Use of structure-directed DNA ligands to probe the binding of recA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing

We have used circular dichroism and structure-directed drugs to identify the role of structural features, wide and narrow grooves in particular, required for the cooperative polymerization, recognition of homologous sequences, and the formation of joint molecules promoted by recA protein. The path of cooperative polymerization of recA protein was deduced by its ability to cause quantitative displacement of distamycin from the narrow groove of duplex DNA. By contrast, methyl green bound to the wide groove was retained by the nucleoprotein filaments comprised of recA protein-DNA. Further, the mode of binding of these ligands and recA protein to DNA was confirmed by DNaseI digestion. More importantly, the formation of joint molecules was prevented by distamycin in the narrow groove while methyl green in the wide groove had no adverse effect. Intriguingly, distamycin interfered with the production of coaggregates between nucleoprotein filaments of recA protein-M13 ssDNA and naked linear M13 duplex DNA, but not with linear phi X174 duplex DNA. Thus, these data, in conjunction with molecular modeling, suggest that the narrow grooves of duplex DNA provide the fundamental framework required for the cooperative polymerization of recA protein and alignment of homologous sequences. These findings and their significance are discussed in relation to models of homologous pairing between two intertwined DNA molecules.

Direct probe of end-segment distribution in tethered polymer chains

End-tethered chains made of an adsorbed diblock copolymer of polystyrene (PS)-polyisoprene (PI) bearing an end-segment including a Ge atom are built by the Langmuir-Schaeffer technique. They are studied both in the dry state and in a good solvent for the PI chain using grazing incidence X-ray standing waves. The analysis of the signal provides a direct measurement of the end-segment distribution which is found to be singular and mostly localized to a plane in the dry case. In the good solvent case, end-segments are found to span the entire assembly and compare very well with results obtained by Kreer et al.

Four group decodable differential scaled unitary linear space-time codes

Differential Unitary Space-Time Block codes (STBCs) offer a means to communicate on the Multiple Input Multiple Output (MIMO) channel without the need for channel knowledge at both the transmitter and the receiver. Recently Yuen-Guan-Tjhung have proposed Single-Symbol-Decodable Differential Space-Time Modulation based on Quasi-Orthogonal Designs (QODs) by replacing the original unitary criterion by a scaled unitary criterion. These codes were also shown to perform better than differential unitary STBCs from Orthogonal Designs (ODs). However the rate (as measured in complex symbols per channel use) of the codes of Yuen-Guan-Tjhung decay as the number of transmit antennas increase. In this paper, a new class of differential scaled unitary STBCs for all even number of transmit antennas is proposed. These codes have a rate of 1 complex symbols per channel use, achieve full diversity and moreover they are four-group decodable, i.e., the set of real symbols can be partitioned into four groups and decoding can be done for the symbols in each group separately. Explicit construction of multidimensional signal sets that yield full diversity for this new class of codes is also given.

Tuning the beta-turn segment in designed peptide beta-hairpins: Construction of a stable type I ' beta-turn nucleus and hairpin-helix transition promoting segments

Designed octapeptides Boc-Leu-Val-Val-Aib-(D)Xxx-Leu- Val-Val-OMe ((D)Xxx = (D)Ala, 3a; (D)Val, 3c and (D)Pro, 5a) and Boc-Leu-Phe-Val-Aib-DAla-Leu-Phe-Val-OMe (3b) have been investigated to construct models of a stable type I' beta-turn nucleated hairpin and to generate systems for investigating helix-hairpin conformational transitions. Peptide 5a, which contains a central Aib-(D)Pro segment, is shown to adopt a stable type I' beta-turn nucleated hairpin structure, stabilized by four cross-strand hydrogen bonds. The stability of the structure in diverse solvents is established by the observation of all diagnostic NOEs expected in a beta-hairpin conformation. Replacement of (D)Pro5 by (D)Ala/(D)Val (3a-c) results in sequences that form beta-hairpins in hydrogen bonding solvents like CD3OH and DMSO-d(6). However, in CDCl3 evidence for population of helical conformations is obtained. Peptide 6b (Boc-Leu-Phe-Val-Aib-Aib-Leu-Phe-Val-OMe), which contains a centrally positioned Aib-Aib segment, provides a clear example of a system, which exhibits a helical conformation in CDCl3 and a significant population of both helices and hairpins in CD3OH and DMSO-d(6). The coexistence of multiple conformations is established by the simultaneous observation of diagnostic NOEs. Control over stereochemistry of the central beta-turn permits generation of models for robust beta-hairpins and also for the construction of systems that may be used to probe helix-hairpin conformational transitions. (c) 2006 Wiley Periodicals, Inc.

