Nonlinear hydrodynamics of a hard-sphere fluid near the glass transition

We conduct a numerical study of the dynamic behavior of a dense hard-sphere fluid by deriving and integrating a set of Langevin equations. The statics of the system is described by a free-energy functional of the Ramakrishnan-Yussouff form. We find that the system exhibits glassy behavior as evidenced through a stretched exponential decay and a two-stage relaxation of the density correlation function. The characteristic times grow with increasing density according to the Vogel-Fulcher law. The wave-number dependence of the kinetics is extensively explored. The connection of our results with experiment, mode-coupling theory, and molecular-dynamics results is discussed.

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Points-to Analysis as a System of Linear Equations

We propose a novel formulation of the points-to analysis as a system of linear equations. With this, the efficiency of the points-to analysis can be significantly improved by leveraging the advances in solution procedures for solving the systems of linear equations. However, such a formulation is non-trivial and becomes challenging due to various facts, namely, multiple pointer indirections, address-of operators and multiple assignments to the same variable. Further, the problem is exacerbated by the need to keep the transformed equations linear. Despite this, we successfully model all the pointer operations. We propose a novel inclusion-based context-sensitive points-to analysis algorithm based on prime factorization, which can model all the pointer operations. Experimental evaluation on SPEC 2000 benchmarks and two large open source programs reveals that our approach is competitive to the state-of-the-art algorithms. With an average memory requirement of mere 21MB, our context-sensitive points-to analysis algorithm analyzes each benchmark in 55 seconds on an average.

Exact-Solutions Of Linear Partial-Differential Equations With Variable-Coefficients

Backlund transformations relating the solutions of linear PDE with variable coefficients to those of PDE with constant coefficients are found, generalizing the study of Varley and Seymour [2]. Auto-Backlund transformations are also determined. To facilitate the generation of new solutions via Backlund transformation, explicit solutions of both classes of the PDE just mentioned are found using invariance properties of these equations and other methods. Some of these solutions are new.

Exact free-surface flows for shallow-water equations .1. - the incompressible case

A comprehensive exact treatment of free surface flows governed by shallow water equations (in sigma variables) is given. Several new families of exact solutions of the governing PDEs are found and are shown to embed the well-known self-similar or traveling wave solutions which themselves are governed by reduced ODEs. The classes of solutions found here are explicit in contrast to those found earlier in an implicit form. The height of the free surface for each family of solutions is found explicitly. For the traveling or simple wave, the free surface is governed by a nonlinear wave equation, but is arbitrary otherwise. For other types of solutions, the height of the free surface is constant either on lines of constant acceleration or on lines of constant speed; in another case, the free surface is a horizontal plane while the flow underneath is a sine wave. The existence of simple waves on shear flows is analytically proved. The interaction of large amplitude progressive waves with shear flow is also studied.

PVU and wave-particle splitting schemes for Euler equations of gas dynamics

A new way of flux-splitting, termed as the wave-particle splitting is presented for developing upwind methods for solving Euler equations of gas dynamics. Based on this splitting, two new upwind methods termed as Acoustic Flux Vector Splitting (AFVS) and Acoustic Flux Difference Splitting (AFDS) methods are developed. A new Boltzmann scheme, which closely resembles the wave-particle splitting, is developed using the kinetic theory of gases. This method, termed as Peculiar Velocity based Upwind (PVU) method, uses the concept of peculiar velocity for upwinding. A special feature of all these methods that the unidirectional and multidirectional parts of the flux vector are treated separately. Extensive computations done using these schemes demonstrate the soundness of the ideas.

A note on a class of singular integro-differential equations

A simplified analysis is employed to handle a class of singular integro-differential equations for their solutions

Exact free-surface flows for shallow-water equations .2. the compressible case

Exact free surface flows with shear in a compressible barotropic medium are found, extending the authors' earlier work for the incompressible medium. The barotropic medium is of finite extent in the vertical direction, while it is infinite in the horizontal direction. The ''shallow water'' equations for a compressible barotropic medium, subject to boundary conditions at the free surface and at the bottom, are solved in terms of double psi-series, Simple wave and time-dependent solutions are found; for the former the free surface is of arbitrary shape while for the latter it is a damping traveling wave in the horizontal direction, For other types of solutions, the height of the free surface is constant either on lines of constant acceleration or on lines of constant speed. In the case of an isothermal medium, when gamma = 1, we again find simple wave and time-dependent solutions.

