Symmetry-breaking transitions in equilibrium shapes of coherent precipitates: Effect of elastic anisotropy and inhomogeneity

We examine the symmetry-breaking transitions in equilibrium shapes of coherent precipitates in two-dimensional (2-D) systems under a plane-strain condition with the principal misfit strain components epsilon(xx)*. and epsilon(yy)*. For systems with cubic elastic moduli, we first show all the shape transitions associated with different values of t = epsilon(yy)*/epsilon(xx)*. We also characterize each of these transitions, by studying its dependence on elastic anisotropy and inhomogeneity. For systems with dilatational misfit (t = 1) and those with pure shear misfit (t = -1), the transition is from an equiaxed shape to an elongated shape, resulting in a break in rotational symmetry. For systems with nondilatational misfit (-1 < t < 1; t not equal 0), the transition involves a break in mirror symmetries normal to the x- and y-axes. The transition is continuous in all cases, except when 0 < t < 1. For systems which allow an invariant line (-1 less than or equal to t < 0), the critical size increases with an increase in the particle stiffness. However, for systems which do not allow an invariant line (0 < t less than or equal to 1), the critical size first decreases, reaches a minimum, and then starts increasing with increasing particle stiffness; moreover, the transition is also forbidden when the particle stiffness is greater than a critical value.

Temperature dependence of infrared and Raman modes in polymeric RbC60

Temperature dependence of the intra-molecular vibrational modes Of C-60 in the quasi-1D polymeric RbC60, across the low temperature transition at similar to50 K, has been probed through infrared (IR) and Raman spectroscopies. With the lowering of temperature, the split IR modes of RbC60 are seen to harden but below 50 K a small but definitive signature of an anomalous softening is observed. In addition, the background IR transmission shows an increase below 50 K with the opening of a well defined gap in the electronic spectrum. The implications of these results, along with those of Raman measurements, are discussed in terms of the interaction of intra-molecular phonons with electrons and spin excitations in the system. (C) 2002 Published by Elsevier Science Ltd.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

Through ring umbrella inversion of a molecular rattle

We report theoretical investigations on some [Ring]Li--(+) compounds, which can exhibit a through ring umbrella like inversion. Our studies predict cyclononatetraenyllithium to be molecular rattle, in which such inversions can occur. The potential energy for the motion is a double well, with an activation barrier of 11.50 kcal/mol. We find that the lithium should go through the ring easily by an excitation to nu = 17 vibrational level. (C) 2002 Elsevier Science B.V. All rights reserved.

Crystal and molecular structure of synthetic cholesterol compounds vitamin D3-analogues (I) 24(S)-hydroxy coprastan-3-one & (II) 24(R)-hydroxy coprastan-3-one

The title compound I (24-(S)-Hydroxy Coprastan-3-one) crystallises in orthorhombic space group P2(1)2(1)2(1) with Z = 4. The unit cell dimensions are a = 6.701(2)Angstrom, b = 11.506(8)Angstrom, c = 32.183(4)Angstrom, V = 2481(2)Angstrom (3), D-cal = 1.077 Mg/m(3). The tide compound II (24-(R)-Hydroxy Coprastan-3-one) crystallises in orthorhombic space group P212121 with two molecules per assymetric unit and with Z = 8. The Unit cell dimensions are a = 10.954(2)Angstrom, b = 21.757(6)Angstrom, c = 21.130(7)Angstrom, V = 5035.0(2)Angstrom (3), D-cal = 1.062 Mg/m(3). In compound I and in both the molecules of compound II, the rings A, B & C are in chair conformation and the five membered ring D is in envelope conformation. The priority sequence attached to the chiral carbon C24 has "S" designation in compound I and "R" designation in compound II. The structures are stabilized by C-H . . .O and O-H---O hydrogen bonds.

A fast quasi-Newton method for semi-supervised SVM

Due to its wide applicability, semi-supervised learning is an attractive method for using unlabeled data in classification. In this work, we present a semi-supervised support vector classifier that is designed using quasi-Newton method for nonsmooth convex functions. The proposed algorithm is suitable in dealing with very large number of examples and features. Numerical experiments on various benchmark datasets showed that the proposed algorithm is fast and gives improved generalization performance over the existing methods. Further, a non-linear semi-supervised SVM has been proposed based on a multiple label switching scheme. This non-linear semi-supervised SVM is found to converge faster and it is found to improve generalization performance on several benchmark datasets. (C) 2010 Elsevier Ltd. All rights reserved.

