INDUCTION OF FOLDED STRUCTURES IN DESIGNED PEPTIDES USING CONFORMATIONALLY CONSTRAINED RESIDUES

Folding into compact globular structures, with well-defined modules of secondary structure, appears to be a characteristic of long polypeptide chains, with a specific patterning of coded amino acid residues along the length of sequence. Cooperative hydrogen bond driven secondary structure formation and solvent forces, which contribute favorably to the entropy of folding, by promoting compaction of the polymeric chain, have long been discussed as major determinants of the folding process. First principles design approaches, which use non-coded amino acids, employ an alternative structure directing strategy, by using amino acid residues which exhibit a strong conformational bias for specific regions of the Ramachandran map. This overview of ongoing studies in the authors' laboratory, attempts to explore the use of conformationally restricted amino acid residues in the design of peptides with well-defined secondary structures. Short peptides composed of 20 genetically coded amino acids usually exist in solution as an ensemble of equilibrating conformations. Apolar peptide sequences, which are readily soluble in organic solvents like chloroform and methanol, facilitate formation of structures which are predominately driven by intramolecular hydrogen bond formation. The choice of sequences containing residues with a limited range of conformational choices strongly favors formation of local turn structures, stabilized by short range intramolecular hydrogen bonds. Two residue beta-turns can nucleate either helical or hairpin folding, depending on the precise conformation of the turn segment Restriction of the conformational space available to amino acid residues is easily achieved by introduction of an additional alkyl group at the C alpha carbon atom or by side chain backbone cyclization, as in proline. Studies of synthetic sequences incorporating two prototype residues alpha-aminoisobutyric acid (Aib) and D-proline (DPro) illustrate the utility of the strategy in construction of helices and hairpins. Extensions to the design of conformationally switchable sequences and structurally defined hybrid peptides containing backbone homologated residues are also surveyed.

CuIn1-xAlxSe2 Solar Cells Fabricated on the Flexible Substrates by CoSputtering and Modified Selenization

CuIn1-xAlxSe2 (CIAS) thin films were grown on the flexible stainless steel substrates, by de co-sputtering from the elemental cathodes. CuInAl alloyed precursor films were selenized both by noble gas assisted Se vapor transport and vacuum evaporation of Se. X-ray diffraction, scanning electron microscopy and UV-visible absorption spectroscopy were used to characterize the selenized films The composition (x=Al/Al+In) with 0 <= x <= 0.65 was varied by substituting Al with indium in CuInSe2. Lattice parameters, average crystallite sizes and compact density of the films compared to CuInSe2, decreased and (112) peak shifted to higher Bragg's angle, with Al incorporation. Cells were fabricated with the device structure SS/Mo/CIAS/CdS/iZno-AZO/Al. Best cell showed the efficiency of 6.8%, with x=0.13, Eg=1.17 eV, fill factor 45.04, short circuit current density J 30 mA/cm(2).

Comparison of CO2 and steam in transcritical Rankine cycles for concentrated solar power

High temperature, high pressure transcritical condensing CO2 cycle (TC-CO2) is compared with transcritical steam (TC-steam) cycle. Performance indicators such as thermal efficiency, volumetric flow rates and entropy generation are used to analyze the power cycle wherein, irreversibilities in turbo-machinery and heat exchangers are taken into account. Although, both cycles yield comparable thermal efficiencies under identical operating conditions, TC-CO2 plant is significantly compact compared to a TC-steam plant. Large specific volume of steam is responsible for a bulky system. It is also found that the performance of a TC-CO2 cycle is less sensitive to source temperature variations, which is an important requirement of a solar thermal system. In addition, issues like wet expansion in turbine and vacuum in condenser are absent in case of a TC-CO2 cycle. External heat addition to working fluid is assumed to take place through a heat transfer fluid (HTF) which receives heat from a solar receiver. A TC-CO2 system receives heat though a single HTF loop, whereas, for TC-steam cycle two HTF loops in series are proposed to avoid high temperature differential between the steam and HTF. (C) 2013 P. Garg. Published by Elsevier Ltd.

Nonlinear analysis of a thin pre-twisted and delaminated anisotropic strip

The present work is aimed at the development of an efficient mathematical model to assess the degradation in the stiffness properties of an anisotropic strip due to delamination. In particular, the motive is to capture those nonlinear effects in a strip that arise due to the geometry of the structure, in the presence of delamination. The variational asymptotic method (VAM) is used as a mathematical tool to simplify the original 3D problem to a 1D problem. Further simplification is achieved by modeling the delaminated structure by a sublaminate approach. By VAM, a 2D nonlinear sectional analysis is carried out to determine compact expression for the stiffness terms. The stiffness terms, both linear and nonlinear, are derived as functions of delamination length and location in closed form. In general, the results from the analysis include fully coupled nonlinear 1D stiffness coefficients, 3D strain field, 3D stress field, and in-plane and warping fields. In this work, the utility of the model is demonstrated for a static case, and its capability to capture the trapeze effect in the presence of delamination is investigated and compared with results available in the literature.

