Structural mobility and transformations in globular proteins

Although globular proteins are endowed with well defined three-dimensional structures, they exhibit substantial mobility within the framework of the given threedimensional structure. The different types of mobility found in proteins by and large correspond to the different levels of organisational hierarchy in protein architecture. They are of considerable structural and functional significance, and can be broadly classified into(a) thermal and conformational fluctuations, (b) segmental mobility, (c) interdomain mobility and (d) intersubunit mobility. Protein crystallographic studies has provided a wealth of information on all of them. The temperature factors derived from X-ray diffraction studies provide a measure of atomic displacements caused by thermal and conformational fluctuations. The variation of displacement along the polypeptide chain have provided functionally significant information on the flexibility of different regions of the molecule in proteins such as myoglobin, lysozyme and prealbumin. Segmental mobility often involves the movement of a region or a segment of a molecule with respect to the rest, as in the transition between the apo and the holo structures of lactate dehydrogenase. It may also involve rigidification of a disordered region of the molecule as in the activation of the zymogens of serine proteases. Transitions between the apo and the holo structures of alcohol dehydrogenase,and between the free and the sugar bound forms of hexokinase, are good examples of interdomain mobility caused by hinge-bending. The capability of different domains to move semi-independently contributes greatly to the versatility of immunoglobulin molecules. Interdomain mobility in citrate synthase appears to be more complex and its study has led to an alternative description of domain closure. The classical and the most thoroughly studied case of intersubunit mobility is that in haemoglobin. The stereochemical mechanism of the action of this allosteric protein clearly brings out the functional subtilities that could be achieved through intersubunit movements. In addition to ligand binding and activation,environmental changes also often cause structural transformations. The reversible transformation between 2 Zn insulin and 4 Zn insulin is caused by changes in the ionic strength of the medium. Adenylate Kinase provides a good example for functionally significant reversible conformational transitions induced by variation in pH. Available evidences indicate that reversible structural transformations in proteins could also be caused by changes in the aqueous environment, including those in the amount of water surrounding protein molecules.

Excited-state structures of molecules with nearby electronic states

Vibronic coupling among the nearby excited electronic states via the in-plane and the out-of-plane nuclear motions is examined in benzene, pyrazine, formaldehyde and thioformaldehyde. Results reveal that in benzene the structure distorts via the most active nuclear bending (planar) motion while in the other molecules the structures distort through an out-of-plane bending motion in their respective lowest excited states.

Nonlinear dynamic analysis of dragonfly inspired piezoelectrically driven flapping and pitching wing

The nonlinear equations for coupled elastic flapping-twisting motion of a dragonfly in- spired smart flapping wing are used for a flapping wing actuated from the root by a PZT unimorph in the piezofan configuration. Excitation by the piezoelectric harmonic force generates only the flap bending motion, which in turn, induces the elastic twist motion due to interaction between flexural and torsional vibrations modes. An unsteady aerodynamic model is used to obtain the aerodynamic forces. Numerical simulations are performed using a wing whose size is the same as the dragonfly Sympetrum Frequens wing. It is found that the value of average lift reaches to its maximum when the smart flapping wing is excited at a frequency closer to the natural frequency in torsion. Moreover, consideration of the elastic twisting of flapping wing leads to an increase in the lift force. It is also found that the flapping wing generates sufficient lift to support its own weight and carry a small pay- load. Therefore, the piezoelectrically actuated smart flapping wing based on the geometry of Sympetrum Frequens wing and undergoing flapping-twisting motions may be considered as a potential candidate for use in MAV applications.

Effect of quantum nuclear motion on hydrogen bonding

This work considers how the properties of hydrogen bonded complexes, X-H center dot center dot center dot Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H center dot center dot center dot O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 angstrom, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends. (C) 2014 AIP Publishing LLC.

Study of motion around a static black hole in Einstein and Lovelock gravity

We study motion around a static Einstein and pure Lovelock black hole in higher dimensions. It is known that in higher dimensions bound orbits exist only for a pure Lovelock black hole in all even dimensions, D = 2N + 2, where N is the degree of Lovelock polynomial action. In particular, we compute periastron shift and light bending, and the latter is given by one of the transverse spatial components of the Riemann curvature tensor. We also consider the pseudo-Newtonian potentials and Kruskal coordinates.

Molecular Origin of the Intrinsic Bending Force for Helical Morphology Observed in Chiral Amphiphilic Assemblies: Concentration and Size Dependence

The formation of the helical morphology in monolayers and bilayers of chiral amphiphilic assemblies is believed to be driven at least partly by the interactions at the chiral centers of the amphiphiles. However, a detailed microscopic understanding of these interactions and their relation with the helix formation is still not clear. In this article a study of the molecular origin of the chirality-driven helix formation is presented by calculating, for the first time, the effective pair potential between a pair of chiral molecules. This effective potential depends on the relative sizes of the groups attached to the two chiral centers, on the orientation of the amphiphile molecules, and also on the distance between them. We find that for the mirror-image isomers (in the racemic modification) the minimum energy conformation is a nearly parallel alignment of the molecules. On the other hand, the same for a pair of molecules of one kind of enantiomer favors a tilt angle between them, thus leading to the formation of a helical morphology of the aggregate. The tilt angle is determined by the size of the groups attached to the chiral centers of the pair of molecules considered and in many cases predicted it to be close to 45 degrees. The present study, therefore, provides a molecular origin of the intrinsic bending force, suggested by Helfrich (J. Chem. Phys. 1986, 85, 1085-1087), to be responsible for the formation of helical structure. This effective potential may explain many of the existing experimental results, such as the size and the concentration dependence of the formation of helical morphology. It is further found that the elastic forces can significantly modify the pitch predicted by the chiral interactions alone and that the modified real pitch is close to the experimentally observed value. The present study is expected to provide a starting point for future microscopic studies.

