Inverse surface melting in confined clusters: Ar-13 in zeolite L

Monte Carlo and molecular dynamics simulations on an Ar-13 cluster in zeolite L have been carried out at a series of temperatures to understand the rigid-nonrigid transition corresponding to the solid-liquid transition exhibited by the free Ar-13 cluster. The icosahedral geometry of the free cluster is no longer preferred when the cluster is confined in the zeolite. The root-mean-squared pair distance fluctuation, delta, exhibits a sharp, well-defined rigid-nonrigid transition at 17 K as compared to 27 K for the free cluster. Multiple peaks in the distribution of short-time averages of the guest-host interaction energy indicate coexistence of two phases.; It is shown that this transition is associated with the inner atoms becoming mobile at 17 K even while the outer layer atoms, which are in close proximity to the zeolitic wall, continue to be comparatively immobile. This may be contrasted with the melting of large free clusters of 40 or more atoms which exhibit surface melting. Guest-host interactions seem to play a predominant role in determining the properties of confined clusters. We demonstrate that the volume of the cluster increases rather sharply at 17 and 27 K respectively for the confined and the free cluster. Power spectra suggest that the motion of the inner atoms is generally parallel to the atoms which form the cage wall.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

Plate-shaped transformation products in zirconium-base alloys

Plate-shaped products resulting from martensitic, diffusional, and mixed mode transformations in zirconium-base alloys are compared. in the present study. These alloys are particularly suitable for the comparison in view of the fact that the lattice correspondence between the parent beta (bcc) and the product alpha (hcp) or gamma-hydride (fct) phases are remarkably similar for different types of transformations. Crystallographic features such as orientation relations, habit planes, and interface structures associated with these transformations have been compared:, with a view toward examining whether the transformation mechanisms have characteristic imprints on these experimental observables. Martensites exhibiting dislocated lath, internally twinned plate, and self-accommodating three-plate cluster morphologies have been encountered in Zr-2.5Nb alloy. Habit planes corresponding to all these morphologies have been found to be consistent with the predictions based on the invariant plane strain (IFS) criterion. Different morphologies have been found to reflect the manner in which the neighboring martensite variants are assembled. Lattice-invariant shears (LISs) for all these cases have been identified to be either {10 (1) over bar 1}(alpha) ((1) over bar 123)(alpha) slip or twinning on (10 (1) over bar 1)(alpha) planes. Widmanstatten alpha precipitates, forming in a step-quenching treatment, have been shown to have a lath morphology, the alpha/beta interface being decorated with a periodic array of (c + a) dislocations at a spacing of 8 to 10 nm. The line vectors of these dislocations are nearly parallel to the invariant lines. The alpha precipitates, forming in the retained beta phase on aging, exhibit an internally twinned structure with a zigzag habit plane. Average habit planes for the morphologies have been found to lie near the {103}(beta) - {113}(beta) poles, which are close to the specific variant of the {112}(beta) plane, which transforms into a prismatic plane of the type {1 (1) over bar 00}(alpha). The crystallography of the formation of the gamma-hydride phase (fct) from both the alpha and beta phases is seen to match the IFS predictions. While the beta-gamma transformation can be treated approximately as a simple shear on the basal plane involving a change in the stacking sequence, the alpha-gamma transformation call be conceptually broken into a alpha --> beta transformation following the Burgers correspondence and the simple beta-gamma shear process. The active eutectoid decomposition in the Zr-Cu system, beta --> alpha + beta', has been described in terms of cooperative growth of the alpha phase from the beta phase through the Burgers correspondence and of the partially ordered beta' (structurally similar to the equilibrium Zr2Cu phase) through an ordering process. Similarities and differences in crystallographic features of these transformations have been discussed. and the importance of the invariant line vector in deciding the geometry of the corresponding habit planes has been pointed out.

The algebra and geometry of SU(3) matrices

We give an elementary treatment of the defining representation and Lie algebra of the three-dimensional unitary unimodular group SU(3). The geometrical properties of the Lie algebra, which is an eight dimensional real Linear vector space, are developed in an SU(3) covariant manner. The f and d symbols of SU(3) lead to two ways of 'multiplying' two vectors to produce a third, and several useful geometric and algebraic identities are derived. The axis-angle parametrization of SU(3) is developed as a generalization of that for SU(2), and the specifically new features are brought out. Application to the dynamics of three-level systems is outlined.

