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Shiv Nadar University

(SoNS) School of Natural Sciences

The InAs quantum structures were formed in silicon by sequential ion implantation and subsequent thermal annealing. Two kinds of crystalline InAs nanostructures were successfully synthesized: nanodots (NDs) and nanopyramids (NPs). The peaks at 215 and 235 cm-1, corresponding to the transverse optical (TO) and longitudinal optical (LO) InAs single-phonon modes, respectively, are clearly visible in the Raman spectra. Moreover, the PL band at around 1.3 μm, due to light emission from InAs NDs with an average diameter 7±2 nm, was observed. The InAs NPs were found only in samples annealed for 20 ms at temperatures ranging from 1000 up to 1200°C. The crystallinity and pyramidal shape of InAs quantum structures were confirmed by HRTEM and XRD techniques. The average size of the NPs is 50 nm base and 50 nm height, and they are oriented parallel to the Si (001) planes. The lattice parameter of the NPs increases from 6.051 to 6.055 Å with the annealing temperature increasing from 1100 to 1200°C, due to lattice relaxation. Energy dispersive spectroscopy (EDS) shows almost stoichiometric composition of the InAs NPs. © 2011 Versita Warsaw and Springer-Verlag Wien.

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Physics

Fulltext

Central European Journal of Physics

Optical and microstructural properties of self-assembled InAs quantum structures in silicon

The entry of dengue viruses is mediated by pH triggering in the host cells. Here we have studied the DENV E protein stability and binding of its units at low and normal pH using MD and MM-PB/SA method for the first time. To investigate the role of pH in dissociation of dimeric protein, we have performed a concise study of hydrogen bonding and other interactions between units of dimer at low and normal pH. The Generalized Born calculation connotes that dimeric unit was relatively less stable and less proned for dimerisation at low pH. Our results provide a theoretical verification for previous assumptions of pH triggering mechanism of dengue envelope protein. During the pH alteration, we found a large decrement in salt bridges which were observed at normal pH. We also compared the flexibility of each unit and found that they exhibit different fluctuations during molecular dynamics simulations. © 2011 Elsevier B.V. All Rights Reserved.

Chemistry

Biochimica et Biophysica Acta - Proteins and Proteomics

Role of pH on dimeric interactions for DENV envelope protein: An insight from molecular dynamics study

We report a Quantum mechanics/Molecular Mechanics-Poisson-Boltzmann/ Surface Area (QM/MM-PB/SA) method to calculate the binding free energy of c-Abl human tyrosine kinase by combining the QM and MM principles where the ligand is treated quantum mechanically and the rest of the receptor by classical molecular mechanics. To study the role of entropy and the flexibility of the protein ligand complex in a solvated environment, molecular dynamics calculations are performed using a hybrid QM/MM approach. This work shows that the results of the QM/MM approach are strongly correlated with the binding affinity. The QM/MM interaction energy in our reported study confirms the importance of electronic and polarization contributions, which are often neglected in classical MM-PB/SA calculations. Moreover, a comparison of semi-empirical methods like DFTB-SCC, PM3, MNDO, MNDO-PDDG, and PDDG-PM3 is also performed. The results of the study show that the implementation of a DFTB-SCC semi-empirical Hamiltonian that is derived from DFT gives better results than other methods. We have performed such studies using the AMBER molecular dynamic package for the first time. The calculated binding free energy is also in agreement with the experimentally determined binding affinity for c-Abl tyrosine kinase complex with Imatinib. © 2010 Springer Science+Business Media B.V.

Journal of Biological Physics

Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor

We investigate complex versions of the Korteweg-deVries equations and an Ito-type nonlinear system with two coupled nonlinear fields. We systematically construct rational, trigonometric/hyperbolic and elliptic solutions for these models including those which are physically feasible in an obvious sense, that is those with real energies, but also those with complex energy spectra. The reality of the energy is usually attributed to different realizations of an antilinear symmetry, as for instance -symmetry. It is shown that the symmetry can be spontaneously broken in two alternative ways either by specific choices of the domain or by manipulating the parameters in the solutions of the model, thus leading to complex energies. Surprisingly, the reality of the energies can be regained in some cases by a further breaking of the symmetry on the level of the Hamiltonian. In many examples, some of the fixed points in the complex solution for the field undergo a Hopf bifurcation in the -symmetry breaking process. By employing several different variants of the symmetries we propose many classes of new invariant extensions of these models and study their properties. The reduction of some of these models yields complex quantum mechanical models previously studied. © 2011 IOP Publishing Ltd.

Journal of Physics A: Mathematical and Theoretical

PT-symmetry breaking in complex nonlinear wave equations and their deformations

Since discovery of graphene, layered materials have drawn considerable attention because of their possible exfoliation into single and multilayer 2D sheets. Because of strong surface effects, the properties of these materials vary drastically with the number of layers in a sheet. We have performed first-principles density functional based calculations to evaluate the electron energy loss spectrum (EELS) of bulk, monolayer, and bilayer configurations of several transition metal dichalcogenides, which include semiconducting as well as metallic compounds. Our investigation shows that the peaks in the EELS spectra move toward larger wavelengths (red shift) with the decrease in number of layers. The π plasmon peak shifts slightly by 0.5-1.0 eV, while a significant shift of around 5.5-13.0 eV is obtained for π + σ plasmon, when exfoliated from bulk to single-layer. This underscores the importance of the interlayer coupling on the loss spectra and the dielectric properties. Our results are found to be in very good agreement with the recent measurements performed by Coleman et al. (Science2011, 331, 568). © 2011 American Chemical Society.

