Interaction of Sesbania Mosaic Virus Movement Protein with VPg and P10: Implication to Specificity of Genome Recognition

Sesbania mosaic virus (SeMV) is a single strand positive-sense RNA plant virus that belongs to the genus Sobemovirus. The mechanism of cell-to-cell movement in sobemoviruses has not been well studied. With a view to identify the viral encoded ancillary proteins of SeMV that may assist in cell-to-cell movement of the virus, all the proteins encoded by SeMV genome were cloned into yeast Matchmaker system 3 and interaction studies were performed. Two proteins namely, viral protein genome linked (VPg) and a 10-kDa protein (P10) c v gft encoded by OFR 2a, were identified as possible interacting partners in addition to the viral coat protein (CP). Further characterization of these interactions revealed that the movement protein (MP) recognizes cognate RNA through interaction with VPg, which is covalently linked to the 59 end of the RNA. Analysis of the deletion mutants delineated the domains of MP involved in the interaction with VPg and P10. This study implicates for the first time that VPg might play an important role in specific recognition of viral genome by MP in SeMV and shed light on the possible role of P10 in the viral movement.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Transferability of Multipole Charge Density Parameters for Supramolecular Synthons: A New Tool for Quantitative Crystal Engineering

The modularity of the supramolecular synthon is used to obtain transferability of charge density derived multipolar parameters for structural fragments, thus creating an opportunity to derive charge density maps for new compounds. On the basis of high resolution X-ray diffraction data obtained at 100 K for three compounds methoxybenzoic acid, acetanilide, and 4-methyl-benzoic acid, multipole parameters for O-H center dot center dot center dot O carboxylic acid dimer and N-H center dot center dot center dot O amide infinite chain synthon fragments have been derived. The robustness associated with these supramolecular synthons has been used to model charge density derived multipolar parameters for 4-(acetylamino)benzoic acid and 4-methylacetanilide. The study provides pointers to the design and fabrication of a synthon library of high resolution X-ray diffraction data sets. It has been demonstrated that the derived charge density features can be exploited in both intra- and intermolecular space for any organic compound based on transferability of multipole parameters. The supramolecular synthon based fragments approach (SBFA) has been compared with experimental charge density data to check the reliability of use of this methodology for transferring charge density derived multipole parameters.

Surface acoustic wave distribution and acousto-optic interaction in proton exchanged LiNbO3 waveguides

The efficiency of acoustooptic (AO) interaction in YZ-cut proton exchanged (PE) LiNbO3 waveguides is theoretically analysed by determining the overlap between the optical and acoustic field distributions. The present analysis takes into account the perturbed SAW field distribution due to the presence of the PE layer on the LiNbO3 substrate determined by the rigorous layered medium approach. The overlap is found to be significant upto very high acoustic frequencies of the order of 5 GHz, whereas in the earlier analysis by vonHelmolt and Schaffer [6] for diffused waveguides, it was shown that the overlap integral rolls down to nearly zero at this high frequency range.

Evidence of gate-tunable topological excitations in two-dimensional electron systems

We report experimental observations of a new mechanism of charge transport in two-dimensional electron systems (2DESs) in the presence of strong Coulomb interaction and disorder. We show that at low enough temperature the conductivity tends to zero at a nonzero carrier density, which represents the point of essential singularity in a Berezinskii-Kosterlitz-Thouless-like transition. Our experiments with many 2DESs in GaAs/AlGaAs heterostructures suggest that the charge transport at low carrier densities is due to the melting of an underlying ordered ground state through proliferation of topological defects. Independent measurement of low-frequency conductivity noise supports this scenario.

