Experimental analysis of shape deformation of evaporating droplet using Legendre polynomials

Experiments involving heating of liquid droplets which are acoustically levitated, reveal specific modes of oscillations. For a given radiation flux, certain fluid droplets undergo distortion leading to catastrophic bag type breakup. The voltage of the acoustic levitator has been kept constant to operate at a nominal acoustic pressure intensity, throughout the experiments. Thus the droplet shape instabilities are primarily a consequence of droplet heating through vapor pressure, surface tension and viscosity. A novel approach is used by employing Legendre polynomials for the mode shape approximation to describe the thermally induced instabilities. The two dominant Legendre modes essentially reflect (a) the droplet size reduction due to evaporation, and (b) the deformation around the equilibrium shape. Dissipation and inter-coupling of modal energy lead to stable droplet shape while accumulation of the same ultimately results in droplet breakup. (C) 2013 Elsevier B.V. All rights reserved.

A Kushner-Stratonovich Monte Carlo filter applied to nonlinear dynamical system identification

A Monte Carlo filter, based on the idea of averaging over characteristics and fashioned after a particle-based time-discretized approximation to the Kushner-Stratonovich (KS) nonlinear filtering equation, is proposed. A key aspect of the new filter is the gain-like additive update, designed to approximate the innovation integral in the KS equation and implemented through an annealing-type iterative procedure, which is aimed at rendering the innovation (observation prediction mismatch) for a given time-step to a zero-mean Brownian increment corresponding to the measurement noise. This may be contrasted with the weight-based multiplicative updates in most particle filters that are known to precipitate the numerical problem of weight collapse within a finite-ensemble setting. A study to estimate the a-priori error bounds in the proposed scheme is undertaken. The numerical evidence, presently gathered from the assessed performance of the proposed and a few other competing filters on a class of nonlinear dynamic system identification and target tracking problems, is suggestive of the remarkably improved convergence and accuracy of the new filter. (C) 2013 Elsevier B.V. All rights reserved.

Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

Copula-Based Modeling of TMI Brightness Temperature With Rainfall Type

Overland rain retrieval using spaceborne microwave radiometer offers a myriad of complications as land presents itself as a radiometrically warm and highly variable background. Hence, land rainfall algorithms of the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) have traditionally incorporated empirical relations of microwave brightness temperature (Tb) with rain rate, rather than relying on physically based radiative transfer modeling of rainfall (as implemented in the TMI ocean algorithm). In this paper, sensitivity analysis is conducted using the Spearman rank correlation coefficient as benchmark, to estimate the best combination of TMI low-frequency channels that are highly sensitive to the near surface rainfall rate from the TRMM Precipitation Radar (PR). Results indicate that the TMI channel combinations not only contain information about rainfall wherein liquid water drops are the dominant hydrometeors but also aid in surface noise reduction over a predominantly vegetative land surface background. Furthermore, the variations of rainfall signature in these channel combinations are not understood properly due to their inherent uncertainties and highly nonlinear relationship with rainfall. Copula theory is a powerful tool to characterize the dependence between complex hydrological variables as well as aid in uncertainty modeling by ensemble generation. Hence, this paper proposes a regional model using Archimedean copulas, to study the dependence of TMI channel combinations with respect to precipitation, over the land regions of Mahanadi basin, India, using version 7 orbital data from the passive and active sensors on board TRMM, namely, TMI and PR. Studies conducted for different rainfall regimes over the study area show the suitability of Clayton and Gumbel copulas for modeling convective and stratiform rainfall types for the majority of the intraseasonal months. Furthermore, large ensembles of TMI Tb (from the most sensitive TMI channel combination) were generated conditional on various quantiles (25th, 50th, 75th, and 95th) of the convective and the stratiform rainfall. Comparatively greater ambiguity was observed to model extreme values of the convective rain type. Finally, the efficiency of the proposed model was tested by comparing the results with traditionally employed linear and quadratic models. Results reveal the superior performance of the proposed copula-based technique.

Energy loss due to adhesion in longitudinal impact of elastic cylinders

Adhesive interaction between impacting bodies can cause energy loss, even in an otherwise elastic impact. Adhesion force induces tensile stress in the bodies, which modifies the stress wave profile and influences the restitution behavior. We investigate this effect by developing a finite element framework, which incorporates a Lennard-Jones-type potential for modeling the adhesive interaction between volume elements. With this framework, the classical problems in contact mechanics can be revisited without the restrictive surface-force approximation. In this paper, we study the longitudinal impact of an elastic cylinder on a rigid half-space with adhesion. In the absence of adhesion, this problem reduces to the impact between two identical cylinders in which there is no energy loss. Adhesion causes a fraction of energy in the stress waves to remain in the cylinder as residual stress waves. This apparent loss in kinetic energy is shown to be a unique function of maximum tensile strain energy. We have developed a 1-D model in terms of interaction force parameters, velocity and material properties to estimate the tensile stain energy. We show that this model can be used to predict practically important phenomena like capture wherein the impacting bodies stick together. (C) 2013 Elsevier Masson SAS. All rights reserved.

