A general procedure for generation of curved DNA molecules.

A general method for generation of base-pairs in a curved DNA structure, for any prescribed values of helical parameters--unit rise (h), unit twist (theta), wedge roll (theta R) and wedge tilt (theta T), propeller twist (theta p) and displacement (D) is described. Its application for generation of uniform as well curved structures is also illustrated with some representative examples. An interesting relationship is observed between helical twist (theta), base-pair parameters theta x, theta y and the wedge parameters theta R, theta T, which has important consequences for the description and estimation of DNA curvature.

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.

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Vortex sheet simulation of a plane �canonical� mixing layer

Discrete vortex simulations of the mixing layer carried out in the past have usually involved large induced velocity fluctuations, and thus demanded rather long time-averaging to obtain satisfactory values of Reynolds stresses and third-order moments. This difficulty has been traced here, in part, to the use of discrete vortices to model what in actuality are continuous vortex sheets. We propose here a novel two-dimensional vortex sheet technique for computing mixing layer flow in the limit of infinite Reynolds number. The method divides the vortex sheet into constant-strength linear elements, whose motions are computed using the Biot-Savart law. The downstream far-field is modelled by a steady vorticity distribution derived by application of conical similarity from the solution obtained in a finite computational domain. The boundary condition on the splitter plate is satisfied rigorously using a doublet sheet. The computed large-scale roll-up of the vortex sheet is qualitatively similar to experimentally obtained shadow-graphs of the plane turbulent mixing layer. The mean streamwise velocity profile and the growth rate agree well with experimental data. The presently computed Reynolds stresses and third-order moments are comparable with experimental and previous vortex-dynamical results, without using any external parameter (such as the vortex core-size) of the kind often used in the latter. The computed autocorrelations are qualitatively similar to experimental results along the top and bottom edges of the mixing layer, and show a well-defined periodicity along the centreline. The accuracy of the present computation is independently established by demonstrating negligibly small changes in the five invariants (including the Hamiltonian) in vortex dynamics.

Modelling plane mixing layers using vortex points and sheets

We present here a critical assessment of two vortex approaches (both two-dimensional) to the modelling of turbulent mixing layers. In the first approach the flow is represented by point vortices, and in the second it is simulated as the evolution of a continuous vortex sheet composed of short linear elements or ''panels''. The comparison is based on fresh simulations using approximately the same number of elements in either model, paying due attention in both to the boundary conditions far downstream as well as those on the splitter plate from which the mixing layer issues. The comparisons show that, while both models satisfy the well-known invariants of vortex dynamics approximately to the same accuracy, the vortex panel model, although ultimately not convergent, leads to smoother roll-up and values of stresses and moments that are in closer agreement with the experiment, and has a higher computational efficiency for a given degree of convergence on moments. The point vortex model, while faster for a given number of elements, produces an unsatisfactory roll-up which (for the number of elements used) is rendered worse by the incorporation of the Van der Vooren correction for sheet curvature.

Response, loads, and stability of interconnected rotor-body systems

A rotor-body system with blades interconnected through viscoelastic elements is analyzed for response, loads, and stability in propulsive trim in ground contact and under forward-flight conditions, A conceptual model of a multibladed rotor with rigid flap and lag motions, and the fuselage with rigid pitch and roll motions is considered, Although the interconnecting elements are placed in the in-plane direction, considerable coupling between the flap-lag motions of the blades can occur in certain ranges of interblade element stiffness, Interblade coupling can yield significant changes in the response, loads, and stability that are dependent on the interblade element and rotor-body parameters, Ground resonance stability investigations show that by tuning the interblade element stiffness, the ground resonance instability problem can be reduced or eliminated, The interblade elements with damping and stiffness provide an effective method to overcome the problems of ground and air resonance.

Command Tracking in High Performance Aircrafts: A New Dynamic Inversion Design

This paper proposes a new straight forward technique based on dynamic inversion, which is applied for tracking the pilot commands in high performance aircrafts.Pilot commands assumed in longitudinal mode are normal acceleration and total velocity(while roll angle and lateral acceleration are maintained at zero). In lateral mode, roll rate and total velocity are used as pilot commands (while climb rate and lateral acceleration are maintained at zero). Ensuring zero lateral acceleration leads to a better turn co-ordination. A six degree-of-freedom model of F-16 aircraft is used for both control design as well as simulation studies. Promising results are obtained which are found to be superior as compared to an existing approach (which is also based on dynamic inversion). The new approach has two potential benefits, namely reduced oscillatory response and reduced control magnitude. Another advantage of this approach is that it leads to a significant reduction of tuning parameters in the control design process.

Modeling of wheeled mobile robots using dextrous manipulation kinematics

Abstract—This document introduces a new kinematic simulation of a wheeled mobile robot operating on uneven terrain. Our modeling method borrows concepts from dextrous manipulation. This allows for an accurate simulation of the way 3-dimensional wheels roll over a smooth ground surface. The purpose of the simulation is to validate a new concept for design of off-road wheel suspensions, called Passive Variable Camber (PVC). We show that PVC eliminates kinematic slip for an outdoor robot. Both forward and inverse kinematics are discussed and simulation results are presented.

Effect of rolling temperature and reduction in thickness on microstructure and mechanical properties of ZM21 magnesium alloy and its subsequent annealing treatment

In this present paper, the effects of non-isothermal rolling temperature and reduction in thickness followed by annealing on microstructure and mechanical properties of ZM21 magnesium alloy were investigated. The alloy rolled at four different temperatures 250 degrees C, 300 degrees C, 350 degrees C and 400 degrees C with reductions of 25%, 50% and 75%. Non-isothermal rolling resulted in grain refinement, introduction of shear bands and twins in the matrix alloy. Partial to full recrystallization was observed when the rolling temperature was above recrystallization temperature. Rolling and subsequent annealing resulted in strain-free equiaxed grains and complete disappearance of shear bands and twins. Maximum ultimate strength (345 MPa) with good ductility (14%) observed in the sample rolled at 250 degrees C with 75% reduction in thickness followed by short annealing. Recrystallization during warm/hot rolling was sluggish, but post-roll treatment gives distinct views about dynamic and static recrystallization. (C) 2011 Elsevier B.V. All rights reserved.