Quantum Properties in Transport Through Nanoscopic Rings:Charge-Spin Separation and Interference Effects

Many of the most intriguing quantum effects are observed or could be measured in transport experiments through nanoscopic systems such as quantum dots, wires and rings formed by large molecules or arrays of quantum dots. In particular, the separation of charge and spin degrees of freedom and interference effects have important consequences in the conductivity through these systems. Charge-spin separation was predicted theoretically in one-dimensional strongly inter-acting systems (Luttinger liquids) and, although observed indirectly in several materials formed by chains of correlated electrons, it still lacks direct observation. We present results on transport properties through Aharonov-Bohmrings (pierced by a magnetic flux) with one or more channels represented by paradigmatic strongly-correlated models. For a wide range of parameters we observe characteristic dips in the conductance as a function of magnetic flux which are a signature of spin and charge separation. Interference effects could also be controlled in certain molecules and interesting properties could be observed. We analyze transport properties of conjugated molecules, benzene in particular, and find that the conductance depends on the lead configuration. In molecules with translational symmetry, the conductance can be controlled by breaking or restoring this symmetry, e.g. by the application of a local external potential. These results open the possibility of observing these peculiar physical properties in anisotropic ladder systems and in real nanoscopic and molecular devices.

The effects of charge density and concentration on the composition of polyelectrolyte complexes

Polyelectrolyte complex formation involving carboxymethylcellulose and quaternized poly(vinylpyridine) as the polyions has been studied using viscosity and u.v. spectroscopic methods. The influence of charge density and molecular weight of two polycations on the composition of the complex has been investigated at two different concentrations. The charge density of the polycation is found to have different influences on the composition at different concentrations. The molecular weight of the polycation and the location of the ionic site on the polycation do not show any effect on the composition. A drastic increase in the viscosity of the polyion mixture containing quaternized poly(2-vinylpyridine) in the non-stoichiometric ratio shows evidence for the existence of the soluble polyelectrolyte complex. The results are analysed on the basis of the relative extension of the polyelectrolyte chains.

Theoretical and experimental investigation of framed structure-layered soil interaction problems

The plane stress solution for the interaction analysis of a framed structure, with a foundation beam, resting on a layered soil has been studied using both theoretical and photoelastic methods. The theoretical analysis has been done by using a combined analytical and finite element method. In this, the analytical solution has been used for the semi-infinite layered medium and finite element method for the framed structure. The experimental investigation has been carried out using two-dimensional photoelasticity in which modelling of the layered semi-infinite plane and a method to obtain contact pressure distribution have been discussed. The theoretical and experimental results in respect of contact pressure distribution between the foundation beam and layered soil medium, the fibre stresses in the foundation beam and framed structure have been compared. These results have also been compared with theoretical results obtained by idealizing the layered semi-infinite plane as (a) a Winkler model and (b) an equivalent homogeneous semi-infinite medium

Synthesis, characterization and photoluminescence properties of CaSiO3: Eu3+ red phosphor

CaSiO3:Eu3+ (1-5 mol%) red emitting phosphors have been synthesized by a low-temperature solution combustion method. The phosphors have been well characterized by powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and optical spectroscopy. PXRD patterns reveal monoclinic CaSiO3 phase can be obtained at 900 degrees C. The SEM micrographs show the crystallites with irregular shape, mostly angular. Upon 254 nm excitation, the phosphor show characteristic fluorescence D-5(0) -> F-7(J) (J = 0, 1, 2, 3, 4) of the Eu3+ ions. The electronic transition located at 614 nm corresponding to D-5(0) -> F-7(2) of Eu3+ ions, which is stronger than the magnetic dipole transition located at 593 nm corresponding to D-5(0) -> F-7(1) of Eu3+ ions. Different pathways involved in emission process have been studied. Concentration quenching has been observed for Eu3+ concentration >4 mol%. UV-visible absorption shows an intense band at 240 nm in undoped and 270 nm in Eu3+ doped CaSiO3 which is attributed to oxygen to silicon (O-Si) ligand-to-metal charge-transfer (LMCT) band in the SiO32- group. The optical energy band gap is widened with increase of Eu3+ ion dopant. (C) 2010 Elsevier B.V. All rights reserved.

Fluorescence and topological gap of conjugated phenylene polymers

We propose that strong fluorescence in conjugated polymers requires a dipole-allowed state to be the lowest singlet. Hückel theory for para-conjugated phenyl rings yields an extended, topologically one-dimensional ?-system with increased alternation, states localized on each ring, and charge-transfer excitations between them. Exact Pariser�Parr�Pople results and molecular spectra for oligomers support a topological contribution and a lowest dipole-allowed singlet in phenylene polymers.

