Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N*) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration (C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N* states. Interestingly, the phase boundaries separating the folded and unfolded states at all C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N* with a disordered solvent-exposed amino-terminal beta-strand. The structure of the N* state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N* state, determined by the free energy gap separating the native structure and the N* state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N* state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain. (C) 2014 Elsevier Ltd. All rights reserved.

Role of spectator ions in influencing the properties of dopant-free ZnO nanocrystals

Towards fundamental studies and potential applications, achieving precise control over the generation of defects in pure ZnO nanocrystals has been always intriguing. Herein, we explored the rote of spectator ions (Co2+ and Ni2+) in influencing the functional properties of ZnO nanocrystals. The crystalline quality, phase purity, and composition of as-prepared samples were thoroughly established by powder X-ray diffraction, electron microscopy (TEM and STEM), and by Raman and X-ray photoelectron spectroscopies (XPS). Despite the presence of Co2+ and Ni2+ ions in the reaction mixture, STEM-energy dispersive spectroscopy (EDS), XPS analysis, and inductively-coupled plasma mass spectrometry (ICP-MS) revealed that the ZnO nanocrystals formed are dopant-free. Even so, their luminescence and magnetic properties were substantially different from those of pure ZnO nanocrystals synthesized using a similar methodology. We attribute the origin of these properties to the defects associated with ZnO nanocrystals generated under different but optimized conditions.

Finite element analysis of free vibration of the delaminated composite plate with variable kinematic multilayered plate elements

Composite laminates are prone to delamination. Implementation of delamination in the Carrera Unified Formulation frame work using nine noded quadrilateral MITC9 element is discussed in this article. MITC9 element is devoid of shear locking and membrane locking. Delaminated as well as healthy structure is analyzed for free mode vibration. The results from the present work are compared with the available experimental or/and research article or/and the three dimensional finite element simulations. The effect of different kinds and different percentages of area of delamination on the first three natural frequencies of the structure is discussed. The presence of open-mode delamination mode shape for large delaminations within the first three natural frequencies is discussed. Also, the switching of places between the second bending mode, with that of the first torsional mode frequency is discussed. Results obtained from different ordered theories are compared in the presence of delamination. Advantage of layerwise theories as compared to equivalent single layer theories for very large delaminations is stated. The effect of different kinds of delamination and their effect on the second bending and first torsional mode shape is discussed. (C) 2014 Elsevier Ltd. All rights reserved.

DIMENSION FREE BOUNDEDNESS OF RIESZ TRANSFORMS FOR THE GRUSHIN OPERATOR

Let G = -Delta(xi) - vertical bar xi vertical bar(2) partial derivative(2)/partial derivative eta(2) be the Grushin operator on R-n x R. We prove that the Riesz transforms associated to this operator are bounded on L-p(Rn+1), 1 < p < infinity, and their norms are independent of dimension n.

An improved free surface modeling for incompressible SPH

In Incompressible Smooth Particle Hydrodynamics (ISPH), a pressure Poisson equation (PPE) is solved to obtain a divergence free velocity field. When free surfaces are simulated using this method a Dirichlet boundary condition for pressure at the free surface has to be applied. In existing ISPH methods this is achieved by identifying free surface particles using heuristically chosen threshold of a parameter such as kernel sum, density or divergence of the position, and explicitly setting their pressure values. This often leads to clumping of particles near the free surface and spraying off of surface particles during splashes. Moreover, surface pressure gradients in flows where surface tension is important are not captured well using this approach. We propose a more accurate semi-analytical approach to impose Dirichlet boundary conditions on the free surface. We show the efficacy of the proposed algorithm by using test cases of elongation of a droplet and dam break. We perform two dimensional simulations of water entry and validate the proposed algorithm with experimental results. Further, a three dimensional simulation of droplet splash is shown to compare well with the Volume-of-Fluid simulations. (C) 2014 Elsevier Ltd. All rights reserved.

