Domain size correlated magnetic properties and electrical impedance of size dependent nickel ferrite nanoparticles

We report here the investigations on the size dependent variation of magnetic properties of nickel ferrite nanoparticles. Nickel ferrite nanoparticles of different sizes (14 to 22 nm) were prepared by the sol-gel route at different annealing temperatures. They are characterized by TGA-DTA, XRD, SEM, TEM and Raman spectroscopy techniques for the confirmation of the temperature of phase formation, thermal stability, crystallinity, morphology and structural status of the nickel ferrite nanoparticles. The magnetization studies revealed that the saturation magnetization (M-s), retentivity (M-r) increase, while coercivity (H-c) and anisotropy (K-eff) decrease as the particle size increases. The observed value of M-s is found to be relatively higher for a particle size of 22 nm. In addition, we have estimated the magnetic domain size using magnetic data and correlated to the average particle size. The calculated magnetic domain size is closely matching with the particle size estimated from XRD. Impedance spectroscopy was employed to study the samples in an equivalent circuit to understand their transport phenomena. It shows that nickel ferrite nanoparticles exhibit a non-Debye behavior with increasing particle size due to the influence of increasing disorders, surface effects, grain size and grain boundaries, etc. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Faster computation of the Karhunen-Loeve expansion using its domain independence property

The goal of this work is to reduce the cost of computing the coefficients in the Karhunen-Loeve (KL) expansion. The KL expansion serves as a useful and efficient tool for discretizing second-order stochastic processes with known covariance function. Its applications in engineering mechanics include discretizing random field models for elastic moduli, fluid properties, and structural response. The main computational cost of finding the coefficients of this expansion arises from numerically solving an integral eigenvalue problem with the covariance function as the integration kernel. Mathematically this is a homogeneous Fredholm equation of second type. One widely used method for solving this integral eigenvalue problem is to use finite element (FE) bases for discretizing the eigenfunctions, followed by a Galerkin projection. This method is computationally expensive. In the current work it is first shown that the shape of the physical domain in a random field does not affect the realizations of the field estimated using KL expansion, although the individual KL terms are affected. Based on this domain independence property, a numerical integration based scheme accompanied by a modification of the domain, is proposed. In addition to presenting mathematical arguments to establish the domain independence, numerical studies are also conducted to demonstrate and test the proposed method. Numerically it is demonstrated that compared to the Galerkin method the computational speed gain in the proposed method is of three to four orders of magnitude for a two dimensional example, and of one to two orders of magnitude for a three dimensional example, while retaining the same level of accuracy. It is also shown that for separable covariance kernels a further cost reduction of three to four orders of magnitude can be achieved. Both normal and lognormal fields are considered in the numerical studies. (c) 2014 Elsevier B.V. All rights reserved.

Crowd Flow Segmentation based on Motion Vectors in H.264 Compressed Domain

In this work, we have explored the prospect of segmenting crowd flow in H. 264 compressed videos by merely using motion vectors. The motion vectors are extracted by partially decoding the corresponding video sequence in the H. 264 compressed domain. The region of interest ie., crowd flow region is extracted and the motion vectors that spans the region of interest is preprocessed and a collective representation of the motion vectors for the entire video is obtained. The obtained motion vectors for the corresponding video is then clustered by using EM algorithm. Finally, the clusters which converges to a single flow are merged together based on the bhattacharya distance measure between the histogram of the of the orientation of the motion vectors at the boundaries of the clusters. We had implemented our proposed approach on the complex crowd flow dataset provided by 1] and compared our results by using Jaccard measure. Since we are performing crowd flow segmentation in the compressed domain using only motion vectors, our proposed approach performs much faster compared to other pixel domain counterparts still retaining better accuracy.