Correlations, quantum entanglement and interference in nanoscopic systems

Several of the most interesting quantum effects can or could be observed in nanoscopic systems. For example, the effect of strong correlations between electrons and of quantum interference can be measured in transport experiments through quantum dots, wires, individual molecules and rings formed by large molecules or arrays of quantum dots. In addition, quantum coherence and entanglement can be clearly observed in quantum corrals. In this paper we present calculations of transport properties through Aharonov-Bohm strongly correlated rings where the characteristic phenomenon of charge-spin separation is clearly observed. Additionally quantum interference effects show up in transport through pi-conjugated annulene molecules producing important effects on the conductance for different source-drain configurations, leading to the possibility of an interesting switching effect. Finally, elliptic quantum corrals offer an ideal system to study quantum entanglement due to their focalizing properties. Because of an enhanced interaction between impurities localized at the foci, these systems also show interesting quantum dynamical behaviour and offer a challenging scenario for quantum information experiments.

Impedance peaks of sealed nickel/cadmium cells at low states-of-charge

The impedance of sealed nickel/cadmium cells is measured at low states-of-charge that correspond to a cell e.m.f. range of 0.0 to 1.3 V. The results show that the impedance exhibits a pronounced maximum between 0.3 and 0.45 V. It is concluded that the impedance maxima are due to physicochemical processes taking place at the nickel oxide electrode. The impedance of the nickel oxide electrode is dominated by three different phenomena: (i) a Ni(II)/Ni(III) reaction between 1.3 and 0.8 V; (ii) a double-layer impedance between 0.8 and 0.3 V; (iii) a hydrogen evolution reaction between 0.3 and 0.0 V.

Dependence of the strength of interaction of carbon monoxide with transition metal clusters on the cluster size

The interaction of CO with Cu, Pd, and Ni at different coverages of the metals on solid substrates has been investigated by He II and core-level spectroscopies, after the nature of variation of the metal core-level binding energies with the coverage or the cluster size is established. The separation between the (1 pi + 5 sigma) and 4 sigma levels of CO increases with a decrease in the size of the metal clusters, accompanied by an increase in the desorption temperature. In the case of Cu, the intramolecular shakeup satellite of CO disappears on small clusters. More importantly, CO dissociates on small Ni clusters, clearly confirming that metal-CO interaction strength increases with a decrease in the cluster size.

Diffusion of sorbates in zeolites Y and A novel dependence on sorbate size and strength of sor ba t e-Zeoli t e interaction

A systematic investigation of monatomic spherical sorbates in the supercages of zeolites Y and A by molecular dynamics technique is presented. Rates of intercage diffusion, rates of cage visits, and the diffusion coefficients have been calculated as a function of the sorbate-zeolite interaction strength. These properties exhibit markedly different dependences on interaction strength for the two zeolites. The observed behavior is shown to be a consequence of the two principal mechanisms of intercage diffusion and the energetic barrier associated with them. The diffusion coefficient and other properties associated with intercage diffusion are found to be directly proportional to the reciprocal of the square of the sorbate diameter when the sorbate diameter is significantly smaller than the window diameter. As the sorbate diameter increases, a peak is observed in all the transport properties investigated including the diffusion coefficient. We call this surprising effect as the ring or levitation effect and it explains several anomalous results reported in the literature and suggests a breakdown of the geometrical criterion for diffusion of sorbates. It shows that under certain conditions nongeometrical factors play a major role and geometrical factors become secondary in the determination of the molecular sieve property. A generalized parameter has been proposed which suggests conditions under which one can expect the ring or levitation effect in any porous medium. Inverse size selectivity becomes operative under these conditions.

Distribution of ionic charge carriers and migration barriers in binary alkali silicate glasses

Likely spatial distributions of network-modifying (and mobile) cations in (oxide) glasses are discussed here. At very low modifier concentrations, the ions form dipoles with non-bridging oxygen centres while, at higher levels of modification, the cations tend to order as a result of Coulombic interactions. Activation energies for cation migration are calculated, assuming that the ions occupy (face-sharing) octahedral sites. It is found that conductivity activation energy decreases markedly with increasing modifier content, in agreement with experiment.