Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Effect of V2O5 on the Surface and Structural Characteristics of Potassium Lithium Niobate

It has been suggested that materials with interesting and useful bulk non-linear optical properties might result by substituting vanadium, the lightest element in the group V of periodic table, for Nb or Ta atoms along with Li and three oxygens. It is with this motivation that we have been making attempts to grow single crystals of LiNbO3 doped with various concentrations of V2O5. Unfortunately the results obtained on the ceramic samples of this material have not been very encouraging, owing to their hygroscopic nature. However, our attempts to prepare both ceramic and single-crystalline samples of potassium lithium niobate (K3Li2Nb5O15; KLN) doped V2O5 were successful. In this letter we report the preliminary results concerning our studies on the effect of V2O5 doping on the structural as well as topographic features of both ceramic and single-crystalline samples of KLN.

Infinite dimensional slow modulations in a well known delayed model for cutting tool vibrations

We apply the method of multiple scales (MMS) to a well-known model of regenerative cutting vibrations in the large delay regime. By ``large'' we mean the delay is much larger than the timescale of typical cutting tool oscillations. The MMS up to second order, recently developed for such systems, is applied here to study tool dynamics in the large delay regime. The second order analysis is found to be much more accurate than the first order analysis. Numerical integration of the MMS slow flow is much faster than for the original equation, yet shows excellent accuracy in that plotted solutions of moderate amplitudes are visually near-indistinguishable. The advantages of the present analysis are that infinite dimensional dynamics is retained in the slow flow, while the more usual center manifold reduction gives a planar phase space; lower-dimensional dynamical features, such as Hopf bifurcations and families of periodic solutions, are also captured by the MMS; the strong sensitivity of the slow modulation dynamics to small changes in parameter values, peculiar to such systems with large delays, is seen clearly; and though certain parameters are treated as small (or, reciprocally, large), the analysis is not restricted to infinitesimal distances from the Hopf bifurcation.

Propagation of quasi-simple waves in a compressible rotating atmosphere

A class of self-propagating linear and nonlinear travelling wave solutions for compressible rotating fluid is studied using both numerical and analytical techiques. It is shown that, in general, a three dimensional linear wave is not periodic. However, for some range of wave numbers depending on rotation, horizontally propagating waves are periodic. When the rotation ohgr is equal to $$\sqrt {(\gamma - 1)/(4\gamma )}$$ , all horizontal waves are periodic. Here, gamma is the ratio of specific heats. The analytical study is based on phase space analysis. It reveals that the quasi-simple waves are periodic only in some plane, even when the propagation is horizontal, in contrast to the case of non-rotating flows for which there is a single parameter family of periodic solutions provided the waves propagate horizontally. A classification of the singular points of the governing differential equations for quasi-simple waves is also appended.

A measurement technique for low frequencies

A technique for the measurement of frequency within a cycle of a periodic input is described. This can be useful for quicker measurement of low frequencies.

A mathematical analysis of nonlinear waves in a fluid filled visco-elastic tube

Our investigations in this paper are centred around the mathematical analysis of a ldquomodal waverdquo problem. We have considered the axisymmetric flow of an inviscid liquid in a thinwalled viscoelastic tube under certain simplifying assumptions. We have first derived the propagation space equations in the long wave limit and also given a general procedure to derive these equations for arbitrary wave length, when the flow is irrotational. We have used the method of operators of multiple scales to derive the nonlinear Schrödinger equation governing the modulation of periodic waves and we have elaborated on the ldquolong modulated wavesrdquo and the ldquomodulated long wavesrdquo. We have also examined the existence and stability of Stokes waves in this system. This is followed by a discussion of the progressive wave solutions of the long wave equations. One of the most important results of our paper is that the propagation space equations are no longer partial differential equations but they are in terms of pseudo-differential operators.Die vorliegenden Untersuchungen beziehen sich auf die mathematische Behandlung des ldquorModalwellenrdquo-Problems. Die achsensymmetrische Strömung einer nichtviskosen Flüssigkeit in einem dünnwandigen viskoelastischen Rohr, unter bestimmten vereinfachenden Annahmen, wird betrachtet. Zuerst werden die Gleichungen des Ausbreitungsraumes im Langwellenbereich abgeleitet und eine allgemeine Methode zur Herleitung dieser Gleichungen für beliebige Wellenlängen bei nichtrotierender Strömung angegeben. Eine Operatorenmethode mit multiplem Maßstab wird verwendet zur Herleitung der nichtlinearen Schrödinger-Gleichung für die Modulation der periodischen Wellen, und die ldquorlangmodulierten Wellenrdquo sowie die ldquormodulierten Langwellenrdquo werden aufgezeigt. Weiters wird die Existenz und die Stabilität der Stokes-Wellen im System untersucht. Anschließend werden die progressiven Wellenlösungen der Langwellengleichungen diskutiert. Eines der wichtigsten Ergebnisse dieser Arbeit ist, daß die Gleichungen des Ausbreitungsraumes keine partiellen Differentialgleichungen mehr sind, sondern Ausdrücke von Pseudo-Differentialoperatoren.