Using heat treatment effects and EBSD analysis to tailor microstructure of hybrid Mg nanocomposite for enhanced overall mechanical response

In this study, a detailed investigation on the effect of heat treatment on the microstructural characteristics, texture evolution and mechanical properties of Mg-(5.6Ti+2.5B(4)C)(BM) hybrid nanocomposite is presented. Optimised heat treatment parameters, namely, heat treatment temperature and heat treatment time, were first identified through grain size and microhardness measurements. Initially, heat treatment of composites was conducted at temperature range between 100 and 300 degrees C for 1 h. Based on optical microscopic analysis and microhardness measurements, it was evident that significant grain growth and reduction in microhardness occurred for temperatures > 200 degrees C. The cutoff temperature that caused significant grain growth/matrix softening was thus identified. Second, at constant temperature (200 degrees C), the effect of variation of heat treatment time was carried out (ranging between 1 and 5 h) so as to identify the range wherein increase in average grain size and reduction in microhardness occurred. Furthering the study, the effect of optimised heat treatment parameters (200 degrees C, 5 h) on the microstructural texture evolution and hence, on the tensile and compressive properties of the Mg-(5.6Ti+2.5B(4)C)(BM) hybrid nanocomposite was carried out. From electron backscattered diffraction (EBSD) analysis, it was identified that the optimised heat treatment resulted in recrystallisation and residual stress relaxation, as evident from the presence of similar to 87% strain free grains, when compared to that observed in the non-heat treated/as extruded condition (i.e. 2.2 times greater than in the as extruded condition). For the heat treated composite, under both tensile and compressive loads, a significant improvement in fracture strain values (similar to 60% increase) was observed when compared to that of the non-heat treated counterpart, with similar to 20% reduction in yield strength. Based on structure-property correlation, the change in mechanical characteristics is identified to be due to: (1) the presence of less stressed matrix/reinforcement interface due to the relief of residual stresses and (2) texture weakening due to matrix recrystallisation effects, both arising due to heat treatment.

Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular a-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36. (C) 2014 AIP Publishing LLC.

Flexibility in flapping foil suppresses meandering of induced jet in absence of free stream

Thrust-generating flapping foils are known to produce jets inclined to the free stream at high Strouhal numbers St = fA/U-infinity, where f is the frequency and A is the amplitude of flapping and U-infinity is the free-stream velocity. Our experiments, in the limiting case of St —> infinity (zero free-stream speed), show that a purely oscillatory pitching motion of a chordwise flexible foil produces a coherent jet composed of a reverse Benard-Karman vortex street along the centreline, albeit over a specific range of effective flap stiffnesses. We obtain flexibility by attaching a thin flap to the trailing edge of a rigid NACA0015 foil; length of flap is 0.79 c where c is rigid foil chord length. It is the time-varying deflections of the flexible flap that suppress the meandering found in the jets produced by a pitching rigid foil for zero free-stream condition. Recent experiments (Marais et al., J. Fluid Mech., vol. 710, 2012, p. 659) have also shown that the flexibility increases the St at which non-deflected jets are obtained. Analysing the near-wake vortex dynamics from flow visualization and particle image velocimetry (PIV) measurements, we identify the mechanisms by which flexibility suppresses jet deflection and meandering. A convenient characterization of flap deformation, caused by fluid-flap interaction, is through a non-dimensional effective stiffness', EI* = 8 EI/(rho V-TEmax(2) s(f) c(f)(3)/2), representing the inverse of the flap deflection due to the fluid-dynamic loading; here, EI is the bending stiffness of flap, rho is fluid density, V-TEmax is the maximum velocity of rigid foil trailing edge, s(f) is span and c(f) is chord length of the flexible flap. By varying the amplitude and frequency of pitching, we obtain a variation in EI* over nearly two orders of magnitude and show that only moderate EI*. (0.1 less than or similar to EI * less than or similar to 1 generates a sustained, coherent, orderly jet. Relatively `stiff' flaps (EI* greater than or similar to 1), including the extreme case of no flap, produce meandering jets, whereas highly `flexible' flaps (EI* less than or similar to 0.1) produce spread-out jets. Obtained from the measured mean velocity fields, we present values of thrust coefficients for the cases for which orderly jets are observed.

Impact of Stone-Wales and lattice vacancy defects on the electro-thermal transport of the free standing structure of metallic ZGNR

We report the effect of topological as well as lattice vacancy defects on the electro-thermal transport properties of the metallic zigzag graphene nano ribbons at their ballistic limit. We employ the density function theory-Non equilibrium green's function combination to calculate the transmission details. We then present an elaborated study considering the variation in the electrical current and the heat current transport with the change in temperature as well as the voltage gradient across the nano ribbons. The comparative analysis shows, that in the case of topological defects, such as the Stone-Wales defect, the electrical current transport is minimum. Besides, for the voltage gradient of 0.5 Volt and the temperature gradient of 300 K, the heat current transport reduces by similar to 62 % and similar to 50% for the cases of Stones-Wales defect and lattice vacancy defect respectively, compared to that of the perfect one.

