Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

Physics based basis function for vibration analysis of high speed rotating beams

The natural frequencies of continuous systems depend on the governing partial differential equation and can be numerically estimated using the finite element method. The accuracy and convergence of the finite element method depends on the choice of basis functions. A basis function will generally perform better if it is closely linked to the problem physics. The stiffness matrix is the same for either static or dynamic loading, hence the basis function can be chosen such that it satisfies the static part of the governing differential equation. However, in the case of a rotating beam, an exact closed form solution for the static part of the governing differential equation is not known. In this paper, we try to find an approximate solution for the static part of the governing differential equation for an uniform rotating beam. The error resulting from the approximation is minimized to generate relations between the constants assumed in the solution. This new function is used as a basis function which gives rise to shape functions which depend on position of the element in the beam, material, geometric properties and rotational speed of the beam. The results of finite element analysis with the new basis functions are verified with published literature for uniform and tapered rotating beams under different boundary conditions. Numerical results clearly show the advantage of the current approach at high rotation speeds with a reduction of 10 to 33% in the degrees of freedom required for convergence of the first five modes to four decimal places for an uniform rotating cantilever beam.

Alternating current conduction and impedance spectroscopy analysis on pulsed excimer laser ablated (Pb, La)TiO3 thin films

Lanthanum doped lead titanate (PLT) thin films were identified as the most potential candidates for the pyroelectric and memory applications. PLT thin films were deposited on Pt coated Si by excimer laser ablation technique. The polarization behavior of PLT thin films has been studied over a temperature range of 300 K to 550 K. A universal power law relation was brought into picture to explain the frequency dependence of ac conductivity. At higher frequency region ac conductivity of PLT thin films become temperature independent. The temperature dependence of ac conductivity and the relaxation time is analyzed in detail. The activation energy obtained from the ac conductivity was attributed to the shallow trap controlled space charge conduction in the bulk of the sample. The impedance analysis for PLT thin films were also performed to get insight of the microscopic parameters, like grain, grain boundary, and film-electrode interface etc. The imaginary component of impedance Z" exhibited different peak maxima at different temperatures. Different types of mechanisms were analyzed in detail to explain the dielectric relaxation behavior in the PLT thin films.

A study on determining the theoretical dispersion curve for Rayleigh wave propagation

A method has been presented to establish the theoretical dispersion curve for performing the inverse analysis for the Rayleigh wave propagation. The proposed formulation is similar to the one available in literature, and is based on the finite difference formulation of the governing partial differential equations of motion. The method is framed in such a way that it ultimately leads to an Eigen value problem for which the solution can be obtained quite easily with respect to unknown frequency. The maximum absolute value of the vertical displacement at the ground surface is formed as the basis for deciding the governing mode of propagation. With the proposed technique, the numerical solutions were generated for a variety of problems, comprising of a number of different layers, associated with both ground and pavements. The results are found to be generally satisfactory. (C) 2011 Elsevier Ltd. All rights reserved.

Scaling analysis of momentum, heat, and mass transfer in binary alloy solidification problems

A systematic approach is developed for scaling analysis of momentum, heat and species conservation equations pertaining to the case of solidification of a binary mixture. The problem formulation and description of boundary conditions are kept fairly general, so that a large class of problems can be addressed. Analysis of the momentum equations coupled with phase change considerations leads to the establishment of an advection velocity scale. Analysis of the energy equation leads to an estimation of the solid layer thickness. Different regimes corresponding to different dominant modes of transport are simultaneously identified. A comparative study involving several cases of possible thermal boundary conditions is also performed. Finally, a scaling analysis of the species conservation equation is carried out, revealing the effect of a non-equilibrium solidification model on solute segregation and species distribution. It is shown that non-equilibrium effects result in an enhanced macrosegregation compared with the case of an equilibrium model. For the sake of assessment of the scaling analysis, the predictions are validated against corresponding computational results.

A scaling analysis of momentum and heat transport in laser surface melting

In this paper, we outline a systematic procedure for scaling analysis of momentum and heat transfer in laser melted pools. With suitable choices of non-dimensionalising parameters, the governing equations coupled with appropriate boundary conditions are first scaled, and the relative significance of various terms appearing in them are accordingly analysed. The analysis is then utilised to predict the orders of magnitude of some important quantities, such as the velocity scale at the top surface, velocity boundary layer thickness, maximum temperature rise in the pool, fully developed pool-depth, and time required for initiation of melting. Using the scaling predictions, the influence of various processing parameters on the system variables can be well recognised, which enables us to develop a deeper insight into the physical problem of interest. Moreover, some of the quantities predicted from the scaling analysis can be utilised for optimised selection of appropriate grid-size and time-steps for full numerical simulation of the process. The scaling predictions are finally assessed by comparison with experimental and numerical results quoted in the literature, and an excellent qualitative agreement is observed.

