Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting

A probe, 9-(anthrylmethyl)trimethylammonium chloride, 1, was prepared. 1 binds to calf-thymus DNA or Escherichia coli genomic DNA with high affinity, as evidenced from the absorption titration. Strong hypochromism, spectral broadening and red-shifts in the absorption spectra were observed. Half-reciprocal plot constructed from this experiment gave binding constant of 5±0.5×104 M−1 in base molarity. We employed this anthryl probe-DNA complex for studying the effects of addition of various surfactant to DNA. Surfactants of different charge types and chain lengths were used in this study and the effects of surfactant addition to such probe-DNA complex were compared with that of small organic cations or salts. Addition of either salts or cationic surfactants led to structural changes in DNA and under these conditions, the probe from the DNA-bound complex appeared to get released. However, the cationic surfactants could induce such release of the probe from the probe-DNA complex at a much lower concentration than that of the small organic cations or salts. In contrast the anionic surfactants failed to promote any destabilization of such probe-DNA complexes. The effects of additives on the probe-DNA complexes were also examined by using a different technique (fluorescence spectroscopy) using a different probe ethidium bromide. The association complexes formed between the cationic surfactants and the plasmid DNA pTZ19R, were further examined under agarose gel electrophoresis and could not be visualized by ethidium bromide staining presumably due to cationic surfactant-induced condensation of DNA. Most of the DNA from such association complexes can be recovered by extraction of surfactants with phenol-chloroform. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA melting temperatures by a few °C and at high [surfactant], the corresponding melting profiles got broadened.

In situ cryocrystallization of low melting chloro and bromo substituted anilines

In situ cryocrystallographic Studies of chloro and bromo substituted anilines have been performed to evaluate the role of halogen...halogen interactions and the subsequent formation of supramolecular assemblies in the solid state. Ortho Cl/Br substituted anilines are isostructural and belong to the trigonal P3(1) space group. Halogen...halogen intermolecular contacts along with stronger N-H center dot center dot center dot N hydrogen bonds generate helical motifs along the crystallographic c-axis. (C) 2009 Elsevier B.V. All rights reserved.

Unsteady Incompressible Three-Dimensional Asymmetric Stagnation-Point Boundary Layers

The unsteady laminar incompressible boundary-layer flow near the three-dimensional asymmetric stagnation point has been studied under the assumptions that the free-stream velocity, wall temperature, and surface mass transfer vary arbitrarily with time. The partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. It is found that in contrast with the symmetric flow, the maximum heat transfer occurs away from the stagnation point due to the decrease in the boundary-layer thickness. The effect of the variation of the wall temperature with time on heat transfer is strong. The skin friction and heat transfer due to asymmetric flow only are comparatively less affected by the mass transfer as compared to those of symmetric flow.

Study of fracture behaviour of bond coats on nickel superalloy by three-point bending of microbeams

A microbeam testing geometry is designed to study the variation in fracture toughness across a compositionally graded NiAl coating on a superalloy substrate. A bi-material analytical model of fracture is used to evaluate toughness by deconvoluting load-displacement data generated in a three-point bending test. It is shown that the surface layers of a diffusion bond coat can be much more brittle than the interior despite the fact that elastic modulus and hardness do not display significant variations. Such a gradient in toughness allows stable crack propagation in a test that would normally lead to unstable fracture in a homogeneous, brittle material. As the crack approaches the interface, plasticity due to the presence of Ni3Al leads to gross bending and crack bifurcation.

Steady mixed convection stagnation-point flow of upper convected Maxwell fluids with magnetic field

The steady MHD mixed convection flow of a viscoelastic fluid in the vicinity of two-dimensional stagnation point with magnetic field has been investigated under the assumption that the fluid obeys the upper-convected Maxwell (UCM) model. Boundary layer theory is used to simplify the equations of motion. induced magnetic field and energy which results in three coupled non-linear ordinary differential equations which are well-posed. These equations have been solved by using finite difference method. The results indicate the reduction in the surface velocity gradient, surface heat transfer and displacement thickness with the increase in the elasticity number. These trends are opposite to those reported in the literature for a second-grade fluid. The surface velocity gradient and heat transfer are enhanced by the magnetic and buoyancy parameters. The surface heat transfer increases with the Prandtl number, but the surface velocity gradient decreases.

