Dynamic origin of the morphotropic phase boundary - Soft modes and phase instability in 0.68Pb(Mg1/3Nb2/3O3)-0.32PbTiO3

We report neutron inelastic scattering on single crystal 0.68Pb(Mg1/3Nb2/3O3)-0.32PbTiO3 (PMN-0.32PT), a relaxor ferroelectric material that lies within the compositional range of the morphotropic phase boundary (MPB). Data were obtained between 100 K and 600 K under zero and non-zero electric field applied along the cubic [001] direction. The lowest energy, zone-center, transverse optic phonon is strongly damped and softens slowly at high temperature; however the square of the soft mode energy begins to increase linearly with temperature as in a conventional ferroelectric, which we term the soft mode "recovery," upon cooling into the tetragonal phase at TC. Our data show that the soft mode in PMN-0.32PT behaves almost identically to that in pure PMN, exhibiting the same temperature dependence and recovery temperature even though PMN exhibits no well-defined structural transition (no TC). The temperature dependence of the soft mode in PMN-0.32PT is also similar to that in PMN-0.60PT; however in PMN-0.60PT the recovery temperature equals TC. These results suggest that the temperature dependence and the energy scale of the soft mode dynamics in PMN-xPT are independent of concentration on the Ti-poor side of the MPB, but scale with TC for Ti-rich compositions. Thus the MPB may be defined in lattice dynamical terms as the concentration where TC first matches the recovery temperature of the soft mode. High-resolution x-ray studies show that the cubic-to-ferroelectric phase boundary shifts to higher temperatures by an abnormal amount within the MPB region in the presence of an electric field. This suggests that an unusual instability exists within the apparently cubic phase at the MPB.Comment: 13 pages, 6 figure

Electronic structure of REREAuMg and REREAgMg (RERE = Eu, Gd, Yb)

We have investigated the electronic structure of the equiatomic EuAuMg, GdAuMg, YbAuMg and GdAgMg intermetallics using x-ray photoelectron spectroscopy. The spectra revealed that the Yb and Eu are divalent while the Gd is trivalent. The spectral weight in the vicinity of the Fermi level is dominated by the mix of Mg $s$, Au/Ag $sp$ and $RE$ $spd$ bands, and not by the $RE$ $4f$. We also found that the Au and Ag $d$ bands are extraordinarily narrow, as if the noble metal atoms were impurities submerged in a low density $sp$ metal host. The experimental results were compared with band structure calculations, and we found good agreement provided that the spin-orbit interaction in the Au an Ag $d$ bands is included and correlation effects in an open $4f$ shell are accounted for using the local density approximation + Hubbard $U$ scheme. Nevertheless, limitations of such a mean-field scheme to explain excitation spectra are also evident.Comment: 4 pages, 3 figures, Brief Repor

Electrostatics of Edge States of Quantum Hall Systems with Constrictions: Metal--Insulator Transition Tuned by External Gates

The nature of a metal--insulator transition tuned by external gates in quantum Hall (QH) systems with point constrictions at integer bulk filling, as reported in recent experiments of Roddaro et al. [1], is addressed. We are particularly concerned here with the insulating behavior--the phenomena of backscattering enhancement induced at high gate voltages. Electrostatics calculations for QH systems with split gates performed here show that observations are not a consequence of interedge interactions near the point contact. We attribute the phenomena of backscattering enhancement to a splitting of the integer edge into conducting and insulating stripes, which enable the occurrence of the more relevant backscattering processes of fractionally charged quasiparticles at the point contact. For the values of the parameters used in the experiments we find that the conducting channels are widely separated by the insulating stripes and that their presence alters significantly the low-energy dynamics of the edges. Interchannel impurity scattering does not influence strongly the tunneling exponents as they are found to be irrelevant processes at low energies. Exponents of backscattering at the point contact are unaffected by interchannel Coulomb interactions since all channels have same chirality of propagation.Comment: 19 pages; To appear in Phys. Rev.

Efficient and accurate greedy search methods for mining functional modules in protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Most computational algorithms mainly focus on detecting highly connected subgraphs in PPI networks as protein complexes but ignore their inherent organization. Furthermore, many of these algorithms are computationally expensive. However, recent analysis indicates that experimentally detected protein complexes generally contain Core/attachment structures.</p> <p>Methods</p> <p>In this paper, a Greedy Search Method based on Core-Attachment structure (GSM-CA) is proposed. The GSM-CA method detects densely connected regions in large protein-protein interaction networks based on the edge weight and two criteria for determining core nodes and attachment nodes. The GSM-CA method improves the prediction accuracy compared to other similar module detection approaches, however it is computationally expensive. Many module detection approaches are based on the traditional hierarchical methods, which is also computationally inefficient because the hierarchical tree structure produced by these approaches cannot provide adequate information to identify whether a network belongs to a module structure or not. In order to speed up the computational process, the Greedy Search Method based on Fast Clustering (GSM-FC) is proposed in this work. The edge weight based GSM-FC method uses a greedy procedure to traverse all edges just once to separate the network into the suitable set of modules.</p> <p>Results</p> <p>The proposed methods are applied to the protein interaction network of S. cerevisiae. Experimental results indicate that many significant functional modules are detected, most of which match the known complexes. Results also demonstrate that the GSM-FC algorithm is faster and more accurate as compared to other competing algorithms.</p> <p>Conclusions</p> <p>Based on the new edge weight definition, the proposed algorithm takes advantages of the greedy search procedure to separate the network into the suitable set of modules. Experimental analysis shows that the identified modules are statistically significant. The algorithm can reduce the computational time significantly while keeping high prediction accuracy.</p

FeCo/Graphite Nanocrystals for Multi-Modality Imaging of Experimental Vascular Inflammation

BACKGROUND: FeCo/graphitic-carbon nanocrystals (FeCo/GC) are biocompatible, high-relaxivity, multi-functional nanoparticles. Macrophages represent important cellular imaging targets for assessing vascular inflammation. We evaluated FeCo/GC for vascular macrophage uptake and imaging in vivo using fluorescence and MRI. METHODS AND RESULTS: Hyperlipidemic and diabetic mice underwent carotid ligation to produce a macrophage-rich vascular lesion. In situ and ex vivo fluorescence imaging were performed at 48 hours after intravenous injection of FeCo/GC conjugated to Cy5.5 (n = 8, 8 nmol of Cy5.5/mouse). Significant fluorescence signal from FeCo/GC-Cy5.5 was present in the ligated left carotid arteries, but not in the control (non-ligated) right carotid arteries or sham-operated carotid arteries (p = 0.03 for ligated vs. non-ligated). Serial in vivo 3T MRI was performed at 48 and 72 hours after intravenous FeCo/GC (n = 6, 270 µg Fe/mouse). Significant T2* signal loss from FeCo/GC was seen in ligated left carotid arteries, not in non-ligated controls (p = 0.03). Immunofluorescence staining showed colocalization of FeCo/GC and macrophages in ligated carotid arteries. CONCLUSIONS: FeCo/GC accumulates in vascular macrophages in vivo, allowing fluorescence and MR imaging. This multi-functional high-relaxivity nanoparticle platform provides a promising approach for cellular imaging of vascular inflammation

pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions.To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data.By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much-needed genome informatics inspired solution to accessing the ever-increasing biomedical literature

Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping

Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58–156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes