Rigid and flexible region in lysozyme and the invariant features in its hydration shell

Water-mediated transformations provide a useful handle for exploring the flexibility in protein molecules and the invariant features in their hydration shells. Low-humidity monoclinic hen egg white lysozyme, resulting from such a transformation, has perhaps the lowest solvent content observed in any protein crystal so far and has a well-ordered structure. A detailed comparison involving this structure, low-humidity tetragonal lysozyme, and the other available refined crystal structures of the enzyme permits the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. The relatively rigid region forms a contiguous structural unit close to the molecular centroid and encompasses parts of of the main beta-structure and three alpha-helices. The hydration shell of the protein contains 30 invariant water molecules. Many of them are involved in holding different parts of the molecule together or in stabilizing local structure. Five of the six invariant water molecules attached to the substrate-binding region form part of a water cluster contiguous with the side-chains of the catalytic residues Glu-35 and Asp-52.

Rocking response of rectangular rigid blocks under random noise base excitations

The response of a rigid rectangular block resting on a rigid foundation and acted upon simultaneously by a horizontal and a vertical random white-noise excitation is considered. In the equation of motion, the energy dissipation is modeled through a viscous damping term. Under the assumption that the body does not topple, the steady-state joint probability density function of the rotation and the rotational velocity is obtained using the Fokker-Planck equation approach. Closed form solution is obtained for a specific combination of system parameters. A more general but approximate solution to the joint probability density function based on the method of equivalent non-linearization is also presented. Further, the problem of overturning of the block is approached in the framework of the diffusion methods for first passage failure studies. The overturning of the block is deemed incipient when the response trajectories in the phase plane cross the separatrix of the conservative unforced system. Expressions for the moments of first passage time are obtained via a series solution to the governing generalized Pontriagin-Vitt equations. Numerical results illustra- tive of the theoretical solutions are presented and their validity is examined through limited amount of digital simulations.

Stereoelectronic control of Cope rearrangement energetics through remote double bonds in novel, rigid polycyclic frames

The presence and orientation of remote double bonds are shown to completely alter the shapes of Cope rearrangement energy profiles in a heptacyclic system.

The scratch hardness and friction of a soft rigid-plastic solid

The paper describes an experimental and analytical study of the normal and scratch hardnesses of a model soft rigid-plastic solid. The material known as ‘Plasticine’, a mixture of dry particles and a mineral oil, has been deformed with a range of rigid conical indentors with included angles of between 30° and 170°. The sliding velocity dependence of the computed scratch hardness and friction has been examined in the velocity range 0.19 mm/s to 7.3 m/s. Data are also described for the time dependence of the normal hardness and also the estimated rate dependence of the intrinsic flow stress. The latter values were estimated from data obtained during the upsetting of right cylinders. Three major conclusions are drawn from these data and the associated analysis. (1) A first-order account of the scratching force may be provided by adopting a model which sums the computed plastic deformation and interfacial sliding contributions to the total sliding work. This is tantamount to the adoption of the two-term non-interacting model of friction. (2) For this system during sliding, at high sliding velocities at least, the interface shear stress which defines the boundary condition is not directly related to the bulk shear stress. The interface rheological characteristics indicate an appreciable dependence on the imposed strain or strain rate. In particular, the relative contributions of the slip and stick boundary conditions appear to be a function of the imposed sliding velocity. (3) The computed normal and scratch hardness values are not simply interrelated primarily because of the evolving boundary conditions which appear to exist in the scratching experiments.

Bile acid based semi-rigid molecular tweezers

The easily constructed bile acid-based semi-rigid molecular tweezer 2 binds guest 8 in chloroform with an association constant of 83 dm(3) mol(-1).

Nonlinear dynamics of a rigid block on a rigid base

The planar rocking of a prismatic rectangular rigid block about either of its corners is considered. The problem of homoclinic intersections of the stable and unstable manifolds of the perturbed separatrix is addressed to and the corresponding Melnikov functions are derived. Inclusion of the vertical forcing in the Hamiltonian permits the construction of a three-dimensional separatrix. The corresponding modified Melnikov function of Wiggins for homoclinic intersections is derived. Further, the 1-period symmetric orbits are predicted analytically using the method of averaging and compared with the simulation results. The stability boundary for such orbits is also established.

Limiting ionic conductance of symmetrical, rigid ions in aqueous solutions: Temperature dependence and solvent isotope effects

Limiting ionic conductance (Lambda(0)) of rigid symmetrical unipositive ions in aqueous solution shows a strong temperature dependence. For example, Lambda(0) more than doubles when the temperature is increased from 283 to 318 K. A marked variation also occurs when the solvent is changed from ordinary water (H2O) to heavy water (D2O). In addition, Lambda(0) shows a nonmonotonic size dependence with a skewed maximum near Cs+. Although these important results have been known for a long time, no satisfactory theoretical explanation exists for these results. In this article we present a simple molecular theory which provides a nearly quantitative explanation in terms of microscopic structure and dynamics of the solvent. A notable feature of this theory is that it does not invoke any nonquantifiable models involving solvent-berg or clatherates. We find the strong temperature dependence of Lambda(0) to arise from a rather large number of microscopic factors, each providing a small but nontrivial contribution, but all acting surprisingly in the same direction. This work, we believe, provides, for the first time, a satisfactory explanation of both the anomalous size and temperature dependencies of Lambda(0) of unipositive ions in molecular terms. The marked change in Lambda(0) as the solvent is changed from H2O to D2O is found to arise partly from a change in the dielectric relaxation and partly from a change in the effective interaction of the ion with the solvent.