Bending Of Circular Plate On Elastic-Foundation

The governing differential equation of linear, elastic, thin, circular plate of uniform thickness, subjected to uniformly distributed load and resting on Winkler-Pasternak type foundation is solved using ``Chebyshev Polynomials''. Analysis is carried out using Lenczos' technique, both for simply supported and clamped plates. Numerical results thus obtained by perturbing the differential equation for plates without foundation are compared and are found to be in good agreement with the available results. The effect of foundation on central deflection of the plate is shown in the form of graphs.

Non-linear flapping vibrations of rotating blades

The non-linear equations of motion of a rotating blade undergoing extensional and flapwise bending vibration are derived, including non-linearities up to O (ε3). The strain-displacement relationship derived is compared with expressions derived by earlier investigators and the errors and the approximations made in some of those are brought out. The equations of motion are solved under the inextensionality condition to obtain the influence of the amplitude on the fundamental flapwise natural frequency of the rotating blade. It is found that large finite amplitudes have a softening effect on the flapwise frequency and that this influence becomes stronger at higher speeds of rotation.

Instabilities of a compressible stratified fluid in horizontal sheared motion

The stability characteristics of a Helmholtz velocity profile in a stably stratified, compressible atmosphere in the presence of a lower boundary are studied. A jump in the Brunt–Väisälä frequency is introduced and the level at which this jump occurs is assumed to be different from the shear zone, to simulate sharp temperature discontinuities in the atmosphere. The results are compared with those of Pellacani, Tebaldi, and Tosi and Lindzen and Rosenthal. In the present configuration, new unstable modes with larger growth rates are found. The wavelengths of the most unstable gravity waves for the parameters pertaining to observed cases of clear air turbulence agree quite closely with the experimental values. Physics of Fluids is copyrighted by The American Institute of Physics

Classification and rating of strong-motion earthquake records

Ninety-two strong-motion earthquake records from the California region, U.S.A., have been statistically studied using principal component analysis in terms of twelve important standardized strong-motion characteristics. The first two principal components account for about 57 per cent of the total variance. Based on these two components the earthquake records are classified into nine groups in a two-dimensional principal component plane. Also a unidimensional engineering rating scale is proposed. The procedure can be used as an objective approach for classifying and rating future earthquakes.

The influence of the motion of a rotor grid on a stator grid

In this paper we have used the method of characteristics developed for two dimensional unsteady flow problems to study a simplified axial turbine problem. The system consists of two sets of blades —the guiding vanes which are fixed and the rotor blades which move perpendicular to these vanes. The initial undisturbed constant flow in the system is perturbed by introducing a small velocity normal to the rotor blades to simulate a slight constant inclination. The resulting perturbed flow is periodic after the first three cycles. We have studied the perturbed density distribution throughout the system during a period.

Stream power criterion and design of sand bed channels at incipient motion

The critical stream power criterion may be used to describe the incipient motion of cohesionless particles of plane sediment beds. The governing equation relating ``critical stream power'' to ``shear Reynolds number'' is developed by using the present experimental data as well as the data from several other sources. Simultaneously, a resistance equation, relating the ``particle Reynolds number'' to the``shear Reynolds number'' is developed for plane sediment beds in wide channels with little or no transport. By making use of these relations, a procedure is developed to design plane sediment beds such that any two of the four design variables, including particle size, energy/friction slope, flow depth, and discharge per unit width in the channel should be known to predict the remaining two variables. Finally, a straightforward design procedure using design tables/design curves and analytical methods is presented to solve six possible design problems.

Motion of a viscous fluid with suspended particles in a curved tube

In this paper we have discussed the motion of a viscous fluid with suspended particles through a curved tube of small curvature ratio. The system is treated as two separate interacting continua. Solutions for axial and secondary velocities are obtained in the form of asymptotic expansions in powers of Dean Number. The streamline pattern for the particulate phase reveals many interesting features. The influence of the particulate continium on the fluid is described by the parameter τ which depends on the density ratio of the two continua. The concentration distribution of the particles in a given cross section is determined. It is noticed that the particles move closer to the wall for certain values of the concentration and the density ratio.

Three-dimensional elastic analysis of cracked thick plates under bending fields

A three-dimensional analysis is presented for the bending problem of finite thick plates with through-the-thickness cracks. A general solution is obtained for Navier's equations of the theory of elasticity. It is found that the in-plane stresses and the transverse normal stress at the crack front are singular with an inverse square root singularity, while the transverse shear stresses are of the order of unity. Results from a numerical study indicate that the stress intensity factor, which varies across the thickness, is influenced by the thickness ratio in a significant manner. Results from a parametric study and those from a comparative study with existing finite element values are presented.

Non-linear flapping vibrations of rotating blades

The non-linear equations of motion of a rotating blade undergoing extensional and flapwise bending vibration are derived, including non-linearities up to O (ε3). The strain-displacement relationship derived is compared with expressions derived by earlier investigators and the errors and the approximations made in some of those are brought out. The equations of motion are solved under the inextensionality condition to obtain the influence of the amplitude on the fundamental flapwise natural frequency of the rotating blade. It is found that large finite amplitudes have a softening effect on the flapwise frequency and that this influence becomes stronger at higher speeds of rotation.