Gap-Dependent Quasiparticle Dynamics and Coherent Acoustic Phonons in CaFe2As2 across Spin Density Wave Phase Transition

We report ultrafast quasiparticle (QP) dynamics and coherent acoustic phonons in undoped CaFe2As2 iron pnictide single crystals exhibiting spin-density wave (SDW) and concurrent structural phase transition at temperature T-SDW similar to 165K using femtosecond time-resolved pump-probe spectroscopy. The contributions in transient differential reflectivity arising from exponentially decaying QP relaxation and oscillatory coherent acoustic phonon mode show large variations in the vicinity of T-SDW. From the temperature-dependence of the QP recombination dynamics in the SDW phase, we evaluate a BCS-like temperature dependent charge gap with its zero-temperature value of similar to(1.6 perpendicular to 0.2)k(B)T(SDW), whereas, much above T-SDW, an electron-phonon coupling constant of similar to 0.13 has been estimated from the linear temperature-dependence of the QP relaxation time. The long-wavelength coherent acoustic phonons with typical time-period of similar to 100 ps have been analyzed in the light of propagating strain pulse model providing important results for the optical constants, sounds velocity and the elastic modulus of the crystal in the whole temperature range of 3 to 300 K.

Generation of extended light-sheets for single and multi-photon fluorescence microscopy

We theoretically propose and computationally demonstrate the generation of extended light-sheet for fluorescence microscopy. This is made possible by the introduction of a specially designed double-window spatial filter that allows the light to pass through the periphery and center of a cylindrical lens. When illuminated with a plane wave, the proposed filter results in an extended depth-of-focus along with side-lobes which are due to other interferences in the transverse focal plane. Computational studies show a maximum extension of light-sheet by 3.38 times for single photon excitation and 3.68 times for multiphoton excitation as compared to state-of-art single plane illumination microscopy system. This technique may facilitate the study of large biological specimens (such as Zebrafish embryo and tissue) with high spatial resolution and reduced photobleaching. (C) 2013 AIP Publishing LLC.

Exploration of deleterious single nucleotide polymorphisms in the components of human P bodies: An in silico approach

P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 60 human proteins have been reported to localize to P bodies. Several human SNPs contribute to complex diseases by altering the structure and function of the proteins. Also, SNPs alter various transcription factors binding, splicing and miRNA regulatory sites. Owing to the essential functions of P bodies in mRNA regulation, we explored computationally the functional significance of SNPs in 7 P body components such as XRN1, DCP2, EDC3, CPEB1, GEMIN5, STAU1 and TRIM71. Computational analyses of non-synonymous SNPs of these components was initiated using well utilized publicly available software programs such as the SIFT, followed by PolyPhen, PANTHER, MutPred, I-Mutant-2.0 and PhosSNP 1.0. Functional significance of noncoding SNPs in the regulatory regions were analysed using FastSNP. Utilizing miRSNP database, we explored the role of SNPs in the context that alters the miRNA binding sites in the above mentioned genes. Our in silico studies have identified various deleterious SNPs and this cataloguing is essential and gives first hand information for further analysis by in vitro and in vivo methods for a better understanding of maintenance, assembly and functional aspects of P bodies in both health and disease. (C) 2013 Elsevier B.V. All rights reserved.

Shape-function-relationship (SFR) framework for semantic interoperability of product model

The problem of semantic interoperability arises while integrating applications in different task domains across the product life cycle. A new shape-function-relationship (SFR) framework is proposed as a taxonomy based on which an ontology is developed. Ontology based on the SFR framework, that captures explicit definition of terminology and knowledge relationships in terms of shape, function and relationship descriptors, offers an attractive approach for solving semantic interoperability issue. Since all instances of terms are based on single taxonomy with a formal classification, mapping of terms requires a simple check on the attributes used in the classification. As a preliminary study, the framework is used to develop ontology of terms used in the aero-engine domain and the ontology is used to resolve the semantic interoperability problem in the integration of design and maintenance. Since the framework allows a single term to have multiple classifications, handling context dependent usage of terms becomes possible. Automating the classification of terms and establishing the completeness of the classification scheme are being addressed presently.