Wigner distributions for finite-state systems without redundant phase-point operators

We set up Wigner distributions for N-state quantum systems following a Dirac-inspired approach. In contrast to much of the work in this study, requiring a 2N x 2N phase space, particularly when N is even, our approach is uniformly based on an N x N phase-space grid and thereby avoids the necessity of having to invoke a `quadrupled' phase space and hence the attendant redundance. Both N odd and even cases are analysed in detail and it is found that there are striking differences between the two. While the N odd case permits full implementation of the marginal property, the even case does so only in a restricted sense. This has the consequence that in the even case one is led to several equally good definitions of the Wigner distributions as opposed to the odd case where the choice turns out to be unique.

On the growth of the Bergman kernel near an infinite-type point

We study diagonal estimates for the Bergman kernels of certain model domains in C-2 near boundary points that are of infinite type. To do so, we need a mild structural condition on the defining functions of interest that facilitates optimal upper and lower bounds. This is a mild condition; unlike earlier studies of this sort, we are able to make estimates for non-convex pseudoconvex domains as well. Thisn condition quantifies, in some sense, how flat a domain is at an infinite-type boundary point. In this scheme of quantification, the model domains considered below range-roughly speaking-from being mildly infinite-type'' to very flat at the infinite-type points.

Melting of an Anchored Bilayer: Phase Transitions in the Organic-Inorganic Hybrid Pervoskite (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n=11, 13, 15, 17)

The conformation, organization, and phase transitions of alkyl chains in organic-inorganic hybrids based on the double pervoskite-slab lead iodides, (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 (n = 11, 13, 15, 17) have been investigated by X-ray diffraction, calorimetry, and infrared vibrational spectroscopy. In these hybrid solids, double pervoskite (CH3NH3)Pb2I7 slabs are interleaved with alkyl ammonium chains with the anchored alkyl chains arranged as tilted bilayers and adopting a planar all-trans conformation at room temperature. The (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 compounds exhibit a single reversible phase transition above room temperature with the associated enthalpy change varying linearly with alkyl chain length. This transition corresponds to the melting in two-dimensions of the alkyl chains of the anchored bilayer and is characterized by increased conformational disorder of the methylene units of the chain and loss of tilt angle coherence leading to an increase in the interslab spacing. By monitoring features in the infrared spectra that are characteristic of the global conformation of the alkyl chains, a quantitative relation between conformational disorder and melting of the anchored bilayer is established. It is found that, irrespective of the alkyl chain length, melting occurs when at least 60% of the chains in the anchored bilayer of (CH3NH3)(CH3(CH2)(n)NH3)(2)Pb2I7 have one or more gauche defects. This concentration is determined by the underlying lattice to which the alkyl chains are anchored.

Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.

Dynamics after a sweep through a quantum critical point

The coherent quantum evolution of a one-dimensional many-particle system after slowly sweeping the Hamiltonian through a critical point is studied using a generalized quantum Ising model containing both integrable and nonintegrable regimes. It is known from previous work that universal power laws of the sweep rate appear in such quantities as the mean number of excitations created by the sweep. Several other phenomena are found that are not reflected by such averages: there are two different scaling behaviors of the entanglement entropy and a relaxation that is power law in time rather than exponential. The final state of evolution after the quench is not characterized by any effective temperature, and the Loschmidt echo converges algebraically for long times, with cusplike singularities in the integrable case that are dynamically broadened by nonintegrable perturbations.

