Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Study of thermal relaxation of Poly (HDDA-co-MMA) by temperature modulated DSC and dielectric spectroscopy

The thermal transitions in the copolymer of 1,6-hexanediol diacrylate (HDDA) and methyl methacrylate (MMA) was investigated to understand its use in microstereolithography. The glass transition temperature and the effect of interaction on this transition process was investigated by means of temperature modulated differential scanning calorimetry (TMDSC). The heat capacities were determined and PHDDA rich phases showed lower heat capacity than PMMA rich phases. The frequency dependence of glass transitions were studied by varying the modulation period of TMDSC and confirmed by dielectric relaxation spectroscopy. Vogel Fulcher Tammann Hesse (VFTH) parameters of homo and copolymers have also been reported.

Accelerated multistress aging of polymer nanocomposites and its condition monitoring

In recent years, the time dependant maintenance of expensive high voltage power equipments is getting replaced by condition based maintenance so as to detect apriori an impending failure of the equipment. For condition based maintenance, most monitoring systems concentrate on the electrical quantities such as measurement and evaluation of partial discharges, tan delta, tip-up test, dielectric strength, insulation resistance, polarization and depolarization current. However, in the case of equipments being developed with novel nanodielectric insulating materials, the variation in these parameters before an impending failure is not available. Hence in this work, accelerated electrothermal aging studies have been conducted on unfilled epoxy as well as epoxy nanocomposite samples of 5 wt% filler loading, and the tan d values were continuously monitored to obtain the condition of the samples under study. It was observed that those samples whose tan d increased at a rapid rate failed first.

Influence of operational and geometrical parameters on the performance of twin thermoacoustic prime mover

Thermoacoustics is the interaction between heat and sound, which are useful in designing heat engines and heat pumps. Research in the field of thermoacoustics focuses on the demand to improve the performance which is achieved by altering operational, geometrical and fluid parameters. The present study deals with improving the performance of twin thermoacoustic prime mover, which has gained the significant importance in the recent years for the production of high amplitude sound waves. The performance of twin thermoacoustic prime mover is evaluated in terms of onset temperature difference, resonance frequency and pressure amplitude of the acoustic waves by varying the resonator length and charge pressures of fluid medium nitrogen. DeltaEC, the free simulation software developed by LANL, USA is employed in the present study to simulate the performance of twin thermoacoustic prime mover. Experimental and simulated results are compared and the deviation is found to be within 10%.

Role of silica nanoparticles in conductivity enhancement of nanocomposite solid polymer electrolytes: (PEG(x) NaBr): ySiO(2)

Nanocomposite solid polymer electrolytes (NCSPEs) with conducting species other than Li ions are being investigated for solid-state battery applications. Pristine solid polymer electrolytes (SPEs) do not show ionic conductivity suitable for batteries. Addition of inert fillers to SPEs is known to enhance the ionic conductivity. In this paper, we present the role of silica nanoparticles in enhancing the ionic conductivity in NCSPEs with sodium as conducting species. Sodium bromide is complexed with the host polyethylene glycol polymer by solution cast method and silica nanoparticles (SiO2, average particle size 7 nm) are incorporated into the complex in small amounts. The composites are characterized by powder XRD and IR spectroscopy. Conductivity measurements are undertaken as a function of concentration of salt and also as a function of temperature using impedance spectroscopy. Addition of silica nanoparticles shows an enhancement in conductivity by 1-2 orders of magnitude. The results are discussed in terms of interaction of nanoparticles with the nonconducting anions.

MODELING AND SIMULATION OF HYDRODYNAMIC INTERACTION OF DNA IN A MICRO-FLUIDIC CHANNEL

The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young's modulus, Poisson's ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.

Glycidyl azide polymer crosslinked through triazoles by click chemistry: curing, mechanical and thermal properties