Synconset Waves and Chains: Spiking Onsets in Synchronous Populations Predict and Are Predicted by Network Structure

Synfire waves are propagating spike packets in synfire chains, which are feedforward chains embedded in random networks. Although synfire waves have proved to be effective quantification for network activity with clear relations to network structure, their utilities are largely limited to feedforward networks with low background activity. To overcome these shortcomings, we describe a novel generalisation of synfire waves, and define `synconset wave' as a cascade of first spikes within a synchronisation event. Synconset waves would occur in `synconset chains', which are feedforward chains embedded in possibly heavily recurrent networks with heavy background activity. We probed the utility of synconset waves using simulation of single compartment neuron network models with biophysically realistic conductances, and demonstrated that the spread of synconset waves directly follows from the network connectivity matrix and is modulated by top-down inputs and the resultant oscillations. Such synconset profiles lend intuitive insights into network organisation in terms of connection probabilities between various network regions rather than an adjacency matrix. To test this intuition, we develop a Bayesian likelihood function that quantifies the probability that an observed synfire wave was caused by a given network. Further, we demonstrate it's utility in the inverse problem of identifying the network that caused a given synfire wave. This method was effective even in highly subsampled networks where only a small subset of neurons were accessible, thus showing it's utility in experimental estimation of connectomes in real neuronal-networks. Together, we propose synconset chains/waves as an effective framework for understanding the impact of network structure on function, and as a step towards developing physiology-driven network identification methods. Finally, as synconset chains extend the utilities of synfire chains to arbitrary networks, we suggest utilities of our framework to several aspects of network physiology including cell assemblies, population codes, and oscillatory synchrony.

The Lovasz θ function, SVMs and finding large dense subgraphs

The Lovasz θ function of a graph, is a fundamental tool in combinatorial optimization and approximation algorithms. Computing θ involves solving a SDP and is extremely expensive even for moderately sized graphs. In this paper we establish that the Lovasz θ function is equivalent to a kernel learning problem related to one class SVM. This interesting connection opens up many opportunities bridging graph theoretic algorithms and machine learning. We show that there exist graphs, which we call SVM−θ graphs, on which the Lovasz θ function can be approximated well by a one-class SVM. This leads to a novel use of SVM techniques to solve algorithmic problems in large graphs e.g. identifying a planted clique of size Θ(n√) in a random graph G(n,12). A classic approach for this problem involves computing the θ function, however it is not scalable due to SDP computation. We show that the random graph with a planted clique is an example of SVM−θ graph, and as a consequence a SVM based approach easily identifies the clique in large graphs and is competitive with the state-of-the-art. Further, we introduce the notion of a ''common orthogonal labeling'' which extends the notion of a ''orthogonal labelling of a single graph (used in defining the θ function) to multiple graphs. The problem of finding the optimal common orthogonal labelling is cast as a Multiple Kernel Learning problem and is used to identify a large common dense region in multiple graphs. The proposed algorithm achieves an order of magnitude scalability compared to the state of the art.

Light transmission through and its complete stoppage in an ultra slow wave optical medium

Light wave transmission - its compression, amplification, and the optical energy storage in an ultra slow wave medium (USWM) is studied analytically. Our phenomenological treatment is based entirely on the continuity equation for the optical energy flux, and the well-known distribution-product property of Dirac delta-function. The results so obtained provide a clear understanding of some recent experiments on light transmission and its complete stoppage in an USWM.

pH sensing by single and multi-layer hydrogel coated Fiber Bragg Grating

In this paper we show a novel chemo-mechanical-optical sensing mechanism in single and multi-layer hydrogel coated Fiber Bragg Grating (FBG) and demonstrate specific application in pH activated processes. The sensing device is based on the ionizable monomers inside the hydrogel which reversibly dissociates as a function of the pH and consequently resulting in osmotic pressure difference between the gel and the solution. This pressure gradient causes the hydrogel to deform which in turn induces secondary strain on the FBG sensor resulting in shift in the Bragg wavelength. We also report on the sensitivity factor of single and multilayer hydrogel coated FBG at various different pH.