Fluctuation-dissipation relation for nonlinear Langevin equations

It is shown that the fluctuation-dissipation theorem is satisfied by the solutions of a general set of nonlinear Langevin equations with a quadratic free-energy functional (constant susceptibility) and field-dependent kinetic coefficients, provided the kinetic coefficients satisfy the Onsager reciprocal relations for the irreversible terms and the antisymmetry relations for the reversible terms. The analysis employs a perturbation expansion of the nonlinear terms, and a functional integral calculation of the correlation and response functions, and it is shown that the fluctuation-dissipation relation is satisfied at each order in the expansion.

The Adomian method applied to some extraordinary differential equations

Several ''extraordinary'' differential equations are considered for their solutions via the decomposition method of Adomian. Verifications are made with the solutions obtained by other methods.

Direct Cartesian-Space Solutions of Generalized Bloch Equations in the Rotating Frame

Analytical solutions of the generalized Bloch equations for an arbitrary set of initial values of the x, y, and z magnetization components are given in the rotating frame. The solutions involve the decoupling of the three coupled differential equations such that a third-order differential equation in each magnetization variable is obtained. In contrast to the previously reported solutions given by Torrey, the present attempt paves the way for more direct physical insight into the behavior of each magnetization component. Special cases have been discussed that highlight the utility of the general solutions. Representative trajectories of magnetization components are given, illustrating their behavior with respect to the values of off-resonance and initial conditions. (C) 1995 Academic Press, Inc.

Characteristic water contents of a fine-grained soil-water system

This paper critically appraises the limitations of the liquid-limit water content of clayey soils determined conventionally either by percussion cup or by the cone penetration method. It is shown that the conventional liquid limit and plastic limit are arbitrary, strength-based water contents and that they cannot represent the plasticity limits, and that the state of the soil-water system at the conventional liquid limit does not correspond to a stress-free reference state. The present investigation identifies three characteristic limiting water contents for a soil-water system which have well-defined, unique mechanisms controlling them, namely the free swell limit, settling limit and shrinkage limit. Simple procedures for the determination of the free swell limit and settling limit of natural soils are presented. The settling limit is shown to be the 'real liquid limit' of any clayey soil. With a number of experimental illustrations, it is clearly shown that the settling limit represents the maximum water-holding capacity of clayey soils and that it corresponds to the stress-free reference state.

Relative performances of textural models in estimating soil moisture characteristic

The soil moisture characteristic (SMC) forms an important input to mathematical models of water and solute transport in the unsaturated-soil zone. Owing to their simplicity and ease of use, texture-based regression models are commonly used to estimate the SMC from basic soil properties. In this study, the performances of six such regression models were evaluated on three soils. Moisture characteristics generated by the regression models were statistically compared with the characteristics developed independently from laboratory and in-situ retention data of the soil profiles. Results of the statistical performance evaluation, while providing useful information on the errors involved in estimating the SMC, also highlighted the importance of the nature of the data set underlying the regression models. Among the models evaluated, the one possessing an underlying data set of in-situ measurements was found to be the best estimator of the in-situ SMC for all the soils. Considerable errors arose when a textural model based on laboratory data was used to estimate the field retention characteristics of unsaturated soils.

Similarity solution of unsteady boundary layer equations with a magnetic field

The unsteady laminar incompressible boundary layer flow of an electrically conducting fluid in the stagnation region of two-dimensional and axisymmetric bodies with an applied magnetic field has been studied. The boundary layer equations which are parabolic partial differential equations with three independent variables have been reduced to a system of ordinary differential equations by using suitable transformations and then solved numerically using a shooting method. Here, we have obtained new solutions which are solutions of both the boundary layer and Navier-Stokes equations.

The Equations of Equilibrium in Orthogonal Curvilinear Reference Coordinates

Analytical solutions to problems in finite elasticity are most often derived using the semi-inverse approach along with the spatial form of the equations of motion involving the Cauchy stress tensor. This procedure is somewhat indirect since the spatial equations involve derivatives with respect to spatial coordinates while the unknown functions are in terms of material coordinates, thus necessitating the use of the chain rule. In this classroom note, we derive compact expressions for the components of the divergence, with respect to orthogonal material coordinates, of the first Piola-Kirchhoff stress tensor. The spatial coordinate system is also assumed to be an orthogonal curvilinear one, although, not necessarily of the same type as the material coordinate system. We show by means of some example applications how analytical solutions can be derived more directly using the derived results.