Wave Propagation in 1-D Spiral geometry

In this article, we investigate the wave equation in spiral geometry and study the modes of vibrations of a one-dimensional (1-D) string in spiral shape. Here we show that the problem of wave propagation along a spiral can be reduced to Bessel differential equation and hence, very closely related to the problem of radial waves of two-dimensional (2-D) vibrating membrane in circular geometry

Probing folding/unfolding kinetics, reaction mechanism and thermodynamic stability of nucleic acid hairpins

2013 Fall.Includes bibliographical references.Nucleic acid hairpins play pivotal roles in biological and cellular processes. The functions of the DNA and RNA hairpins depend upon the conformational changes they adopt during the biological process. Therefore, a clear understanding of their conformational dynamics such as folding and unfolding kinetics, reaction mechanism as well as thermodynamic stability is essential to understand their biological functions. This dissertation describes folding kinetics, reaction mechanism and thermodynamic stability of stem-loop nucleic acid hairpins by using rapid-mixing stopped-flow kinetics and other spectroscopic techniques. Firstly, the folding kinetics and reaction mechanism of a five base-paired stem and twenty one polythymidine loop DNA hairpin as a function of varying monovalent counter ion concentrations have been discussed. The important observation of this investigation is that the DNA hairpin folding is not simply a two-state process, and based on our experiments and kinetic modeling, we proposed a three-state reaction mechanism, wherein, the intermediate formation occurs on microsecond time scale and the complete hairpin formation occurs on millisecond time scale. Secondly, the loop length and counter ion dependent thermodynamic stability and folding of DNA hairpins have been described. This investigation provides a detailed understanding of how the stability and folding changes as a function of loop length and counter ion concentrations. The most important conclusion of this part of the investigation is that the thermodynamic stability of tetraloop hairpins depend upon counter ion concentration regimes and we explained the exceptional stability of a tetraloop hairpin in the higher concentration regime, compared to longer loop length hairpins on the basis of base-stacking effect. Finally, the folding and unfolding kinetics of RNA hairpins with identical four base-paired stem but different nucleotide loop sequence is discussed. Here we observed that the RNA hairpin folding and unfolding can be much more complex than previously thought and also RNA hairpin folding process can be different than DNA hairpin folding process

Foodborne pathogens in poultry production and post-harvest control

A comprehensive ecological survey was conducted from April 1997 to June 1999 on four turkey flocks (F5-F8) to identify the preharvest sources of Salmonella colonization. Generic E. coli and total coliforms were enumerated as indicators of fecal contamination in F7 and F8. Turkey cecal and crop contents, litter, drinkers, air, feed, feeder contents, and environmental swabs were sampled and tested for Salmonella and E. coli. Salmonella was isolated from 13% of litter, 11% of turkey ceca, 10% of drinkers, and 5% of swabs. Escherichia coli and total coliforms were detected in 45 and 53% of samples, respectively. Salmonella heidelberg was the major serotype isolated from the sampled flocks. About 25% of the Salmonella isolates were resistant to antibiotic(s). Identifying preharvest sources of Salmonella and E. coli colonization would assist integrators and producers in designing hazard analysis and critical control point (HACCP) Protocols. On-farm reduction of these pathogens will assist processors in reducing positive carcasses at the plant.;A skin attachment model was used to examine the ability of ZnCl 2 to reverse or inhibit Salmonella attachment to broiler skin. In reversal experiments, skin samples were first treated with 1 mL of S. typhimurium culture (108 CFU/mL) for 30 min, followed by the addition of 1 mL of 25 or 50 mM ZnCl2 for 5 or 15 min. For inhibition experiments, this order was reversed. Firmly and loosely attached salmonellae were enumerated on the skin. Treated skin samples were observed under a scanning electron microscope. In reversal experiments, 25 and 50 mM ZnCl2 reduced (p \u3c 0.01) firmly attached cells by 77 and 89%, respectively, when compared to the control (water). At 25 and 50 mM concentration, ZnCl2 reduced (p \u3c 0.0001) cells in the discard by 99.4 and 99.9%, respectively. Micrographs indicated that 25 and 50 mM ZnCl2 reduced (p \u3c 0.1) Salmonella attachment by 69 and 99.9%, respectively, in the reversal experiments. In the inhibition experiments, 25 and 50 mM ZnCl2 reduced (p \u3c 0.01) firmly attached cells by 82 and 91%, respectively. Reduction of Salmonella may be attributed, in part, to the bactericidal activity of ZnCl2 in addition to detachment of the bacterial cells on skin