A Genetic Analysis of the Functional Interactions within Mycobacterium tuberculosis Single-Stranded DNA Binding Protein

Single-stranded DNA binding proteins (SSBs) are vital in all organisms. SSBs of Escherichia coli (EcoSSB) and Mycobacterium tuberculosis (MtuSSB) are homotetrameric. The N-terminal domains (NTD) of these SSBs (responsible for their tetramerization and DNA binding) are structurally well defined. However, their C-terminal domains (CTD) possess undefined structures. EcoSSB NTD consists of beta 1-beta 1'-beta 2-beta 3-alpha-beta 4-beta 45(1)-beta 45(2)-beta 5 secondary structure elements. MtuSSB NTD includes an additional beta-strand (beta 6) forming a novel hook-like structure. Recently, we observed that MtuSSB complemented an E. coli Delta ssb strain. However, a chimeric SSB (m beta 4-beta 5), wherein only the terminal part of NTD (beta 4-beta 5 region possessing L-45 loop) of EcoSSB was substituted with that from MtuSSB, failed to function in E. coli in spite of its normal DNA binding and oligomerization properties. Here, we designed new chimeras by transplanting selected regions of MtuSSB into EcoSSB to understand the functional significance of the various secondary structure elements within SSB. All chimeric SSBs formed homotetramers and showed normal DNA binding. The m beta 4-beta 6 construct obtained by substitution of the region downstream of beta 5 in m beta 4-beta 5 SSB with the corresponding region (beta 6) of MtuSSB complemented the E. coli strain indicating a functional interaction between the L-45 loop and the beta 6 strand of MtuSSB.

Frequency Domain Based Solution for Certain Class of Wave Equations: An exhaustive study of Numerical Solutions

The paper discusses the frequency domain based solution for a certain class of wave equations such as: a second order partial differential equation in one variable with constant and varying coefficients (Cantilever beam) and a coupled second order partial differential equation in two variables with constant and varying coefficients (Timoshenko beam). The exact solution of the Cantilever beam with uniform and varying cross-section and the Timoshenko beam with uniform cross-section is available. However, the exact solution for Timoshenko beam with varying cross-section is not available. Laplace spectral methods are used to solve these problems exactly in frequency domain. The numerical solution in frequency domain is done by discretisation in space by approximating the unknown function using spectral functions like Chebyshev polynomials, Legendre polynomials and also Normal polynomials. Different numerical methods such as Galerkin Method, Petrov- Galerkin method, Method of moments and Collocation method or the Pseudo-spectral method in frequency domain are studied and compared with the available exact solution. An approximate solution is also obtained for the Timoshenko beam with varying cross-section using Laplace Spectral Element Method (LSEM). The group speeds are computed exactly for the Cantilever beam and Timoshenko beam with uniform cross-section and is compared with the group speeds obtained numerically. The shear mode and the bending modes of the Timoshenko beam with uniform cross-section are separated numerically by applying a modulated pulse as the shear force and the corresponding group speeds for varying taper parameter in are obtained numerically by varying the frequency of the input pulse. An approximate expression for calculating group speeds corresponding to the shear mode and the bending mode, and also the cut-off frequency is obtained. Finally, we show that the cut-off frequency disappears for large in, for epsilon > 0 and increases for large in, for epsilon < 0.

Dynamic Site Characterization and Correlation of Shear Wave Velocity with Standard Penetration Test `N' Values for the City of Agartala, Tripura State, India

Seismic site characterization is the basic requirement for seismic microzonation and site response studies of an area. Site characterization helps to gauge the average dynamic properties of soil deposits and thus helps to evaluate the surface level response. This paper presents a seismic site characterization of Agartala city, the capital of Tripura state, in the northeast of India. Seismically, Agartala city is situated in the Bengal Basin zone which is classified as a highly active seismic zone, assigned by Indian seismic code BIS-1893, Indian Standard Criteria for Earthquake Resistant Design of Structures, Part-1 General Provisions and Buildings. According to the Bureau of Indian Standards, New Delhi (2002), it is the highest seismic level (zone-V) in the country. The city is very close to the Sylhet fault (Bangladesh) where two major earthquakes (M (w) > 7) have occurred in the past and affected severely this city and the whole of northeast India. In order to perform site response evaluation, a series of geophysical tests at 27 locations were conducted using the multichannel analysis of surface waves (MASW) technique, which is an advanced method for obtaining shear wave velocity (V (s)) profiles from in situ measurements. Similarly, standard penetration test (SPT-N) bore log data sets have been obtained from the Urban Development Department, Govt. of Tripura. In the collected data sets, out of 50 bore logs, 27 were selected which are close to the MASW test locations and used for further study. Both the data sets (V (s) profiles with depth and SPT-N bore log profiles) have been used to calculate the average shear wave velocity (V (s)30) and average SPT-N values for the upper 30 m depth of the subsurface soil profiles. These were used for site classification of the study area recommended by the National Earthquake Hazard Reduction Program (NEHRP) manual. The average V (s)30 and SPT-N classified the study area as seismic site class D and E categories, indicating that the city is susceptible to site effects and liquefaction. Further, the different data set combinations between V (s) and SPT-N (corrected and uncorrected) values have been used to develop site-specific correlation equations by statistical regression, as `V (s)' is a function of SPT-N value (corrected and uncorrected), considered with or without depth. However, after considering the data set pairs, a probabilistic approach has also been presented to develop a correlation using a quantile-quantile (Q-Q) plot. A comparison has also been made with the well known published correlations (for all soils) available in the literature. The present correlations closely agree with the other equations, but, comparatively, the correlation of shear wave velocity with the variation of depth and uncorrected SPT-N values provides a more suitable predicting model. Also the Q-Q plot agrees with all the other equations. In the absence of in situ measurements, the present correlations could be used to measure V (s) profiles of the study area for site response studies.