Glycidyl azide polymer (GAP) was cured through click chemistry by reaction of the azide group with bispropargyl succinate (BPS) through a 1,3-dipolar cycloaddition reaction to form 1,2,3-triazole network. The properties of GAP-based triazole networks are compared with the urethane cured GAP-systems. The glass transition temperature (T-g), tensile strength, and modulus of the system increased with crosslink density, controlled by the azide to propargyl ratio. The triazole incorporation has a higher T-g in comparison to the GAP-urethane system (T-g-20 degrees C) and the networks exhibit biphasic transitions at 61 and 88 degrees C. The triazole curing was studied using Differential Scanning Calorimetry (DSC) and the related kinetic parameters were helpful for predicting the cure profile at a given temperature. Density functional theory (DFT)-based theoretical calculations implied marginal preference for 1,5-addition over 1,4-addition for the cycloaddition between azide and propargyl group. Thermogravimetic analysis (TG) showed better thermal stability for the GAP-triazole and the mechanism of decomposition was elucidated using pyrolysis GC-MS studies. The higher heat of exothermic decomposition of triazole adduct (418kJmol(-1)) against that of azide (317kJmol(-1)) and better mechanical properties of the GAP-triazole renders it a better propellant binder than the GAP-urethane system.

Tuning the parameters to establish Quenching and enhancement regimes in hybrid Gold nanoparticles and CdSe Quantum dots monolayer

The multi-component nanomaterials combine the individual properties and give rise to emergent phenomenon. Optical excitations in such hybrid nonmaterial's ( for example Exciton in semiconductor quantum dots and Plasmon in Metal nanomaterials) undergo strong weak electromagnetic coupling. Such exciton-plasmon interactions allow design of absorption and emission properties, control of nanoscale energy-transfer processes, and creation of new excitations in the strong coupling regime.This Exciton plasmon interaction in hybrid nanomaterial can lead to both enhancement in the emission as well as quenching. In this work we prepared close-packed hybrid monolayer of thiol capped CdSe and gold nanoparticles. They exhibit both the Quenching and enhancements the in PL emission.The systematic variance of PL from such hybrid nanomaterials monolayer is studied by tuning the Number ratio of Gold per Quantum dots, the surface density of QDs and the spectral overlap of emission spectrum of QD and absorption spectrum of Gold nanoparticles. Role of Localized surface Plasmon which not only leads to quenching but strong enhancements as well, is explored.

Antimicrobial and conducting polymer substrate derived from hybrid structures of silver nanoparticles and multiwall carbon nanotubes

Hybrid nanocomposites of polycaprolactone (PCL) with multiwall carbon nanotubes (MWNTs) and silver nanoparticles (nAg) were prepared by melt mixing. Synergetic effect of the two nanofillers (MWNT and nAg) in PCL matrix was evaluated for dielectric and antibacterial properties. Dielectric results showed that the addition of nAg as filler in PCL matrix (PCL/nAg) had no effect on conductivity, whereas addition of MWNT in PCL matrix (PCL/MWNT) caused a sharp increase in conductivity of PCL. Interestingly, the hybrid nanocomposite (PCL/MWNT/nAg) incorporating MWNT and nAg also exhibited high electrical conductivity. The hybrid composite was found to have antibacterial property similar to that of PCL/nAg composite for lower loading of nAg. This study demonstrates that the synergetic interaction of the nanofillers in the hybrid nanocomposite improves both electrical conductivity and antibacterial properties of PCL.

Conducting polymer-carbon black nanocomposite sensor for volatile organic compounds and correlating sensor response by molecular dynamics

Volatile organic compounds (VOCs) are present in our every day used products such as plastics, cosmetics, air fresheners, paint, etc. The determination of amount of VOC present in atmosphere can be carried out via various sensors. In this work a nanocomposite of a novel thiophene based conducting polymer and carbon black is used as a volatile organic compound sensor. The fabricated 2 lead chemiresistor sensor was tested for vapours of toluene, acetone, cylcohexane, and carbon tetrachloride. The sensor responds to all the vapours, however, exhibit maximum response to toluene vapours. The sensor was evaluated for various concentrations of toluene. The lower limit of detection of the sensor is 15 +/- 10 ppm. The study of the effect of humidity on senor response to toluene showed that the response decreases at higher humidity conditions. The surface morphology of the nanocomposite was characterized by scanning electron microscopy. Diffuse reflectance spectroscopy was used to investigate the absorption of vapours by the nanocomposite film. Contact angle measurements were used to present the effect of water vapour on the toluene response of nanocomposite film. Solubility parameter of the conducting polymer is predicted by molecular dynamics. The sensing behaviour of the conducting polymer is correlated with solubility parameter of the polymer. Dispersion interaction of conducting polymer with toluene is believed to be the reason for the selective response towards toluene. (C) 2014 Elsevier B.V. All rights reserved.