ACS Nano

Tunable dielectric properties of transition metal dichalcogenides

To modulate the electronic and optical properties of graphene oxide via controlled deoxidation, a proper understanding of the role of the individual functional group in determining these properties is required. We, therefore, have performed ab initio density functional theory based calculations to study the electronic and optical properties of model structures of graphene oxide with different coverages and compositions. In particular, we considered various concentrations of major functional groups like epoxides, hydroxyls, and carbonyls, which mainly consititute the graphene oxide and the reduced graphene oxide. Our calculated electron energy loss spectra (EELS) demonstrate the π plasmon peak to be less sensitive, while π + θ plasmon is found to have a significant blue shift of about 1.0-3.0 eV, when the concentration of epoxy and hydroxyl functional groups in graphene oxide vary from 25% to 75%. However, the increase in carbonyl groups in the center of the graphene sheet creates holes, which lead to the red shift of the EELS. In the case of 37.5% of oxygen-to-carbon ratio, we find the π plasmon peak to be shifted by roughly 1.0 eV as compared to that of the pristine graphene. Our results agree well with the experimental findings which suggest a blue shift in the EELS of graphene oxide and an absorption feature due to a π electron transition of the carbonyl groups at a lower energy than that of epoxy and hydroxyl groups. We also show that the increase in the width of the hole created by the carbonyl groups significantly decreases the optical gap and opens the band gap, and thus, we argue that reduced graphene oxide with mostly carbonyl groups could be a useful material for developing tunable opto-electronic nanodevices. © 2011 American Chemical Society.

Modulating optical properties of graphene oxide: Role of prominent functional groups

Useful electronic, magnetic, and optical properties have been proposed and observed in thin films of Ti1-x Mx O2 (M=Ta,Nb,V). In this work, we have studied phase formation for films of Ti 1-x Tax O2 prepared by pulsed laser deposition. We show that substitutional Ta in TiO2 results in a different material system in terms of its electronic properties. Moss-Burstein shift is ruled out by comparing the electrical transport data of anatase and rutile TiO2. Vegard's law fit to the blueshift data and the high energy optical reflectivity studies confirm the formation of an alloy with a distinct band structure. © 2011 American Institute of Physics.

Applied Physics Letters

Multifunctional Ti1-x Tax O2: Ta doping or alloying?

Recently Yousefi and Hesameddini [13] have obtained a characterization for shift invariant subspaces of a special class of Hilbert spaces contained in the Hardy space H2. In the present note we settle an open problem posed by them in their paper. In fact, by discussing invariance under multiplication by finite Blaschke factors we prove a far more general result than the main result of [13]. We prove our results under much weaker assumptions than the assumptions of [13] and with a simpler proof. © 2011 The Japan Academy.

Mathematics

Proceedings of the Japan Academy Series A: Mathematical Sciences

Invariant subspaces of certain sub hilbert spaces of H2

Highly luminescent micrometre-sized fine particles of a Zn(ii) metal-organic framework (MOF) of a new $\pi$-electron rich tricarboxylate dispersed in ethanol is demonstrated as a selective sensory material for the detection of nitroaromatic explosives via a fluorescence quenching mechanism. {\textcopyright} The Royal Society of Chemistry 2011.

Chemical Communications

Fluorescent metal-organic framework for selective sensing of nitroaromatic explosives

The 34 grapevine genotypes grown in India were studied for the genetic relatedness using RAPD, markers. Out of 120 primers tested, 31 were found polymorphic for all the genotypes. The molecular diversity of these genotypes was estimated based on 205 RAPD bands using Jaccard's and Dice's similarity coefficients. The two diversity indices for RAPD marker system depicted a high level of correlation (>99%). The resolving power (Rp) and polymorphism information content (PIC) was found highest for primers OPB-15 (16.7) and OPG-15 (9.17), respectively. The UPGMA dendrogram obtained from the cluster analysis using Jaccard's similarity matrix showed two clusters at 35% genetic similarity. In the dendrogram, all the seedless varieties clustered together and other grouped at different similarity levels that suggest the development of seedless grapevine cultivars from related ancestor(s). The RAPD primers OPG-7, OPB-12, OPB-3 and OPB-4 amplified a unique band for Hybrid 72-51 (Angoor Kalan x Pusa Seedless) whereas, OPW-19 and OPB-4 amplified unique band for Bharat Early and Julesky Muscat, respectively. The Mantel's test between the Dice's and Jaccard's similarity matrices provided r = 0.99518 (t value = 8.45) for RAPD, suggesting very good correlation between the two similarity indices. The analysis with RAPD markers provides a quick, reliable and highly informative system to establish genetic relationship among grape genotypes.