Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Selective-Area Atomic Layer Deposition

Atomic layer deposition (ALD) is a method to deposit thin films from gaseous precursors to the substrate layer-by-layer so that the film thickness can be tailored with atomic layer accuracy. Film tailoring is even further emphasized with selective-area ALD which enables the film growth to be controlled also on the substrate surface. Selective-area ALD allows the decrease of a process steps in preparing thin film devices. This can be of a great technological importance when the ALD films become into wider use in different applications. Selective-area ALD can be achieved by passivation or activation of a surface. In this work ALD growth was prevented by octadecyltrimethoxysilane, octadecyltrichlorosilane and 1-dodecanethiol SAMs, and by PMMA (polymethyl methacrylate) and PVP (poly(vinyl pyrrolidone) polymer films. SAMs were prepared from vapor phase and by microcontact printing, and polymer films were spin coated. Microcontact printing created patterned SAMs at once. The SAMs prepared from vapor phase and the polymer mask layers were patterned by UV lithography or lift-off process so that after preparation of a continuous mask layer selected areas of them were removed. On these areas the ALD film was deposited selectively. SAMs and polymer films prevented the growth in several ALD processes such as iridium, ruthenium, platinum, TiO2 and polyimide so that the ALD films did grow only on areas without SAM or polymer mask layer. PMMA and PVP films also protected the surface against Al2O3 and ZrO2 growth. Activation of the surface for ALD of ruthenium was achieved by preparing a RuOX layer by microcontact printing. At low temperatures the RuCp2-O2 process nucleated only on this oxidative activation layer but not on bare silicon.

Fuzzy Coherence: Making Sense of Continuity in Hypertext Narratives

Hypertexts are digital texts characterized by interactive hyperlinking and a fragmented textual organization. Increasingly prominent since the early 1990s, hypertexts have become a common text type both on the Internet and in a variety of other digital contexts. Although studied widely in disciplines like hypertext theory and media studies, formal linguistic approaches to hypertext continue to be relatively rare. This study examines coherence negotiation in hypertext with particularly reference to hypertext fiction. Coherence, or the quality of making sense, is a fundamental property of textness. Proceeding from the premise that coherence is a subjectively evaluated property rather than an objective quality arising directly from textual cues, the study focuses on the processes through which readers interact with hyperlinks and negotiate continuity between hypertextual fragments. The study begins with a typological discussion of textuality and an overview of the historical and technological precedents of modern hypertexts. Then, making use of text linguistic, discourse analytical, pragmatic, and narratological approaches to textual coherence, the study takes established models developed for analyzing and describing conventional texts, and examines their applicability to hypertext. Primary data derived from a collection of hyperfictions is used throughout to illustrate the mechanisms in practice. Hypertextual coherence negotiation is shown to require the ability to cognitively operate between local and global coherence by means of processing lexical cohesion, discourse topical continuities, inferences and implications, and shifting cognitive frames. The main conclusion of the study is that the style of reading required by hypertextuality fosters a new paradigm of coherence. Defined as fuzzy coherence, this new approach to textual sensemaking is predicated on an acceptance of the coherence challenges readers experience when the act of reading comes to involve repeated encounters with referentially imprecise hyperlinks and discourse topical shifts. A practical application of fuzzy coherence is shown to be in effect in the way coherence is actively manipulated in hypertext narratives.

A Cache coherence protocol for MIN-based multiprocessors

In this paper we present a cache coherence protocol for multistage interconnection network (MIN)-based multiprocessors with two distinct private caches: private-blocks caches (PCache) containing blocks private to a process and shared-blocks caches (SCache) containing data accessible by all processes. The architecture is extended by a coherence control bus connecting all shared-block cache controllers. Timing problems due to variable transit delays through the MIN are dealt with by introducing Transient states in the proposed cache coherence protocol. The impact of the coherence protocol on system performance is evaluated through a performance study of three phases. Assuming homogeneity of all nodes, a single-node queuing model (phase 3) is developed to analyze system performance. This model is solved for processor and coherence bus utilizations using the mean value analysis (MVA) technique with shared-blocks steady state probabilities (phase 1) and communication delays (phase 2) as input parameters. The performance of our system is compared to that of a system with an equivalent-sized unified cache and with a multiprocessor implementing a directory-based coherence protocol. System performance measures are verified through simulation.

A Molecular Dynamics Study of Atomic Correlations in Glassy BzS3t

Glassy B&, the parent compound of the superionic conductor LiI-Li&B& has been studied by the molecular dynamics technique using a new potential model. The results suggest that the glass is made up of local units of four-membered B2S2 rings bridged by sulfur atoms, leading to a chainlike structure. Various pair correlation functions have been analyzed, and the B2Sz rings have been found to be planar. The calculated neutron structure factor shows a peak at 1.4 A-' which has been attributed to B-B correlations at 5.6 A. The glass transition temperature of the simulated system has been calculated to be around 800 K.

