Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by B97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 134-147, 2015.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.

Fragility correlates thermodynamic and kinetic properties of glass forming liquids

In our earlier communication we proposed a simple fragility determining function, (NBO]/(VmTg)-T-3), which we have now used to analyze several glass systems using available thermal data. A comparison with similar fragility determining function, Delta C-p/C-p(1), introduced by Chryssikos et al. in their investigation of lithium borate glasses has also been performed and found to be more convenient quantity for discussing fragilities. We now propose a new function which uses both Delta C-p and Delta T and which gives a numerical fragility parameter, F whose value lies between 0 and 1 for glass forming liquids. F can be calculated through the use of measured thermal parameters Delta C-p, C-p(1), T-g and T-m. Use of the new fragility values in reduced viscosity equation reproduces the whole range of viscosity curves of the Angell plot. The reduced viscosity equation can be directly compared with the Adam-Gibbs viscosity equation and a heat capacity function can be formulated which reproduces satisfactorily the Delta C-p versus In(T-r) curves and hence the configurational entropy. (C) 2014 Elsevier Ltd. All rights reserved.

Designing Elastic Organic Crystals: Highly Flexible Polyhalogenated N-Benzylideneanilines

The intermolecular interactions and structural features in crystals of seven halogenated N-benzylideneanilines (Schiff bases), all of which exhibit remarkable flexibility, were examined to identify the common packing features that are the raison d'etre for the observed elasticity. The following two features, in part related, were identified as essential to obtain elastic organic crystals: 1)A multitude of weak and dispersive interactions, including halogen bonds, which may act as structural buffers for deformation through easy rupture and reformation during bending; and 2)corrugated packing patterns that would get interlocked and, in the process, prevent long-range sliding of molecular planes.

Stability of Filaments in Star-Forming Clouds and the Formation of Prestellar Cores in Them

The exact process(es) that generate(s) dense filaments which then form prestellar cores within them is unclear. Here we study the formation of a dense filament using a relatively simple set-up of a pressure-confined, uniform-density cylinder. We examine if its propensity to form a dense filament and further, to the formation of prestellar cores along this filament, bears on the gravitational state of the initial volume of gas. We report a radial collapse leading to the formation of a dense filamentary cloud is likely when the initial volume of gas is at least critically stable (characterised by the approximate equality between the mass line-density for this volume and its maximum value). Though self-gravitating, this volume of gas, however, is not seen to be in free-fall. This post-collapse filament then fragments along its length due to the growth of a Jeans-like instability to form prestellar cores. We suggest dense filaments in typical star-forming clouds classified as gravitationally super-critical under the assumption of: (i) isothermality when in fact, they are not, and (ii) extended radial profiles as against pressure-truncated, that significantly over-estimates their mass line-density, are unlikely to experience gravitational free-fall. The radial density and temperature profile derived for this post-collapse filament is consistent with that deduced for typical filamentary clouds mapped in recent surveys of nearby star-forming regions.

Unusual Fragility and Cooperativity in Glass-Forming and Crystalline PVDF/PMMA Blends in the Presence of Multiwall Carbon Nanotubes