Fabrication and characterization of sub 100 nm period polymer gratings for photonics applications

We report on the fabrication of polymethylmethacrylate (PMMA) nanogratings on silicon (Si) and glass substrates using electron beam lithography technique. Various aspects of proximity corrections using Monte Carlo simulation have been discussed. The fabrication process parameters such as proximity gap of exposure, exposure dosage and developing conditions have been optimized for high-density PMMA nanogratings structure on Si and glass substrates. Electron beam exposure is adjusted in such a way that PMMA acts as a negative tone resist and at the same time resolution loss due to proximity effect is minimum. Both reflection and transmission-type, nanometre period gratings have been fabricated and their diffraction characteristics are evaluated.

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

Dispersion of polymer grafted nanoparticles in polymer nanocomposite films: Insights from surface x-ray scattering and microscopy

Dispersion of nanoparticles in polymer nanocomposite films determines the application potential of these systems as novel materials with unique physical properties. Grafting polymers to, mostly inorganic, nanoparticles has been suggested as an effective strategy to enhance dispersion and hence the efficacy of materials. In this review, we discuss the various parameters which control dispersion of polymer grafted nanoparticles in polymer nanocomposite films. We discuss how surface x-ray scattering and microscopy can provide complementary and unique information in thin polymer nanocomposite films to unravel the subtle interplay of entropic and surface interactions, mediated by confinement, that leads to enhanced dispersion of the nanoparticles in these films. (C) 2014 AIP Publishing LLC.

Heterogeneity in Dye-TiO2 Interactions Dictate Charge Transfer Efficiencies for Diketopyrrolopyrrole-Based Polymer Sensitized Solar Cells

Power conversion efficiency of a solar cell is a complex parameter which usually hides the molecular details of the charge generation process. For rationally tailoring the overall device efficiency of the dye-sensitized solar cell, detailed molecular understanding of photoinduced reactions at the dye-TiO2 interface has to be achieved. Recently, near-IR absorbing diketopyrrolopyrrole-based (DPP) low bandgap polymeric dyes with enhanced photostabilities have been used for TiO2 sensitization with moderate efficiencies. To improve the reported device performances, a critical analysis of the polymerTiO(2) interaction and electron transfer dynamics is imperative. Employing a combination of time-resolved optical measurements complemented by low temperature EPR and steady-state Raman spectroscopy on polymerTiO(2) conjugates, we provide direct evidence for photoinduced electron injection from the TDPP-BBT polymer singlet state into TiO2 through the C-O group of the DPP-core. A detailed excited state description of the electron transfer process in films reveals instrument response function (IRF) limited (<110 fs) charge injection from a minor polymer fraction followed by a picosecond recombination. The major fraction of photoexcited polymers, however, does not show injection indicating pronounced ground state heterogeneity induced due to nonspecific polymerTiO(2) interactions. Our work therefore underscores the importance of gathering molecular-level insight into the competitive pathways of ultrafast charge generation along with probing the chemical heterogeneity at the nanoscale within the polymerTiO2 films for optimizing photovoltaic device efficiencies.

Actin-Curcumin Interaction: Insights into the Mechanism of Actin Polymerization Inhibition

Curcumin, derived from rhizomes of the Curcuma longa plant, is known to possess a wide range of medicinal properties. We have examined the interaction of curcumin with actin and determined their binding and thermodynamic parameters using isothermal titration calorimetry. Curcumin is weakly fluorescent in aqueous solution, and binding to actin enhances fluorescence several fold with a large blue shift in the emission maximum. Curcumin inhibits microfilament formation, which is similar to its role in inhibiting microtubule formation. We synthesized a series of stable curcumin analogues to examine their affinity for actin and their ability to inhibit actin self-assembly. Results show that curcumin is a ligand with two symmetrical halves, each of which possesses no activity individually. Oxazole, pyrazole, and acetyl derivatives are less effective than curcumin at inhibiting actin self-assembly, whereas a benzylidiene derivative is more effective. Cell biology studies suggest that disorganization of the actin network leads to destabilization of filaments in the presence of curcumin. Molecular docking reveals that curcumin binds close to the cytochalasin binding site of actin. Further molecular dynamics studies reveal a possible allosteric effect in which curcumin binding at the barbed end of actin is transmitted to the pointed end, where conformational changes disrupt interactions with the adjacent actin monomer to interrupt filament formation. Finally, the recognition and binding of actin by curcumin is yet another example of its unique ability to target multiple receptors.