DNA polymorphism and local variation in base-pair orientation: a theoretical rationale

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B --> A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.

Dynamics of sheared inelastic dumbbells

We study the dynamical properties of the homogeneous shear flow of inelastic dumbbells in two dimensions as a first step towards examining the effect of shape on the properties of flowing granular materials. The dumbbells are modelled as smooth fused disks characterized by the ratio of the distance between centres (L) and the disk diameter (D), with an aspect ratio (L/D) varying between 0 and 1 in our simulations. Area fractions studied are in the range 0.1-0.7, while coefficients of normal restitution (e(n)) from 0.99 to 0.7 are considered. The simulations use a modified form of the event-driven methodology for circular disks. The average orientation is characterized by an order parameter S, which varies between 0 (for a perfectly disordered fluid) and 1 (for a fluid with the axes of all dumbbells in the same direction). We investigate power-law fits of S as a function of (L D) and (1 - e(n)(2)) There is a gradual increase in ordering as the area fraction is increased, as the aspect ratio is increased or as the coefficient of restitution is decreased. The order parameter has a maximum value of about 0.5 for the highest area fraction and lowest coefficient of restitution considered here. The mean energy of the velocity fluctuations in the flow direction is higher than that in the gradient direction and the rotational energy, though the difference decreases as the area fraction increases, due to the efficient collisional transfer of energy between the three directions. The distributions of the translational and rotational velocities are Gaussian to a very good approximation. The pressure is found to be remarkably independent of the coefficient of restitution. The pressure and dissipation rate show relatively little variation when scaled by the collision frequency for all the area fractions studied here, indicating that the collision frequency determines the momentum transport and energy dissipation, even at the lowest area fractions studied here. The mean angular velocity of the particles is equal to half the vorticity at low area fractions, but the magnitude systematically decreases to less than half the vorticity as the area fraction is increased, even though the stress tensor is symmetric.

Orientation dependence of the indentation impression morphology in a Mg alloy

The formation of anomalous indentations, with two opposite faces describing a pin-cushion effect and the other two faces normal, in long elongated grains of an extruded Mg-2Al-1Zn alloy is reported. Subsurface microstructural observations combined with Schmid factor calculations suggest that extension twinning accompanied by basal slip are the reasons for these. Johnson's expanding cavity model is invoked for further substantiation. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Sanomattakin selvää? : "Ja", "mutta" ja "että" puheenvuoron lopussa

This study describes the use of utterances ending in the conjunctions "ja" (‘and’), "mutta" (‘but’) or "että" (‘that’/‘so’) in Finnish conversation. It argues that in spoken interaction, these conjunctions are not only used as linking elements but also as final elements in interactional and linguistic units. In contrast to more traditional views, the study shows that final conjunctions do not always indicate incompleteness or project continuation, but that they can also form recognizable points for turn-transition. In these contexts they can be reanalyzed as final particles that leave some aspect of the turn implicit. The data for the study consist of audio-taped telephone conversations and videotaped service encounters. Situated within the framework of conversation analysis and interactional linguistics, the study discusses the interactional uses of conjunction-final turns and their recognizability as possibly complete units in talk-in-interaction. The analysis of conjunction-final utterances focuses on 1) participant orientation, and 2) their recurrent contexts of use. The results show that the recipients of conjunction-final utterances often treat them as sufficient and complete in their contexts by displaying understanding or agreement. When the same speaker continues after a pause, it is not always clear that the continuation was "planned" in advance; it can also be reactive to lack of expected uptake. In these cases, a turn can be analyzed as potentially complete even if the same speaker decides to continue after a pause. In the light of these observations, the study confirms the incremental nature of spoken language. All the final conjunctions under examination have recurrent and recognizable contexts of use. Most typically, a conjunction-final utterance is produced in the service of some earlier claim by the same speaker. The conjunction-final utterance may 1) specify the earlier claim with a detailing list ("ja"), 2) legitimize it by presenting grounds ("että") or 3) partly back down from it by making a concession ("mutta"). Together with the earlier claim, conjunction-final utterances form recognizable discourse patterns that are used for argumentative purposes. In these contexts, conjunctions are used to relinquish the floor instead of functioning as turn-holding devices. In conclusion, the study discusses the emergence of conjunctions as final particles – how their development can be explained. Conjunction-type final particles emerge from recurring situations in which the future course of the conjunction-final turn-so-far is clear enough to remain unsaid, to be left to inference. More specifically, this ability to leave something to inference often lies in the fixed discourse patterns that are conventionalized and predictable and thus reducible.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