A Proportional plus Multiresonant Controller for Three-Phase Four-Wire High-Frequency Link Inverter

A new solution for unbalanced and nonlinear loads in terms of power circuit topology and controller structure is proposed in this paper. A three-phase four-wire high-frequency ac-link inverter is adopted to cater to such loads. Use of high-frequency transformer results in compact and light-weight systems. The fourth wire is taken out from the midpoint of the isolation transformer in order to avoid the necessity of an extra leg. This makes the converter suitable for unbalanced loads and eliminates the requirements of bulky capacitor in half-bridge inverter. The closed-loop control is carried out in stationary reference frame using proportional + multiresonant controller (three separate resonant controller for fundamental, fifth and seventh harmonic components). The limitations on improving steady-state response of harmonic resonance controllers is investigated and mitigated using a lead-lag compensator. The proposed voltage controller is used along with an inner current loop to ensure excellent performance of the power converter. Simulation studies and experimental results with 1 kVA prototype under nonlinear and unbalanced loading conditions validate the proposed scheme.

Analysis of the binding of polymyxin B to endotoxic lipid A and core glycolipid using a fluorescent displacement probe

Dansylcadaverine, a cationic fluorescent probe binds to bacterial lipopolysaccharide and lipid A, and is displaced competitively by other compounds which possess affinity toward endotoxins. The binding parameters of dansylcadaverine for lipid A were determined by Scatchard analysis to be two apparently equivalent sites with apparent dissociation constants (Kd) ranging between 16 μM to 26 μM, while that obtained for core glycolipid from Salmonella minnesota Re595 yielded a Kd of 22 μM to 28 μM with three binding sites. The Kd of polymyxin B for lipid A was computed from dansylcadaverine displacement by the method of Horovitz and Levitzki (Horovitz, A., and Levitzki, A. (1987) Proc. Natl. Acad. Sci. USA 84, 6654–6658). The applicability of this method for analyzing fluorescence data was validated by comparing the Kds of melittin for lipid A obtained by direct Scatchard analysis, and by the Horovitz-Levitzki method. The displacement of dansylcadaverine from lipid A by polymyxin B was distinctly biphasic with Kds for polymyxin B-lipid A interactions corresponding to 0.4 μM and 1.5 μM, probably resulting as a consequence of lipid A being a mixture of mono- and di-phosphoryl species. This was not observed with core glycolipid, for which the Kd for polymyxin was estimated to range from 1.1 μM to 5.8 μM. The use of dansylcadaverine as a displacement probe offers a novel and convenient method of quantitating the interactions of a wide variety of substances with lipid A.

N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yI)colcemid, a probe for different classes of colchincine-binding site on tubulin

The nature of binding of 7-nitrobenz-2-oxa-1,3-diazol-4-yl-colcemid (NBD-colcemid), an environment-sensitive fluorescent analogue of colchicine, to tubulin was tested. This article reports the first fluorometric study where two types of binding site of colchincine analogue on tubulin were detected. Binding of NBD-colcemid to one of these sites equilibrates slsowly. NBD-colcemid competes with colchicine for this site. Binding of NBD-colcemid to this site also causes inhibition of tubulin self-assembly. In contrast, NBD-colcemid binding to the other site is characterised by rapid equilibration and lack of competition with colchicine. Nevertheless, binding to this site is highly specific for the cholchicine nucleus, as alkyl-NBD analogues have no significant binding activity. Fast-reaction-kinetic studies gave 1.76 × 105 M–1 s–1 for the association and 0.79 s–1 for the dissociation rate constants for the binding of NBD-colcemid to the fast site of tubulin. The association rate constants for the two phases of the slow site are 0.016 × 10–4 M–1 s–1 and 3.5 × 10–4 M–1 respectively. These two sites may be related to the two sites of colchicine reported earlier, with binding characteristics altered by the increased hydrophobic nature of NBD-colcemid.

Four generations: SUSY and SUSY breaking

We revisit four generations within the context of supersymmetry. Wecompute the perturbativity limits for the fourth generation Yukawa couplings and show that if the masses of the fourth generation lie within reasonable limits of their present experimental lower bounds, it is possible to have perturbativity only up to scales around 1000 TeV. Such low scales are ideally suited to incorporate gauge mediated supersymmetry breaking, where the mediation scale can be as low as 10-20 TeV. The minimal messenger model, however, is highly constrained. While lack of electroweak symmetry breaking rules out a large part of the parameter space, a small region exists, where the fourth generation stau is tachyonic. General gauge mediation with its broader set of boundary conditions is better suited to accommodate the fourth generation.

Four-dimensional current algebra from Chern-Simons theory

We study an abelian Chern-Simons theory on a five-dimensional manifold with boundary. We find it to be equivalent to a higher-derivative generalization of the abelian Wess-Zumino-Witten model on the boundary. It contains a U(1) current algebra with an operational extension.