General relativistic treatment of LISA optical links

LISA is a joint space mission of the NASA and the ESA for detecting low frequency gravitational waves in the band $10^{-5} - 1$ Hz. In order to attain the requisite sensitivity for LISA, the laser frequency noise must be suppressed below the other secondary noises such as the optical path noise, acceleration noise etc. This is achieved by combining time-delayed data for which precise knowledge of time-delays is required. The gravitational field, mainly that of the Sun and the motion of LISA affect the time-delays and the optical links. Further, the effect of the gravitational field of the Earth on the orbits of spacecraft is included. This leads to additional flexing over and above that of the Sun. We have written a numerical code which computes the optical links, that is, the time-delays with great accuracy $\sim 10^{-2}$ metres - more than what is required for time delay interferometry (TDI) - for most of the orbit and with sufficient accuracy within $\sim 10$ metres for an integrated time window of about six days, when one of the arms tends to be tangent to the orbit. Our analysis of the optical links is fully general relativistic and the numerical code takes into account effects such as the Sagnac, Shapiro delay, etc.. We show that with the deemed parameters in the design of LISA, there are symmetries inherent in the configuration of LISA and in the physics, which may be used effectively to suppress the residual laser noise in the modified first generation TDI. We demonstrate our results for some important TDI variables

Standard Coupling Unification in SO(10), Hybrid Seesaw Neutrino Mass and Leptogenesis, Dark Matter, and Proton Lifetime Predictions

We discuss gauge coupling unification of the SM descending directly from SO(10) while providing solutions to the three outstanding problems: neutrino masses, dark matter, and the baryon asymmetry of the universe. Conservation of matter parity as gauged discrete symmetry in the model calls for high-scale spontaneous symmetry breaking through ${126}_H$ Higgs representation. This naturally leads to the hybrid seesaw formula for neutrino masses mediated by heavy scalar triplet and right-handed neutrinos. The seesaw formula predicts two distinct patterns of RH$\nu$ masses, one hierarchical and another not so hierarchical (or compact) when fitted with the neutrino oscillation data. Predictions of the baryon asymmetry via leptogenesis are investigated through the decays of both the patterns of RH$\nu$ masses. A complete flavor analysis has been carried out to compute CP-asymmetries and solutions to Boltzmann equations have been utilized to predict the baryon asymmetry. The additional contribution to vertex correction mediated by the heavy left-handed triplet scalar is noted to contribute as dominantly as other Feynman diagrams. We have found successful predictions of the baryon asymmetry for both the patterns of RH$\nu$ masses. The triplet fermionic dark matter at the TeV scale carrying even matter parity is naturally embedded into the non-standard fermionic representation ${45}_F$ of SO(10). In addition to the triplet scalar and the triplet fermion, the model needs a nonstandard color octet fermion of mass $\sim 10^7$ GeV to achieve precision gauge coupling unification. Threshold corrections due to superheavy components of ${126}_H$ and other representations are estimated and found to be substantial. It is noted that the proton life time predicted by the model is accessible to the ongoing and planned experiments over a wide range of parameter space.Comment: 58 pages PDFLATEX, 19 Figures, Revised as suggested by JHEP Revie

Multipole interactions with an extended object

In this article, we study the motion of an extended object in various spacetime geometries consists of the monopole, dipole as well as quadrupole moment within the framework of the general theory of relativity. We focus on a compelling limiting case, in which the acceleration of extended object vanishes and therefore, it becomes indistinguishable from a geodesic trajectory. In this case, both dipole, as well as the quadrupole moment of the extended object, would necessarily interact with the various moments of the central object, resulting in zero acceleration. We show that an object with monopole and dipole moment, namely the spin, can have a limit where the dipole-monopole and dipole-dipole interaction between that particle and the central object respectively vanishes. However, the introduction of quadrupole moment leads to more complicated situations and only the quadrupole-monopole interaction consists of a well-posed vanishing limit, while other interactions such as dipole-quadrupole or quadrupole-quadrupole, in general, remain nonzero. We expand on these scenarios in detail with their possible physical implications.Comment: 22 pages, 1 tabl

Swarm-intelligent search for gravitational waves from eccentric binary mergers

We implement an eccentric search for compact binary mergers based on particle swarm optimization. The orbital eccentricity is an invaluable input for understanding the formation scenarios of the binary mergers and can play a pivotal role in finding their electromagnetic counterparts. Current modelled searches rely on pre-computed template banks that are computationally expensive and resistant towards expanding the search parameter space dimensionality. On the other hand, particle swarm optimization offers a straightforward algorithm that dynamically selects template points while exploring an arbitrary dimensional parameter space. Through extensive evaluation using simulated signals from spin-aligned eccentric binary mergers, we discovered that the search exhibits a remarkable autonomy in capturing the effects of both eccentricity and spin. We describe our search pipeline and revisit some of the merger candidates from the gravitational wave transient catalogs