Hexamethylenetetramine mediated simultaneous nitrogen doping and reduction of graphene oxide for a metal-free SERS substrate

We report a one-pot hydrothermal synthesis of nitrogen doped reduced graphene oxide (N-rGO) and Ag nanoparticle decorated N-rGO hybrid nanostructures from graphene oxide (GO), metal ions and hexamethylenetetramine (HMT). HMT not only reduces GO and metal ions simultaneously but also acts as the source for the nitrogen (N) dopant. We show that the N-rGO can be used as a metal-free surface enhanced Raman spectroscopy (SERS) substrate, while the Ag nano-particles decorated N-rGO can be used as an effective SERS substrate as well as a template for decorating various other nanostructures on N-rGO.

Beyond classical dynamic structural plasticity using mesh-free modelling techniques

The problem of modelling the transient response of an elastic-perfectly-plastic cantilever beam, carrying an impulsively loaded tip mass, is,often referred to as the Parkes cantilever problem 25]; The permanent deformation of a cantilever struck transversely at its tip, Proc. R. Soc. A., 288, pp. 462). This paradigm for classical modelling of projectile impact on structures is re-visited and updated using the mesh-free method, smoothed particle hydrodynamics (SPH). The purpose of this study is to investigate further the behaviour of cantilever beams subjected to projectile impact at its tip, by considering especially physically real effects such as plastic shearing close to the projectile, shear deformation, and the variation of the shear strain along the length and across the thickness of the beam. Finally, going beyond macroscopic structural plasticity, a strategy to incorporate physical discontinuity (due to crack formation) in SPH discretization is discussed and explored in the context of tip-severance of the cantilever beam. Consequently, the proposed scheme illustrates the potency for a more refined treatment of penetration mechanics, paramount in the exploration of structural response under ballistic loading. The objective is to contribute to formulating a computational modelling framework within which transient dynamic plasticity and even penetration/failure phenomena for a range of materials, structures and impact conditions can be explored ab initio, this being essential for arriving at suitable tools for the design of armour systems. (C) 2014 Elsevier Ltd. All rights reserved.

Enhanced electric field tunable magnetic properties of lead-free Na0.5Bi0.5TiO3-MnFe2O4 multiferroic composites

Strong magnetoelectric (ME) interaction was exhibited at both dc and microwave frequencies in a lead-free multiferroic particulate composites of Na0.5Bi0.5TiO3 (NBT) and MnFe2O4 (MFO) multiferroic, which were prepared by sol-gel route. The room temperature permeability measurements were carried out in the frequency range of 1 MHz-1 GHz. A systematic study of structural, magnetic and ME properties were undertaken. The room temperature ferromagnetic resonance (FMR) was studied. Strong ME coupling is demonstrated in 70NBT-30MFO composite by an electrostatically tunable FMR field shift up to 428 Oe (at E = 4 kV/cm), which increases to a large value of 640 Oe at E = 8 kV/cm. Furthermore, these lead-free multiferroic composites exhibiting electrostatically induced magnetic resonance field at microwave frequencies provide great opportunities for electric field tunable microwave devices.

High quality oxide-free metallic nanoparticles: a strategy for synthesis through laser ablation in aqueous medium

The paper explores the synthesis of oxide-free nanoparticles of Ag and Cu through laser ablation of pure targets under aqueous medium and tuning the quality and size through addition of Polyvinylpyrrolidone (PVP) in the medium. The size distribution of nanoparticles reduces from 37 +/- 30 nm and 13 +/- 5 nm to 32 +/- 12 nm and 4 +/- 1 nm for Ag and Cu with changes in PVP concentration from 0.00 to 0.02 M, respectively. Irregular shaped particles of Ag with Ag2O phase and a Cu-Cu2O core-shell particles form without the addition of PVP, while oxide layer is absent with 0.02 M of PVP. The recent understanding of the mechanism of particle formation during laser ablation under liquid medium allows us to rationalize our observation.

A metal-free and a solvent-free synthesis of thio-amides and amides: an efficient Friedel-Crafts arylation of isothiocyanates and isocyanates

A rapid, metal-free and solvent-free (very low loading of solvent in few cases) reaction conditions for synthesizing thioamides and amides using a Bronsted super acid such as triflic acid has been developed. This method shows a broad substrate scope with a variety of electron-rich arenes including thiophene derivatives. The reaction works well for both aromatic as well as aliphatic isothiocyanates. Most of the thioamides are obtained in excellent yields in short reaction times and in most of the examples, a simple work up procedure has been developed which does not require further purification.