Empirical torsional potential functions from protiesn structure DATA Phi- and Psi-Potentials for Non-glycyl Amino Acid Residues

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα-C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)-plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l-configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°). The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Effect of wall thickness on the end corrections of the extended inlet and outlet of a double-tuned expansion chamber

Simple expansion chambers, the simplest of the muffler configurations, have very limited practical application due to the presence of periodic troughs in the transmission loss spectrum which drastically lower the overall transmission loss of the muffler. Tuned extended inlet and outlet can be designed to nullify three-fourths of these troughs, making use of the plane wave theory. These cancellations would not occur unless one altered the geometric lengths for the extended tube in order to incorporate the effect of evanescent higher-order modes (multidimensional effect) through end corrections or lumped inertance approximation at the area discontinuities or junctions. End corrections of the extended inlet and outlet have been studied by several researchers. However the effect of wall thickness of the inlet/outlet duct on end correction has not been studied explicitly. This has significant effect on the tuning of an extended inlet/outlet expansion chamber. It is investigated here experimentally as well as numerically (through use of 3-D FEM software) for stationary medium. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved.

A study of symbolic processing and computational aspects in helicopter dynamics

Even research models of helicopter dynamics often lead to a large number of equations of motion with periodic coefficients; and Floquet theory is a widely used mathematical tool for dynamic analysis. Presently, three approaches are used in generating the equations of motion. These are (1) general-purpose symbolic processors such as REDUCE and MACSYMA, (2) a special-purpose symbolic processor, DEHIM (Dynamic Equations for Helicopter Interpretive Models), and (3) completely numerical approaches. In this paper, comparative aspects of the first two purely algebraic approaches are studied by applying REDUCE and DEHIM to the same set of problems. These problems range from a linear model with one degree of freedom to a mildly non-linear multi-bladed rotor model with several degrees of freedom. Further, computational issues in applying Floquet theory are also studied, which refer to (1) the equilibrium solution for periodic forced response together with the transition matrix for perturbations about that response and (2) a small number of eigenvalues and eigenvectors of the unsymmetric transition matrix. The study showed the following: (1) compared to REDUCE, DEHIM is far more portable and economical, but it is also less user-friendly, particularly during learning phases; (2) the problems of finding the periodic response and eigenvalues are well conditioned.

Hysteresis in model spin system

The aim of this paper is to construct a nonequilibrium statistical‐mechanics theory to study hysteresis in ferromagnetic systems. We study the hysteretic response of model spin systems to periodic magnetic fields H(t) as a function of the amplitude H0 and frequency Ω. At fixed H0, we find conventional, squarelike hysteresis loops at low Ω, and rounded, roughly elliptical loops at high Ω, in agreement with experiments. For the O(N→∞), d=3, (Φ2)2 model with Langevin dynamics, we find a novel scaling behavior for the area A of the hysteresis loop, of the form A∝H0.660Ω0.33. We carry out a Monte Carlo simulation of the hysteretic response of the two‐dimensional, nearest‐neighbor, ferromagnetic Ising model. These results agree qualitatively with the results obtained for the O(N) model.

Hopping and non-hopping localized ionic motion: β-AgI and β-Ag3SI

In β-AgI and β-Ag3SI the ionic conductivity has been measured at frequencies from 1kHz to 2.6 GHz and from 10 MHz to 10 THz, respectively. In both phases we observe a conductivity increase of some orders of magnitude, due to localized types of motion of the silver ions. In β-AgI the increase is found at about 1 MHz and reflects cooperative back-and-forth hopping processes between adjacent tetrahedral sites. In β-Ag3SI the phenomenon occurs at microwave frequencies. Here it is caused by a non-hopping, non-periodic localized Ag+-motion within shallow potentials.

Exact traveling- wave solution for model geophysical systems

Exact traveling-wave solutions of time-dependent nonlinear inhomogeneous PDEs, describing several model systems in geophysical fluid dynamics, are found. The reduced nonlinear ODEs are treated as systems of linear algebraic equations in the derivatives. A variety of solutions are found, depending on the rank of the algebraic systems. The geophysical systems include acoustic gravity waves, inertial waves, and Rossby waves. The solutions describe waves which are, in general, either periodic or monoclinic. The present approach is compared with the earlier one due to Grundland (1974) for finding exact solutions of inhomogeneous systems of nonlinear PDEs.

Exact nonlinear travelling hydromagnetic wave solutions

Exact travelling wave solutions for hydromagnetic waves in an exponentially stratified incompressible medium are obtained. With the help of two integrals it becomes possible to reduce the system of seven nonlinear PDE's to a second order nonlinear ODE which describes an one dimensional harmonic oscillator with a nonlinear friction term. This equation is studied in detail in the phase plane. The travelling waves are periodic only when they propagate either horizontally or vertically. The reduced second order nonlinear differential equation describing the travelling waves in inhomogeneous conducting media has rather ubiquitous nature in that it also appears in other geophysical systems such as internal waves, Rossby waves and topographic Rossby waves in the ocean.

Analysis of reflection characteristics of a normal incidence plane wave on resonant sound absorbers: A finite element approach

Resonant sound absorbers are used widely as anechoic coatings in underwater applications. In this paper a finite element scheme based on the Galerkin technique is used to analyze the reflection characteristics of the resonant absorber when insonified by a normal incidence plane wave. A waveguide theory coupled with an impedance matching condition in the fluid is used to model the problem. It is shown in this paper that the fluid medium encompassing the absorber can be modeled as an elastic medium with equivalent Lamé constants. Quarter symmetry conditions within the periodic unit cell are exploited. The finite element results are compared with analytical results, and with results published elsewhere in the literature. It is shown in the process that meshing of the fluid domain can be obviated if the transmission coefficients or reflection coefficients only are desired as is often the case. Finally, some design curves for thin resonant absorbers with water closure are presented in this paper.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.