Poly(vinylidene fluoride) (PVDF) and poly(methyl methacrylate) (PMMA) are completely miscible below 50 wt % PVDF in the blends. In this work, an attempt was made to understand the fragility/cooperativity relation in glass-forming and crystalline blends of PVDF/PMMA and in the presence of a heteronucleating agent, multiwall carbon nanotubes (CNTs). Hence, three representative blends were chosen: a completely amorphous (10/90 by wt, PVDF/PMMA), on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA), and crystalline (60/40 by wt, PVDF/PMMA) blends. The intermolecular cooperativity/coupling, fragility, and configurational entropy near the glass transition temperature (T-g) were studied using differential scanning calorimetry (DSC) and broadband dielectric relaxation spectroscopy (DRS). It was observed that the blends with higher concentration of PMMA were more fragile (fragility index m = 141) and those with higher concentration of PVDF were more strong (m = 78). Interestingly, the coupling was less in the glass-forming blends (10/90 by wt, PVDF/PMMA) than the crystalline blends as manifested from DRS. This observation was also supported by DSC measurements which reflected that the cooperative rearranging region (CRR) existed over a smaller length scales in fragile blends as compared to strong blends, possibly due to restricted amorphous mobility. This effect was more prominent in the presence of CNTs, in particular for 50/50 (by wt) and 60/40 (by wt) PVDF/PMMA blends. Further, the configurational entropy, as manifested from DRS, decreased significantly in the strong blends in striking contrast to the fragile blends, supported by DSC, which manifested in an increase in the volume of cooperativity in the strong blends. The higher coupling in the crystalline blends can be attributed to good packing of the amorphous regions. While this is understood for crystalline blends (60/40 by wt, PVDF/PMMA), it is envisaged that enhanced dynamic heterogeneity is accountable for increased coupling in the case of blends which are on the verge of amorphous miscibility (50/50 by wt, PVDF/PMMA). The latter is also supported by broad relaxations near the T-g in DRS. Interestingly, the intermolecular coupling in the blends in the presence of CNTs has reduced, though the potential energy barrier hindering the rearrangement of CRR is lower than the blends without CNTs. In addition, the amorphous packing is not as effective as the blends without CNTs. This is manifested from reduced volume of cooperativity in particular, for 50/50 (by wt) and 60/40 (by wt) blends.

Thermally flexible epoxy/cellulose blends mediated by an ionic liquid

Blends between the widely used thermoset resin, epoxy, and the most abundant organic material, natural cellulose are demonstrated for the first time. The blending modification induced by charge transfer complexes using a room temperature ionic liquid, leads to the formation of thermally flexible thermoset materials. The blend materials containing low concentrations of cellulose were optically transparent which indicates the miscibility at these compositions. We observed the existence of intermolecular hydrogen bonding between epoxy and cellulose in the presence of the ionic liquid, leading to partial miscibility between these two polymers. The addition of cellulose improves the tensile mechanical properties of epoxy. This study reveals the use of ionic liquids as a compatible processing medium to prepare epoxy thermosets modified with natural polymers.

Dynamics of Glass Forming Liquids with Randomly Pinned Particles

It is frequently assumed that in the limit of vanishing cooling rate, the glass transition phenomenon becomes a thermodynamic transition at a temperature T-K. However, with any finite cooling rate, the system falls out of equilibrium at temperatures near T-g(> T-K), implying that the very existence of the putative thermodynamic phase transition at T-K can be questioned. Recent studies of systems with randomly pinned particles have hinted that the thermodynamic glass transition may be observed for liquids with randomly pinned particles. This expectation is based on the results of approximate calculations that suggest that the thermodynamic glass transition temperature increases with increasing concentration of pinned particles and it may be possible to equilibrate the system at temperatures near the increased transition temperature. We test the validity of this prediction through extensive molecular dynamics simulations of two model glass-forming liquids in the presence of random pinning. We find that extrapolated thermodynamic transition temperature T-K does not show any sign of increasing with increasing pinning concentration. The main effect of pinning is found to be a rapid decrease in the kinetic fragility of the system with increasing pin concentration. Implications of these observations for current theories of the glass transition are discussed.

Flexible implementation of power system corrective topology control

This paper proposes a novel decision making framework for optimal transmission switching satisfying the AC feasibility, stability and circuit breaker (CB) reliability requirements needed for practical implementation. The proposed framework can be employed as a corrective tool in day to day operation planning scenarios in response to potential contingencies. The switching options are determined using an efficient heuristic algorithm based on DC optimal power flow, and are presented in a multi-branch tree structure. Then, the AC feasibility and stability checks are conducted and the CB condition monitoring data are employed to perform a CB reliability and line availability assessment. Ultimately, the operator will be offered multiple AC feasible and stable switching options with associated benefits. The operator can use this information, other operating conditions not explicitly considered in the optimization, and his/her own experience to implement the best and most reliable switching action(s). The effectiveness of the proposed approach is validated on the IEEE-118 bus test system. (C) 2015 Elsevier B.V. All rights reserved.