A Short-Channel Common Double-Gate MOSFET Model Adapted to Gate Oxide Thickness Asymmetry

Existing compact models for common double-gate (CDG) MOSFETs are based on the fundamental assumption of having symmetric gate oxide thickness. In this paper, we demonstrate that using the unique quasi-linear relationship between the surface potentials, it is possible to develop compact model for CDG-MOSFETs without such approximation while preserving the mathematical complexity at the same level of the existing models. In the proposed model, the surface potential relationship is used to include the drain-induced barrier lowering, channel length modulation, velocity saturation, and quantum mechanical effect in the long-channel model and good agreement is observed with the technology computer aided design simulation results.

A general methodology for calculating mixed mode stress intensity factors and fracture toughness of solder joints with interfacial cracks

Solder joints in electronic packages undergo thermo-mechanical cycling, resulting in nucleation of micro-cracks, especially at the solder/bond-pad interface, which may lead to fracture of the joints. The fracture toughness of a solder joint depends on material properties, process conditions and service history, as well as strain rate and mode-mixity. This paper reports on a methodology for determining the mixed-mode fracture toughness of solder joints with an interfacial starter-crack, using a modified compact mixed mode (CMM) specimen containing an adhesive joint. Expressions for stress intensity factor (K) and strain energy release rate (G) are developed, using a combination of experiments and finite element (FE) analysis. In this methodology, crack length dependent geometry factors to convert for the modified CMM sample are first obtained via the crack-tip opening displacement (CTOD)-based linear extrapolation method to calculate the under far-field mode I and II conditions (f(1a) and f(2a)), (ii) generation of a master-plot to determine a(c), and (iii) computation of K and G to analyze the fracture behavior of joints. The developed methodology was verified using J-integral calculations, and was also used to calculate experimental fracture toughness values of a few lead-free solder-Cu joints. (C) 2014 Elsevier Ltd. All rights reserved.

Direct regulation of topoisomerase activity by a nucleoid-associated protein

The topological homeostasis of bacterial chromosomes is maintained by the balance between compaction and the topological organization of genomes. Two classes of proteins play major roles in chromosome organization: the nucleoid-associated proteins (NAPs) and topoisomerases. The NAPs bind DNA to compact the chromosome, whereas topoisomerases catalytically remove or introduce supercoils into the genome. We demonstrate that HU, a major NAP of Mycobacterium tuberculosis specifically stimulates the DNA relaxation ability of mycobacterial topoisomerase I (TopoI) at lower concentrations but interferes at higher concentrations. A direct physical interaction between M. tuberculosis HU (MtHU) and TopoI is necessary for enhancing enzyme activity both in vitro and in vivo. The interaction is between the amino terminal domain of MtHU and the carboxyl terminal domain of TopoI. Binding of MtHU did not affect the two catalytic trans-esterification steps but enhanced the DNA strand passage, requisite for the completion of DNA relaxation, a new mechanism for the regulation of topoisomerase activity. An interaction-deficient mutant of MtHU was compromised in enhancing the strand passage activity. The species-specific physical and functional cooperation between MtHU and TopoI may be the key to achieve the DNA relaxation levels needed to maintain the optimal superhelical density of mycobacterial genomes.

Capturability Analysis of a 3-D Retro-PN Guidance Law for Higher Speed Nonmaneuvering Targets

This brief presents the capturability analysis of a 3-D Retro-proportional navigation (Retro-PN) guidance law, which uses a negative navigation constant (as against the usual positive one), for intercepting targets having higher speeds than interceptors. This modification makes it possible to achieve collision conditions that were inaccessible to the standard PN law. A modified polar coordinate system, that makes the model more compact, is used in this brief for capturability analysis. In addition to the ratio of the target to interceptor speeds, the directional cosines of the interceptor, and target velocity vectors play a crucial role in the capturability. The existence of nontrivial capture zone of the Retro-PN guidance law and necessary and sufficient conditions, for capturing the target in finite time, are presented. A sufficient condition on the navigation constant is derived to ensure finiteness of the line-of-sight turn rate. The results are more extensive than those available for 2-D engagements, which can be obtained as special cases of this brief. Simulation results are given to support the analytical results.