Membrane-based deformable mirror: intrinsic aberrations and alignment issues

A deformable mirror (DM) is an important component of an adaptive optics system. It is known that an on-axis spherical/parabolic optical component, placed at an angle to the incident beam introduces defocus as well as astigmatism in the image plane. Although the former can be compensated by changing the focal plane position, the latter cannot be removed by mere optical realignment. Since the DM is to be used to compensate a turbulence-induced curvature term in addition to other aberrations, it is necessary to determine the aberrations induced by such (curved DM surface) an optical element when placed at an angle (other than 0 deg) of incidence in the optical path. To this effect, we estimate to a first order the aberrations introduced by a DM as a function of the incidence angle and deformation of the DM surface. We record images using a simple setup in which the incident beam is reflected by a 37 channel micro-machined membrane deformable mirror for various angles of incidence. It is observed that astigmatism is a dominant aberration, which was determined by measuring the difference between the tangential and sagittal focal planes. We justify our results on the basis of theoretical simulations and discuss the feasibility of using such a system for adaptive optics considering a trade-off between wavefront correction and astigmatism due to deformation. (C) 2015 Optical Society of America

Conservation Properties of the Trapezoidal Rule in Linear Time Domain Analysis of Acoustics and Structures

The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and energy in the case of undamped linear elastodynamics problems, and an ``energy-like measure'' in the case of undamped acoustic problems. These conservation properties, thus, provide a rational basis for using this algorithm. In linear elastodynamics problems, variants of the trapezoidal rule that incorporate ``high-frequency'' dissipation are often used, since the higher frequencies, which are not approximated properly by the standard displacement-based approach, often result in unphysical behavior. Instead of modifying the trapezoidal algorithm, we propose using a hybrid finite element framework for constructing the stiffness matrix. Hybrid finite elements, which are based on a two-field variational formulation involving displacement and stresses, are known to approximate the eigenvalues much more accurately than the standard displacement-based approach, thereby either bypassing or reducing the need for high-frequency dissipation. We show this by means of several examples, where we compare the numerical solutions obtained using the displacement-based and hybrid approaches against analytical solutions.

Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance

In many organisms ``Universal Stress Proteins'' CUSPS) are induced in response to a variety of environmental stresses. Here we report the structures of two USPs, YnaF and YdaA from Salmonella typhimurium determined at 1.8 angstrom and 2.4 angstrom resolutions, respectively. YnaF consists of a single USP domain and forms a tetrameric organization stabilized by interactions mediated through chloride ions. YdaA is a larger protein consisting of two tandem USP domains. Two protomers of YdaA associate to form a structure similar to the YnaF tetramer. YdaA showed ATPase activity and an ATP binding motif G-2X-G-9X-G(S/T/N) was found in its C-terminal domain. The residues corresponding to this motif were not conserved in YnaF although YnaF could bind ATP. However, unlike YdaA, YnaF did not hydrolyse ATP in vitro. Disruption of interactions mediated through chloride ions by selected mutations converted YnaF into an ATPase. Residues that might be important for ATP hydrolysis could be identified by comparing the active sites of native and mutant structures. Only the C-terminal domain of YdaA appears to be involved in ATP hydrolysis. The structurally similar N-terminal domain was found to bind a zinc ion near the segment equivalent to the phosphate binding loop of the C-terminal domain. Mass spectrometric analysis showed that YdaA might bind a ligand of approximate molecular weight 800 daltons. Structural comparisons suggest that the ligand, probably related to an intermediate in lipid A biosynthesis, might bind at a site close to the zinc ion. Therefore, the N-terminal domain of YdaA binds zinc and might play a role in lipid metabolism. Thus, USPs appear to perform several distinct functions such as ATP hydrolysis, altering membrane properties and chloride sensing. (C) 2015 Elsevier Inc. All rights reserved.

Modification of crosslinked chitosan membrane using NaY zeolite for pervaporation separation of water-isopropanol mixtures

The blocked diisocyanate crosslinked chitosan membrane was modified by incorporating different mass% of NaY zeolite. The physico-chemical properties of resulting composite membranes were studied using Fourier transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (WAXD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). The mechanical properties of the membranes were studied using universal testing machine (UTM). After measuring the equilibrium swelling, membranes were subjected to pervaporation for separation of water-isopropanol mixtures. Both flux and selectivity were increased with increasing NaY zeolite content in the membranes. The membrane containing 40 mass% of NaY zeolite exhibited the highest separation selectivity of 11,241 with a flux of 11.37 x 10(-2) kg/m(2) h for 10 mass% of water in the feed. The total flux and flux of water are almost overlapping each other, suggesting that these membranes could be effectively used to break the azeotropic point of water-isopropanol mixture. From the temperature dependent diffusion and permeation values, the Arrhenius activation parameters were estimated. All the composite membranes exhibited lower activation energy compared to crosslinked membrane, indicating that the permeants require less energy during the process because of molecular sieving action attributed to the presence of sodalite and super cages in the framework of Nay zeolite. The Henry's mode of sorption dominates the process, giving an endothermic contribution. (C) 2014 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.

Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Ser/Thr and Tyr protein kinases orchestrate many signalling pathways and hence loss in this balance leads to many disease phenotypes. Due to their high abundance, diversity and importance, efforts have been made in the past to classify kinases and annotate their functions at both gross and fine levels. These kinases are conventionally classified into subfamilies based on the sequences of catalytic domains. Usually the domain architecture of a full-length kinase is consistent with the subfamily classification made based on the sequence of kinase domain. Important contributions of modular domains to the overall function of the kinase are well known. Recently occurrence of two kinds of outlier kinases-''Hybrid'' and ``Rogue'' has been reported. These show considerable deviations in their domain architectures from the typical domain architecture known for the classical kinase subfamilies. This article provides an overview of the different subfamilies of human kinases and the role of non-kinase domains in functions and diseases. Importantly this article provides analysis of hybrid and rogue kinases encoded in the human genome and highlights their conservation in closely related primate species. These kinases are examples of elegant rewiring to bring about subtle functional differences compared to canonical variants.

Response to ``Comment on `Frequency-domain stimulated and spontaneous light emission signals at molecular junctions''' J. Chem. Phys. 142, 137101 (2015)]

In a recent work [U. Harbola, B. K. Agrawalla, and S. Mukamel, J. Chem. Phys. 141, 074107 (2014)], we have presented a superoperator (Liouville space) diagrammatic formulation of spontaneous and stimulated optical signals from current-carrying molecular junctions. We computed the diagrams that contribute to the spontaneous light emission SLE (fluorescence and Raman) signal using a diagrammatic method which clearly distinguishes between the Raman and the fluorescence contributions. We pointed out some discrepancies with the work of Galperin, Ratner and Nitzan (GRN) [M. Galperin, M. A. Ratner and, A. Nitzan, J. Chem. Phys. 130, 144109 (2009)]. In their response [M. Galperin, M. A. Ratner and A. Nitzan, “Comment on‘ Frequency-domain stimulated and spontaneous light emission signals at molecular junctions’” [J. Chem. Phys. 141, 074107 (2014)], J. Chem. Phys. 142, 137101 (2015)] to our work, GRN have argued that there are no differences in the choice of Raman diagrams in both works. Here we reply to their points and show where the differences exist.

Cyclic nucleotide binding and structural changes in the isolated GAF domain of Anabaena adenylyl cyclase, CyaB2

GAF domains are a large family of regulatory domains, and a subset are found associated with enzymes involved in cyclic nucleotide (cNMP) metabolism such as adenylyl cyclases and phosphodiesterases. CyaB2, an adenylyl cyclase from Anabaena, contains two GAF domains in tandem at the N-terminus and an adenylyl cyclase domain at the C-terminus. Cyclic AMP, but not cGMP, binding to the GAF domains of CyaB2 increases the activity of the cyclase domain leading to enhanced synthesis of cAMP. Here we show that the isolated GAFb domain of CyaB2 can bind both cAMP and cGMP, and enhanced specificity for cAMP is observed only when both the GAFa and the GAFb domains are present in tandem(GAFab domain). In silico docking and mutational analysis identified distinct residues important for interaction with either cAMP or cGMP in the GAFb domain. Structural changes associated with ligand binding to the GAF domains could not be detected by bioluminescence resonance energy transfer (BRET) experiments. However, amide hydrogen-deuterium exchange mass spectrometry (HDXMS) experiments provided insights into the structural basis for cAMP-induced allosteric regulation of the GAF domains, and differences in the changes induced by cAMP and cGMP binding to the GAF domain. Thus, our findings could allow the development of molecules that modulate the allosteric regulation by GAF domains present in pharmacologically relevant proteins.