Ultra-small sulphur nanoparticles configured inside a flexible organic mixed conducting network as a cathode for lithium-sulphur batteries

The major challenges in Li-S batteries are the formation of soluble polysulphides during the reversible conversion of S-8 <-> Li2S, large changes in sulphur particle volume during lithiation and extremely poor charge transport in sulphur. We demonstrate here a novel and simple strategy to overcome these challenges towards practical realization of a stable high performance Li-S battery. For the first time, a strategy is developed which does away with the necessity of pre-fabricated high surface area hollow-structured adsorbates and also multiple nontrivial synthesis steps related to sulphur loading inside such adsorbates. A lithiated polyethylene glycol (PEG) based surfactant tethered on ultra-small sulphur nanoparticles and wrapped up with polyaniline (PAni) (abbreviated as S-MIEC) is demonstrated here as an exceptional cathode for Li-S batteries. The PEG and PAni network around the sulphur nanoparticles serves as an efficient flexible trap for sulphur and polysulphides and also provides distinct pathways for electrons (through PAni) and ions (through PEG) during battery operation. Contrary to the cathodes demonstrated based on various carbon-sulphur composites, the mixed conducting S-MIEC showed an extremely high loading of 75%. The S-MIEC exhibited a stable capacity of nearly 900 mA h g(-1) at the end of 100 cycles at a 1C current rate.

Synthesis of ZnO nanorods on a flexible Phynox alloy substrate: influence of growth temperature on their properties

A novel flexible alloy substrate (Phynox, 50 mm thick) was used for the synthesis of zinc oxide (ZnO) nanorods via a low-temperature solution growth method. The growth of ZnO nanorods was observed over a low temperature range of 60-90 degrees C for a growth duration of 4 hours. The as-synthesized nanorods were characterized using field-emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) for their morphology, crystallinity, microstructure and composition. The as-grown ZnO nanorods were observed to be relatively vertical to the substrate. However, the morphology of the ZnO nanorods in terms of their length, diameter and aspect ratio was found to vary with the growth temperature. The morphological variation was mainly due to the effects of the various relative growth rates observed at the different growth temperatures. The growth temperature influenced ZnO nanorods were also analyzed for their wetting (either hydrophobic or hydrophilic) properties. After carrying out multiple wetting behaviour analyses, it has been found that the as-synthesized ZnO nanorods are hydrophobic in nature. The ZnO nanorods have potential application possibilities in self-cleaning devices, sensors and actuators as well as energy harvesters such as nanogenerators.

Length scales in glass-forming liquids and related systems: a review

The central problem in the study of glass-forming liquids and other glassy systems is the understanding of the complex structural relaxation and rapid growth of relaxation times seen on approaching the glass transition. A central conceptual question is whether one can identify one or more growing length scale(s) associated with this behavior. Given the diversity of molecular glass-formers and a vast body of experimental, computational and theoretical work addressing glassy behavior, a number of ideas and observations pertaining to growing length scales have been presented over the past few decades, but there is as yet no consensus view on this question. In this review, we will summarize the salient results and the state of our understanding of length scales associated with dynamical slow down. After a review of slow dynamics and the glass transition, pertinent theories of the glass transition will be summarized and a survey of ideas relating to length scales in glassy systems will be presented. A number of studies have focused on the emergence of preferred packing arrangements and discussed their role in glassy dynamics. More recently, a central object of attention has been the study of spatially correlated, heterogeneous dynamics and the associated length scale, studied in computer simulations and theoretical analysis such as inhomogeneous mode coupling theory. A number of static length scales have been proposed and studied recently, such as the mosaic length scale discussed in the random first-order transition theory and the related point-to-set correlation length. We will discuss these, elaborating on key results, along with a critical appraisal of the state of the art. Finally we will discuss length scales in driven soft matter, granular fluids and amorphous solids, and give a brief description of length scales in aging systems. Possible relations of these length scales with those in glass-forming liquids will be discussed.