Block coherence: a method for measuring the interdependence between two blocks of neurobiological time series

Multisensor recordings are becoming commonplace. When studying functional connectivity between different brain areas using such recordings, one defines regions of interest, and each region of interest is often characterized by a set (block) of time series. Presently, for two such regions, the interdependence is typically computed by estimating the ordinary coherence for each pair of individual time series and then summing or averaging the results over all such pairs of channels (one from block 1 and other from block 2). The aim of this paper is to generalize the concept of coherence so that it can be computed for two blocks of non-overlapping time series. This quantity, called block coherence, is first shown mathematically to have properties similar to that of ordinary coherence, and then applied to analyze local field potential recordings from a monkey performing a visuomotor task. It is found that an increase in block coherence between the channels from V4 region and the channels from prefrontal region in beta band leads to a decrease in response time.

Chopped nonlinear magneto-optic rotation: A technique for precision measurements

We have developed a technique for precise measurement of small magnetic fields using nonlinear magneto-optic rotation (NMOR). The technique relies on the resonant laser beam being chopped. During the on time, the atoms are optically pumped into an aligned ground state (Delta m=2 coherence). During the off time, they freely precess around the magnetic field at the Larmor frequency. If the on-off modulation frequency matches (twice) the Larmor precession frequency, the rotation is resonantly enhanced in every cycle, thereby making the process like a repeated Ramsey measurement of the Larmor frequency. We study chopped-NMOR in a paraffin-coated Cs vapor cell. The out-of-phase demodulated rotation shows a Lorentzian peak of linewidth 85 mu G, corresponding to a sensitivity of 0.15nG/root Hz. We discuss the potential of this technique for the measurement of an atomic electric-dipole moment. Copyright (C) EPLA, 2011

Coherence of the real symmetric Hardy algebra

Let D denote the open unit disk in C centered at 0. Let H-R(infinity) denote the set of all bounded and holomorphic functions defined in D that also satisfy f(z) = <(f <(z)over bar>)over bar> for all z is an element of D. It is shown that H-R(infinity) is a coherent ring.

Structural and transport properties of high energy ion irradiated YBCO

The effects of 100 MeV Oxygen and 200 MeV Silver ions on the structural and transport properties of YBCO thin films are reported. Both normal state and superconducting properties were studied on Laser ablated and high pressure oxygen sputtered films. Precise electrical resistance and critical current measurements near T-c were made and the data obtained were analysed in the light of existing models of para-coherence near T-c and the other aspects of radiation damage arising from microstructural studies such as atomic force microscopy (AFM). There was evidence of sputtering by high energy ions from AFM measurement. (C) 1998 Elsevier Science Ltd. All rights reserved.

Radiation induced modifications on microstructure and related properties of high temperature superconductor YBCO

Role of swift heavy ion irradiation on the modification of transport and structural properties of high temperature superconductors is studied. Good quality YBCO thin films prepared by high pressure oxygen sputtering and laser ablation were used in this investigation. Resistivity and atomic force microscopy (AFM) were mainly used to probe superconducting and microstructural modifications resulted from the irradiation of high energy and heavy ions like 100 MeV oxygen and 200 MeV silver. Radiation induced sputtering or erosion is likely to be a major disastrous component of such high energy irradiation that could be powerful in masking phase coherence effects, atleast in grain boundaries. The extent of damage/nature of defects other than columnar defects produced by swift heavy ions is discussed in the light of AFM measurements. The effect of high energy oxygen ion irradiation is anomalous. A clear annealing effect at higher doses is seen. (C) 1999 Elsevier Science B.V. All rights reserved.

A token-based distributed algorithm for total order atomic broadcast

In this paper, we propose a new token-based distributed algorithm for total order atomic broadcast. We have shown that the proposed algorithm requires lesser number of messages compared to the algorithm where broadcast servers use unicasting to send messages to other broadcast servers. The traditional method of broadcasting requires 3(N - 1) messages to broadcast an application message, where N is the number of broadcast servers present in the system. In this algorithm, the maximum number of token messages required to broadcast an application message is 2N. For a heavily loaded system, the average number of token messages required to broadcast an application message reduces to 2, which is a substantial improvement over the traditional broadcasting approach.

Growth mechanism of phases by interdiffusion and atomic mechanism of diffusion in the molybdenum-silicon system

Tracer diffusion coefficients are calculated in different phases in the Mo-Si system from diffusion couple experiments using the data available on thermodynamic parameters. Following, possible atomic diffusion mechanism of the species is discussed based on the crystal structure. Unusual diffusion behaviour is found in the Mo(5)Si(3) and Mo(3)Si phases, which indicate the nature of defects present on different sublattices. Further the growth mechanism of the phases is discussed and morphological evolution during interdiffusion is explained. (C) 2011 Elsevier Ltd. All rights reserved.

Effect of Post-Metallization Hydrogen Annealing on C-V Characteristic of Zirconia Grown Using Atomic Layer Deposition

Substantial amount of fixed charge present in most of the alternative gate dielectrics gives rise to large shifts in the flat-band voltage (VFB) and charge trapping and de-trapping causes hysterectic changes on voltage cycling. Both phenomena affect stable and reliable transistor operation. In this paper we have studied for the first time the effect of post-metallization hydrogen annealing on the C-V curve of MOS capacitors employing zirconia, one of the most promising gate dielectric. Samples were annealed in hydrogen ambient for up to 30 minutes at different temperatures ranging from room temperature to 400°C. C-V measurements were done after annealing at each temperature and the hysteresis width was calculated from the C-V curves. A minimum hysteresis width of ∼35 mV was observed on annealing the sample at 200°C confirming the excellent suitability of this dielectric