Ni Nano-particle Encapsulated in Hollow Carbon Sphere Electrocatalyst in Polymer Electrolyte Membrane Water Electrolyzer

The present study evaluates the synthesis by solvo-thermal method and electrocatalytic activity of nickel nano-particles encapsulated in hollow carbon sphere, in hydrogen and oxygen evolution reaction in PEM water electrolyzer. The XRD patterns have ascertained the formation of nickel metal with different planes in face centered cubic (fcc) and hexagonal closed pack (hcp) form. SEM and TEM images have confirmed the nickel nano-particles with diameter of 10-50 nm inside the 0.2 mu m sized hollow carbon spheres. The BET surface area values gradually decreased with greater encapsulation of nickel; although the electrochemical active surface area (ECSA) values have been calculated as quite higher. It confirms the well dispersion of nickel in the materials and induces their electrocatalytic performance through the active surface sites. The cyclic voltammetric studies have evaluated hydrogen desorption peaks as five times more intense in nickel encapsulated materials, in comparison to the pure hollow carbon spheres. The anodic peak current density value has reached the highest level of 1.9 A cm(-2) for HCSNi10, which gradually decreases with lesser amount of nickel in the electrocatalysts. These electrocatalysts have been proved electrochemically stable during their usage for 48 h long duration under potentiostatic condition. (C) 2015 Elsevier Ltd. All rights reserved.

Functional characterization of heat-shock protein 90 from Oryza sativa and crystal structure of its N-terminal domain

Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. It plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. In plants, Hsp90s are required for normal plant growth and development. Hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. Although there are several studies elucidating the physiological role of Hsp90s in plants, their molecular mechanism of action is still unclear. In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 angstrom resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 from Dictyostelium discoideum, which shares 70% sequence identity with OsHsp90-NTD. This is the second reported structure of a domain of Hsp90 from a plant source.

The nuclease activities of both the Smr domain and an additional LDLK motif are required for an efficient anti-recombination function of Helicobacter pyloriMutS2

Helicobacter pylori, a human pathogen, is a naturally and constitutively competent bacteria, displaying a high rate of intergenomic recombination. While recombination events are essential for evolution and adaptation of H.pylori to dynamic gastric niches and new hosts, such events should be regulated tightly to maintain genomic integrity. Here, we analyze the role of the nuclease activity of MutS2, a protein that limits recombination during transformation in H.pylori. In previously studied MutS2 proteins, the C-terminal Smr domain was mapped as the region responsible for its nuclease activity. We report here that deletion of Smr domain does not completely abolish the nuclease activity of HpMutS2. Using bioinformatics analysis and mutagenesis, we identified an additional and novel nuclease motif (LDLK) at the N-terminus of HpMutS2 unique to Helicobacter and related epsilon-proteobacterial species. A single point mutation (D30A) in the LDLK motif and the deletion of Smr domain resulted in approximate to 5-10-fold loss of DNA cleavage ability of HpMutS2. Interestingly, the mutant forms of HpMutS2 wherein the LDLK motif was mutated or the Smr domain was deleted were unable to complement the hyper-recombination phenotype of a mutS2(-) strain, suggesting that both nuclease sites are indispensable for an efficient anti-recombinase activity of HpMutS2.

Human Action Recognition in Compressed Domain using PBL-McRBFN Approach

Large variations in human actions lead to major challenges in computer vision research. Several algorithms are designed to solve the challenges. Algorithms that stand apart, help in solving the challenge in addition to performing faster and efficient manner. In this paper, we propose a human cognition inspired projection based learning for person-independent human action recognition in the H.264/AVC compressed domain and demonstrate a PBL-McRBEN based approach to help take the machine learning algorithms to the next level. Here, we use gradient image based feature extraction process where the motion vectors and quantization parameters are extracted and these are studied temporally to form several Group of Pictures (GoP). The GoP is then considered individually for two different bench mark data sets and the results are classified using person independent human action recognition. The functional relationship is studied using Projection Based Learning algorithm of the Meta-cognitive Radial Basis Function Network (PBL-McRBFN) which has a cognitive and meta-cognitive component. The cognitive component is a radial basis function network while the Meta-Cognitive Component(MCC) employs self regulation. The McC emulates human cognition like learning to achieve better performance. Performance of the proposed approach can handle sparse information in compressed video domain and provides more accuracy than other pixel domain counterparts. Performance of the feature extraction process achieved more than 90% accuracy using the PTIL-McRBFN which catalyzes the speed of the proposed high speed action recognition algorithm. We have conducted twenty random trials to find the performance in GoP. The results are also compared with other well known classifiers in machine learning literature.