A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands

Angiogenin is a protein belonging to the superfamily of RNase A. The RNase activity of this protein is essential for its angiogenic activity. Although members of the RNase A family carry out RNase activity, they differ markedly in their strength and specificity. In this paper, we address the problem of higher specificity of angiogenin towards cytosine against uracil in the first base binding position. We have carried out extensive nano-second level molecular dynamics(MD) computer simulations on the native bovine angiogenin and on the CMP and UMP complexes of this protein in aqueous medium with explicit molecular solvent. The structures thus generated were subjected to a rigorous free energy component analysis to arrive at a plausible molecular thermodynamic explanation for the substrate specificity of angiogenin.

A nonlinear spectral finite element model for analysis of wave propagation in solid with internal friction and dissipation

A geometrically non-linear Spectral Finite Flement Model (SFEM) including hysteresis, internal friction and viscous dissipation in the material is developed and is used to study non-linear dissipative wave propagation in elementary rod under high amplitude pulse loading. The solution to non-linear dispersive dissipative equation constitutes one of the most difficult problems in contemporary mathematical physics. Although intensive research towards analytical developments are on, a general purpose cumputational discretization technique for complex applications, such as finite element, but with all the features of travelling wave (TW) solutions is not available. The present effort is aimed towards development of such computational framework. Fast Fourier Transform (FFT) is used for transformation between temporal and frequency domain. SFEM for the associated linear system is used as initial state for vector iteration. General purpose procedure involving matrix computation and frequency domain convolution operators are used and implemented in a finite element code. Convergnence of the spectral residual force vector ensures the solution accuracy. Important conclusions are drawn from the numerical simulations. Future course of developments are highlighted.

On the solution of the problem of scattering of surface water waves by a sharp discontinuity in the surface boundary conditions

Closed-form analytical expressions are derived for the reflection and transmission coefficients for the problem of scattering of surface water waves by a sharp discontinuity in the surface-boundary-conditions, for the case of deep water. The method involves the use of the Havelock-type expansion of the velocity potential along with an analysis to solve a Carleman-type singular integral equation over a semi-infinite range. This method of solution is an alternative to the Wiener-Hopf technique used previously.

Solving a part classification problem using simulated annealing-like hybrid

Part classification and coding is still considered as laborious and time-consuming exercise. Keeping in view, the crucial role, which it plays, in developing automated CAPP systems, the attempts have been made in this article to automate a few elements of this exercise using a shape analysis model. In this study, a 24-vector directional template is contemplated to represent the feature elements of the parts (candidate and prototype). Various transformation processes such as deformation, straightening, bypassing, insertion and deletion are embedded in the proposed simulated annealing (SA)-like hybrid algorithm to match the candidate part with their prototype. For a candidate part, searching its matching prototype from the information data is computationally expensive and requires large search space. However, the proposed SA-like hybrid algorithm for solving the part classification problem considerably minimizes the search space and ensures early convergence of the solution. The application of the proposed approach is illustrated by an example part. The proposed approach is applied for the classification of 100 candidate parts and their prototypes to demonstrate the effectiveness of the algorithm. (C) 2003 Elsevier Science Ltd. All rights reserved.

Comparative Analysis of Pilot-Assisted Distributed Cophasing Approaches in Wireless Sensor Networks

This paper compares and analyzes the performance of distributed cophasing techniques for uplink transmission over wireless sensor networks. We focus on a time-division duplexing approach, and exploit the channel reciprocity to reduce the channel feedback requirement. We consider periodic broadcast of known pilot symbols by the fusion center (FC), and maximum likelihood estimation of the channel by the sensor nodes for the subsequent uplink cophasing transmission. We assume carrier and phase synchronization across the participating nodes for analytical tractability. We study binary signaling over frequency-flat fading channels, and quantify the system performance such as the expected gains in the received signal-to-noise ratio (SNR) and the average probability of error at the FC, as a function of the number of sensor nodes and the pilot overhead. Our results show that a modest amount of accumulated pilot SNR is sufficient to realize a large fraction of the maximum possible beamforming gain. We also investigate the performance gains obtained by censoring transmission at the sensors based on the estimated channel state, and the benefits obtained by using maximum ratio transmission (MRT) and truncated channel inversion (TCI) at the sensors in addition to cophasing transmission. Simulation results corroborate the theoretical expressions and show the relative performance benefits offered by the various schemes.