Synthesis, spectral characterization and in vitro microbiological evaluation of novel glyoxal, biacetyl and benzil bis-hydrazone macrocyclic Schiff bases and their Co(II), Ni(II) and Cu(II) complexes

A series of binuclear Co(II), Ni(II) and Cu(II) complexes were synthesized by the template condensation of glyoxal, biacetyl or benzil bis-hydrazide, 2,6-diformyl-4-methylphenol and Co(11), Ni(II) or Cu(II) chloride in a 2:2:2 M ratio in ethanol. These 22-membered macrocyclic complexes were characterized by elemental analyses, magnetic, molar conductance, spectral, thermal and fluorescence studies. Elemental analyses suggest the complexes have a 2:1 stoichiometry of the type (M2LX2]center dot nH(2)O and Ni(2)LX(2)2H(2)O]center dot nH(2)O (where M = Co(II) and Cu(II); L = H2L1, H2L2 and H2L3; X = Cl; n = 2). From the spectroscopic and magnetic studies, it has been concluded that the Co(11) and Cu(11) complexes display a five coordinated square pyramidal geometry and the Ni(II) complexes have a six coordinated octahedral geometry. The Schiff bases and their metal complexes have also been screened for their antibacterial and antifungal activities by the MIC method. (C) 2011 Elsevier Ltd. All rights reserved.

Role of Hetero-Halogen (F center dot center dot center dot X, X = Cl, Br, and I) or Homo-Halogen (X center dot center dot center dot X, X = F, Cl, Br, and I) Interactions in Substituted Benzanilides

A series of halogen-substituted benzanilides have been synthesized and characterized, and crystallization studies directed toward generation of polymorphs have been performed to delineate the importance of interactions involving halogens. The effect of halogen substitution on the molecular conformation and supramolecular packing has been investigated. The N-H center dot center dot center dot O H-bond is a key structure-directing element acting in conjunction with C-H center dot center dot center dot O and C-H center dot center dot center dot pi interactions. In addition, it is of importance to note that organic fluorine prefers Type I F center dot center dot center dot F contacts, whereas Cl, Br, and I prefer Type II contacts. Hetero-halogen center dot center dot center dot halogen interactions on the other hand are predominately of Type II geometry, and this is due to the greater polarizability of the electron density associated with the heavier halogens. It is of importance to evaluate the contributing role of these interactions in crystal structure packing and the co-operativity associated with such interactions in the solid state.

Numerical simulations of fracture initiation in ductile solids under mode I, dynamic loading

In this paper, an overview of some recent computational studies by the authors on ductile crack initiation under mode I, dynamic loading is presented. In these studies, a large deformation finite element procedure is employed along with the viscoplastic version of the Gurson constitutive model that accounts for the micro-mechanical processes of void nucleation, growth and coalescence. A three-point bend fracture specimen subjected to impact, and a single edge notched specimen loaded by a tensile stress pulse are analysed. Several loading rates are simulated by varying the impact speed or the rise time and magnitude of the stress pulse. A simple model involving a semi-circular notch with a pre-nucleated circular hole situated ahead of it is considered. The growth of the hole and its interaction with the notch tip, which leads to plastic strain and porosity localization in the ligament connecting them, is simulated. The role of strain-rate dependence on ductile crack initiation at high loading rates, and the specimen geometry effect on the variation of dynamic fracture toughness with loading rate are Investigated.

Characterization of alkyl chain conformation in an intercalated cationic lipid bilayer by IR spectroscopy

A structural analysis of alkyl chain conformation of an intercalated cationic lipid bilayer is described. Dialkyl dimethylammonium ions (di-C(n)DA) were ion exchanged into the galleries of layered cadmium thiophosphate to give Cd0.83PS3(di-C(n)DA)(0.34). The grafting density and interlayer expansions were identical to those for the intercalated single chain alkyl trimethylammonium (C(n)TA) bilayers. The increased methylene chain density in the galleries, however, forces the intercalated lipid to adopt a more trans ordered structure. Progression bands arising from the coupling of vibrational modes of trans methylene units are used to establish the extent of trans registry. Two types of ordered structures of the intercalated cationic lipid may be distinguished. One in which both alkyl chains adopt an all-trans geometry, and one in which the methylene bond adjacent to the headgroup on one of the alkyl chains is gauche. The latter structure is typically found in the crystalline state of these cationic lipids. The concentrations of the two structures were determined from the ratio of the intensities of the progression bands and were found to remain unchanged with temperature.

