Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

A characteristic based numerical method with tracking for nonlinear wave equations

Many physical problems can be modeled by scalar, first-order, nonlinear, hyperbolic, partial differential equations (PDEs). The solutions to these PDEs often contain shock and rarefaction waves, where the solution becomes discontinuous or has a discontinuous derivative. One can encounter difficulties using traditional finite difference methods to solve these equations. In this paper, we introduce a numerical method for solving first-order scalar wave equations. The method involves solving ordinary differential equations (ODEs) to advance the solution along the characteristics and to propagate the characteristics in time. Shocks are created when characteristics cross, and the shocks are then propagated by applying analytical jump conditions. New characteristics are inserted in spreading rarefaction fans. New characteristics are also inserted when values on adjacent characteristics lie on opposite sides of an inflection point of a nonconvex flux function, Solutions along characteristics are propagated using a standard fourth-order Runge-Kutta ODE solver. Shocks waves are kept perfectly sharp. In addition, shock locations and velocities are determined without analyzing smeared profiles or taking numerical derivatives. In order to test the numerical method, we study analytically a particular class of nonlinear hyperbolic PDEs, deriving closed form solutions for certain special initial data. We also find bounded, smooth, self-similar solutions using group theoretic methods. The numerical method is validated against these analytical results. In addition, we compare the errors in our method with those using the Lax-Wendroff method for both convex and nonconvex flux functions. Finally, we apply the method to solve a PDE with a convex flux function describing the development of a thin liquid film on a horizontally rotating disk and a PDE with a nonconvex flux function, arising in a problem concerning flow in an underground reservoir.

Graphical method to determine the parameters of the two-parameter fracture model for concrete

To evaluate the parameters in the two-parameter fracture model, i.e. the critical stress intensity factor and critical crack tip opening displacement for the fracture of plain concrete in Mode 1 for the given test configuration and geometry, considerable computational effort is necessary. A simple graphical method has been proposed using normalized fracture parameters for the three-point bend (3PB) notched specimen and the double-edged notched (DEN) specimen. A similar graphical method is proposed to compute the maximum load carrying capacity of a specimen, using the critical fracture parameters both for 3PB and DEN configurations.

A finite element method for compressible viscous fluid flows

This work presents a mixed three-dimensional finite element formulation for analyzing compressible viscous flows. The formulation is based on the primitive variables velocity, density, temperature and pressure. The goal of this work is to present a `stable' numerical formulation, and, thus, the interpolation functions for the field variables are chosen so as to satisfy the inf-sup conditions. An exact tangent stiffness matrix is derived for the formulation, which ensures a quadratic rate of convergence. The good performance of the proposed strategy is shown in a number of steady-state and transient problems where compressibility effects are important such as high Mach number flows, natural convection, Riemann problems, etc., and also on problems where the fluid can be treated as almost incompressible. Copyright (C) 2010 John Wiley & Sons, Ltd.

Modeling of concrete cracking-A hybrid technique of using displacement discontinuity element method and direct boundary element method

This paper presents a new approach by making use of a hybrid method of using the displacement discontinuity element method and direct boundary element method to model concrete cracking by incorporating fictitious crack model. Fracture mechanics approach is followed using the Hillerborg's fictitious crack model. A boundary element based substructure method and a hybrid technique of using displacement discontinuity element method and direct boundary element method are compared in this paper. In order to represent the process zone ahead of the crack, closing forces are assumed to act in such a way that they obey a linear normal stress-crack opening displacement law. Plain concrete beams with and without initial crack under three-point loading were analyzed by both the methods. The numerical results obtained were shown to agree well with the results from existing finite element method. The model is capable of reproducing the whole range of load-deflection response including strain-softening and snap-back behavior as illustrated in the numerical examples. (C) 2011 Elsevier Ltd. All rights reserved.

A method of tracking the peak power points for a variable speed wind energy conversion system

In this paper, a method of tracking the peak power in a wind energy conversion system (WECS) is proposed, which is independent of the turbine parameters and air density. The algorithm searches for the peak power by varying the speed in the desired direction. The generator is operated in the speed control mode with the speed reference being dynamically modified in accordance with the magnitude and direction of change of active power. The peak power points in the P-omega curve correspond to dP/domega = 0. This fact is made use of in the optimum point search algorithm. The generator considered is a wound rotor induction machine whose stator is connected directly to the grid and the rotor is fed through back-to-back pulse-width-modulation (PWM) converters. Stator flux-oriented vector control is applied to control the active and reactive current loops independently. The turbine characteristics are generated by a dc motor fed from a commercial dc drive. All of the control loops are executed by a single-chip digital signal processor (DSP) controller TMS320F240. Experimental results show that the performance of the control algorithm compares well with the conventional torque control method.

