Quorum Sensing and Biofilm Formation in Mycobacteria: Role of c-di-GMP and Methods to Study This Second Messenger

Bacteria have evolved to survive the ever-changing environment using intriguing mechanisms of quorum sensing (QS). Very often, QS facilitates formation of biofilm to help bacteria to persist longer and the formation of such biofilms is regulated by c-di-GMP. It is a well-known second messenger also found in mycobacteria. Several methods have been developed to study c-di-GMP signaling pathways in a variety of bacteria. In this review, we have attempted to highlight a connection between c-di-GMP and biofilm formation and QS in mycobacteria and several methods that have helped in better understanding of c-di-GMP signaling. (c) 2014 IUBMB Life, 66(12):823-834, 2014

Stability of the flow in a soft tube deformed due to an applied pressure gradient

A linear stability analysis is carried out for the flow through a tube with a soft wall in order to resolve the discrepancy of a factor of 10 for the transition Reynolds number between theoretical predictions in a cylindrical tube and the experiments of Verma and Kumaran J. Fluid Mech. 705, 322 (2012)]. Here the effect of tube deformation (due to the applied pressure difference) on the mean velocity profile and pressure gradient is incorporated in the stability analysis. The tube geometry and dimensions are reconstructed from experimental images, where it is found that there is an expansion and then a contraction of the tube in the streamwise direction. The mean velocity profiles at different downstream locations and the pressure gradient, determined using computational fluid dynamics, are found to be substantially modified by the tube deformation. The velocity profiles are then used in a linear stability analysis, where the growth rates of perturbations are calculated for the flow through a tube with the wall modeled as a neo-Hookean elastic solid. The linear stability analysis is carried out for the mean velocity profiles at different downstream locations using the parallel flow approximation. The analysis indicates that the flow first becomes unstable in the downstream converging section of the tube where the flow profile is more pluglike when compared to the parabolic flow in a cylindrical tube. The flow is stable in the upstream diverging section where the deformation is maximum. The prediction for the transition Reynolds number is in good agreement with experiments, indicating that the downstream tube convergence and the consequent modification in the mean velocity profile and pressure gradient could reduce the transition Reynolds number by an order of magnitude.

Novel Transmit Precoding Methods for Rayleigh Fading Multiuser TDD-MIMO Systems With CSIT and No CSIR

In this paper, we present novel precoding methods for multiuser Rayleigh fading multiple-input-multiple-output (MIMO) systems when channel state information (CSI) is available at the transmitter (CSIT) but not at the receiver (CSIR). Such a scenario is relevant, for example, in time-division duplex (TDD) MIMO communications, where, due to channel reciprocity, CSIT can be directly acquired by sending a training sequence from the receiver to the transmitter(s). We propose three transmit precoding schemes that convert the fading MIMO channel into a fixed-gain additive white Gaussian noise (AWGN) channel while satisfying an average power constraint. We also extend one of the precoding schemes to the multiuser Rayleigh fading multiple-access channel (MAC), broadcast channel (BC), and interference channel (IC). The proposed schemes convert the fading MIMO channel into fixed-gain parallel AWGN channels in all three cases. Hence, they achieve an infinite diversity order, which is in sharp contrast to schemes based on perfect CSIR and no CSIT, which, at best, achieve a finite diversity order. Further, we show that a polynomial diversity order is retained, even in the presence of channel estimation errors at the transmitter. Monte Carlo simulations illustrate the bit error rate (BER) performance obtainable from the proposed precoding scheme compared with existing transmit precoding schemes.

Interphase anisotropy effects on lamellar eutectics: A numerical study

In directional solidification of binary eutectics, it is often observed that two-phase lamellar growth patterns grow tilted with respect to the direction z of the imposed temperature gradient. This crystallographic effect depends on the orientation of the two crystal phases alpha and beta with respect to z. Recently, an approximate theory was formulated that predicts the lamellar tilt angle as a function of the anisotropy of the free energy of the solid(alpha)-solid(beta) interphase boundary. We use two different numerical methods-phase field (PF) and dynamic boundary integral (BI)-to simulate the growth of steady periodic patterns in two dimensions as a function of the angle theta(R) between z and a reference crystallographic axis for a fixed relative orientation of alpha and beta crystals, that is, for a given anisotropy function (Wulff plot) of the interphase boundary. For Wulff plots without unstable interphase-boundary orientations, the two simulation methods are in excellent agreement with each other and confirm the general validity of the previously proposed theory. In addition, a crystallographic ``locking'' of the lamellae onto a facet plane is well reproduced in the simulations. When unstable orientations are present in the Wulff plot, it is expected that two distinct values of the tilt angle can appear for the same crystal orientation over a finite theta(R) range. This bistable behavior, which has been observed experimentally, is well reproduced by BI simulations but not by the PF model. Possible reasons for this discrepancy are discussed.