A four-timescale algorithm for constrained stochastic optimization of RED

The overall performance of random early detection (RED) routers in the Internet is determined by the settings of their associated parameters. The non-availability of a functional relationship between the RED performance and its parameters makes it difficult to implement optimization techniques directly in order to optimize the RED parameters. In this paper, we formulate a generic optimization framework using a stochastically bounded delay metric to dynamically adapt the RED parameters. The constrained optimization problem thus formulated is solved using traditional nonlinear programming techniques. Here, we implement the barrier and penalty function approaches, respectively. We adopt a second-order nonlinear optimization framework and propose a novel four-timescale stochastic approximation algorithm to estimate the gradient and Hessian of the barrier and penalty objectives and update the RED parameters. A convergence analysis of the proposed algorithm is briefly sketched. We perform simulations to evaluate the performance of our algorithm with both barrier and penalty objectives and compare these with RED and a variant of it in the literature. We observe an improvement in performance using our proposed algorithm over RED, and the above variant of it.

Structural, dielectric and ferroelectric properties of four-layer Aurivillius phase Na0.5La0.5Bi4Ti4O15

Monophasic Na0.5La0.5Bi4Ti4O15 powders were synthesized via the conventional solid-state reaction route. The X-ray powder diffraction (XRD), selected area electron diffraction (SAED) and high resolution transmission electron microscopy (HRTEM) studies carried out on the as synthesized powdered samples confirmed the phase to be a four-layer Aurivillius that crystallizes in an orthorhombic A2(1)am space group. The microstructure and the chemical composition of the sintered sample were examined by scanning electron microscope (SEM) equipped with an energy dispersive X-ray analyzer (EDX). The dielectric properties of the ceramics have been studied in the 27-700 degrees C temperature range at various frequencies (100 Hz to 1 MHz). A sharp dielectric anomaly was observed at 580 degrees C for all the frequencies corresponding to the ferroelectric to paraelectric phase transition. Saturated ferroelectric hysteresis loops were observed at 200 degrees C and the associated remnant polarization (P-r) and coercive field (E-c) were found to be 7.4 mu C/cm(2) and 34.8 kV/cm, respectively. AC conductivity analysis confirmed the existence of two different conduction mechanisms in the ferroelectric region. Activation energies calculated from the Arrhenius plots were similar to 0.24 eV and similar to 0.84 eV in the 300-450 degrees C and 450-580 degrees C temperature ranges, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Fabrication of device quality films of high loaded PPy/MWCNT nanocomposites using pulsed laser deposition

Polypyrrole (PPy) - multiwalled carbonnanotubes (MWCNT) nanocomposites with various MWCNT loading were prepared by in situ inversion emulsion polymerization technique. High loading of the nano filler were evaluated because of available inherent high interface area for charge separation in the nanocomposites. Solution processing of these conducting polymer nanocomposites is difficult because, most of them are insoluble in organic solvents. Device quality films of these composites were prepared by using pulsed laser deposition techniques (PLD). Comparative study of X-ray photoelectron spectroscopy (XPS) of bulk and film show that there is no chemical modification of polymer on ablation with laser. TEM images indicate PPy layer on MWCNT surface. SEM micrographs indicate that the MWCNT's are distributed throughout the film. It was observed that MWCNT in the composite held together by polymer matrix. Further more MWCNT diameter does not change from bulk to film indicating that the polymer layer remains intact during ablation. Even for very high loadings (80 wt.% of MWCNT's) of nanocomposites device quality films were fabricated, indicating laser ablation is a suitable technique for fabrication of device quality films. Conductivity of both bulk and films were measured using collinear four point probe setup. It was found that overall conductivity increases with increase in MWCNT loading. Comparative study of thickness with conductivity indicates that maximum conductivity was observed around 0.2 mu m. (C) 2010 Elsevier B.V. All rights reserved.

A Five-Level Inverter Scheme for a Four-Pole Induction Motor Drive by Feeding the Identical Voltage-Profile Windings From Both Sides

This paper presents a five-level inverter scheme with four two-level inverters for a four-pole induction motor (IM) drive. In a conventional three-phase four-pole IM, there exists two identical voltage-profile winding coil groups per phase around the armature, which are connected in series and spatially apart by two pole pitches. In this paper, these two identical voltage-profile pole-pair winding coils in each phase of the IM are disconnected and fed from four two-level inverters from four sides of the windings with one-fourth dc-link voltage as compared to a conventional five-level neutral-point-clamped inverter. The scheme presented in this paper does not require any special design modification for the induction machine. For this paper, a four-pole IM drive is used, and the scheme can be easily extended to IMs with more than four poles. The proposed scheme is experimentally verified on a four-pole 5-hp IM drive.

Coplanar Capacitively Coupled Probe Fed Microstrip Antennas for Wideband Applications

The design and analysis of a coplanar capacitive fed microstrip antenna suspended above the ground plane is presented. It is demonstrated that the proposed approach can be used for designing antennas with impedance bandwidth of about 50% and a good gain to operate in various microwave bands. The model of the antenna incorporates the capacitive feed strip which is fed by a coaxial probe using equivalent circuit approach, and matches simulation and experimental results. The capacitive feed strip used here is basically a rectangular microstrip capacitor formed from a truncated microstrip transmission line and all its open ends are represented by terminal or edge capacitances. The error analysis was carried out for validity of the model for different design parameters. The antenna configuration can be used where unidirectional radiation patterns are required over a wide bandwidth.