X-ray structure of a galactose-specific lectin from Spatholobous parviflorous

A galactose-specific seed lectin from Spatholobous parviflorus (SPL) has been purified, crystallized and its X-ray structure solved. It is the first lectin purified and crystallized from the genus Spatholobus (family: Fabaceae). The crystals belong to the space group P1, with a = 60.792 angstrom, b = 60.998 angstrom, c = 78.179 angstrom, alpha = 78.68 degrees, beta = 88.62 degrees, gamma = 104.32 degrees. The data were collected at 2.04 angstrom resolution under cryocondition, on a MAR image-plate detector system, mounted on a rotating anode X-ray generator. The coordinates of Dolichos biflorus lectin (1lu1) were successfully used for the structure solution by molecular replacement method. The primary structure of the SPL was not known earlier and it was unambiguously visible in the electron density. S. parviflorus lectin is a hetero-dimeric-tetramer with two alpha and two beta chains of 251 and 239 residues respectively. SPL has two metal ions, Ca(2+) and Mn(2+), bound to a loop region of each chain. The SPL monomers are in jelly roll form. (C) 2011 Elsevier B.V. All rights reserved.

Enhancing fluorescence signals from aluminium thin films and foils using polyelectrolyte multilayers

In this paper we investigate the application of polyelectrolyte multilayer (PEM) coated metal slides in enhancing fluorescence signal. We observed around eight-fold enhancement in fluorescence for protein incubated on PEM coated on aluminium mirror surface with respect to that of functionalized bare glass slides. The fluorescence intensities were also compared with commercially available FAST (R) slides (Whatman) offering 3D immobilization of proteins and the results were found to be comparable. We also showed that PEM coated on low-cost and commonly available aluminium foils also results in comparable fluorescence enhancement as sputtered aluminium mirrors. Immunoassay was also performed, using model proteins, on aluminium mirror as well as on aluminium foil based devices to confirm the activity of proteins. This work demonstrated the potential of PEMs in the large-scale, roll-to-roll manufacturing of fluorescence enhancements substrates for developing disposable, low-cost devices for fluorescence based diagnostic methods.

Evolution of microstructure and texture during deformation and recrystallization of heavily rolled Cu-Cu multilayer

A Cu-Cu multilayer processed by accumulative roll bonding was deformed to large strains and further annealed. The texture of the deformed Cu-Cu multilayer differs from the conventional fcc rolling textures in terms of higher fractions of Bs and RD-rotated cube components, compared with the volume fraction of Cu component. The elongated grain shape significantly affects the deformation characteristics. Characteristic microstructural features of both continuous dynamic recrystallization and discontinuous dynamic recrystallization were observed in the microtexture measurements. X-ray texture measurements of annealing of heavily deformed multilayer demonstrate constrained recrystallization and resulted in a bimodal grain size distribution in the annealed material at higher strains. The presence of cube- and BR-oriented grains in the deformed material confirms the oriented nucleation as the major influence on texture change during recrystallization. Persistence of cube component throughout the deformation is attributed to dynamic recrystallization. Evolution of RD-rotated cube is attributed to the deformation of cube components that evolve from dynamic recrystallization. The relaxation of strain components leads to Bs at larger strains. Further, the Bs component is found to recover rather than recrystallize during deformation. The presence of predominantly Cu and Bs orientations surrounding the interface layer suggests constrained annealing behavior.

Transition and acoustic response of recirculation structures in an unconfined co-axial isothermal swirling flow

This paper reports the first observations of transition from a pre-vortex breakdown (Pre-VB) flowreversal to a fully developed central toroidal recirculation zone in a non-reacting, double-concentric swirling jet configuration and its response to longitudinal acoustic excitation. This transition proceeds with the formation of two intermediate, critical flow regimes. First, a partially penetrated vortex breakdown bubble (VBB) is formed that indicates the first occurrence of an enclosed structure as the centre jet penetration is suppressed by the growing outer roll-up eddy; resulting in an opposed flow stagnation region. Second, a metastable transition structure is formed that marks the collapse of inner mixing vortices. In this study, the time-averaged topological changes in the coherent recirculation structures are discussed based on the non-dimensional modified Rossby number (Ro(m)) which appears to describe the spreading of the zone of swirl influence in different flow regimes. Further, the time-mean global acoustic response of pre-VB and VBB is measured as a function of pulsing frequency using the relative aerodynamic blockage factor (i.e., maximum radial width of the inner recirculation zone). It is observed that all flow modes except VBB are structurally unstable as they exhibit severe transverse radial shrinkage (similar to 20%) at the burner Helmholtz resonant modes (100-110 Hz). In contrast, all flow regimes show positional instability as seen by the large-scale, asymmetric spatial shifting of the vortex core centres. Finally, the mixing transfer function M (f) and magnitude squared coherence lambda(2)(f) analysis is presented to determine the natural couplingmodes of the system dynamic parameters (u', p'), i.e., local acoustic response. It is seen that the pre-VB flow mode exhibits a narrow-band, low pass filter behavior with a linear response window of 100-105 Hz. However, in the VBB structure, presence of critical regions such as the opposed flow stagnation region alters the linearity range with the structure showing a response even at higher pulsing frequencies (100-300 Hz). (C) 2013 AIP Publishing LLC.

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.