Evaluating Methods to Predict Streamflow at Ungauged Sites using Regional Flow Duration Curves: A Case Study

Precise information on streamflows is of major importance for planning and monitoring of water resources schemes related to hydro power, water supply, irrigation, flood control, and for maintaining ecosystem. Engineers encounter challenges when streamflow data are either unavailable or inadequate at target locations. To address these challenges, there have been efforts to develop methodologies that facilitate prediction of streamflow at ungauged sites. Conventionally, time intensive and data exhaustive rainfall-runoff models are used to arrive at streamflow at ungauged sites. Most recent studies show improved methods based on regionalization using Flow Duration Curves (FDCs). A FDC is a graphical representation of streamflow variability, which is a plot between streamflow values and their corresponding exceedance probabilities that are determined using a plotting position formula. It provides information on the percentage of time any specified magnitude of streamflow is equaled or exceeded. The present study assesses the effectiveness of two methods to predict streamflow at ungauged sites by application to catchments in Mahanadi river basin, India. The methods considered are (i) Regional flow duration curve method, and (ii) Area Ratio method. The first method involves (a) the development of regression relationships between percentile flows and attributes of catchments in the study area, (b) use of the relationships to construct regional FDC for the ungauged site, and (c) use of a spatial interpolation technique to decode information in FDC to construct streamflow time series for the ungauged site. Area ratio method is conventionally used to transfer streamflow related information from gauged sites to ungauged sites. Attributes that have been considered for the analysis include variables representing hydrology, climatology, topography, land-use/land- cover and soil properties corresponding to catchments in the study area. Effectiveness of the presented methods is assessed using jack knife cross-validation. Conclusions based on the study are presented and discussed. (C) 2015 The Authors. Published by Elsevier B.V.

Simulations using meshfree methods

In this paper, attempt is made to solve a few problems using the Polynomial Point Collocation Method (PPCM), the Radial Point Collocation Method (RPCM), Smoothed Particle Hydrodynamics (SPH), and the Finite Point Method (FPM). A few observations on the accuracy of these methods are recorded. All the simulations in this paper are three dimensional linear elastostatic simulations, without accounting for body forces.

Panchromatic Borane-aza-BODIPY Conjugate: Synthesis, Intriguing Optical Properties, and Selective Fluorescent Sensing of Fluoride Anions

A new triarylborane-aza-BODIPY conjugate is reported. The compound consists of two blue emissive dimesitylarylborane moieties and a near-infrared (NIR) emissive aza-BOIDPY core and shows panchromatic absorption spanning approximately 300-800 nm. DFT computational studies suggest limited electronic communication between the individual fluorophore units. Hence, the partial energy transfer from blue fluorophore triarylborane to NIR chromophore aza-BODIPY unit leads to a broad dual-emissive feature covering a large part of visible and NIR region. Furthermore, the broadband emissive compound can act as a selective sensor for fluoride anion as a result of fluorescence quenching response in both visible and NIR spectral regions.

Markov chain splitting methods in structural reliability integral estimation

Monte Carlo simulation methods involving splitting of Markov chains have been used in evaluation of multi-fold integrals in different application areas. We examine in this paper the performance of these methods in the context of evaluation of reliability integrals from the point of view of characterizing the sampling fluctuations. The methods discussed include the Au-Beck subset simulation, Holmes-Diaconis-Ross method, and generalized splitting algorithm. A few improvisations based on first order reliability method are suggested to select algorithmic parameters of the latter two methods. The bias and sampling variance of the alternative estimators are discussed. Also, an approximation to the sampling distribution of some of these estimators is obtained. Illustrative examples involving component and series system reliability analyses are presented with a view to bring out the relative merits of alternative methods. (C) 2015 Elsevier Ltd. All rights reserved.