A differential geometric method for kinematic analysis of two- and three-degree-of-freedom rigid body motions

In this paper, we present a novel differential geometric characterization of two- and three-degree-of-freedom rigid body kinematics, using a metric defined on dual vectors. The instantaneous angular and linear velocities of a rigid body are expressed as a dual velocity vector, and dual inner product is defined on this dual vector, resulting in a positive semi-definite and symmetric dual matrix. We show that the maximum and minimum magnitude of the dual velocity vector, for a unit speed motion, can be obtained as eigenvalues of this dual matrix. Furthermore, we show that the tip of the dual velocity vector lies on a dual ellipse for a two-degree-of-freedom motion and on a dual ellipsoid for a three-degree-of-freedom motion. In this manner, the velocity distribution of a rigid body can be studied algebraically in terms of the eigenvalues of a dual matrix or geometrically with the dual ellipse and ellipsoid. The second-order properties of the two- and three-degree-of-freedom motions of a rigid body are also obtained from the derivatives of the elements of the dual matrix. This results in a definition of the geodesic motion of a rigid body. The theoretical results are illustrated with the help of a spatial 2R and a parallel three-degree-of-freedom manipulator.

Boundary conditions at a rigid wall for rough granular gases

We derive boundary conditions at a rigid wall for a granular material comprising rough, inelastic particles. Our analysis is confined to the rapid flow, or granular gas, regime in which grains interact by impulsive collisions. We use the Chapman-Enskog expansion in the kinetic theory of dense gases, extended for inelastic and rough particles, to determine the relevant fluxes to the wall. As in previous studies, we assume that the particles are spheres, and that the wall is corrugated by hemispheres rigidly attached to it. Collisions between the particles and the wall hemispheres are characterized by coefficients of restitution and roughness. We derive boundary conditions for the two limiting cases of nearly smooth and nearly perfectly rough spheres, as a hydrodynamic description of granular gases comprising rough spheres is appropriate only in these limits. The results are illustrated by applying the equations of motion and boundary conditions to the problem of plane Couette flow.

Thermal instability in a three-dimensional rigid container with prescribed heat flux at lower boundary

The Bénard–Marangoni convection is studied in a three-dimensional container with thermally insulated lateral walls and prescribed heat flux at lower boundary. The upper surface of the incompressible, viscous fluid is assumed to be flat with temperature dependent surface tension. A Galerkin–Tau method with odd and even trial functions satisfying all the essential boundary conditions except the natural boundary conditions at the free surface has been used to solve the problem. The critical Marangoni and Rayleigh numbers are determined for the onset of steady convection as a function of aspect ratios x0 and y0 for the cases of Bénard–Marangoni, pure Marangoni and pure Bénard convections. It is observed that critical parameters are decreasing with an increase in aspect ratios. The flow structures corresponding to the values of the critical parameters are presented in all the cases. It is observed that the critical parameters are higher for case with heat flux prescribed than those corresponding to the case with prescribed temperature. The critical Marangoni number for pure Marangoni convection is higher than critical Rayleigh number corresponding to pure Bénard convection for a given aspect ratio whereas the reverse was observed for two-dimensional infinite layer.

Theory of Gas Hydrates: Effect of the Approximation of Rigid Water Lattice

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory. Our study shows that even if the exact intermolecular potential between the guest molecules and water is known, the dissociation temperatures predicted by the theory are significantly higher. This has serious implications to the modeling of gas hydrate thermodynamics, and in spite of the several impressive efforts made toward obtaining an accurate description of intermolecular interactions in gas hydrates, the theory will suffer from the problem of robustness if the issue of movement of water molecules is not adequately addressed.

Energy Loss in the Impact of Elastic Spheres on a Rigid Half-Space in Presence of Adhesion

Adhesion can cause energy losses in asperities or particles coming into dynamic contact resulting in frictional dissipation, even if the deformation occurring is purely elastic. Such losses are of special significance in impact of nanoparticles and friction between surfaces under low contact pressure to hardness ratio. The objective of this work is to study the effect of adhesion during the normal impact of elastic spheres on a rigid half-space, with an emphasis on understanding the mechanism of energy loss. We use finite element method for modeling the impact phenomenon, with the adhesion due to van der Waals force and the short-range repulsion included as body forces distributed over the volume of the sphere. This approach, in contrast with commonly used surface force approximation, helps to model the interactions in a more precise way. We find that the energy loss in impact of elastic spheres is negligible unless there are adhesion-induced instabilities. Significant energy loss through elastic stress waves occurs due to jump-to-contact and jump-out-of-contact instabilities and can even result in capture of the elastic sphere on the half-space.

Multiobjective Optimization of Piezoelectric Bimorph Actuator with Rigid Extension

Production of high tip deflection in a piezoelectric bimorph laminar actuator by applying high voltage is limited by many physical constraints. Therefore, piezoelectric bimorph actuator with a rigid extension of non-piezoelectric material at its tip is used to increase the tip deflection of such an actuator. Research on this type of piezoelectric bending actuator is either limited to first order constitutive relations, which do not include non-linear behavior of piezoelectric element at high electric field, or limited to curve fitting techniques. Therefore, this paper considers high electric field, and analytically models tapered piezoelectric bimorph actuator with a rigid extension of non-piezoelectric material at its tip. The stiffness, capacitance, effective tip deflection, block force, output strain energy, output energy density, input electrical energy and energy efficiency of the actuator are calculated analytically. The paper also discusses the multi-objective optimization of this type of actuator subjected to the mechanical and electrical constraints.