Phonon spectrum and vibrational characteristics of linear nanostructures in solid matrices

The atomic dynamics of linear chains embedded in a crystalline matrix or adsorbed on its surface is studied. A linear chain formed by substitutional impurities in a surface layer and at the same time offsetting from this layer was analyzed particularly. This system models the actively studied experimentally structures in which gas molecules are adsorbed on the walls of the bundles of carbon nanotubes located in certain medium. It is shown that the quasi-1D features are typical for the chains in which the interatomic interaction is higher than the interaction between the atoms of the chain and the atoms of the crystal matrix. On the local phonon density of atoms of the chain, the transition to quasi-one-dimensional behavior has the form of the kink. In other words, it is the first (lowest-frequency) van Hove singularity, which in 3D structures (the system under consideration is generally three-dimensional) corresponds to the transition from closed to open constant-frequency (quasi-plane) surfaces. The local phonon densities of atoms in the chain have one-dimensional character at frequencies higher than the frequency of the van Hove singularity. The rms-amplitude of embedded chains atoms vibrations is calculated and the behavior of the atomic vibrations contribution in the low-temperature heat capacity of the system is analyzed.Comment: 14 pages, 7 figure

Low Temperature Specific Heat of BiOX (X = Cl, Br, and I) Single Crystals

Low temperature specific heat of layered bismuth oxyhalide crystals has been studied in the temperature range from 2 to 50 K in zero and 8 T magnetic field. The expected Debye-like behaviour at the lowest temperatures (below 4-5 K) is established. Linear dependences of entropy and the Debye temperature as cross-correlation parameters are established. The small values of the Debye temperature and peculiarities of phonon spectra at lowest temperatures are discussed

Low-frequency properties of the phonon spectra, and low-temperature thermodynamics of disordered solid solutions

This is an analysis of the properties of quasi-local vibrations, and the conditions of the formation thereof, in a realistic model of the crystal lattice on a microscopic scale. The evolution of quasi-local vibrations with an increase in the concentration of impurity atoms, is examined. It is shown that the formation of boson peaks occurs mainly due to the additional dispersion of high-velocity acoustic phonons (connected to the atomic vibrations of the main lattice), caused by the scattering of these phonons by the quasi-local vibrations localized at the impurities. We demonstrate a connection between the boson peaks in disordered systems, and the first van Hove singularity, in regular crystal structures. We analyze the manifestation of quasi-local vibrations and boson peaks, as it relates to the behavior of low-temperature heat capacity, and how it changes with an increasing impurity concentration

Low-temperature vibration characteristics in InSe single crystals intercalated by Ni

The theoretical and experimental study of low-temperature heat capacity of InSe intercalated by nickel as a function of temperature has been carried out in range 0.3–30 K. The effect of intercalation by nickel on phonon heat capacity (Cph) of InSe has been investigated. Two peaks observed in relative change of phonon specific heat (∆Cph/Cph) suggested non-Debye excess in heat capacity for all intercalated NixInSe systems

zrp2: a novel maize gene whose mRNA accumulates in the root cortex and mature stems

A near full-length cDNA clone (pZRP2) was isolated from a cDNA library constructed from maize root mRNAs. The predicted polypeptide has a calculated molecular mass of 66 975 Da, is largely hydrophilic, and contains 26 repeats of a motif the consensus sequence of which is RKATTSYG[S][D/E][D/E][D/E][D/E][P]. The function of the putative protein remains to be elucidated. The ZRP2 mRNA accumulates to the highest levels in young roots, and is also present in mature roots and stems of maize. Further analysis of young roots indicates that the lowest level of ZRP2 mRNA is near the root tip, with relatively high levels throughout the remainder of the root. In situ hybridization reveals that ZRP2 mRNA accumulates predominantely in the cortical parenchyma cells of the root. In vitro nuclear run-on transcription experiments indicate a dramatically higher level of zrp2 gene transcription in 3-day old roots than in 5-day old leaves. A zrp2 genomic clone, which includes the transcribed region and 4.7 kb of upstream sequence, was isolated and characterized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43444/1/11103_2004_Article_142986.pd

Multiferroic Bi 0.65 La 0.35 Fe 0.5 Sc 0.5 O 3 perovskite:Magnetic and thermodynamic properties

Magnetic and thermodynamic properties of polycrystalline multiferroic Bi 0.65 La 0.35 Fe 0.5 Sc 0.5 O 3 synthesized under high-pressure and high-temperature conditions are reported. Magnetic properties were studied using a SQUID magnetometer technique over the temperature range of 5−300 K in magnetic fields up to H=10 kOe. The field dependent magnetization M(H) was measured in magnetic fields up to 50 kOe at different temperatures up to 230 K after zero-field cooling procedure. A long-range magnetic ordering of the AFM type with a weak FM contribution occurs below the Néel temperature T N ~237 K. Magnetic hysteresis loops taken below T N show a huge coercive field up to H c ~10 kOe. A strong effect of magnetic field on the magnetic properties of the compound has been found. Derivative of the initial magnetization curves demonstrates a temperature-dependent anomaly in fields of H=15−25 kOe. Besides, an anomaly of the temperature dependent zero-field cooled magnetization measured in magnetic fields of 6−7 kOe has been found. Origin of both anomalies is associated with inhomogeneous magnetic state of the compound. The heat capacity has been measured from 2 K up to room temperature and a significant contribution from the magnon excitations at low temperatures has been detected. From the low-temperature heat capacity, an anisotropy gap of the magnon modes of the order 3.7 meV and Debye temperature T D =189 K have been determined

MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis

MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly available software in development for analysis of genome-wide RNA, protein and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis, combined with gene expression profiling data. It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler captures input from MetNetDB in a graphical form. Sub-networks can be identified and interpreted using simple fuzzy cognitive maps. FCModeler is intended to develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently being extended to three-dimensional virtual reality display. The MetNet map, together with gene expression data, can be viewed using multivariate graphics tools in GGobi linked with the data analytic tools in R. Users can highlight different parts of the metabolic network and see the relevant expression data highlighted in other data plots. Multi-dimensional expression data can be rotated through different dimensions. Statistical analysis can be computed alongside the visual. MetNet is designed to provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term provide the basis for identification of metabolic and regulatory networks that control plant composition and development

Epitaxial Catalyst-Free Growth of InN Nanorods onc-Plane Sapphire

We report observation of catalyst-free hydride vapor phase epitaxy growth of InN nanorods. Characterization of the nanorods with transmission electron microscopy, and X-ray diffraction show that the nanorods are stoichiometric 2H–InN single crystals growing in the [0001] orientation. The InN rods are uniform, showing very little variation in both diameter and length. Surprisingly, the rods show clear epitaxial relations with thec-plane sapphire substrate, despite about 29% of lattice mismatch. Comparing catalyst-free with Ni-catalyzed growth, the only difference observed is in the density of nucleation sites, suggesting that Ni does not work like the typical vapor–liquid–solid catalyst, but rather functions as a nucleation promoter by catalyzing the decomposition of ammonia. No conclusive photoluminescence was observed from single nanorods, while integrating over a large area showed weak wide emissions centered at 0.78 and at 1.9 eV

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

<p>Abstract</p> <p>Background</p> <p>Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server.</p> <p>Results</p> <p>MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only.</p> <p>Conclusions</p> <p>An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at <url>http://www.metnetonline.org/api</url>.</p