Propensity of formation of zipper architecture vs. Lincoln log arrangement in solvated molecular complexes of melamine with hydroxybenzoic acids

Molecular complexes of melamine with hydroxy and dihydroxybenzoic acids have been analyzed to assess the collective role of the hydroxyl (OH) and carboxyl (COOH) functionalities in the recognition process. In most cases, solvents of crystallization do play a major role in self-assembly and structure stabilization. Hydrated compounds generate linear chains of melamine molecules with acid molecules pendant resulting in a zipper architecture. However, anhydrous and solvated compounds generate tetrameric units consisting of melamine dimers together with acid molecules. These tetramers in turn interweave to form a Lincoln log arrangement in the crystal. The salt/co-crystal formation in these complexes cannot be predicted apriori on the basis of Delta pK(a) values as there exists a salt-to-co-crystal continuum.

Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA

The protein MsRbpA from Mycobacterium smegmatis rescues RNA polymerase (RNAP) from the inhibitory effect of rifampicin (Rif). We have reported previously that MsRbpA interacts with the beta-subunit of RNAP and that the effect of MsRbpA on Rif-resistant (Rif(R)) RNAP is minimal. Here we attempted to gain molecular insights into the mechanism of action of this protein with respect to its role in rescuing RNAP from Rif-mediated transcription inhibition. Our experimental approach comprised multiple-round transcription assays, fluorescence spectroscopy, MS and surface plasmon resonance in order to meet the above objective. Based on our molecular studies we propose here that Rif is released from its binding site in the RNAP-Rif complex in the presence of MsRbpA. Biophysical studies reveal that the location of MsRbpA on RNAP is at the junction of the beta- and beta'-subunits, close to the Rif-binding site and the (i + 1) site on RNAP.

Indium Nitride Nanometric-Objects on c-Sapphire Grown by Plasma-Assisted Molecular Beam Epitaxy

The indium nitride (InN)-based nanometric-objects were grown directly on a c-sapphire substrate by using plasma-assisted molecular beam epitaxy (PAMBE) at different substrate temperatures. High resolution X-ray diffraction (HRXRD) reveals the InN (0002) reflection and full width at half maximum (FWHM) found to be decreased with increasing the growth temperature. The size, height and density of the grown nanometric-objects studied by scanning electron microscopy (SEM) has remarkable differences, evidencing the decisive role of substrate temperature. Photoluminescence (PL) studies revealed that the emission energy is shifted towards the higher side from the bulk value, i.e., a blue shift in the PL spectra was observed. The temperature dependence of the PL peak position shows an ``S-shaped'' emission energy shift, which can be attributed to the localization of carriers in the nanometric-objects.

Simulation of the infrared spectra of N-methylformamide and N-methylacetamide by the extended molecular mechanics method

The infrared spectra of the matrix isolated species of N-methylformamide (NMF) and N-methylacetamide (NMA) and their N-deuterated molecules have been simulated by the extended molecular mechanics method using an empirical force field which includes charges and charge fluxes as coulombic potential parameters. The structural parameters and dipole. moments of NMF and NMA have. also been computed in satisfactory agreement with the experiment. Good agreement between experimental and calculated vibrational frequencies and infrared absorption band intensities for NMF and NMA and their deuterated molecules has been obtained. The vibrational assignments of NMF and NMA are-discussed taking also into account the infrared absorption intensities.

Electric Field Directed Growth of Molecular Wires of Charge Transfer Molecules on Prefabricated Metal Electrodes

Molecular wires of charge transfer molecules were formed by co-evaporating the 7 7 8 8-Tetracyanoquinodimethane [TCNQ] (acceptor) and Tetrathiafulvalene [TTF] (donor) molecules across prefabricated metal electrodes. Molecular wires of TTF TCNQ were also formed by evaporating single complex of TTF:TCNQ across prefabricated metal electrodes The prefabricated metal electrodes were made using electron beam lithography on SiO2 and glass cover slip substrates. Even though TTF: TCNQ wires grown from both co-evaporation and evaporation techniques show semiconductor like behavior in temperature dependence of resistance they show different activation energies due the difference in stoichiometry of TTF and TCNQ.