Pseudodynamic systems approach based on a quadratic approximation of update equations for diffuse optical tomography

We explore a pseudodynamic form of the quadratic parameter update equation for diffuse optical tomographic reconstruction from noisy data. A few explicit and implicit strategies for obtaining the parameter updates via a semianalytical integration of the pseudodynamic equations are proposed. Despite the ill-posedness of the inverse problem associated with diffuse optical tomography, adoption of the quadratic update scheme combined with the pseudotime integration appears not only to yield higher convergence, but also a muted sensitivity to the regularization parameters, which include the pseudotime step size for integration. These observations are validated through reconstructions with both numerically generated and experimentally acquired data. (C) 2011 Optical Society of America

Linear stability, transient growth and the role of viscosity stratification in compressible Couette flow

Linear stability and the nonmodal transient energy growth in compressible plane Couette flow are investigated for two prototype mean flows: (a) the uniform shear flow with constant viscosity, and (b) the nonuniform shear flow with stratified viscosity. Both mean flows are linearly unstable for a range of supersonic Mach numbers (M). For a given M, the critical Reynolds number (Re) is significantly smaller for the uniform shear flow than its nonuniform shear counterpart; for a given Re, the dominant instability (over all streamwise wave numbers, α) of each mean flow belongs to different modes for a range of supersonic M. An analysis of perturbation energy reveals that the instability is primarily caused by an excess transfer of energy from mean flow to perturbations. It is shown that the energy transfer from mean flow occurs close to the moving top wall for “mode I” instability, whereas it occurs in the bulk of the flow domain for “mode II.” For the nonmodal transient growth analysis, it is shown that the maximum temporal amplification of perturbation energy, Gmax, and the corresponding time scale are significantly larger for the uniform shear case compared to those for its nonuniform counterpart. For α=0, the linear stability operator can be partitioned into L∼L̅ +Re2 Lp, and the Re-dependent operator Lp is shown to have a negligibly small contribution to perturbation energy which is responsible for the validity of the well-known quadratic-scaling law in uniform shear flow: G(t∕Re)∼Re2. In contrast, the dominance of Lp is responsible for the invalidity of this scaling law in nonuniform shear flow. An inviscid reduced model, based on Ellingsen-Palm-type solution, has been shown to capture all salient features of transient energy growth of full viscous problem. For both modal and nonmodal instability, it is shown that the viscosity stratification of the underlying mean flow would lead to a delayed transition in compressible Couette flow.

Estimation of missing data using windowed linear prediction in laterally truncated projection & in cone beam CT

In this paper, we address the reconstruction problem from laterally truncated helical cone-beam projections. The reconstruction problem from lateral truncation, though similar to that of interior radon problem, is slightly different from it as well as the local (lambda) tomography and pseudo-local tomography in the sense that we aim to reconstruct the entire object being scanned from a region-of-interest (ROI) scan data. The method proposed in this paper is a projection data completion approach followed by the use of any standard accurate FBP type reconstruction algorithm. In particular, we explore a windowed linear prediction (WLP) approach for data completion and compare the quality of reconstruction with the linear prediction (LP) technique proposed earlier.

An adaptive MAC protocol in MANETs: a democratic approach

Mobile ad-hoc networks (MANETs) have recently drawn significant research attention since they offer unique benefits and versatility with respect to bandwidth spatial reuse, intrinsic fault tolerance, and low-cost rapid deployment. This paper addresses the issue of delay sensitive realtime data transport in these type of networks. An effective QoS mechanism is thereby required for the speedy transport of the realtime data. QoS issue in MANET is an open-end problem. Various QoS measures are incorporated in the upperlayers of the network, but a few techniques addresses QoS techniques in the MAC layer. There are quite a few QoS techniques in the MAC layer for the infrastructure based wireless network. The goal and the challenge is to achieve a QoS delivery and a priority access to the real time traffic in adhoc wireless environment, while maintaining democracy in the resource allocation. We propose a MAC layer protocol called "FCP based FAMA protocol", which allocates the channel resources to the needy in a more democratic way, by examining the requirements, malicious behavior and genuineness of the request. We have simulated both the FAMA as well as FCP based FAMA and tested in various MANET conditions. Simulated results have clearly shown a performance improvement in the channel utilization and a decrease in the delay parameters in the later case. Our new protocol outperforms the other QoS aware MAC layer protocols.