Constraint loss under dynamic loading in rate independent plastic solids

The objectives of this paper are to examine the loss of crack tip constraint in dynamically loaded fracture specimens and to assess whether it can lead to enhancement in the fracture toughness at high loading rates which has been observed in several experimental studies. To this end, 2-D plane strain finite element analyses of single edge notched (tension) specimen and three point bend specimen subjected to time varying loads are performed. The material is assumed to obey the small strain J(2) flow theory of plasticity with rate independent behaviour. The results demonstrate that a valid J-Q field exists under dynamic loading irrespective of the crack length and specimen geometry. Further, the constraint parameter Q becomes strongly negative at high loading rates, particularly in deeply cracked specimens. The variation of dynamic fracture toughness K-dc with stress intensity rate K for cleavage cracking is predicted using a simple critical stress criterion. It is found that inertia-driven constraint loss can substantially enhance K-dc for (K) over dot > 10(5) MPa rootm/s.

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight < 1.5 KDa). The prediction accuracy of DEPTH is comparable to that of other geometry-based prediction methods including LIGSITE, SURFNET and Pocket-Finder (all with Matthew's correlation coefficient of similar to 0.4) over a testing set of 225 single and multi-chain protein structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

Helical structures: The geometry of protein helices and nanotubes

In nature, helical structures arise when identical structural subunits combine sequentially, the orientational and translational relation between each unit and its predecessor remaining constant. A helical structure is thus generated by the repeated action of a screw transformation acting on a subunit. A plane hexagonal lattice wrapped round a cylinder provides a useful starting point for describing the helical conformations of protein molecules, for investigating the geometrical properties of carbon nanotubes, and for certain types of dense packings of equal spheres.

Three-dimensional computational modeling of momentum, heat, and mass transfer in a laser surface alloying process

A three- dimensional, transient model is developed for studying heat transfer, fluid flow, and mass transfer for the case of a single- pass laser surface alloying process. The coupled momentum, energy, and species conservation equations are solved using a finite volume procedure. Phase change processes are modeled using a fixed-grid enthalpy-porosity technique, which is capable of predicting the continuously evolving solid- liquid interface. The three- dimensional model is able to predict the species concentration distribution inside the molten pool during alloying, as well as in the entire cross section of the solidified alloy. The model is simulated for different values of various significant processing parameters such as laser power, scanning speed, and powder feedrate in order to assess their influences on geometry and dynamics of the pool, cooling rates, as well as species concentration distribution inside the substrate. Effects of incorporating property variations in the numerical model are also discussed.

Surfaces of Bounded Mean Curvature In Riemannian Manifolds

Consider a sequence of closed, orientable surfaces of fixed genus g in a Riemannian manifold M with uniform upper bounds on the norm of mean curvature and area. We show that on passing to a subsequence, we can choose parametrisations of the surfaces by inclusion maps from a fixed surface of the same genus so that the distance functions corresponding to the pullback metrics converge to a pseudo-metric and the inclusion maps converge to a Lipschitz map. We show further that the limiting pseudo-metric has fractal dimension two. As a corollary, we obtain a purely geometric result. Namely, we show that bounds on the mean curvature, area and genus of a surface F subset of M, together with bounds on the geometry of M, give an upper bound on the diameter of F. Our proof is modelled on Gromov's compactness theorem for J-holomorphic curves.

Analytical Study of Low-Field Diffusive Transport in Highly Asymmetric Bilayer Graphene Nanoribbon

We present a simplified theory of carrier backscattering coefficient in a twofold degenerate asymmetric bilayer graphene nanoribbon (BGN) under the application of a low static electric field. We show that for a highly asymmetric BGN(Delta = gamma), the density of states in the lower subband increases more that of the upper, in which Delta and gamma are the gap and the interlayer coupling constant, respectively. We also demonstrate that under the acoustic phonon scattering regime, the formation of two distinct sets of energy subbands signatures a quantized transmission coefficient as a function of ribbon width and provides an extremely low carrier reflection coefficient for a better Landauer conductance even at room temperature. The well-known result for the ballistic condition has been obtained as a special case of the present analysis under certain limiting conditions which forms an indirect validation of our theoretical formalism.

Qualitative theorem proving in linear constraints

We know, from the classical work of Tarski on real closed fields, that elimination is, in principle, a fundamental engine for mechanized deduction. But, in practice, the high complexity of elimination algorithms has limited their use in the realization of mechanical theorem proving. We advocate qualitative theorem proving, where elimination is attractive since most processes of reasoning take place through the elimination of middle terms, and because the computational complexity of the proof is not an issue. Indeed what we need is the existence of the proof and not its mechanization. In this paper, we treat the linear case and illustrate the power of this paradigm by giving extremely simple proofs of two central theorems in the complexity and geometry of linear programming.