C-13 MAS NMR spectra of cis,cis-mucononitrile in liquid-crystalline media and in the solid state. Orientation of the carbon chemical-shift tensors

The spinning sidebands observed in the C-13 MAS NMR spectra of cis,cis-mucononitrile oriented in liquid-crystalline media and of the neat sample in the solid state are studied. There are differences in the sideband intensity patterns in the two cases. These differences arise because the order parameters which characterize the orientation of the solute in the liquid-crystalline media differ for different axes. It is shown that, in general, the relative intensities of the sidebands contain information on the sign and magnitude of an effective chemical-shift parameter which is a function of the sum of the products of the principal components of the chemical-shift tensor and the corresponding order parameters with respect to the director. A method for obtaining the orientation of the carbon chemical-shift tensor is proposed. The carbon chemical-shift tensors obtained from gauge-including atomic orbital calculations are also presented for comparison. (C) 1996 Academic Press, Inc.

Microscopic origin of the chirality driven morphologies of the amphiphilic monolayers and bilayers

It is widely known that the compressed monolayers and bilayers of chiral lipids or fatty acids form helical morphologies, while the corresponding racemic modification gives only flat platelets without twist. No molecular explanation of this phenomenon is yet available, although subtle interactions at the chiral centers have often been proposed as the driving force behind the morphology of the aggregate to form a particular shape. In the present study, the morphologies of the chiral amphiphilic assemblies have been predicted on the basis of an effective pair potential between the molecules, which depends on the relative sizes of the groups attached to the chiral centers, the orientation of the amphiphilic molecules and also on the distance between them. It is shown that fur a pair of same kind of enantiomers, the minimum energy conformation favours a twist angle between them. This twist between the neighbouring molecules gives rise to the helicity of the aggregate. The present theory also shows from the molecular considerations that for a pair of mirror-image isomers (i.e. the racemic modification) the minimum energy conformation corresponds to the zero angle between the molecules, thus giving rise to flat platelets as observed in experiments. Another fascinating aspect of such chirality driven helical structures is that the sense (or the handedness) of the helix is highly specific about the chirality of the monomer concerned. The molecular theory shows, for the first time, that the sense of the helical structures in many cases is determined by the sizes of the groups attached to the chiral centers and the effective potential between them. The predicted senses of the helical structures are in complete agreement with the experimental results.

Vibration and buckling of hybrid laminated curved panels

Vibration and buckling of curved plates, made of hybrid laminated composite materials, are studied using first-order shear deformation theory and Reissner's shallow shell theory. For an initial study, only simply-supported boundary conditions are considered. The natural frequencies and critical buckling loads are calculated using the energy method (Lagrangian approach) by assuming a combination of sine and cosine functions in the form of double Fourier series. The effects of curvature, aspect ratio, stacking sequence and ply-orientation are studied. The non-dimensional frequencies and critical buckling load of a hybrid laminate lie in between the values for laminates made of all plies of higher strength and lower strength fibres. Curvature enhances natural frequencies and it is more predominant for a thin panel than a thick one.

Conformation and orientation of alkyl chains in the layered organic-inorganic hybrids: (CnH2n+1NH3)(2)PbI4 (n=12,16,18)

Layered organic inorganic hybrids based on perovskite-derived alkylammonium lead halides have been demonstrated as important new materials in the construction of molecular electronic devices. Typical of this class of materials are the single-perovskite slab lead iodides of the general formula (CnH2n+1NH3)(2)PbI4. While for small n, these compounds are amenable to single-crystal structure determination, the increasing degree of disorder in the long chain (n = 12,14...) compounds makes such an analysis difficult. In this study, we use powder X-ray diffraction, and vibrational and C-13 NMR spectroscopies to establish the conformation, orientation and organization of hydrocarbon chains in the series of layered alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4 (n = 12,16,18). We find that the alkyl chains adopt a tilted bilayer arrangement, while the structure of the inorganic layer remains invariant with respect to the value of n. Conformation-sensitive methylene stretching modes in the infrared and Raman spectra, as well as the C-13 NMR spectra indicate that bonds in the methylene chain are in trans configuration. The skeletal modes of the alkyl chain in the Raman spectra establish that there is a high degree of all-trans conformational registry for the values of n studied here. From the orientation dependence of the infrared spectra of crystals of (CnH2n+1NH3)(2)PbI4 ( n = 12,16), we find that the molecular axis of the all-trans alkyl chains are tilted away from the interlayer normal by an angle of 55degrees. This value of this tilt angle is consistent with the dependence of the c lattice expansion as a function of n, as determined from powder X-ray diffraction.