Nonlinear Dynamics of a Rotating Flexible Link

This paper deals with the study of the nonlinear dynamics of a rotating flexible link modeled as a one dimensional beam, undergoing large deformation and with geometric nonlinearities. The partial differential equation of motion is discretized using a finite element approach to yield four nonlinear, nonautonomous and coupled ordinary differential equations (ODEs). The equations are nondimensionalized using two characteristic velocities-the speed of sound in the material and a velocity associated with the transverse bending vibration of the beam. The method of multiple scales is used to perform a detailed study of the system. A set of four autonomous equations of the first-order are derived considering primary resonances of the external excitation and one-to-one internal resonances between the natural frequencies of the equations. Numerical simulations show that for certain ranges of values of these characteristic velocities, the slow flow equations can exhibit chaotic motions. The numerical simulations and the results are related to a rotating wind turbine blade and the approach can be used for the study of the nonlinear dynamics of a single link flexible manipulator.

Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses

Tobacco streak virus (TSV), the type member of Ilarvirus genus, is a major plant pathogen. TSV purified from infected plants consists of a ss-RNA genome encapsidated in spheroidal particles with diameters of 27, 30 and 33 nm constructed from multiple copies of a single species of coat protein (CP) subunits. Apart from protecting the viral genome, CPs of ilarviruses play several key roles in the life cycle of these viruses. Unlike the related bromo and cucumoviruses, ilarvirus particles are labile and pleomorphic, which has posed difficulties in their crystallization and structure determination. In the current study, a truncated TSV-CP was crystallized in two distinct forms and their structures were determined at resolutions of 2.4 angstrom and 2.1 angstrom, respectively. The core of TSV CP was found to possess the canonical beta-barrel jelly roll tertiary structure observed in several other viruses. Dimers of CP with swapped C-terminal arms (C-arm) were observed in both the crystal forms. The C-arm was found to be flexible and is likely to be responsible for the polymorphic and pleomorphic nature of TSV capsids. Consistent with this observation, mutations in the hinge region of the C-arm that reduce the flexibility resulted in the formation of more uniform particles. TSV CP was found to be structurally similar to that of Alfalfa mosaic virus (AMV) accounting for similar mechanism of genome activation in alfamo and ilar viruses. This communication represents the first report on the structure of the CP from an ilarvirus. (C) 2015 Elsevier Inc. All rights reserved.

Two-Phase Metallic Thermal Interface Materials Processed Through Liquid Phase Sintering Followed by Accumulative Roll Bonding

Thermal interface materials (TIMs) form a mechanical and thermal link between a heat source and a heat sink. Thus, they should have high thermal conductivity and high compliance to efficiently transfer heat and accommodate any differential strain between the heat source and the sink, respectively. This paper reports on the processing and the characterization of potential metallic TIM composite solders comprising of Cu, a high conductivity phase, uniformly embedded in In matrix, a highly compliant phase. We propose the fabrication of such a material by a two-step fabrication technique comprising of liquid phase sintering (LPS) followed by accumulative roll bonding (ARB). To demonstrate the efficacy of the employed two-step processing technique, an In-40 vol. % Cu composite solder was produced first using LPS with short sintering periods (30 or 60 s at 160 degrees C) followed by ARB up to five passes, each pass imposing a strain of 50%. Mechanical response and electrical and thermal conductivities of the fabricated samples were evaluated. It was observed that processing through ARB homogenizes the distribution of Cu in an In matrix, disintegrates the agglomerates of Cu powders, and also significantly increases thermal and electrical conductivities, almost attaining theoretically predicted values, without significantly increasing the flow stress. Furthermore, the processing technique also allows the insertion of desired foreign species, such as reduced graphene oxide, in In-Cu for further enhancing a target property, such as electrical conductivity.