Topology Optimization of Electrostatically Actuated Micromechanical Structures with Accurate Electrostatic Modeling of the Interpolated Material Model

In this paper, we present a novel formulation for performing topology optimization of electrostatically actuated constrained elastic structures. We propose a new electrostatic-elastic formulation that uses the leaky capacitor model and material interpolation to define the material state at every point of a given design domain continuously between conductor and void states. The new formulation accurately captures the physical behavior when the material in between a conductor and a void is present during the iterative process of topology optimization. The method then uses the optimality criteria method to solve the optimization problem by iteratively pushing the state of the domain towards that of a conductor or a void in the appropriate regions. We present examples to illustrate the ability of the method in creating the stiffest structure under electrostatic force for different boundary conditions.

Characterization of Clean and Fouled Rail Track Ballast Subsurface Using Seismic Surface Survey Method: Model and Field Studies

The efficiency of track foundation material gradually decreases due to insufficient lateral confinement, ballast fouling, and loss of shear strength of the subsurface soil under cyclic loading. This paper presents characterization of rail track subsurface to identify ballast fouling and subsurface layers shear wave velocity using seismic survey. Seismic surface wave method of multi-channel analysis of surface wave (MASW) has been carried out in the model track and field track for finding out shear wave velocity of the clean and fouled ballast and track subsurface. The shear wave velocity (SWV) of fouled ballast increases with increase in fouling percentage, and reaches a maximum value and then decreases. This character is similar to typical compaction curve of soil, which is used to define optimum and critical fouling percentage (OFP and CFP). Critical fouling percentage of 15 % is noticed for Coal fouled ballast and 25 % is noticed for clayey sand fouled ballast. Coal fouled ballast reaches the OFP and CFP before clayey sand fouled ballast. Fouling of ballast reduces voids in ballast and there by decreases the drainage. Combined plot of permeability and SWV with percentage of fouling shows that after critical fouling point drainage condition of fouled ballast goes below acceptable limit. Shear wave velocities are measured in the selected location in the Wollongong field track by carrying out similar seismic survey. In-situ samples were collected and degrees of fouling were measured. Field SWV values are more than that of the model track SWV values for the same degree of fouling, which might be due to sleeper's confinement. This article also highlights the ballast gradation widely followed in different countries and presents the comparison of Indian ballast gradation with international gradation standards. Indian ballast contains a coarser particle size when compared to other countries. The upper limit of Indian gradation curve matches with lower limit of ballast gradation curves of America and Australia. The ballast gradation followed by Indian railways is poorly graded and more favorable for the drainage conditions. Indian ballast engineering needs extensive research to improve presents track conditions.

An operator-splitting finite element method for the efficient parallel solution of multidimensional population balance systems

A finite element method for solving multidimensional population balance systems is proposed where the balance of fluid velocity, temperature and solute partial density is considered as a two-dimensional system and the balance of particle size distribution as a three-dimensional one. The method is based on a dimensional splitting into physical space and internal property variables. In addition, the operator splitting allows to decouple the equations for temperature, solute partial density and particle size distribution. Further, a nodal point based parallel finite element algorithm for multi-dimensional population balance systems is presented. The method is applied to study a crystallization process assuming, for simplicity, a size independent growth rate and neglecting agglomeration and breakage of particles. Simulations for different wall temperatures are performed to show the effect of cooling on the crystal growth. Although the method is described in detail only for the case of d=2 space and s=1 internal property variables it has the potential to be extendable to d+s variables, d=2, 3 and s >= 1. (C) 2011 Elsevier Ltd. All rights reserved.

Construction of equivalent circuit of a transformer winding from driving-point impedance function - analytical approach

Analytical solution is presented to convert a given driving-point impedance function (in s-domain) into a physically realisable ladder network with inductive coupling between any two sections and losses considered. The number of sections in the ladder network can vary, but its topology is assumed fixed. A study of the coefficients of the numerator and denominator polynomials of the driving-point impedance function of the ladder network, for increasing number of sections, led to the identification of certain coefficients, which exhibit very special properties. Generalised expressions for these specific coefficients have also been derived. Exploiting their properties, it is demonstrated that the synthesis method essentially turns out to be an exercise of solving a set of linear, simultaneous, algebraic equations, whose solution directly yields the ladder network elements. The proposed solution is novel, simple and guarantees a unique network. Presently, the formulation can synthesise a unique ladder network up to six sections.