Orientation dependent electrocatalysis using self-assembled molecular films

Surface orientation of self-assembled molecular films of 2,9,6,23-tetraamino cobalt phthalocyanine on gold and silver is shown to determine the nature and the products of the electrocatalytic reduction of oxygen.

The absolute orientation of a molecule in space: Extension of the 'CIP' system

A scheme for denoting the absolute spatial orientation of molecules and molecular fragments is presented; this is based on three angular deviations - one for each spatial dimension - with respect to a reference orientation, which is itself defined with the help of certain features of the Cahn-Ingold-Prelog stereochemical notation. The new scheme helps in reconstructing the three-dimensional characteristics of molecules from purely verbal descriptors, and may thus find application in various information storage and retrieval processes (e.,-. encrypting holograms, etc.).

Effect of lattice orientation on crack tip constraint in ductile single crystals

In this work, the effect of lattice orientation on the fields prevailing near a notch tip is investigated pertaining to various constraint levels in FCC single crystals. A modified boundary layer formulation is employed and numerical solutions under mode I, plane strain conditions are generated by assuming an elastic-perfectly plastic FCC single crystal. The analysis is carried out corresponding to different lattice orientations with respect to the notch line. It is found that the near-tip deformation field, especially the development of kink or slip shear bands is sensitive to the constraint level. The stress distribution and the size and shape of the plastic zone near the notch tip are also strongly influenced by the level of T-stress. The present results clearly establish that ductile single crystal fracture geometries would progressively lose crack tip constraint as the T-stress becomes more negative irrespective of lattice orientation. Also, the near-tip field for a range of constraint levels can be characterized by two-parameters such as K-T or J-Q as in isotropic plastic solids.

Beta-structure of polypeptides in non-aqueous solutions. II. Side-chain orientation

The specific side-chain orientations of the phenyl group in the polypeptides poly-S-benzyl-L-cysteine, poly-S-carbobenzoxy-L-cysteine and poly-O-carbobenzoxy-L-serine in the beta-structure have been studied by spectral measurements in solutions. All the three polypeptides exhibit aromatic CD bands, indicating the asymmetric placement of the side-chain phenyl rings when the polypeptide backbone takes up the antiparallel beta-structure. Supporting evidence for this is derived from n.m.r. spectra of the polypeptides, which show upfield shift of the phenyl protons due to the stacking of the aromatic rings. Molecular model building studies reveal the stacking of alternate phenyl groups along the polypeptide chain.

Topology Optimization of Micromachined Structures with the Manufacturing Constraints of KOH Etching of (110) Silicon

The focus of this paper is on designing useful compliant micro-mechanisms of high-aspect-ratio which can be microfabricated by the cost-effective wet etching of (110) orientation silicon (Si) wafers. Wet etching of (110) Si imposes constraints on the geometry of the realized mechanisms because it allows only etch-through in the form of slots parallel to the wafer's flat with a certain minimum length. In this paper, we incorporate this constraint in the topology optimization and obtain compliant designs that meet the specifications on the desired motion for given input forces. Using this design technique and wet etching, we show that we can realize high-aspect-ratio compliant micro-mechanisms. For a (110) Si wafer of 250 µm thickness, the minimum length of the etch opening to get a slot is found to be 866 µm. The minimum achievable width of the slot is limited by the resolution of the lithography process and this can be a very small value. This is studied by conducting trials with different mask layouts on a (110) Si wafer. These constraints are taken care of by using a suitable design parameterization rather than by imposing the constraints explicitly. Topology optimization, as is well known, gives designs using only the essential design specifications. In this work, we show that our technique also gives manufacturable mechanism designs along with lithography mask layouts. Some designs obtained are transferred to lithography masks and mechanisms are fabricated on (110) Si wafers.

Measurement of Electron Spin Lifetime and Optical Orientation Efficiency in Germanium Using Electrical Detection of Radio Frequency Modulated Spin Polarization

We propose and demonstrate a technique for electrical detection of polarized spins in semiconductors in zero applied magnetic fields. Spin polarization is generated by optical injection using circularly polarized light which is modulated rapidly using an electro-optic cell. The modulated spin polarization generates a weak time-varying magnetic field which is detected by a sensitive radio-frequency coil. Using a calibrated pickup coil and amplification electronics, clear signals were obtained for bulk GaAs and Ge samples from which an optical spin orientation efficiency of 4.8% could be determined for Ge at 1342 nm excitation wavelength. In the presence of a small external magnetic field, the signal decayed according to the Hanle effect, from which a spin lifetime of 4.6 +/- 1.0 ns for electrons in bulk Ge at 127 K was extracted.