A relook at Reissner's theory of plates in bending

Shear deformation and higher order theories of plates in bending are (generally) based on plate element equilibrium equations derived either through variational principles or other methods. They involve coupling of flexure with torsion (torsion-type) problem and if applied vertical load is along one face of the plate, coupling even with extension problem. These coupled problems with reference to vertical deflection of plate in flexure result in artificial deflection due to torsion and increased deflection of faces of the plate due to extension. Coupling in the former case is eliminated earlier using an iterative method for analysis of thick plates in bending. The method is extended here for the analysis of associated stretching problem in flexure.

Implementation of a phase array diffuse optical tomographic imager

Diffuse optical tomography (DOT) using near-infrared (NIR) light is a promising tool for noninvasive imaging of deep tissue. This technique is capable of quantitative reconstructions of absorption coefficient inhomogeneities of tissue. The motivation for reconstructing the optical property variation is that it, and, in particular, the absorption coefficient variation, can be used to diagnose different metabolic and disease states of tissue. In DOT, like any other medical imaging modality, the aim is to produce a reconstruction with good spatial resolution and accuracy from noisy measurements. We study the performance of a phase array system for detection of optical inhomogeneities in tissue. The light transport through a tissue is diffusive in nature and can be modeled using diffusion equation if the optical parameters of the inhomogeneity are close to the optical properties of the background. The amplitude cancellation method that uses dual out-of-phase sources (phase array) can detect and locate small objects in turbid medium. The inverse problem is solved using model based iterative image reconstruction. Diffusion equation is solved using finite element method for providing the forward model for photon transport. The solution of the forward problem is used for computing the Jacobian and the simultaneous equation is solved using conjugate gradient search. The simulation studies have been carried out and the results show that a phase array system can resolve inhomogeneities with sizes of 5 mm when the absorption coefficient of the inhomogeneity is twice that of the background tissue. To validate this result, a prototype model for performing a dual-source system has been developed. Experiments are carried out by inserting an inhomogeneity of high optical absorption coefficient in an otherwise homogeneous phantom while keeping the scattering coefficient same. The high frequency (100 MHz) modulated dual out-of-phase laser source light is propagated through the phantom. The interference of these sources creates an amplitude null and a phase shift of 180° along a plane between the two sources with a homogeneous object. A solid resin phantom with inhomogeneities simulating the tumor is used in our experiment. The amplitude and phase changes are found to be disturbed by the presence of the inhomogeneity in the object. The experimental data (amplitude and the phase measured at the detector) are used for reconstruction. The results show that the method is able to detect multiple inhomogeneities with sizes of 4 mm. The localization error for a 5 mm inhomogeneity is found to be approximately 1 mm.

Federated Search Service for OAI-compliant, Open-Access Repositories in India

Many of the research institutions and universities across the world are facilitating open-access (OA) to their intellectual outputs through their respective OA institutional repositories (IRs) or through the centralized subject-based repositories. The registry of open access repositories (ROAR) lists more than 2850 such repositories across the world. The awareness about the benefits of OA to scholarly literature and OA publishing is picking up in India, too. As per the ROAR statistics, to date, there are more than 90 OA repositories in the country. India is doing particularly well in publishing open-access journals (OAJ). As per the directory of open-access journals (DOAJ), to date, India with 390 OAJs, is ranked 5th in the world in terms of numbers of OAJs being published. Much of the research done in India is reported in the journals published from India. These journals have limited readership and many of them are not being indexed by Web of Science, Scopus or other leading international abstracting and indexing databases. Consequently, research done in the country gets hidden not only from the fellow countrymen, but also from the international community. This situation can be easily overcome if all the researchers facilitate OA to their publications. One of the easiest ways to facilitate OA to scientific literature is through the institutional repositories. If every research institution and university in India set up an open-access IR and ensure that copies of the final accepted versions of all the research publications are uploaded in the IRs, then the research done in India will get far better visibility. The federation of metadata from all the distributed, interoperable OA repositories in the country will serve as a window to the research done across the country. Federation of metadata from the distributed OAI-compliant repositories can be easily achieved by setting up harvesting software like the PKP Harvester. In this paper, we share our experience in setting up a prototype metadata harvesting service using the PKP harvesting software for the OAI-compliant repositories in India.

Homogenization of eigenvalue problems in perforated domains

In this paper, we treat some eigenvalue problems in periodically perforated domains and study the asymptotic behaviour of the eigenvalues and the eigenvectors when the number of holes in the domain increases to infinity Using the method of asymptotic expansion, we give explicit formula for the homogenized coefficients and expansion for eigenvalues and eigenvectors. If we denote by ε the size of each hole in the domain, then we obtain the following aysmptotic expansion for the eigenvalues: Dirichlet: λε = ε−2 λ + λ0 +O (ε), Stekloff: λε = ελ1 +O (ε2), Neumann: λε = λ0 + ελ1 +O (ε2).Using the method of energy, we prove a theorem of convergence in each case considered here. We briefly study correctors in the case of Neumann eigenvalue problem.

Robust Approach for Identification of Bad Data in State Estimation Using SLP Technique

This paper proposes a new approach for solving the state estimation problem. The approach is aimed at producing a robust estimator that rejects bad data, even if they are associated with leverage-point measurements. This is achieved by solving a sequence of Linear Programming (LP) problems. Optimization is carried via a new algorithm which is a combination of “upper bound optimization technique" and “an improved algorithm for discrete linear approximation". In this formulation of the LP problem, in addition to the constraints corresponding to the measurement set, constraints corresponding to bounds of state variables are also involved, which enables the LP problem more efficient in rejecting bad data, even if they are associated with leverage-point measurements. Results of the proposed estimator on IEEE 39-bus system and a 24-bus EHV equivalent system of the southern Indian grid are presented for illustrative purpose.

A Numerical Scheme for Three-Dimensional Front Propagation and Control of Jordan Mode

As an example of a front propagation, we study the propagation of a three-dimensional nonlinear wavefront into a polytropic gas in a uniform state and at rest. The successive positions and geometry of the wavefront are obtained by solving the conservation form of equations of a weakly nonlinear ray theory. The proposed set of equations forms a weakly hyperbolic system of seven conservation laws with an additional vector constraint, each of whose components is a divergence-free condition. This constraint is an involution for the system of conservation laws, and it is termed a geometric solenoidal constraint. The analysis of a Cauchy problem for the linearized system shows that when this constraint is satisfied initially, the solution does not exhibit any Jordan mode. For the numerical simulation of the conservation laws we employ a high resolution central scheme. The second order accuracy of the scheme is achieved by using MUSCL-type reconstructions and Runge-Kutta time discretizations. A constrained transport-type technique is used to enforce the geometric solenoidal constraint. The results of several numerical experiments are presented, which confirm the efficiency and robustness of the proposed numerical method and the control of the Jordan mode.

Nonlinear viscoelasticity of freestanding and polymer-anchored vertically aligned carbon nanotube foams

Vertical arrays of carbon nanotubes (VACNTs) show unique mechanical behavior in compression, with a highly nonlinear response similar to that of open cell foams and the ability to recover large deformations. Here, we study the viscoelastic response of both freestanding VACNT arrays and sandwich structures composed of a VACNT array partially embedded between two layers of poly(dimethylsiloxane) (PDMS) and bucky paper. The VACNTs tested are similar to 2 mm thick foams grown via an injection chemical vapor deposition method. Both freestanding and sandwich structures exhibit a time-dependent behavior under compression. A power-law function of time is used to describe the main features observed in creep and stress-relaxation tests. The power-law exponents show nonlinear viscoelastic behavior in which the rate of creep is dependent upon the stress level and the rate of stress relaxation is dependent upon the strain level. The results show a marginal effect of the thin PDMS/bucky paper layers on the viscoelastic responses. At high strain levels (epsilon - 0.8), the peak stress for the anchored CNTs reaches similar to 45 MPa, whereas it is only similar to 15MPa for freestanding CNTs, suggesting a large effect of PDMS on the structural response of the sandwich structures. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.3699184]

Catalysis of tRNA Aminoacylation: Single Turnover to Steady-State Kinetics of tRNA Synthetases

Aminoacyl-tRNA synthetases (aaRS) catalyze the bimolecular association reaction between amino acid and tRNA by specifically and unerringly choosing the cognate amino acid and tRNA. There are two classes of such synthetases that perform tRNA-aminoacylation reaction. Interestingly, these two classes of aminoacyl-tRNA synthetases differ not only in their structures but they also exhibit remarkably distinct kinetics under pre-steady-state condition. The class I synthetases show initial burst of product formation followed by a slower steady-state rate. This has been argued to represent the influence of slow product release. In contrast, there is no burst in the case of class H enzymes. The tight binding of product with enzyme for class I enzymes is correlated with the enhancement of rate in presence of elongation factor. EF-TU. In spite of extensive experimental studies, there is no detailed theoretical analysis that can provide a quantitative understanding of this important problem. In this article, we present a theoretical investigation of enzyme kinetics for both classes of aminoacyl-tRNA synthetases. We present an augmented kinetic scheme and then employ the methods of time-dependent probability statistics to obtain expressions for the first passage time distribution that gives both the time-dependent and the steady-state rates. The present study quantitatively explains all the above experimental observations. We propose an alternative path way in the case of class II enzymes showing the tRNA-dependent amino acid activation and the discrepancy between the single-turnover and steady-state rate.

Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Background: Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism. Results: Here we report kinetic characterization of S. typhimurium AckA (StAckA) and structures of its unliganded (Form-I, 2.70 angstrom resolution) and citrate-bound (Form-II, 1.90 angstrom resolution) forms. The enzyme showed broad substrate specificity with k(cat)/K-m in the order of acetate > propionate > formate. Further, the K-m for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5'-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I StAckA represents the first structural report of an unliganded AckA. StAckA protomer consists of two domains with characteristic beta beta beta alpha beta alpha beta alpha topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (MtAckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II StAckA structure showed a drastic change in the conformation of residues 230-300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II StAckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I StAckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes. Conclusions: The biochemical and structural characterization of StAckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of StAckA led to identification of a putative ligand-binding pocket at the dimeric interface of StAckA with implications for enzymatic function.

Nonlocal continuum mechanics based ultrasonic flexural wave dispersion characteristics of a monolayer graphene embedded in polymer matrix

Wave propagation in graphene sheet embedded in elastic medium (polymer matrix) has been a topic of great interest in nanomechanics of graphene sheets, where the equivalent continuum models are widely used. In this manuscript, we examined this issue by incorporating the nonlocal theory into the classical plate model. The influence of the nonlocal scale effects has been investigated in detail. The results are qualitatively different from those obtained based on the local/classical plate theory and thus, are important for the development of monolayer graphene-based nanodevices. In the present work, the graphene sheet is modeled as an isotropic plate of one-atom thick. The chemical bonds are assumed to be formed between the graphene sheet and the elastic medium. The polymer matrix is described by a Pasternak foundation model, which accounts for both normal pressure and the transverse shear deformation of the surrounding elastic medium. When the shear effects are neglected, the model reduces to Winkler foundation model. The normal pressure or Winkler elastic foundation parameter is approximated as a series of closely spaced, mutually independent, vertical linear elastic springs where the foundation modulus is assumed equivalent to stiffness of the springs. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of flexural wave propagation model is also derived and the results of the wave dispersion analysis are shown for both local and nonlocal elasticity calculations. From this analysis we show that the elastic matrix highly affects the flexural wave mode and it rapidly increases the frequency band gap of flexural mode. The flexural wavenumbers obtained from nonlocal elasticity calculations are higher than the local elasticity calculations. The corresponding wave group speeds are smaller in nonlocal calculation as compared to local elasticity calculation. The effect of y-directional wavenumber (eta(q)) on the spectrum and dispersion relations of the graphene embedded in polymer matrix is also observed. We also show that the cut-off frequencies of flexural wave mode depends not only on the y-direction wavenumber but also on nonlocal scaling parameter (e(0)a). The effect of eta(q) and e(0)a on the cut-off frequency variation is also captured for the cases of with and without elastic matrix effect. For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(0)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this article. (c) 2012 Elsevier Ltd. All rights reserved.

Microwave-assisted, surfactant-free synthesis of air-stable copper nanostructures and their SERS study

A simple, rapid, and surfactant-free synthesis of crystalline copper nanostructures has been carried out through microwave irradiation of a solution of copper acetylacetonate in benzyl alcohol. The structures are found to be stable against oxidation in ambient air for several months. High-resolution electron microscopy (SEM and TEM) reveals that the copper samples comprise nanospheres measuring about 150 nm in diameter, each made of copper nanocrystals similar to 7 nm in extension. The nanocrystals are densely packed into spherical aggregates, the driving force being minimization of surface area and surface energy, and are thus immune to oxidation in ambient air. Such aggregates can also be adherently supported on SiO2 and Al2O3 when these substrates are immersed in the irradiated solution. The air-stable copper nanostructures exhibit surface enhanced Raman scattering, as evidenced by the detection of 4-mercaptobenzoic acid at 10(-6) M concentrations.