Spiral-wave dynamics in ionically realistic mathematical models for human ventricular tissue: the effects of periodic deformation

We carry out an extensive numerical study of the dynamics of spiral waves of electrical activation, in the presence of periodic deformation (PD) in two-dimensional simulation domains, in the biophysically realistic mathematical models of human ventricular tissue due to (a) ten-Tusscher and Panfilov (the TP06 model) and (b) ten-Tusscher, Noble, Noble, and Panfilov (the TNNPO4 model). We first consider simulations in cable-type domains, in which we calculate the conduction velocity theta and the wavelength lambda of a plane wave; we show that PD leads to a periodic, spatial modulation of theta and a temporally periodic modulation of lambda; both these modulations depend on the amplitude and frequency of the PD. We then examine three types of initial conditions for both TP06 and TNNPO4 models and show that the imposition of PD leads to a rich variety of spatiotemporal patterns in the transmembrane potential including states with a single rotating spiral (RS) wave, a spiral-turbulence (ST) state with a single meandering spiral, an ST state with multiple broken spirals, and a state SA in which all spirals are absorbed at the boundaries of our simulation domain. We find, for both TP06 and TNNPO4 models, that spiral-wave dynamics depends sensitively on the amplitude and frequency of PD and the initial condition. We examine how these different types of spiral-wave states can be eliminated in the presence of PD by the application of low-amplitude pulses by square- and rectangular-mesh suppression techniques. We suggest specific experiments that can test the results of our simulations.

Transverse Single Spin Asymmetries and Charmonium Production

We estimate transverse spin single spin asymmetry(TSSA) in the process e + p(up arrow) -> J/psi + X using color evaporation model of charmonium production. We take into account transverse momentum dependent(TMD) evolution of Sivers function and parton distribution function and show that the there is a reduction in the asymmetry as compared to our earlier estimates wherein the Q(2) - evolution was implemented only through DGLAP evolution of unpolarized gluon densities.

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.

A spectral element for wave propagation in honeycomb sandwich construction considering core flexibility

Spectral elements are found to be extremely resourceful to study the wave propagation characteristics of structures at high frequencies. Most of the aerospace structures use honeycomb sandwich constructions. The existing spectral elements use single layer theories for a sandwich construction wherein the two face sheets vibrate together and this model is sufficient for low frequency excitations. At high frequencies, the two face sheets vibrate independently. The Extended Higher order SAndwich Plate theory (EHSaPT) is suitable for representing the independent motion of the face sheets. A 1D spectral element based on EHSaPT is developed in this work. The wave number and the wave speed characteristics are obtained using the developed spectral element. It is shown that the developed spectral element is capable of representing independent wave motions of the face sheets. The propagation speeds of a high frequency modulated pulse in the face sheets and the core of a honeycomb sandwich are demonstrated. Responses of a typical honeycomb sandwich beam to high frequency shock loads are obtained using the developed spectral element and the response match very well with the finite element results. It is shown that the developed spectral element is able to represent the flexibility of the core resulting into independent wave motions in the face sheets, for which a finite element method needs huge degrees of freedom. (C) 2015 Elsevier Ltd. All rights reserved.