Performance evaluation of typical approximation algorithms for nonconvex l(p)-minimization in diffuse optical tomography

The sparse estimation methods that utilize the l(p)-norm, with p being between 0 and 1, have shown better utility in providing optimal solutions to the inverse problem in diffuse optical tomography. These l(p)-norm-based regularizations make the optimization function nonconvex, and algorithms that implement l(p)-norm minimization utilize approximations to the original l(p)-norm function. In this work, three such typical methods for implementing the l(p)-norm were considered, namely, iteratively reweighted l(1)-minimization (IRL1), iteratively reweighted least squares (IRLS), and the iteratively thresholding method (ITM). These methods were deployed for performing diffuse optical tomographic image reconstruction, and a systematic comparison with the help of three numerical and gelatin phantom cases was executed. The results indicate that these three methods in the implementation of l(p)-minimization yields similar results, with IRL1 fairing marginally in cases considered here in terms of shape recovery and quantitative accuracy of the reconstructed diffuse optical tomographic images. (C) 2014 Optical Society of America

Inhibition of Mycobacterium tuberculosis topoisomerase I by m-AMSA, a eukaryotic type II topoisomerase poison

m-AMSA, an established inhibitor of eukaryotic type II topoisomerases, exerts its cidal effect by binding to the enzyme-DNA complex thus inhibiting the DNA religation step. The molecule and its analogues have been successfully used as chemotherapeutic agents against different forms of cancer. After virtual screening using a homology model of the Mycobacterium tuberculosis topoisomerase I, we identified m-AMSA as a high scoring hit. We demonstrate that m-AMSA can inhibit the DNA relaxation activity of topoisomerase I from M. tuberculosis and Mycobacterium smegmatis. In a whole cell assay, m-AMSA inhibited the growth of both the mycobacteria. (C) 2014 Elsevier Inc. All rights reserved.

UNIQUENESS OF SOLUTIONS TO SCHRODINGER EQUATIONS ON H-TYPE GROUPS

This paper deals with the Schrodinger equation i partial derivative(s)u(z, t; s) - Lu(z, t; s) = 0; where L is the sub-Laplacian on the Heisenberg group. Assume that the initial data f satisfies vertical bar f(z, t)vertical bar less than or similar to q(alpha)(z, t), where q(s) is the heat kernel associated to L. If in addition vertical bar u(z, t; s(0))vertical bar less than or similar to q(beta)(z, t), for some s(0) is an element of R \textbackslash {0}, then we prove that u(z, t; s) = 0 for all s is an element of R whenever alpha beta < s(0)(2). This result holds true in the more general context of H-type groups. We also prove an analogous result for the Grushin operator on Rn+1.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) approximate to 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) approximate to 0.05. We note that ``islands'' of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) approximate to 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level. (C) 2014 AIP Publishing LLC.

Estimation of the 2.0(5) helix type i -> i hydrogen bond energy at Aib*-Oxa motif: an isodesmic approach

Bending at the valence angle N-C-alpha-C' (tau) is a known control feature for attenuating the stability of the rare intramolecular hydrogen bonded pseudo five-membered ring C-5 structures, the so called 2.0(5) helices, at Aib. The competitive 3(10)-helical structures still predominate over the C5 structures at Aib for most values of tau. However at Aib*, a mimic of Aib where the carbonyl 0 of Aib is replaced with an imidate N (in 5,6-dihydro-4H-1,3-oxazine = Oxa), in the peptidomimic Piv-Pro-Aib*-Oxa (1), the C(5)i structure is persistent in both crystals and in solution. Here we show that the i -> i hydrogen bond energy is a more determinant control for the relative stability of the C5 structure and estimate its value to be 18.5 +/- 0.7 kJ/mol at Aib* in 1, through the computational isodesmic reaction approach, using two independent sets of theoretical isodesmic reactions. (C) 2014 Elsevier Ltd. All rights reserved.

Asymptotic expansions for wavenumbers in orthotropic fluid-filled circular cylindrical shells for intermediate fluid loading

Coupled wavenumbers in infinite fluid-filled isotropic and orthotropic cylindrical shells are considered. Using the Donnell-Mushtari (DM) theory for thin shells, compact and elegant asymptotic expansions for the wavenumbers are found at an intermediate fluid loading for both the coupled rigid-duct modes (''fluid-originated'') and the coupled structural wavenumbers (''structure-originated modes'') over the entire frequency range where DM theory is valid. The coupled rigid-duct expansions are found to be valid for O(1) orthotropy and for all circumferential orders, whereas the coupled structural wavenumber expansions are valid for small orthotropy and for low circumferential orders. These two above results are then used to derive the expansions for a set of multiple complex roots that display a locking behavior at this intermediate fluid-loading. The expansions are matched with the numerical solutions of the coupled dispersion relation and the match is found to be good over most of the frequency range. (C) 2014 Acoustical Society of America.

Novel Rearrangements in the Staphylococcal Cassette Chromosome Mec Type V Elements of Indian ST772 and ST672 Methicillin Resistant Staphylococcus aureus Strains

Staphylococcus aureus is a commensal gram positive bacteria which causes severe and non severe infections in humans and livestock. In India, ST772 is a dominant and ST672 is an emerging clone of Staphylococcus aureus. Both cause serious human diseases, and carry type V SCCmec elements. The objective of this study was to characterize SCCmec type V elements of ST772 and ST672 because the usual PCR methods did not amplify all primers specific to the type. Whole genome sequencing analysis of seven ST772 and one ST672 S. aureus isolates revealed that the SCCmec elements of six of the ST772 isolates were the smallest of the extant type V elements and in addition have several other novel features. Only one ST772 isolate and the ST672 isolate carried bigger SCCmec cassettes which were composites carrying multiple ccrC genes. These cassettes had some similarities to type V SCCmec element from M013 isolate (ST59) from Taiwan in certain aspects. SCCmec elements of all Indian isolates had an inversion of the mec complex, similar to the bovine SCCmec type X. This study reveals that six out of seven ST772 S. aureus isolates have a novel type V (5C2) SCCmec element while one each of ST772 and ST672 isolates have a composite SCCmec type V element (5C2&5) formed by the integration of type V SCCmec into a MSSA carrying a SCC element, in addition to the mec gene complex inversions and extensive recombinations.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.