve increasingly cooperative relaxation dynamics as the temperature approaches that of the glass transition. However, the precise nature of this motion is unclear, and a complete understanding of vitrification thus remains elusive. Of the numerous theoretical perspectives(1-4) devised to explain the process, random first-order theory (RFOT; refs 2,5) is a well-developed thermodynamic approach, which predicts a change in the shape of relaxing regions as the temperature is lowered. However, the existence of an underlying `ideal' glass transition predicted by RFOT remains debatable, largely because the key microscopic predictions concerning the growth of amorphous order and the nature of dynamic correlations lack experimental verification. Here, using holographic optical tweezers, we freeze a wall of particles in a two-dimensional colloidal glass-forming liquid and provide direct evidence for growing amorphous order in the form of a static point-to-set length. We uncover the non-monotonic dependence of dynamic correlations on area fraction and show that this non-monotonicity follows directly from the change in morphology and internal structure of cooperatively rearranging regions(6,7). Our findings support RFOT and thereby constitute a crucial step in distinguishing between competing theories of glass formation.

COMPUTATIONAL MODELING OF A MULTI-LAYERED PIEZO-COMPOSITE BEAM MADE UP OF MFC

The Variational Asymptotic Method (VAM) is used for modeling a coupled non-linear electromechanical problem finding applications in aircrafts and Micro Aerial Vehicle (MAV) development. VAM coupled with geometrically exact kinematics forms a powerful tool for analyzing a complex nonlinear phenomena as shown previously by many in the literature 3 - 7] for various challenging problems like modeling of an initially twisted helicopter rotor blades, matrix crack propagation in a composite, modeling of hyper elastic plates and various multi-physics problems. The problem consists of design and analysis of a piezocomposite laminate applied with electrical voltage(s) which can induce direct and planar distributed shear stresses and strains in the structure. The deformations are large and conventional beam theories are inappropriate for the analysis. The behavior of an elastic body is completely understood by its energy. This energy must be integrated over the cross-sectional area to obtain the 1-D behavior as is typical in a beam analysis. VAM can be used efficiently to approximate 3-D strain energy as closely as possible. To perform this simplification, VAM makes use of thickness to width, width to length, width multiplied by initial twist and strain as small parameters embedded in the problem definition and provides a way to approach the exact solution asymptotically. In this work, above mentioned electromechanical problem is modeled using VAM which breaks down the 3-D elasticity problem into two parts, namely a 2-D non-linear cross-sectional analysis and a 1-D non-linear analysis, along the reference curve. The recovery relations obtained as a by-product in the cross-sectional analysis earlier are used to obtain 3-D stresses, displacements and velocity contours. The piezo-composite laminate which is chosen for an initial phase of computational modeling is made up of commercially available Macro Fiber Composites (MFCs) stacked together in an arbitrary lay-up and applied with electrical voltages for actuation. The expressions of sectional forces and moments as obtained from cross-sectional analysis in closed-form show the electro-mechanical coupling and relative contribution of electric field in individual layers of the piezo-composite laminate. The spatial and temporal constitutive law as obtained from the cross-sectional analysis are substituted into 1-D fully intrinsic, geometrically exact equilibrium equations of motion and 1-D intrinsic kinematical equations to solve for all 1-D generalized variables as function of time and an along the reference curve co-ordinate, x(1).

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.

Structure-Based Phylogenetic Analysis of the Lipocalin Superfamily

Lipocalins constitute a superfamily of extracellular proteins that are found in all three kingdoms of life. Although very divergent in their sequences and functions, they show remarkable similarity in 3-D structures. Lipocalins bind and transport small hydrophobic molecules. Earlier sequence-based phylogenetic studies of lipocalins highlighted that they have a long evolutionary history. However the molecular and structural basis of their functional diversity is not completely understood. The main objective of the present study is to understand functional diversity of the lipocalins using a structure-based phylogenetic approach. The present study with 39 protein domains from the lipocalin superfamily suggests that the clusters of lipocalins obtained by structure-based phylogeny correspond well with the functional diversity. The detailed analysis on each of the clusters and sub-clusters reveals that the 39 lipocalin domains cluster based on their mode of ligand binding though the clustering was performed on the basis of gross domain structure. The outliers in the phylogenetic tree are often from single member families. Also structure-based phylogenetic approach has provided pointers to assign putative function for the domains of unknown function in lipocalin family. The approach employed in the present study can be used in the future for the functional identification of new lipocalin proteins and may be extended to other protein families where members show poor sequence similarity but high structural similarity.

Crystallographic studies of the extracytoplasmic function sigma factor sigma(J) from Mycobacterium tuberculosis

Mycobacterium tuberculosis has multiple sigma factors which enable the bacterium to reprogram its transcriptional machinery under diverse environmental conditions. sigma(J), an extracytoplasmic function sigma factor, is upregulated in late stationary phase cultures and during human macrophage infection. sigma(J) governs the cellular response to hydrogen peroxide-mediated oxidative stress. sigma(J) differs from other canonical sigma factors owing to the presence of a SnoaL_2 domain at the C-terminus. sigma(J) crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 133.85, c = 75.08 angstrom. Diffraction data were collected to 2.16 angstrom resolution on the BM14 beamline at the European Synchrotron Radiation Facility (ESRF).

Human action recognition in H.264/AVC compressed domain using meta-cognitive radial basis function network

In this paper, we propose a H.264/AVC compressed domain human action recognition system with projection based metacognitive learning classifier (PBL-McRBFN). The features are extracted from the quantization parameters and the motion vectors of the compressed video stream for a time window and used as input to the classifier. Since compressed domain analysis is done with noisy, sparse compression parameters, it is a huge challenge to achieve performance comparable to pixel domain analysis. On the positive side, compressed domain allows rapid analysis of videos compared to pixel level analysis. The classification results are analyzed for different values of Group of Pictures (GOP) parameter, time window including full videos. The functional relationship between the features and action labels are established using PBL-McRBFN with a cognitive and meta-cognitive component. The cognitive component is a radial basis function, while the meta-cognitive component employs self-regulation to achieve better performance in subject independent action recognition task. The proposed approach is faster and shows comparable performance with respect to the state-of-the-art pixel domain counterparts. It employs partial decoding, which rules out the complexity of full decoding, and minimizes computational load and memory usage. This results in reduced hardware utilization and increased speed of classification. The results are compared with two benchmark datasets and show more than 90% accuracy using the PBL-McRBFN. The performance for various GOP parameters and group of frames are obtained with twenty random trials and compared with other well-known classifiers in machine learning literature. (C) 2015 Elsevier B.V. All rights reserved.

Towards an exact factorization of the molecular wave function

An exact single-product factorisation of the molecular wave function for the timedependent Schrodinger equation is investigated by using an ansatz involving a phasefactor. By using the Frenkel variational method, we obtain the Schrodinger equations for the electronic and nuclear wave functions. The concept of a potential energy surface (PES) is retained by introducing a modified Hamiltonian as suggested earlier by Cederbaum. The parameter in the phase factor is chosen such that the equations of motion retain the physically appealing Born- Oppenheimer-like form, and is therefore unique.