Reduced graphene oxide-titania based platform for label-free biosensor

A label-free biosensor has been fabricated using a reduced graphene oxide (RGO) and anatase titania (ant-TiO2) nanocomposite, electrophoretically deposited onto an indium tin oxide coated glass substrate. The RGO-ant-TiO2 nanocomposite has been functionalized with protein (horseradish peroxidase) conjugated antibodies for the specific recognition and detection of Vibrio cholerae. The presence of Ab-Vc on the RGO-ant-TiO2 nanocomposite has been confirmed using electron microscopy, Fourier transform infrared spectroscopy and electrochemical techniques. Electrochemical studies relating to the fabricated Ab-Vc/RGO-ant-TiO2/ITO immunoelectrode have been conducted to investigate the binding kinetics. This immunosensor exhibits improved biosensing properties in the detection of Vibrio cholerae, with a sensitivity of 18.17 x 10(6) F mol(-1) L-1 m(-2) in the detection range of 0.12-5.4 nmol L-1, and a low detection limit of 0.12 nmol L-1. The association (k(a)), dissociation (k(d)) and equilibrium rate constants have been estimated to be 0.07 nM, 0.002 nM and 0.41 nM, respectively. This Ab-Vc/RGO-ant-TiO2/ITO immunoelectrode could be a suitable platform for the development of compact diagnostic devices.

Monopoles, Dirac operator, and index theory for fuzzy SU(3) / (U(1) x U(1))

The intersection of the ten-dimensional fuzzy conifold Y-F(10) with S-F(5) x S-F(5) is the compact eight-dimensional fuzzy space X-F(8). We show that X-F(8) is (the analogue of) a principal U(1) x U(1) bundle over fuzzy SU(3) / U(1) x U(1)) ( M-F(6)). We construct M-F(6) using the Gell-Mann matrices by adapting Schwinger's construction. The space M-F(6) is of relevance in higher dimensional quantum Hall effect and matrix models of D-branes. Further we show that the sections of the monopole bundle can be expressed in the basis of SU(3) eigenvectors. We construct the Dirac operator on M-F(6) from the Ginsparg-Wilson algebra on this space. Finally, we show that the index of the Dirac operator correctly reproduces the known results in the continuum.

Interpreting the upper level structure of the Madden-Julian oscillation

The nonlinear response of a spherical shallow water model to an imposed heat source in the presence of realistic zonal mean zonal winds is investigated numerically. The solutions exhibit elongated, meridionally tilted ridges and troughs indicative of a poleward dispersion of wave activity. As the speed of the jets is increased, the equatorial Kelvin wave is unaffected but the global Rossby wave train coalesces to form a compact, amplified quadrupole structure that bears a striking resemblance to the observed upper level structure of the Madden-Julian oscillation. In the presence of strong subtropical westerly jets, the advection of planetary vorticity by the meridional flow and relative vorticity by the zonally averaged background flow conspire to create the distinctive quadrupole configuration of flanking Rossby waves.

Sparse coding based VLAD for efficient image retrieval

Representing images and videos in the form of compact codes has emerged as an important research interest in the vision community, in the context of web scale image/video search. Recently proposed Vector of Locally Aggregated Descriptors (VLAD), has been shown to outperform the existing retrieval techniques, while giving a desired compact representation. VLAD aggregates the local features of an image in the feature space. In this paper, we propose to represent the local features extracted from an image, as sparse codes over an over-complete dictionary, which is obtained by K-SVD based dictionary training algorithm. The proposed VLAD aggregates the residuals in the space of these sparse codes, to obtain a compact representation for the image. Experiments are performed over the `Holidays' database using SIFT features. The performance of the proposed method is compared with the original VLAD. The 4% increment in the mean average precision (mAP) indicates the better retrieval performance of the proposed sparse coding based VLAD.

On the curvature ODE associated to the Ricci flow

In the vector space of algebraic curvature operators we study the reaction ODE which is associated to the evolution equation of the Riemann curvature operator along the Ricci flow. More precisely, we give a partial classification of the zeros of this ODE up to suitable normalization and analyze the stability of a special class of zeros of the same. In particular, we show that the ODE is unstable near the curvature operators of the Riemannian product spaces where is an Einstein (locally) symmetric space of compact type and not a spherical space form when .

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).

A gap theorem for Ricci-flat 4-manifolds

Let (M, g) be a compact Ricci-fiat 4-manifold. For p is an element of M let K-max(P) (respectively K-min(p)) denote the maximum (respectively the minimum) of sectional curvatures at p. We prove that if K-max(p) <= -cK(min)(P) for all p is an element of M, for some constant c with 0 <= c < 2+root 6/4 then (M, g) is fiat. We prove a similar result for compact Ricci-flat Kahler surfaces. Let (M, g) be such a surface and for p is an element of M let H-max(p) (respectively H-min(P)) denote the maximum (respectively the minimum) of holomorphic sectional curvatures at p. If H-max(P) <= -cH(min)(P) for all p is an element of M, for some constant c with 0 <= c < 1+root 3/2, then (M, g) is flat. (C) 2015 Elsevier B.V. All rights reserved.