Turbulence-induced melting of a nonequilibrium vortex crystal in a forced thin fluid film

To gain a better understanding of recent experiments on the turbulence-induced melting of a periodic array of vortices in a thin fluid film, we perform a direct numerical simulation of the two-dimensional Navier-Stokes equations forced such that, at low Reynolds numbers, the steady state of the film is a square lattice of vortices. We find that as we increase the Reynolds number, this lattice undergoes a series of nonequilibrium phase transitions, first to a crystal with a different reciprocal lattice and then to a sequence of crystals that oscillate in time. Initially, the temporal oscillations are periodic; this periodic behaviour becoming more and more complicated with increasing Reynolds number until the film enters a spatially disordered nonequilibrium statistical steady state that is turbulent. We study this sequence of transitions using fluid-dynamics measures, such as the Okubo-Weiss parameter that distinguishes between vortical and extensional regions in the flow, ideas from nonlinear dynamics, e.g. Poincare maps, and theoretical methods that have been developed to study the melting of an equilibrium crystal or the freezing of a liquid and that lead to a natural set of order parameters for the crystalline phases and spatial autocorrelation functions that characterize short- and long-range order in the turbulent and crystalline phases, respectively.

Average-Delay Optimal Policies for the Point-to-Point Channel

Average-delay optimal scheduflng of messages arriving to the transmitter of a point-to-point channel is considered in this paper. We consider a discrete time batch-arrival batch-service queueing model for the communication scheme, with service time that may be a function of batch size. The question of delay optimality is addressed within the semi-Markov decision-theoretic framework. Approximations to the average-delay optimal policy are obtained.

New insights from a fixed-point analysis of single cell IEEE 802.11 WLANs

We study a fixed-point formalization of the well-known analysis of Bianchi. We provide a significant simplification and generalization of the analysis. In this more general framework, the fixed-point solution and performance measures resulting from it are studied. Uniqueness of the fixed point is established. Simple and general throughput formulas are provided. It is shown that the throughput of any flow will be bounded by the one with the smallest transmission rate. The aggregate throughput is bounded by the reciprocal of the harmonic mean of the transmission rates. In an asymptotic regime with a large number of nodes, explicit formulas for the collision probability, the aggregate attempt rate, and the aggregate throughput are provided. The results from the analysis are compared with ns2 simulations and also with an exact Markov model of the backoff process. It is shown how the saturated network analysis can be used to obtain TCP transfer throughputs in some cases.

Melting of an Anchored Bilayer: Molecular Dynamics Simulations of the Structural Transition in (CnH2n+1NH3)(2)PbI4 (n=12, 14, 16, 18)

The thermally driven Structural phase transition in the organic-inorganic hybrid perovskite (CnH2n+1NH3)(2)PbI4 has been investigated using molecular dynamics (MD) simulations. This system consists of positively charged alkyl-amine chains anchored to a rigid negatively charged PbI4 sheet with the chains organized as bilayers with a herringbone arrangement. Atomistic simulations were performed using ail isothermal-isobaric ensemble over a wide temperature range from 65 to 665 K for different alkyl chain lengths, n = 12, 14, 16, and 18. The simulations are able to reproduce the essential Features of the experimental observations of this system, including the existence of a transition, the linear variation of the transition temperature with alkyl chain length, and the expansion of the bilayer thickness at the transition. By use of the distance fluctuation Criteria, it is Shown that the transition is associated With a Melting of the alkyl chains of the anchored bilayer. Ail analysis of the conformation of the alkyl chains shows increased disorder in the form of gauche defects above due melting transition. Simulations also show that the melting transition is characterized by the complete disappearance of all-trans alkyl chains in the anchored bilayer, in agreement with experimental observations. A conformationally disordered chain has a larger effective cross-sectional area, and above due transition a uniformly tilted arrangement of the anchored chains call no longer be Sustained. At the melt the angular distribution of the orientation of the chains are 110 longer uniform; the chains are splayed allowing for increased space for individual chains of the anchored bilayer. This is reflected in a sharp rise in the ratio of the mean head-to-head to tail-to-tail distance of the chains of the bilayer at the transition resulting in in expansion of the bilayer thickness. The present MD simulations provide a simple explanation as to how changes in conformation of individual alkyl-chains gives rise to the observed increase in the interlayer lattice spacing of (CnH2n+1NH3)(2)PbI4 at the melting transition.