Regionalization of precipitation in data sparse areas using large scale atmospheric variables - A fuzzy clustering approach

Delineation of homogeneous precipitation regions (regionalization) is necessary for investigating frequency and spatial distribution of meteorological droughts. The conventional methods of regionalization use statistics of precipitation as attributes to establish homogeneous regions. Therefore they cannot be used to form regions in ungauged areas, and they may not be useful to form meaningful regions in areas having sparse rain gauge density. Further, validation of the regions for homogeneity in precipitation is not possible, since the use of the precipitation statistics to form regions and subsequently to test the regional homogeneity is not appropriate. To alleviate this problem, an approach based on fuzzy cluster analysis is presented. It allows delineation of homogeneous precipitation regions in data sparse areas using large scale atmospheric variables (LSAV), which influence precipitation in the study area, as attributes. The LSAV, location parameters (latitude, longitude and altitude) and seasonality of precipitation are suggested as features for regionalization. The approach allows independent validation of the identified regions for homogeneity using statistics computed from the observed precipitation. Further it has the ability to form regions even in ungauged areas, owing to the use of attributes that can be reliably estimated even when no at-site precipitation data are available. The approach was applied to delineate homogeneous annual rainfall regions in India, and its effectiveness is illustrated by comparing the results with those obtained using rainfall statistics, regionalization based on hard cluster analysis, and meteorological sub-divisions in India. (C) 2011 Elsevier B.V. All rights reserved.

Two Dimensional Principal Component Analysis for Online Tamil Character Recognition

This paper presents a new application of two dimensional Principal Component Analysis (2DPCA) to the problem of online character recognition in Tamil Script. A novel set of features employing polynomial fits and quartiles in combination with conventional features are derived for each sample point of the Tamil character obtained after smoothing and resampling. These are stacked to form a matrix, using which a covariance matrix is constructed. A subset of the eigenvectors of the covariance matrix is employed to get the features in the reduced sub space. Each character is modeled as a separate subspace and a modified form of the Mahalanobis distance is derived to classify a given test character. Results indicate that the recognition accuracy using the 2DPCA scheme shows an approximate 3% improvement over the conventional PCA technique.

Fully Comprehensive Geometrically Non-Linear Dynamic Analysis of Multi-Body Beam Systems with Elastic Couplings

This paper is concerned with the dynamic analysis of flexible,non-linear multi-body beam systems. The focus is on problems where the strains within each elastic body (beam) remain small. Based on geometrically non-linear elasticity theory, the non-linear 3-D beam problem splits into either a linear or non-linear 2-D analysis of the beam cross-section and a non-linear 1-D analysis along the beam reference line. The splitting of the three-dimensional beam problem into two- and one-dimensional parts, called dimensional reduction,results in a tremendous savings of computational effort relative to the cost of three-dimensional finite element analysis,the only alternative for realistic beams. The analysis of beam-like structures made of laminated composite materials requires a much more complicated methodology. Hence, the analysis procedure based on Variational Asymptotic Method (VAM), a tool to carry out the dimensional reduction, is used here.The analysis methodology can be viewed as a 3-step procedure. First, the sectional properties of beams made of composite materials are determined either based on an asymptotic procedure that involves a 2-D finite element nonlinear analysis of the beam cross-section to capture trapeze effect or using strip-like beam analysis, starting from Classical Laminated Shell Theory (CLST). Second, the dynamic response of non-linear, flexible multi-body beam systems is simulated within the framework of energy-preserving and energy-decaying time integration schemes that provide unconditional stability for non-linear beam systems. Finally,local 3-D responses in the beams are recovered, based on the 1-D responses predicted in the second step. Numerical examples are presented and results from this analysis are compared with those available in the literature.

Vegetation Analysis in Uttara Kannada District Using GIS and Remote Sensing Techniques

Uttara Kannada is the only district in Karnataka, which has a forested area of about 80% and falls in the region of the Western Ghats. It is considered to be a very resourceful in terms of abundant natural resources and constitutes an important district in Karnataka. The forest resources of the district are under pressure as a large portion of the forested area has been converted to non-forestry activities since independence owing to the increased demands from human and animal population resulting in degradation of the forest ecosystem. This has led to poor productivity and regenerative capacity which is evident in the form of barren hill tops, etc in Coastal taluks of Uttara Kannada, entailing regular monitoring of the forest resources very essential. The classification of forest is a prerequisite for managing forest resources. Geographical Information System (GIS), allows the spatial and temporal analysis of the features of interest, and helps in solving the problem of deforestation and associated environmental and ecological problems. Spatial and temporal tools such as GIS and remotely sensed data helps the planners and decision makers in evolving the sustainable strategies for management and conservation of natural resources. Uttara Kannada district was classified on the basis of the land-use using supervised hard classifiers. The land use categories identified were urban area, water bodies, agricultural land, forest cover, and waste land. Further classification was carried out on the basis of forest type. The types of forest categorised were semi-evergreen, evergreen, moist deciduous, dry deciduous, plantations and scrub, thorny and non-forested area. The identified classes were correlated with the ground data collected during field visits. The observed results were compared with the historic data and the changes in the forest cover were analysed. From the assessment made it was clear that there has been a considerable degree of forest loss in certain areas of the district. It was also observed that plantations and social forests have increased drastically over the last fifteen years,and natural forests have declined.