A novel variable resolution global spectral method on the sphere

A variable resolution global spectral method is created on the sphere using High resolution Tropical Belt Transformation (HTBT). HTBT belongs to a class of map called reparametrisation maps. HTBT parametrisation of the sphere generates a clustering of points in the entire tropical belt; the density of the grid point distribution decreases smoothly in the domain outside the tropics. This variable resolution method creates finer resolution in the tropics and coarser resolution at the poles. The use of FFT procedure and Gaussian quadrature for the spectral computations retains the numerical efficiency available with the standard global spectral method. Accuracy of the method for meteorological computations are demonstrated by solving Helmholtz equation and non-divergent barotropic vorticity equation on the sphere. (C) 2011 Elsevier Inc. All rights reserved.

Fracture Analysis of High strength and Ultra high strength Concrete beams by using Finite Element Method

This paper presents the details of nonlinear finite element analysis (FEA) of three point bending specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete (UHSC). Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Cracking strength criterion has been used for simulation of crack propagation by conducting nonlinear FEA. The description about FEA using crack strength criterion has been outlined. Bi-linear tension softening relation has been used for modeling the cohesive stresses ahead of the crack tip. Numerical studies have been carried out on fracture analysis of three point bending specimens. It is observed from the studies that the computed values from FEA are in very good agreement with the corresponding experimental values. The computed values of stress vs crack width will be useful for evaluation of fracture energy, crack tip opening displacement and fracture toughness. Further, these values can also be used for crack growth study, remaining life assessment and residual strength evaluation of concrete structural components.

Directional Diffusion Regulator (DDR) for some numerical solvers of hyperbolic conservation laws

A computational tool called ``Directional Diffusion Regulator (DDR)'' is proposed to bring forth real multidimensional physics into the upwind discretization in some numerical schemes of hyperbolic conservation laws. The direction based regulator when used with dimension splitting solvers, is set to moderate the excess multidimensional diffusion and hence cause genuine multidimensional upwinding like effect. The basic idea of this regulator driven method is to retain a full upwind scheme across local discontinuities, with the upwind bias decreasing smoothly to a minimum in the farthest direction. The discontinuous solutions are quantified as gradients and the regulator parameter across a typical finite volume interface or a finite difference interpolation point is formulated based on fractional local maximum gradient in any of the weak solution flow variables (say density, pressure, temperature, Mach number or even wave velocity etc.). DDR is applied to both the non-convective as well as whole unsplit dissipative flux terms of some numerical schemes, mainly of Local Lax-Friedrichs, to solve some benchmark problems describing inviscid compressible flow, shallow water dynamics and magneto-hydrodynamics. The first order solutions consistently improved depending on the extent of grid non-alignment to discontinuities, with the major influence due to regulation of non-convective diffusion. The application is also experimented on schemes such as Roe, Jameson-Schmidt-Turkel and some second order accurate methods. The consistent improvement in accuracy either at moderate or marked levels, for a variety of problems and with increasing grid size, reasonably indicate a scope for DDR as a regular tool to impart genuine multidimensional upwinding effect in a simpler framework. (C) 2012 Elsevier Inc. All rights reserved.

Sum rules and three point functions

Sum rules constraining the R-current spectral densities are derived holographically for the case of D3-branes, M2-branes and M5-branes all at finite chemical potentials. In each of the cases the sum rule relates a certain integral of the spectral density over the frequency to terms which depend both on long distance physics, hydrodynamics and short distance physics of the theory. The terms which which depend on the short distance physics result from the presence of certain chiral primaries in the OPE of two it-currents which are turned on at finite chemical potential. Since these sum rules contain information of the OPE they provide an alternate method to obtain the structure constants of the two R-currents and the chiral primary. As a consistency check we show that the 3 point function derived from the sum rule precisely matches with that obtained using Witten diagrams.

Partial delamination modeling in composite beams using a finite element method

A new method of modeling partial delamination in composite beams is proposed and implemented using the finite element method. Homogenized cross-sectional stiffness of the delaminated beam is obtained by the proposed analytical technique, including extension-bending, extension-twist and torsion-bending coupling terms, and hence can be used with an existing finite element method. A two noded C1 type Timoshenko beam element with 4 degrees of freedom per node for dynamic analysis of beams is implemented. The results for different delamination scenarios and beams subjected to different boundary conditions are validated with available experimental results in the literature and/or with the 3D finite element simulation using COMSOL. Results of the first torsional mode frequency for the partially delaminated beam are validated with the COMSOL results. The key point of the proposed model is that partial delamination in beams can be analyzed using a beam model, rather than using 3D or plate models. (c) 2013 Elsevier B.V. All rights reserved.